Functional Biology Final review
BIO- FINAL EXAM REVEW SHEET
This is a comprehensive review of material from exams 1-3. Please study your class notes/powerpoint slides and read the chapters listed in your syllabus to study for all new material.
What are the characteristics of living organisms?
Acquire and use energy
Made up of other cells
Process information
Can replicate itself (can reproduce)
Population evolves (they evolve)
What are the characteristics of cells?
Contain genetic information
Can duplicate themselves
Have a cell membrane
Have a cytoplasm
Have ribosomes
The structure of a cell is closely correlated with its function
Cells are dynamic thousands of chemical reactions occur in each second
Most cells are capable of division
What is a scientific theory? How does this differ from everyday usage of the term “theory”?
An explanation for a very general class of phenomena or observations that are supported by a wide body of evidence.
A scientific theory summarizes a hypothesis of group of hypotheses that have been supported with repeated testing. If enough evidence accumulates to support a hypothesis, it moves to the next step- known as a theory- in the scientific method and becomes accepted as a valid explanation of a phenomenon
When used in non-scientific context, the word “theory” implies that something is unproven or speculative. As used in science, however, a theory is an explanation or model based on observation, experimentation, and reasoning, especially one that has been tested and confirmed as a general principle helping to explain and predict natural phenomena
Scientific theories are testable explanations, not speculative guesses
What are the two components of a scientific theory?
Null hypothesis
Alternative hypothesis
Pattern component (based on observation)
Process component (based on experimentation)
The two critical components of a scientific theory is that it provides explanations and predictions that can be trusted
Describe the cell theory
All organisms are made of cells.
The cell theory and theory of evolution address fundamental questions:
What are organisms made of?
Where do they come from?
It also states that all organisms are made of cells (this formed only the first part of the cell theory). The complete cell theory can be stated as follows: “All organisms are made of cells, and all cells come from preexisting cells.”
The cell theory was a direct challenge to the prevailing explanation of where cells come from, called spontaneous generation
Pattern- all material is made of cells
Organisms and their characteristics change; living populations change
Process- Pasteur’s experiment that rejected spontaneous
Field studies have proved this
What are the two main types of cells?
Prokaryotes
Eukaryotes
Describe prokaryotic cells with regard to: DNA storage/organization, site of protein synthesis, membranes.
Have no membrane bound organelles
DNA is circular, organized in a nucleoid region
Protein synthesis takes place in ribosomes
DNA storage/organization DOES NOT have a nucleus but contains a nucleoid region where DNA is stored
Site of protein synthesis: Proteins are synthesized in the ribosomes found in the prokaryotic cell
Describe eukaryotic cells with regard to: DNA storage/organization, site of protein synthesis, membranes.
Membrane bound organelles
DNA located in the nucleus
Proteins synthesized in both rough ER and ribosomes
What type of cells from Q6 have membrane bound organelles?
Eukaryotes
Nucleus
ER
Golgi apparatus
Lysosomes
Endosomes
Mitochondria
What are the advantages of membrane-bound organelles?
Reactions occur more efficiently
Has the ability to protect the cell from unwanted side effects
For the following cellular organelles (1) be able to identify and (2) describe their function: ribosomes, nucleus, endoplasmic reticulum (rough and smooth), peroxisome, lysosome, mitochondria, vacuoles, chloroplast
Ribosomes- Synthesize proteins
Nucleus- Carries chromosomes in nucleolus
Rough ER- Has ribosomes, produce proteins to export
Breaks down toxins and synthesized lipids, stores calcium
Peroxisome- Fatty acid processing with catalase to breakdown H202
Lysosome- Break down macromolecules and mitochondria with hydrolytic enzymes
Mitochondria- Site of ATP production, and undergoes cellular respiration
Vacuoles- Storage of water, toxins, oils and carbohydrates
Chloroplast- Site of photosynthesis and ATP production ONLY in plant cells
For the organelles in Q11, which are present in only eukaryotes or in both prokaryotes and eukaryotes?
Eukaryotes-
HAS Nucleolus
HAS Smooth and rough ER
HAS Mitochondria
HAS Chloroplasts
HAS Ribosomes- relatively large
HAS Lysosomes
HAS Peroxisomes
HAS Vacuoles
HAS Golgi
HAS Nuclear envelope
HAS microtubules, intermediate filaments and microfilaments
Multiple, linear chromosomes with wound on nucleosomes
Prokaryotes (don’t have membrane bound organelles)-
HAS Ribosomes- relatively small
HAS Nucleoid
NO Golgi
NO ER
NO Lysosomes
NO Peroxisomes
NO Mitochondria
NO microtubules, intermediate filaments or microfilaments
NO nuclear envelope
Single, circular chromosomes with no nucleosomes
Describe how the structure of a cell is correlated with its function?
A cells shape is related to its function
What are the most abundant elements in living organisms?
Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur (CHNOPS)
What is the structure of an atom?
There is a nucleus made up of protons(+) and neutrons(no charge) surrounded by a cloud or ring of electrons(-)
In a neutral charges atom, there is one proton for every electron
What is the atomic number? Mass number?
Atomic number- number of protons in an atom (# never varies)
Mass number- number of protons and neutrons (this can vary- isotopes)
What are valence electrons? How are they contributing to an atom’s reactivity?
Valence electrons- unpaired electrons in the outermost orbital or shell
Atoms become stable once there are no longer outer orbitals that only contain single electrons
The further away the valence electron, the more reactive
What are covalent bonds – polar and non-polar?
Covalent can be polar or non-polar
Non polar- two atoms share the electrons equally
Polar- if one atom is more electronegative it will pull the electron closer to its nucleus
What are ionic bonds?
One atom loses an unpaired electron, and another element gains an electron to fill its orbital
What is a hydrogen bond?
Involves the bonding between H and one of three different elements: N, O, or F (Nitrogen, Oxygen, or Fluorine)
These bonds are fairly weak and are easily broken
What type of bond(s) are most often found in living organisms?
Polar/non-polar covalent bonds
What types of bonds are found in water?
Covalent
Hydrogen bonding
Has polarity
Hydrogen bonding
Gives water structure: cohesion
High specific heat (amount of heat to raise T 1 degree Celsius)
High heat of vaporization
It is a good solvent for ionic, polar molecules
Nonpolar molecules do not dissolve in water
Define hydrophobic and hydrophilic.
Hydrophobic- “Water fearing”
Hydrophilic- “Water loving”
28. What is potential energy? Entropy?
Potential energy- the amount of energy stored in the reacting molecules
Entropy- The amount of disorder in the reacting molecules
29. What happens to the two in Q28 over the course of a chemical reaction?
Endergonic reaction- ^S decreases; ^H increases
Exergonic reaction- S increases; H decreases
30. What determines if a particular reaction is spontaneous?
If delta G is (-), then it is spontaneous
If delta G is (+), then it is nonspontaneous
For delta G to be (-) (regardless of T), delta H needs to be (-) and delta S would need to be (+)
31. What is the formula for Gibb’s free energy of a reaction? Define the variables.
Delta G = Delta H – (T Delta S)
Delta G- Total free energy change in a reaction
Delta H- Change in potential energy
T- temperature
Delta S- change in entropy
32. Define endergonic, exergonic, endothermic, exothermic reactions. Which are spontaneous?
Endergonic- Energy must be absorbed into system; this would be nonspontaneous (also anabolic)
Exergonic- gives off energy (energy is released); this would be spontaneous (also catabolic)
Endothermic- energy, in the form of heat, being absorbed (absorbs heat); this would be nonspontaneous
Exothermic- energy, in the form of heat, being released (gives off heat); this would be spontaneous
Exothermic and Exergonic are spontaneous
33. Draw a graph of the change in free energy of a reaction for both a spontaneous and non-spontaneous reaction.
34. What are the monomers of a protein?
Amino acids
35. What kind of bond joins Q34 together?
Peptide bonds
36. Draw a generalized amino acid with a “R” representing the side group. Label the amino and carboxyl groups.
37. How are side groups important?
Side groups determine properties of particular amino acids
Side groups could be any one of the following: polar, acidic, basic, or nonpolar.
The sequence of the amino acids (and therefore the side groups) determines how these side groups will interact with each other and will affect what shape the overall protein takes
38. Describe the primary, secondary and tertiary structure of a protein.
Primary- this structure has to do with just the sequence of the amino acids themselves
Secondary- this structure deals with the folding of the amino acid chain due to H-bonding
Tertiary- this structure deals with the folding of the amino acid chain specifically due to side group interactions
39. What kind(s) of bonds are important to each level of structure in Q38?
Primary- covalent bond
Secondary- alpha helix, beta sheet
Tertiary- van der wals, H-bonds, covalent
Quaternary- aggregation of polypeptide subunits
40. What is the quaternary structure of a protein?
Structure made up of multiple polypeptide chains together (there would need to be more than one protein involved to make this structure)
41. List 5 functions of proteins in a cell.
1. Catalysts reactions (speeds up reaction)
2. Defense (antibodies in immune system)
3. Movement (actin and myosin)
4. Signaling (insulin receptors)
5. Cell structure (keratin in hair)
Also.. 6. Transport (Na+ K+ exchangers across membranes)
42. How are form and function related with respect to proteins?
Since shape determines function and function is part of what dictates it’s shape, each one informs us about the other
One cannot exist without the other
43. What are catalysts?
Something that speeds up reactions by reducing the activation energy required for spontaneous reactions.
Increases the rate of a chemical reaction without undergoing a chemical change itself
44. How do enzymes catalyze biological reactions?
By reducing the activation energy required for spontaneous reactions
45. Draw a graph of the free energy of a reaction with an enzyme. Label the transition state and activation energy.
46. How do enzymes affect the transition state & activation energy?
It lowers both of them
47. Do enzymes change the overall free energy change of a reaction?
No
48. What are cofactors? Coenzymes?
Cofactors- Inorganic ions such as Zn, Mg, or Fe, that helps bind the substrate to the active site better
Coenzymes- small organic molecules, often within active site
Both of these help increase levels of reaction within enzymes
49. Describe competitive inhibition of an enzyme.
The competitive inhibitor will bind to the active site
It can do this because it often has a similar shape to the substrate
It “competes” with the substrate to bind to the active site
50. What is allosteric activation? Deactivation?
Either will bind to someplace on the enzyme other than the active site
Allosteric activator or deactivator will bind to someplace on the enzyme other than the active site. Depending on how and where it binds, the molecule could change the shape of the enzyme to make it better able to bind with substrates (allosteric activation) or it could change its shape so that substrate have a hard time to bind (allosteric deactivation)
51. In Q49 & Q50 are the active sites involved? Explain.
^Explained in Q50
55. What are the two types of nucleic acids?
1. DNA
2. RNA
56. What are the monomers of nucleic acids?
Nucleotides
57. What are the 3 components of Q56?
1. One 5-carbon sugar
2. A phosphate group
3. A nitrogenous base
58. How do the sugars and nitrogenous bases differ between DNA and RNA?
Three of the nitrogenous bases are the same for both RNA and DNA; guanine, adenine, and cytosine.
Thymine, the fourth base pair found in DNA, is replaced by uracil in RNA.
DNA has deoxyribose sugar while RNA has ribose sugar.
The deoxyribose sugar has one less oxygen atom than the ribose sugar.
59. What are pyrimidines? Purines? Draw one example of each.
The bases thymine and cytosine present in DNA are pyrimidines.
Purines are the bases adenine and guanine present in DNA and RNA
Purines- Adenine, Guanine
Pyrimadines- Uracil, Thymine, Cytosine
60. How many strands is DNA? RNA?
DNA is two stands, and RNA is one strand
61. If 2 strands in Q60, what holds the strands together?
Hydrogen bonds
H+ bonds between nitrogen containing rings of nucleotide base pairs
With opposing bases
62. What are the base pairing rules? Which pairs have 2 hydrogen bonds? Three?
AT, CG, AU in RNA
Adenine and thymine held by two
Cytosine and Guanine held by three
63. Why is DNA said to be antiparallel?
One end runs three prime to five prime (3’5’) while the other runs five prime to three prime (5’3’) (two DNA strands running in opposite directions will bond together via H-bonding and stick together)
One strand of the original DNA is preserved and one is newly made
64. What is the function of DNA?
Contains all genetic material
Stores genetic information and directs protein synthesis
65. What are four functions of RNA?
1.Messenger RNA (mRNA) contains the codons for peptide chain synthesis
2.Transfer RNA (tRNA) transports amino acids to the ribosome during protein synthesis
3.MicroRNA destroys mRNA
4.Ribosomal RNA (rRNA) structural component of ribosomes
66. Can DNA or RNA act as catalysts? Why?
RNA because it can act as a catalyst to itself, ribosomal RNA (rRNA)
67. What elements make up carbohydrates?
Carbon, Hydrogen, and Oxygen
68. What are three functions of carbohydrates in cells?
1. Carbohydrates are the ready source of energy
2. They also play a structural role (e.g.. Cellulose in plants and chitin in arthropods)
3. They combine with certain classes of lipids (to form glycolipid) and proteins (to form glycoprotein) to confer on them the biological function
4. They continue the overcoat of the plasma membrane and thus help in conferring on it the property of recognition, cell sociology, and antigenic property
-Provide identity to cells
-Energy source for cells
-Energy storage for cells
69. Contrast mon-, di-, oligo- and poly-saccharides.
Monosaccharides consist of a single sugar
Disaccharides consists of two sugars
Polysaccharides consists of a chain of monosaccharides
70. Simple sugars are in which class from Q69?
Monosaccharides
71. What is the bond between sugars in oligo- and polysaccharides?
Glycocidic bonds
72. For starch, glycogen, cellulose and chitin, describe (1)structure and components; (2) type of cells that contain the particular polysaccharide and (3) function.
Polysaccharide- polymers of hundreds to thousands of monosaccharides linked together by dehydration reactions
Function as storage molecules or as structural compounds
Starch- found in plants and is served as storages for energy or the plant’s building materials
Glycogen- found in animals and act as a storage for energy and release glucose when needed
Cellulose- major component of plant cell walls
73. What are lipids? Are they hydrophobic or hydrophilic?
Category of compounds containing carbon, hydrogen and oxygen that are hydrophobic
Insoluble in water
Non-polar (fats, oils, cholesterol)
Soluble in non-polar solvent
4 main groups of lipids (fats, phospholipids, waxes and steroids)
Used to store long-term energy
74. Draw the basic structure of a fat and label the glycerol and fatty acid tails.
75. What is the difference between saturated and unsaturated fats? Which are liquid at room temperature?
Saturated fats are solid at room temperature and unsaturated fats are liquid at room temperature
76. What are steroids?
Lipids derived from cholesterol
77. What are phospholipids? How are they amphipathic?
Phospholipids: form a phospholipid bilayer (cellular membranes)
Phospholipids are a class of lipids that make up the main component in cell membranes
Forms two distinct layers- polar heads facing water in the interior and exterior of the cell (hydrophilic); Non-polar tails facing each other on the interior of the membrane (hydrophobic)
Contains two fatty acids in the hydrophobic regions
Fatty acids for micelles in water (single layer droplet)
Provides biosynthetic activities in smooth ER
78. What kind of reaction builds all biological macromolecules discussed in class? What type of reaction breaks them?
Builds- dehydration reactions (water is removed)
Breaking- hydrolysis (water is added)
79. What are cellular membranes comprised of?
Phospholipids and the mosaic model (proteins, carbohydrates, and cholesterol)
80. Describe the terms “fluid” and “selectively permeable” with respect to cell membranes.
Fluid- no bond
Phospholipids are not bound together; Independent molecules
Selectively permeable- only allow certain things to enter or exit the cell
81. Are biological membranes highly permeable, moderately permeable or impermeable to the following molecules: (1) small nonpolar (like carbon dioxide), small uncharged polar (like water), large uncharged polar (like sugars and amino acids) and charged ions.
Small non-polar- highly permeable
Small, uncharged polar- moderately permeable
Large, uncharged polar- moderately permeable
Charged ions- impermeable
82. How do the following affect membrane permeability: (1) saturation of tails; (2) cholesterol and (3) temperature.
1.Saturation of fatty acid tail- lowers permeability; more saturated = less fluid membrane
2. More cholesterol = less fluid membrane
3. Temperature- lower fluidity with lower temperature due to closer packing of fatty acid tails
83. What is diffusion? Osmosis?
Diffusion- molecules going from high to low concentrations
Osmosis- water diffusing from high to low concentration
84. If cells are placed in a (1) hypertonic, (2) isotonic, or (3) hypotonic solution will water move into or out of the cell? Define the terms 1-3.
Hypertonic- there is too much water outside the cell and not enough inside the cell causing the cell to shrivel up
Hypertonic- there is too much water in the cell and not enough outside the cell, causes cell to swell and burst; water will flow out of the cell and the cell will shrink
Isotonic- water moves throughout the cell evenly; the difference between channel and carrier proteins; at equilibrium
All are involved in osmosis!
Hypotonic- water will flow into the cell and the cell will swell
85. Describe the fluid mosaic model of cell membrane structure.
The fluid mosaic model states that proteins float in a sea of lipids.
A cell membrane is composed of lipids arranged with their hydrophobic tails touching each other, with proteins scattered
The membrane surrounds these cells has two layers (a bilayer) of phospholipids (fats with phosphorous attached).
Both layers have the hydrophilic heads pointing toward the outside; the hydrophobic tails form the inside of the bilayer
86. What is facilitated diffusion? What types of molecules are transported in this manner?
It is an active process
Against gradient
87. What is the difference between channel and carrier proteins and in what type of transport are they involved?
Isotonic; osmosis
88. Is diffusion an active or passive process? Facilitated diffusion?
Diffusion is a passive process
Facilitated diffusion is an active process
89. What types of transport move molecules down their concentration gradients? Against their concentration gradients?
Passive transport
Carrier proteins- carry large/uncharged molecules across a membrane (very selective)
Channel- carry ions across a membrane (slightly selective)
Against gradient- active transport (facilitated diffusion)
90. What is endocytosis? Exocytosis?
Endo- into the cell (engulf)
Exo- out of the cell (excrete)
92. What structures in the nuclear envelope controls transport of substances into and out of the nucleus?
Membrane bound transport proteins
Nuclear pores
93. What must a molecule have in order to be transported into the nucleus? Endoplasmic reticulum?
Nucleus- must have a nuclear localization signal
ER- must have an ER signal sequence
94. How is importin involved in transport into/out of the nucleus? SRP into the endoplasmic reticulum?
NLS interacts with importin Which interacts with the pore complex.
Exportin- brings molecules out of the nucleus.
SRP binds to signal sequence which then a ribosome docks to the signal sequence.
95. Trace the pathway of a protein made in the rough endoplasmic reticulum that is destined to be exported from the cell. Explain what happens to the protein along its journey.
SRP binds to the ER signal sequence ribosome docks with the ER protein is deposited into lumen of ER (Rough ER) = proteins in the lumen get folded into tertiary shape (Smooth ER)= proteins get glycosylated (sugar tag added) Proteins enter transport vesicles.
96. How is the golgi apparatus critical for proteins transport to the correct places within the cell?
The golgi assigns additional sugar tags to the proteins and then they get shipped to their specific destination that matches their sugar tag.
97. What are the three components of the cytoskeleton and their relative sizes? Which one is most stable?
1.Microfilaments= smallest
2.Intermediate filaments= middle (most stable)
3.Microtubules= largest
98. What cellular processes are myosin-actin filaments involved?
Movement in muscle cells
99. Which of Q97 have polarity? What is polarity associated with?
Microfilaments
Polarity is what makes them dynamic (able to grow/shrink)
100. What are nuclear lamins? What type of cytoskeletal element from Q97 are they?
Class V intermediate filaments
Fibrous proteins, providing structural function and transcriptional regulation in the cell nucleus
Nuclear lamins interact with membrane-associated proteins to form the nuclear lamina on the interior of the nuclear envelope
From intermediate filaments and holds shape of nucleus and strengthens pores
101. What are microtubule tracks and how is kinesin involved in their function?
Move transport vesicles along microtubules
Kinesin- motor protein associated with this
102. What are cilia and flagella composed of? What is the internal structural arrangement of these components?
Composed of microtubules
9+2 inner arrangement of microtubules with Dynein arms (9 outer and 2 inner)
103. How is dynein involved in the movement of cilia and flagella?
Dynein is a motor protein
104. How are microtubules essential to mitosis?
Microtubules form centromeres of a tetrad
105. What are 3 purposes of cell junctions?
1.Provides a tight seal between adjacent cells (tight junctions)
2.A removable anchor between cells (anchoring junctions)
3.Allows nutrients, etc. between cells (gap junctions)
106. Contrast tight, anchoring, and gap junctions.
Tight- plasma membranes of neighboring cells are tightly pressed against each other and knit together by proteins, prevent leakage of fluid across a layer of cells.
Anchoring- fasten cells together into strong sheets, intermediate filaments made of sturdy keratin proteins anchor these junctions in the cytoplasm, coming in tissues subject to stretching or mechanical stress, such as skin.
Gap- channels that allow small molecules to flow through protein-lined pore between cells. Common in embryos
Although both tight and gap junctions are made up of membrane-spanning proteins, tight junctions seal adjacent animal cells together while gap junctions allow a flow of material between them
107. What are desmosomes? What proteins link the cells in these structures?
Desmosomes- cell- cell attachments (most common anchoring junction)
Cadherin- Proteins link cells
108. What are plasmodesmata?
Gap junctions in plants where the ER extends between cells
109. What is the overall purpose of cellular respiration?
The production of large amounts of ATP
110. What is the general equation of aerobic cellular respiration?
6H12O6 + 6 O2 6 CO2 + 6 H2O
111. In what organelle does cellular respiration in eukaryotes occur? Draw and label the components of this organelle.
Mitochondria (makes ATP)
Glycolysis- cytosol
Pyruvate processing and Krebs Cycle- in mitochondrial matrix
Electron transport. Chemiosmosis & oxidative phosphorylation- in inner mitochondrial membrane
112. What is ATP used for? Draw it.
ATP is the energy currency for cells; it is used for cellular respiration, glycolysis and many other biological processes.
Phosphate- phosphate- phosphate- ribose- adenine
113. How is ATP used? Include the following terms in your explanation: coupled reactions, exergonic & endergonic reactions.
ATP is used to fuel all of the other cycles/processes but the more ATP is out into the cycle, the more ATP is yielded.
Exergonic- ATP is released
Endergonic- ATP is absorbed
Coupled reactions- ATP is both lost and gained
114. What is a redox reaction?
A reaction in which there is a transfer of electrons. One is reduced and another is oxidized.
OIL RIG- oxidation is losing electrons; reduction is gaining electrons
115. What is being oxidized and what is being reduced in the equation in Q110?
Oxygen is being oxidized and Glucose is being reduced
116. What are the 4 overall steps in aerobic cellular respiration and where do they occur in the cell?
Glycolysis- cytoplasm
Pyruvate processing, Krebs Cycle, ETC- mitochondria
117. What is NAD+?
An electron carrier
118. For glycolysis, pyruvate processing and Kreb’s cycle, list (1) reactants and products; (2) ATP formation? ; (3) CO2 released?; (4) electron carrier reduced?; (5) overall purpose.
Glycolysis- glucose Pyruvate (4 ATP made, NAD is reduced to NADH)
Pyruvate processing= pyruvate acetyl coA (NAD is reduced to NADH, 1 CO2 is released)
Kreb’s Cycle- Acetyl group CO2 (1 GTP made and 2 CO2 are released per cycle)
119. Where do electron carriers bring electrons in aerobic respiration?
Electron carriers bring electrons into mitochondrial inner membrane
Electron transport chain 120. What happens to energy as electrons are passed between proteins in Q119?
Energy is being released
121. What is the final electron acceptor in Q119?
Oxygen
122. How does the electron transport chain create a proton gradient in the intermembrane space?
Proton accumulation inside cristae builds up a proton gradient
123. Describe Mitchell’s chemiosmotic hypothesis of ATP production.
Protons try to force back into the matrix along the concentration gradient (proton motive force)
Basically, builds up energy
124. In which step from Q116 are most ATP generate?
Chemiosmosis and Oxidative Phosphorylation
125. Why can’t aerobic respiration occur in one or just a few steps?
Because the cycle needs to be broken down into those steps in order for the most ATP to be made
126. Respiration in the absence of oxygen is called?
Anaerobic respiration
127. What is the final electron acceptor in lactic acid fermentation? What is the product of this process?
Pyruvic acid product- 2 lactate
128. What is the final electron acceptor in alcohol fermentation? What it the product of this process?
Acetaldehyde product- 2 ethanol
129. Does aerobic or anaerobic respiration generate more ATP per glucose molecule?
Aerobic
130. What is the overall equation for photosynthesis?
CO2 + H2O + light energy sugars + O2
131. Draw and label the structures of a chloroplast including thylakoid and grana.
132. What are the photosynthetic pigments? Where are they located? What colors do they absorb and reflect?
Inside thylakoid membranes
Absorb light
Chlorophylls- green
Carotenoids- orange/yellow
Blue and red are absorbed and green is reflected
133. What happens to electrons in pigment molecules when they absorb light energy?
Electrons jump, then fall down (they are excited)
134. What is a photosystem? Reaction center?
Photosystem- II and I are pigment clusters on the membrane.
Reaction center receives light energy
135. In PSII, what is the fate of electrons boosted from the reaction center?
Electrons go to electron transport proteins and are then released as energy
136. How is ATP generated from the movement of the electron from Q135?
Light absorbed by the LHC energizes the photosystems and stimulates linear electron flow, resulting in production of ATP and NADPH
137. In PSI, what is the fate of electrons boosted from the reaction center?
The electron is given to the electron transport chain
138. What replaces electrons that are lost from PSI? PSII?
The electron lost from PSI is replaced by an electron transferred from PSII via another electron transport chain.
PSII replaces its electrons by extracting electrons from water molecules, releasing O2 as byproduct
139. What is the fate of water in photosynthesis?
Water separates into O2, H+ ions, and electrons
140. What two reactions are produced in the light reactions that will proceed to the light independent reactions?
ATP, and NADPH
141. What occurs in the carbon fixation phase of the light independent reactions of photosynthesis? What enzyme is involved?
The process of photorespiration also known as C2 cycle, is also coupled to the dark reactions, as it results from an alternative reaction of the Rubisco enzyme, and its final byproduct is also another gyceraldehyde.
142. What occurs in the reduction phase of the light independent reactions? Regeneration phase?
3- Phosphoglycerate is reduced to glyceraldehyde- 3- phosphate (G3P)
143. What molecules are generated by the light independent reactions and will be used to make glucose?
G3P, 1 of 6 will make sugars
144. What molecule is a competitive inhibitor of the enzyme in Q141? Define photorespiration.
Oxygen is a competitive inhibitor of the Rubisco enzyme
Photorespiration- a light dependent process in some plants resulting in the oxidation of glycolic acid and release of carbon dioxide that under some environmental conditions (as high temperature) tends to inhibit photosynthesis.
145. What type of cell undergoes mitosis? Meiosis?
Mitosis- Somatic cells
Meiosis- Gametes (sex cells)
146. What occurs in G1 of the cell cycle? S phase? G2? M stages?
G1- “Growth 1”- Normal cell activity, making proteins and growing
S phase- “Synthesis”- DNA is replicated
G2- “Growth 2”- Cell continues to grow
M stages- “Mitotic”- Cell divides into daughter cells and go back to G1 phase
G1- Gap for growth
S- DNA replication
G2- gap for growth
M- mitosis
147. What is a chromosome composed of?
DNA wrapped around proteins called histones
Linear strands of DNA complexed with proteins
148. When in the cell cycle do chromosomes replicate? What holds the two sister chromatids together?
After S phase, chromosomes are replicated and the sister chromatids connect at the centromere
The centromere holds the sister chromatids together
149. Draw and describe what occurs in the following mitotic stages: prophase, prometaphase, metaphase, anaphase, telophase.
Prophase- Chromosomes condense, and spindle apparatus begins to form
Replicated chromosomes condense. Mitotic spindle forms; Sister chromatids are visible; Nuclear envelope starts to breakdown.
Prometaphase- Nuclear envelope breaks down and microtubules contact chromosomes at kinetochores
Spindle fibers reach chromosomes and contact kinetochores.
Metaphase- Chromosomes complete migration to the metaphase plate
Chromosomes line up at the middle.
Anaphase- Sister chromatids separate into daughter chromosomes and are pulled to opposite poles of the spindle apparatus
Spindle fibers shorten
Telophase- Nuclear envelope re-forms and chromosomes elongate
Spindle disappears; nuclear envelope reforms and chromosomes begin to unwind.
150. What is cytokinesis?
Division of the cytoplasm and cell membrane.
Splitting of the cell membrane to form two new cells.
Plant cells form a cell plate while animal cells exhibit a cleavage furrow to do so.
151. Chromosomes that code for the same traits are said to be___________ chromosomes.
Homologous
152. Cells that contain a complete set of chromosomes from Q151 are said to be _____________ whereas cells that only contain one set of chromosomes are said to be __________________.
Diploid
Haploid
153. What occurs in prophase I of meiosis, and how is it important?
Chromosomes condense, bivalents form (homologous chromosome pairs joined together at chiasmata). It is important because the chiasmata mark the site of crossing over which promotes genetic diversity.
Homologous chromosomes come together (synapsis) and form a tetrad. Crossing over at chiasmata- homologous chromosomes exchanges segments.
154. Do homologous chromosomes separate in meiosis II or I?
Meiosis I
155. Mitosis produces ___________ (#) daughter cells that are ______________(chromosome #) and genetically ____________ whereas meiois produces ____________(#) daughter cells that are ____________________(chromosome #) and genetically __________________.
2 (46)
Diploid
Identical
4 (23)
Haploid
Different
156. What is nondisjunction?
When chromosomes fail to separate completely, or correctly during M phase of meiosis. (If both homologs in meiosis I or both sister chromatids in meiosis II move to the same pole of the parent cell.)
Failure of one or more pairs of homologous chromosomes to separate normally during nuclear division, usually resulting in an abnormal product of meiosis.
157. Describe the following chromosomal alterations: deletion, duplication, and inversion.
Deletion- Mutation in which during replication, part of the sequence of DNA is missing.
Loss of one or more nucleotides from a gene by mutation (the loss of a fragment of a chromosome)
Duplication- Mutation in which during replication, part of the sequence of DNA is repeated.
Repetition of part of a chromosome resulting from fusion with a fragment from a homologous chromosome, resulting from reattachment of a chromosome fragment to the original chromosome, but in a reverse direction.
Inversion- Mutation in which during replication, part of the sequence of DNA is reversed.
158. How does meiosis lead to genetic variation and why is genetic variation often advantageous?
Meiosis leads to genetic variation through RANDOM crossing over of homologous chromosomes from each parent cell. Advantageous because the more variety, the higher chance a species has to adapt to a changing environment
It leads to genetic variation, because you get 23 chromosomes from each your mother and your father. So there is some variation. That way, people are not exactly the same as their family members.
159.What enzyme builds new strands of DNA? Onto what end 5’ or 3’ can it add new nucleotides?
DNA polymerase III builds new strands of DNA
5’- 3’
160. Describe how DNA replication is semi-conservative.
Produces two copies that each contain one original strand of DNA and one new strand of DNA
When two strands become four strands after replication, then each double helix has a new strand and one old strand. This means that the newly formed double helix is half new and half old.
161. What are origins of replication/replication bubbles?
Specific sequence of bases. Bacterial chromosomes have one origin while eukaryotes have several.
Bacterial chromosomes have a single location where the replication process begins and a single bubble forms. Eukaryotes have multiple sites where each DNA synthesis begins, so it has multiple origins for replication bubbles.
162. What must first be placed so that the enzyme in Q159 can build a new DNA strand? What enzyme catalyzes this?
A primer must be added (DNA/RNA fragment)
163. What enzyme catalyzes the opening of DNA during replication?
DNA helicase
164. What is the leading strand? Lagging strand?
Leading- The strand being synthesized in the 5>3 direction towards the replication fork
In DNA replication, the strand of new DNA that is synthesized in one continuous piece, with nucleotides added to the 3’ end of the growing molecule (continuous strand)
Lagging- The strand being synthesized in the 5>3 direction away from the replication fork
In DNA replication, the strand of new DNA that is synthesized discontinuously in a series of short pieces that are later joined together (discontinuous strand)
165. What are Okasaki fragments?
Segments of synthesized DNA on the lagging strand made because the lagging strand must be synthesized backwards. Are later joined together to form a complete strand of newly synthesized DNA.
Short fragments of DNA synthesized on the lagging strand during DNA replicaion
166. What enzyme catalyzes the joining of fragments from Q165 together?
DNA ligase
167. What enzyme catalyzes the removal of primers and synthesis of DNA in place of the primers?
DNA polymerase
168. Contrast the starting of prokaryotic and eukaryotic DNA replication.
Location: In prokaryotes- occurs in the cytoplasm; in eukaryotes- occurs in the nucleus
Prokaryotic DNA is organized into circular chromosomes while eukaryotic DNA is organized into linear chromosomes
Prokaryotic have one replication bubble while eukaryotes have several
Prokaryotes have a single termination site
Prokaryotic- DNA is arranged in a circular shape and there is only one replication origin when replication starts. Eukaryotic chromosomes have multiple origins of replication.
169. What are some causes of DNA damage?
Chemicals in tobacco, cell divides when not ready, high levels of proto-oncogenes or mitogens, defective cyclins and CDK.
170. Describe the excision repair system.
Four steps in the nucleotide excision repair:
1.Error detection- enzymes detect an irregularity in DNA structure and cut the damaged strand.
2.Nucleotide excision- an enzyme excises a stretch of nucleotides that includes the damage.
3.Nucleotide replacement- DNA polymerase fills in the gap in the 5’3’ direction.
4.Nucleotide linkage- DNA ligase links the new and old nucleotides.
171. What molecule brings information on how to construct a protein from the nucleus to ribosomes in the cytoplasm? mRNA 172. What is the process of making the molecule from Q171 called?
Transcription
173. What is the process of synthesizing a protein by reading the molecule from Q171 called?
Translation
174. What is the central dogma of molecular biology? What are two exceptions?
Central dogma summarizes the flow of information in cells
DNA codes for RNA, which codes for proteins.
Information in cells flows in one direction: DNA (info storage)RNA (info carrier)Proteins (active cell machinery)
Exceptions:
Many genes code for RNA molecules that do not function as mRNA, they are not translated into proteins
In some cases, information flows in reverse – RNA back to DNA
175. What is the genetic code? Is it universal or different between different species?
Genetic code is different between species
Region of DNA that carries information for a discrete hereditary characteristic.
176. Why is the genetic code said to be redundant yet specific?
Because there are several different codons for only a few proteins
1 protein can code for multiple things
Ratio- 61 codons: 20 amino acids
177. What are codons?
Short sequences of DNA that code for a specific amino acid
3 base sequence
Each code for a specific amino acid
178. What is a mutation?
A change in the normal base sequence of DNA
179. Describe the following types of mutations and how they would affect a protein: silent, substitution, nonsense, frameshift.
Silent- does not affect final protein (often in 3rd base of codon)
Missense- changes sequence of amino acid (replacement)
Nonsense- results in a STOP codon (shortened- truncated protein)
Frameshift- insertion or deletion of a base shifts the reading frame of the codons which changes the sequence of amino acids
180. What enzyme catalyzes the building of RNA from a DNA template?
RNA polymerase
181. What is a gene? Promoter? Terminator?
Gene- region of DNA that carries hereditary information
Promoter- starts transcription
Terminator- ends transcription (causes everything to disassociate and translation stops)
182. What is the function of the -35 and -10 boxes of a prokaryotic promoter?
It is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand.
183. What is the job of sigma in prokaryotic transcription?
Binds to the promoter and opens the double helix
184. What is RNA processing? Does it occur in prokaryotics, eukaryotics or both?
The processing or post-transcriptional mods of mRNA before entering cytoplasm.
In eukaryotes- in the nucleus; after the pre-mRNA is processed, it exits the nucleus and is translated
185. What is removed during in the process of RNA processing?
Introns
186. What is added onto the ends of RNA during RNA processing? Why?
5’ caps and 3’ poly A tails in order to keep enzymes from chewing it up
187. What is alternative splicing and how does it contribute to the diversity of proteins within a cell?
Producing several proteins from a single gene
Splicing- removal of introns
188. What organelle is central to the process of translation? What is composed of?
Ribosome- large subunit and small subunit
189. What are tRNA? What is their main function?
Transfer RNA, bring amino acids to ribosomes in the cytoplasm for protein synthesis
190. What is an anticodon?
A specific three-base nucleotide sequence on tRNA that is complementary to a mRNA codon
Pairs to codon
On tRNA
191. There are more codons than tRNAs – how does the wobble hypothesis account for this.
61 codons; 40 tRNAs
Wobbling occurs at the 3rd position of the codon
A third base in each sequence is interchangeable (redundant but specific)
192. What are the roles of the E, P and A sites within the large ribosomal subunit?
E- holds a tRNA that will exit
P- holds the tRNA with growing polypeptide attached
A- holds an aminoacyl tRNA
193. Describe what occurs during translation in (1) initiation; (2) elongation and (3) termination.
Initiation- mRNA binds to small subunit, tRNA binds to AUG codon, large subunit binds to complete assemble
Elongation- 2nd tRNA binds to A site, peptide bond forms between 1st and 2nd amino acids, ribosome moves in 3’ direction, tRNA that was in P site no longer has an attached amino acid and enters E site, new tRNA moves into A site, peptide bond forms between amino acid in A site and the growing chain in the P site, chain is transferred by the formation of bond to the A site, ribosome moves in the 3’ direction, tRNA in E site exits and empty tRNA in P site is transferred to E site
Termination- ribosome reaches a stop codon, protein is released, ribosomal subunits separate and mRNA is released
194. When in the cell cycle does a cell undergo replication? Transcription? Translation?
Replication- during interphase or s phase
Transcription and translation- G1 and G2
195. What is a tumor? What is the difference between a benign and malignant tumor? Which have differences in cell division, cell differentiation? Both?
A tumor is a region of uncontrolled cell growth
Benign is not cancerous, malignant is
Benign tumors have not metastasized
Malignant tumors have spread to other regions in the body
Malignant tumors have problems in both cell differentiation and cell division
Benign tumors are well differentiated but have no problems with cell division
196.What is the role of checkpoints throughout the cell cycle?
To make sure that the damaged DNA does not replicate
Also to check that the cell is big enough, that organelles within the cell have matured enough before and after replication, or that DNA is replicated properly
197.What class of proteins promotes the cell cycle? Sets breaks to the cell cycle?
P class proteins
Proto-oncogenes
Lac I gene and repressor protein
Sets breaks- P53
198. What are oncogenes?
Genes that when mutated or expressed at high levels helps turn a normal cell into a tumor cell
Various genes that control cell growth that are inappropriately activated
Tumor inducing genes
Gene that when mutated or expressed at abnormally high levels contributes to converting a normal cell into a cancer cell
199. What is the maturation-promoting factor (MPF) comprised of? When is it highest? What is its function?
Made of cyclin B and cyclin-dependent kinase (CDK). MPF promotes the entrance into mitosis (the M phase) from the G2 phase by phosphorylating multiple proteins needed during mitosis. MPF is activated at the end of G2 by a phosphate, which removes an inhibitory phosphate group added earlier.
The MPF is also called the M phase kinase because of its ability to phosphorylate target proteins at a specific point in the cell cycle and thus control their ability to function
200. How does cyclin dependent kinase (cdk) become activated? How does MPF become inactivated after mitosis?
When CDKs and cyclin form a complex and activate CDK, it is called an MPF or maturation-promoting factor.
The presence of enough MPFs will cause the cell to move from the G phase into the mitotic of M phase.
Towards the end of mitosis, the MPF deactivates itself by promoting the degradation of cyclin.
The CDKs remain for later use but are now inactive because of the lack of cyclin
201. How do growth factors induce the cell cycle (ie. Cause mitosis)?
MPF-induces mitosis in all eukaryotes
MPF is a dimer consisting of a cyclin and a cyclin-dependent kinase (CDK)
CDK catalyzes phosphorylation of other proteins to start mitosis
202. What types of proteins are mutated in familial cancer syndromes (ie. Breast-ovarian; colo-rectal)?
Breast-ovarian-tumor suppressors that help in DNA repair
Colo-rectal- mutations in denes for mismatch repair system
203. What is the role of p53?
“Breaks” pushes cell into cycle arrest
Tumor suppressor
Prevents uncontrolled cell growth
Inhibit cell cycling by induction of p21 transcription
Detect DNA damage, telomere shortening, hypoxia, hyperproliferative signals
Initiate apoptosis
203. What makes cells different from other cells?
Structure
Function
204. What is a stem cell?
Eukaryote
An undifferentiated cell that can differentiate into any cell type
A cell capable of self renewal
Can produce daughter cells that can differentiate
205. What are the three levels of control of protein expression/function in prokaryotes?
Transcriptional, translational, and post-translational
206. What is the role of transcription factors? How are they regulated?
Inhibit or initiate gene expression
We do not know the mechanism for it (biggest problem with DNA)
They are nuclear proteins that, when activated, bind specific DNA regions (response elements) near a gene’s promoter and activate or repress the transcription of that gene, leading to increased OR decreased synthesis of the encoded protein
Regulated:
Phosphorylation of a kinase
Concentration
Activity
207. Under what environmental conditions is transcription of the lac operon at low levels? What occurs at the lac operon to account for this?
Lactose present/ glucose absent
Under low glucose levels, transcription of lac operon increases
Needed for transcription- lactose, empty o-site (lactose inhibits repressor protein), full capsite (glucose not there to inhibit CAP protein)
Presence of cAMP increases the transcription of lac operon
Activator- CRP
208. Under what environmental conditions is transcription of the lac operon turned off? What occurs at the lac operon to account for this?
No glucose/ lactose/ cap bond
In the lac operon with the presence of lactose, transcription is turned on
Off- repressor protein is locked to operator to prevent production of enzymes that would be used for breaking down abundant nutrients
209. Under what environmental conditions is transcription of the lac operon at its highest? What signaling system accounts for this and what is occurring at the lac operon?
High lactose/ low glucose (glucose absent/ lactose present)
If lactose is absent, LacR blocks access to the promoter
If glucose levels are high, cAMP levels will be low
Lactose removes repressor
Low glucose activates adenylyl cyclase and increases cAMP cAMP binds to catabolite activator protein (CAP)
CAP-cAMP binds to a specific promoter sequence and facilitates binding of RNA pol to activate transcription
210. What is a riboswitch?
Single stranded RNA that regulates gene translation
Causes molecules to bind and affect secondary structure
An mRNA that controls gene expression in response to concentration of small molecules. The gene controlled is involved in the synthesis of the metabolite which regulates the riboswitch
Found in un-translated parts of a bacteria mRNA
211. Give examples of post-translational modifications of proteins that can affect protein activity.
Phosphorylation- Ser, Thr, Tyr (the Hydroxyl groups)
Hydroxylation- Pro, Lys (the N groups)
Glycosylation- Ser, Thr, Asn for membrane or secreted proteins
Carboxylation- In clot formation
Prenylation- Addition of hydrophobic groups
This is a comprehensive review of material from exams 1-3. Please study your class notes/powerpoint slides and read the chapters listed in your syllabus to study for all new material.
What are the characteristics of living organisms?
Acquire and use energy
Made up of other cells
Process information
Can replicate itself (can reproduce)
Population evolves (they evolve)
What are the characteristics of cells?
Contain genetic information
Can duplicate themselves
Have a cell membrane
Have a cytoplasm
Have ribosomes
The structure of a cell is closely correlated with its function
Cells are dynamic thousands of chemical reactions occur in each second
Most cells are capable of division
What is a scientific theory? How does this differ from everyday usage of the term “theory”?
An explanation for a very general class of phenomena or observations that are supported by a wide body of evidence.
A scientific theory summarizes a hypothesis of group of hypotheses that have been supported with repeated testing. If enough evidence accumulates to support a hypothesis, it moves to the next step- known as a theory- in the scientific method and becomes accepted as a valid explanation of a phenomenon
When used in non-scientific context, the word “theory” implies that something is unproven or speculative. As used in science, however, a theory is an explanation or model based on observation, experimentation, and reasoning, especially one that has been tested and confirmed as a general principle helping to explain and predict natural phenomena
Scientific theories are testable explanations, not speculative guesses
What are the two components of a scientific theory?
Null hypothesis
Alternative hypothesis
Pattern component (based on observation)
Process component (based on experimentation)
The two critical components of a scientific theory is that it provides explanations and predictions that can be trusted
Describe the cell theory
All organisms are made of cells.
The cell theory and theory of evolution address fundamental questions:
What are organisms made of?
Where do they come from?
It also states that all organisms are made of cells (this formed only the first part of the cell theory). The complete cell theory can be stated as follows: “All organisms are made of cells, and all cells come from preexisting cells.”
The cell theory was a direct challenge to the prevailing explanation of where cells come from, called spontaneous generation
Pattern- all material is made of cells
Organisms and their characteristics change; living populations change
Process- Pasteur’s experiment that rejected spontaneous
Field studies have proved this
What are the two main types of cells?
Prokaryotes
Eukaryotes
Describe prokaryotic cells with regard to: DNA storage/organization, site of protein synthesis, membranes.
Have no membrane bound organelles
DNA is circular, organized in a nucleoid region
Protein synthesis takes place in ribosomes
DNA storage/organization DOES NOT have a nucleus but contains a nucleoid region where DNA is stored
Site of protein synthesis: Proteins are synthesized in the ribosomes found in the prokaryotic cell
Describe eukaryotic cells with regard to: DNA storage/organization, site of protein synthesis, membranes.
Membrane bound organelles
DNA located in the nucleus
Proteins synthesized in both rough ER and ribosomes
What type of cells from Q6 have membrane bound organelles?
Eukaryotes
Nucleus
ER
Golgi apparatus
Lysosomes
Endosomes
Mitochondria
What are the advantages of membrane-bound organelles?
Reactions occur more efficiently
Has the ability to protect the cell from unwanted side effects
For the following cellular organelles (1) be able to identify and (2) describe their function: ribosomes, nucleus, endoplasmic reticulum (rough and smooth), peroxisome, lysosome, mitochondria, vacuoles, chloroplast
Ribosomes- Synthesize proteins
Nucleus- Carries chromosomes in nucleolus
Rough ER- Has ribosomes, produce proteins to export
Breaks down toxins and synthesized lipids, stores calcium
Peroxisome- Fatty acid processing with catalase to breakdown H202
Lysosome- Break down macromolecules and mitochondria with hydrolytic enzymes
Mitochondria- Site of ATP production, and undergoes cellular respiration
Vacuoles- Storage of water, toxins, oils and carbohydrates
Chloroplast- Site of photosynthesis and ATP production ONLY in plant cells
For the organelles in Q11, which are present in only eukaryotes or in both prokaryotes and eukaryotes?
Eukaryotes-
HAS Nucleolus
HAS Smooth and rough ER
HAS Mitochondria
HAS Chloroplasts
HAS Ribosomes- relatively large
HAS Lysosomes
HAS Peroxisomes
HAS Vacuoles
HAS Golgi
HAS Nuclear envelope
HAS microtubules, intermediate filaments and microfilaments
Multiple, linear chromosomes with wound on nucleosomes
Prokaryotes (don’t have membrane bound organelles)-
HAS Ribosomes- relatively small
HAS Nucleoid
NO Golgi
NO ER
NO Lysosomes
NO Peroxisomes
NO Mitochondria
NO microtubules, intermediate filaments or microfilaments
NO nuclear envelope
Single, circular chromosomes with no nucleosomes
Describe how the structure of a cell is correlated with its function?
A cells shape is related to its function
What are the most abundant elements in living organisms?
Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur (CHNOPS)
What is the structure of an atom?
There is a nucleus made up of protons(+) and neutrons(no charge) surrounded by a cloud or ring of electrons(-)
In a neutral charges atom, there is one proton for every electron
What is the atomic number? Mass number?
Atomic number- number of protons in an atom (# never varies)
Mass number- number of protons and neutrons (this can vary- isotopes)
What are valence electrons? How are they contributing to an atom’s reactivity?
Valence electrons- unpaired electrons in the outermost orbital or shell
Atoms become stable once there are no longer outer orbitals that only contain single electrons
The further away the valence electron, the more reactive
What are covalent bonds – polar and non-polar?
Covalent can be polar or non-polar
Non polar- two atoms share the electrons equally
Polar- if one atom is more electronegative it will pull the electron closer to its nucleus
What are ionic bonds?
One atom loses an unpaired electron, and another element gains an electron to fill its orbital
What is a hydrogen bond?
Involves the bonding between H and one of three different elements: N, O, or F (Nitrogen, Oxygen, or Fluorine)
These bonds are fairly weak and are easily broken
What type of bond(s) are most often found in living organisms?
Polar/non-polar covalent bonds
What types of bonds are found in water?
Covalent
Hydrogen bonding
Has polarity
Hydrogen bonding
Gives water structure: cohesion
High specific heat (amount of heat to raise T 1 degree Celsius)
High heat of vaporization
It is a good solvent for ionic, polar molecules
Nonpolar molecules do not dissolve in water
Define hydrophobic and hydrophilic.
Hydrophobic- “Water fearing”
Hydrophilic- “Water loving”
28. What is potential energy? Entropy?
Potential energy- the amount of energy stored in the reacting molecules
Entropy- The amount of disorder in the reacting molecules
29. What happens to the two in Q28 over the course of a chemical reaction?
Endergonic reaction- ^S decreases; ^H increases
Exergonic reaction- S increases; H decreases
30. What determines if a particular reaction is spontaneous?
If delta G is (-), then it is spontaneous
If delta G is (+), then it is nonspontaneous
For delta G to be (-) (regardless of T), delta H needs to be (-) and delta S would need to be (+)
31. What is the formula for Gibb’s free energy of a reaction? Define the variables.
Delta G = Delta H – (T Delta S)
Delta G- Total free energy change in a reaction
Delta H- Change in potential energy
T- temperature
Delta S- change in entropy
32. Define endergonic, exergonic, endothermic, exothermic reactions. Which are spontaneous?
Endergonic- Energy must be absorbed into system; this would be nonspontaneous (also anabolic)
Exergonic- gives off energy (energy is released); this would be spontaneous (also catabolic)
Endothermic- energy, in the form of heat, being absorbed (absorbs heat); this would be nonspontaneous
Exothermic- energy, in the form of heat, being released (gives off heat); this would be spontaneous
Exothermic and Exergonic are spontaneous
33. Draw a graph of the change in free energy of a reaction for both a spontaneous and non-spontaneous reaction.
34. What are the monomers of a protein?
Amino acids
35. What kind of bond joins Q34 together?
Peptide bonds
36. Draw a generalized amino acid with a “R” representing the side group. Label the amino and carboxyl groups.
37. How are side groups important?
Side groups determine properties of particular amino acids
Side groups could be any one of the following: polar, acidic, basic, or nonpolar.
The sequence of the amino acids (and therefore the side groups) determines how these side groups will interact with each other and will affect what shape the overall protein takes
38. Describe the primary, secondary and tertiary structure of a protein.
Primary- this structure has to do with just the sequence of the amino acids themselves
Secondary- this structure deals with the folding of the amino acid chain due to H-bonding
Tertiary- this structure deals with the folding of the amino acid chain specifically due to side group interactions
39. What kind(s) of bonds are important to each level of structure in Q38?
Primary- covalent bond
Secondary- alpha helix, beta sheet
Tertiary- van der wals, H-bonds, covalent
Quaternary- aggregation of polypeptide subunits
40. What is the quaternary structure of a protein?
Structure made up of multiple polypeptide chains together (there would need to be more than one protein involved to make this structure)
41. List 5 functions of proteins in a cell.
1. Catalysts reactions (speeds up reaction)
2. Defense (antibodies in immune system)
3. Movement (actin and myosin)
4. Signaling (insulin receptors)
5. Cell structure (keratin in hair)
Also.. 6. Transport (Na+ K+ exchangers across membranes)
42. How are form and function related with respect to proteins?
Since shape determines function and function is part of what dictates it’s shape, each one informs us about the other
One cannot exist without the other
43. What are catalysts?
Something that speeds up reactions by reducing the activation energy required for spontaneous reactions.
Increases the rate of a chemical reaction without undergoing a chemical change itself
44. How do enzymes catalyze biological reactions?
By reducing the activation energy required for spontaneous reactions
45. Draw a graph of the free energy of a reaction with an enzyme. Label the transition state and activation energy.
46. How do enzymes affect the transition state & activation energy?
It lowers both of them
47. Do enzymes change the overall free energy change of a reaction?
No
48. What are cofactors? Coenzymes?
Cofactors- Inorganic ions such as Zn, Mg, or Fe, that helps bind the substrate to the active site better
Coenzymes- small organic molecules, often within active site
Both of these help increase levels of reaction within enzymes
49. Describe competitive inhibition of an enzyme.
The competitive inhibitor will bind to the active site
It can do this because it often has a similar shape to the substrate
It “competes” with the substrate to bind to the active site
50. What is allosteric activation? Deactivation?
Either will bind to someplace on the enzyme other than the active site
Allosteric activator or deactivator will bind to someplace on the enzyme other than the active site. Depending on how and where it binds, the molecule could change the shape of the enzyme to make it better able to bind with substrates (allosteric activation) or it could change its shape so that substrate have a hard time to bind (allosteric deactivation)
51. In Q49 & Q50 are the active sites involved? Explain.
^Explained in Q50
55. What are the two types of nucleic acids?
1. DNA
2. RNA
56. What are the monomers of nucleic acids?
Nucleotides
57. What are the 3 components of Q56?
1. One 5-carbon sugar
2. A phosphate group
3. A nitrogenous base
58. How do the sugars and nitrogenous bases differ between DNA and RNA?
Three of the nitrogenous bases are the same for both RNA and DNA; guanine, adenine, and cytosine.
Thymine, the fourth base pair found in DNA, is replaced by uracil in RNA.
DNA has deoxyribose sugar while RNA has ribose sugar.
The deoxyribose sugar has one less oxygen atom than the ribose sugar.
59. What are pyrimidines? Purines? Draw one example of each.
The bases thymine and cytosine present in DNA are pyrimidines.
Purines are the bases adenine and guanine present in DNA and RNA
Purines- Adenine, Guanine
Pyrimadines- Uracil, Thymine, Cytosine
60. How many strands is DNA? RNA?
DNA is two stands, and RNA is one strand
61. If 2 strands in Q60, what holds the strands together?
Hydrogen bonds
H+ bonds between nitrogen containing rings of nucleotide base pairs
With opposing bases
62. What are the base pairing rules? Which pairs have 2 hydrogen bonds? Three?
AT, CG, AU in RNA
Adenine and thymine held by two
Cytosine and Guanine held by three
63. Why is DNA said to be antiparallel?
One end runs three prime to five prime (3’5’) while the other runs five prime to three prime (5’3’) (two DNA strands running in opposite directions will bond together via H-bonding and stick together)
One strand of the original DNA is preserved and one is newly made
64. What is the function of DNA?
Contains all genetic material
Stores genetic information and directs protein synthesis
65. What are four functions of RNA?
1.Messenger RNA (mRNA) contains the codons for peptide chain synthesis
2.Transfer RNA (tRNA) transports amino acids to the ribosome during protein synthesis
3.MicroRNA destroys mRNA
4.Ribosomal RNA (rRNA) structural component of ribosomes
66. Can DNA or RNA act as catalysts? Why?
RNA because it can act as a catalyst to itself, ribosomal RNA (rRNA)
67. What elements make up carbohydrates?
Carbon, Hydrogen, and Oxygen
68. What are three functions of carbohydrates in cells?
1. Carbohydrates are the ready source of energy
2. They also play a structural role (e.g.. Cellulose in plants and chitin in arthropods)
3. They combine with certain classes of lipids (to form glycolipid) and proteins (to form glycoprotein) to confer on them the biological function
4. They continue the overcoat of the plasma membrane and thus help in conferring on it the property of recognition, cell sociology, and antigenic property
-Provide identity to cells
-Energy source for cells
-Energy storage for cells
69. Contrast mon-, di-, oligo- and poly-saccharides.
Monosaccharides consist of a single sugar
Disaccharides consists of two sugars
Polysaccharides consists of a chain of monosaccharides
70. Simple sugars are in which class from Q69?
Monosaccharides
71. What is the bond between sugars in oligo- and polysaccharides?
Glycocidic bonds
72. For starch, glycogen, cellulose and chitin, describe (1)structure and components; (2) type of cells that contain the particular polysaccharide and (3) function.
Polysaccharide- polymers of hundreds to thousands of monosaccharides linked together by dehydration reactions
Function as storage molecules or as structural compounds
Starch- found in plants and is served as storages for energy or the plant’s building materials
Glycogen- found in animals and act as a storage for energy and release glucose when needed
Cellulose- major component of plant cell walls
73. What are lipids? Are they hydrophobic or hydrophilic?
Category of compounds containing carbon, hydrogen and oxygen that are hydrophobic
Insoluble in water
Non-polar (fats, oils, cholesterol)
Soluble in non-polar solvent
4 main groups of lipids (fats, phospholipids, waxes and steroids)
Used to store long-term energy
74. Draw the basic structure of a fat and label the glycerol and fatty acid tails.
75. What is the difference between saturated and unsaturated fats? Which are liquid at room temperature?
Saturated fats are solid at room temperature and unsaturated fats are liquid at room temperature
76. What are steroids?
Lipids derived from cholesterol
77. What are phospholipids? How are they amphipathic?
Phospholipids: form a phospholipid bilayer (cellular membranes)
Phospholipids are a class of lipids that make up the main component in cell membranes
Forms two distinct layers- polar heads facing water in the interior and exterior of the cell (hydrophilic); Non-polar tails facing each other on the interior of the membrane (hydrophobic)
Contains two fatty acids in the hydrophobic regions
Fatty acids for micelles in water (single layer droplet)
Provides biosynthetic activities in smooth ER
78. What kind of reaction builds all biological macromolecules discussed in class? What type of reaction breaks them?
Builds- dehydration reactions (water is removed)
Breaking- hydrolysis (water is added)
79. What are cellular membranes comprised of?
Phospholipids and the mosaic model (proteins, carbohydrates, and cholesterol)
80. Describe the terms “fluid” and “selectively permeable” with respect to cell membranes.
Fluid- no bond
Phospholipids are not bound together; Independent molecules
Selectively permeable- only allow certain things to enter or exit the cell
81. Are biological membranes highly permeable, moderately permeable or impermeable to the following molecules: (1) small nonpolar (like carbon dioxide), small uncharged polar (like water), large uncharged polar (like sugars and amino acids) and charged ions.
Small non-polar- highly permeable
Small, uncharged polar- moderately permeable
Large, uncharged polar- moderately permeable
Charged ions- impermeable
82. How do the following affect membrane permeability: (1) saturation of tails; (2) cholesterol and (3) temperature.
1.Saturation of fatty acid tail- lowers permeability; more saturated = less fluid membrane
2. More cholesterol = less fluid membrane
3. Temperature- lower fluidity with lower temperature due to closer packing of fatty acid tails
83. What is diffusion? Osmosis?
Diffusion- molecules going from high to low concentrations
Osmosis- water diffusing from high to low concentration
84. If cells are placed in a (1) hypertonic, (2) isotonic, or (3) hypotonic solution will water move into or out of the cell? Define the terms 1-3.
Hypertonic- there is too much water outside the cell and not enough inside the cell causing the cell to shrivel up
Hypertonic- there is too much water in the cell and not enough outside the cell, causes cell to swell and burst; water will flow out of the cell and the cell will shrink
Isotonic- water moves throughout the cell evenly; the difference between channel and carrier proteins; at equilibrium
All are involved in osmosis!
Hypotonic- water will flow into the cell and the cell will swell
85. Describe the fluid mosaic model of cell membrane structure.
The fluid mosaic model states that proteins float in a sea of lipids.
A cell membrane is composed of lipids arranged with their hydrophobic tails touching each other, with proteins scattered
The membrane surrounds these cells has two layers (a bilayer) of phospholipids (fats with phosphorous attached).
Both layers have the hydrophilic heads pointing toward the outside; the hydrophobic tails form the inside of the bilayer
86. What is facilitated diffusion? What types of molecules are transported in this manner?
It is an active process
Against gradient
87. What is the difference between channel and carrier proteins and in what type of transport are they involved?
Isotonic; osmosis
88. Is diffusion an active or passive process? Facilitated diffusion?
Diffusion is a passive process
Facilitated diffusion is an active process
89. What types of transport move molecules down their concentration gradients? Against their concentration gradients?
Passive transport
Carrier proteins- carry large/uncharged molecules across a membrane (very selective)
Channel- carry ions across a membrane (slightly selective)
Against gradient- active transport (facilitated diffusion)
90. What is endocytosis? Exocytosis?
Endo- into the cell (engulf)
Exo- out of the cell (excrete)
92. What structures in the nuclear envelope controls transport of substances into and out of the nucleus?
Membrane bound transport proteins
Nuclear pores
93. What must a molecule have in order to be transported into the nucleus? Endoplasmic reticulum?
Nucleus- must have a nuclear localization signal
ER- must have an ER signal sequence
94. How is importin involved in transport into/out of the nucleus? SRP into the endoplasmic reticulum?
NLS interacts with importin Which interacts with the pore complex.
Exportin- brings molecules out of the nucleus.
SRP binds to signal sequence which then a ribosome docks to the signal sequence.
95. Trace the pathway of a protein made in the rough endoplasmic reticulum that is destined to be exported from the cell. Explain what happens to the protein along its journey.
SRP binds to the ER signal sequence ribosome docks with the ER protein is deposited into lumen of ER (Rough ER) = proteins in the lumen get folded into tertiary shape (Smooth ER)= proteins get glycosylated (sugar tag added) Proteins enter transport vesicles.
96. How is the golgi apparatus critical for proteins transport to the correct places within the cell?
The golgi assigns additional sugar tags to the proteins and then they get shipped to their specific destination that matches their sugar tag.
97. What are the three components of the cytoskeleton and their relative sizes? Which one is most stable?
1.Microfilaments= smallest
2.Intermediate filaments= middle (most stable)
3.Microtubules= largest
98. What cellular processes are myosin-actin filaments involved?
Movement in muscle cells
99. Which of Q97 have polarity? What is polarity associated with?
Microfilaments
Polarity is what makes them dynamic (able to grow/shrink)
100. What are nuclear lamins? What type of cytoskeletal element from Q97 are they?
Class V intermediate filaments
Fibrous proteins, providing structural function and transcriptional regulation in the cell nucleus
Nuclear lamins interact with membrane-associated proteins to form the nuclear lamina on the interior of the nuclear envelope
From intermediate filaments and holds shape of nucleus and strengthens pores
101. What are microtubule tracks and how is kinesin involved in their function?
Move transport vesicles along microtubules
Kinesin- motor protein associated with this
102. What are cilia and flagella composed of? What is the internal structural arrangement of these components?
Composed of microtubules
9+2 inner arrangement of microtubules with Dynein arms (9 outer and 2 inner)
103. How is dynein involved in the movement of cilia and flagella?
Dynein is a motor protein
104. How are microtubules essential to mitosis?
Microtubules form centromeres of a tetrad
105. What are 3 purposes of cell junctions?
1.Provides a tight seal between adjacent cells (tight junctions)
2.A removable anchor between cells (anchoring junctions)
3.Allows nutrients, etc. between cells (gap junctions)
106. Contrast tight, anchoring, and gap junctions.
Tight- plasma membranes of neighboring cells are tightly pressed against each other and knit together by proteins, prevent leakage of fluid across a layer of cells.
Anchoring- fasten cells together into strong sheets, intermediate filaments made of sturdy keratin proteins anchor these junctions in the cytoplasm, coming in tissues subject to stretching or mechanical stress, such as skin.
Gap- channels that allow small molecules to flow through protein-lined pore between cells. Common in embryos
Although both tight and gap junctions are made up of membrane-spanning proteins, tight junctions seal adjacent animal cells together while gap junctions allow a flow of material between them
107. What are desmosomes? What proteins link the cells in these structures?
Desmosomes- cell- cell attachments (most common anchoring junction)
Cadherin- Proteins link cells
108. What are plasmodesmata?
Gap junctions in plants where the ER extends between cells
109. What is the overall purpose of cellular respiration?
The production of large amounts of ATP
110. What is the general equation of aerobic cellular respiration?
6H12O6 + 6 O2 6 CO2 + 6 H2O
111. In what organelle does cellular respiration in eukaryotes occur? Draw and label the components of this organelle.
Mitochondria (makes ATP)
Glycolysis- cytosol
Pyruvate processing and Krebs Cycle- in mitochondrial matrix
Electron transport. Chemiosmosis & oxidative phosphorylation- in inner mitochondrial membrane
112. What is ATP used for? Draw it.
ATP is the energy currency for cells; it is used for cellular respiration, glycolysis and many other biological processes.
Phosphate- phosphate- phosphate- ribose- adenine
113. How is ATP used? Include the following terms in your explanation: coupled reactions, exergonic & endergonic reactions.
ATP is used to fuel all of the other cycles/processes but the more ATP is out into the cycle, the more ATP is yielded.
Exergonic- ATP is released
Endergonic- ATP is absorbed
Coupled reactions- ATP is both lost and gained
114. What is a redox reaction?
A reaction in which there is a transfer of electrons. One is reduced and another is oxidized.
OIL RIG- oxidation is losing electrons; reduction is gaining electrons
115. What is being oxidized and what is being reduced in the equation in Q110?
Oxygen is being oxidized and Glucose is being reduced
116. What are the 4 overall steps in aerobic cellular respiration and where do they occur in the cell?
Glycolysis- cytoplasm
Pyruvate processing, Krebs Cycle, ETC- mitochondria
117. What is NAD+?
An electron carrier
118. For glycolysis, pyruvate processing and Kreb’s cycle, list (1) reactants and products; (2) ATP formation? ; (3) CO2 released?; (4) electron carrier reduced?; (5) overall purpose.
Glycolysis- glucose Pyruvate (4 ATP made, NAD is reduced to NADH)
Pyruvate processing= pyruvate acetyl coA (NAD is reduced to NADH, 1 CO2 is released)
Kreb’s Cycle- Acetyl group CO2 (1 GTP made and 2 CO2 are released per cycle)
119. Where do electron carriers bring electrons in aerobic respiration?
Electron carriers bring electrons into mitochondrial inner membrane
Electron transport chain 120. What happens to energy as electrons are passed between proteins in Q119?
Energy is being released
121. What is the final electron acceptor in Q119?
Oxygen
122. How does the electron transport chain create a proton gradient in the intermembrane space?
Proton accumulation inside cristae builds up a proton gradient
123. Describe Mitchell’s chemiosmotic hypothesis of ATP production.
Protons try to force back into the matrix along the concentration gradient (proton motive force)
Basically, builds up energy
124. In which step from Q116 are most ATP generate?
Chemiosmosis and Oxidative Phosphorylation
125. Why can’t aerobic respiration occur in one or just a few steps?
Because the cycle needs to be broken down into those steps in order for the most ATP to be made
126. Respiration in the absence of oxygen is called?
Anaerobic respiration
127. What is the final electron acceptor in lactic acid fermentation? What is the product of this process?
Pyruvic acid product- 2 lactate
128. What is the final electron acceptor in alcohol fermentation? What it the product of this process?
Acetaldehyde product- 2 ethanol
129. Does aerobic or anaerobic respiration generate more ATP per glucose molecule?
Aerobic
130. What is the overall equation for photosynthesis?
CO2 + H2O + light energy sugars + O2
131. Draw and label the structures of a chloroplast including thylakoid and grana.
132. What are the photosynthetic pigments? Where are they located? What colors do they absorb and reflect?
Inside thylakoid membranes
Absorb light
Chlorophylls- green
Carotenoids- orange/yellow
Blue and red are absorbed and green is reflected
133. What happens to electrons in pigment molecules when they absorb light energy?
Electrons jump, then fall down (they are excited)
134. What is a photosystem? Reaction center?
Photosystem- II and I are pigment clusters on the membrane.
Reaction center receives light energy
135. In PSII, what is the fate of electrons boosted from the reaction center?
Electrons go to electron transport proteins and are then released as energy
136. How is ATP generated from the movement of the electron from Q135?
Light absorbed by the LHC energizes the photosystems and stimulates linear electron flow, resulting in production of ATP and NADPH
137. In PSI, what is the fate of electrons boosted from the reaction center?
The electron is given to the electron transport chain
138. What replaces electrons that are lost from PSI? PSII?
The electron lost from PSI is replaced by an electron transferred from PSII via another electron transport chain.
PSII replaces its electrons by extracting electrons from water molecules, releasing O2 as byproduct
139. What is the fate of water in photosynthesis?
Water separates into O2, H+ ions, and electrons
140. What two reactions are produced in the light reactions that will proceed to the light independent reactions?
ATP, and NADPH
141. What occurs in the carbon fixation phase of the light independent reactions of photosynthesis? What enzyme is involved?
The process of photorespiration also known as C2 cycle, is also coupled to the dark reactions, as it results from an alternative reaction of the Rubisco enzyme, and its final byproduct is also another gyceraldehyde.
142. What occurs in the reduction phase of the light independent reactions? Regeneration phase?
3- Phosphoglycerate is reduced to glyceraldehyde- 3- phosphate (G3P)
143. What molecules are generated by the light independent reactions and will be used to make glucose?
G3P, 1 of 6 will make sugars
144. What molecule is a competitive inhibitor of the enzyme in Q141? Define photorespiration.
Oxygen is a competitive inhibitor of the Rubisco enzyme
Photorespiration- a light dependent process in some plants resulting in the oxidation of glycolic acid and release of carbon dioxide that under some environmental conditions (as high temperature) tends to inhibit photosynthesis.
145. What type of cell undergoes mitosis? Meiosis?
Mitosis- Somatic cells
Meiosis- Gametes (sex cells)
146. What occurs in G1 of the cell cycle? S phase? G2? M stages?
G1- “Growth 1”- Normal cell activity, making proteins and growing
S phase- “Synthesis”- DNA is replicated
G2- “Growth 2”- Cell continues to grow
M stages- “Mitotic”- Cell divides into daughter cells and go back to G1 phase
G1- Gap for growth
S- DNA replication
G2- gap for growth
M- mitosis
147. What is a chromosome composed of?
DNA wrapped around proteins called histones
Linear strands of DNA complexed with proteins
148. When in the cell cycle do chromosomes replicate? What holds the two sister chromatids together?
After S phase, chromosomes are replicated and the sister chromatids connect at the centromere
The centromere holds the sister chromatids together
149. Draw and describe what occurs in the following mitotic stages: prophase, prometaphase, metaphase, anaphase, telophase.
Prophase- Chromosomes condense, and spindle apparatus begins to form
Replicated chromosomes condense. Mitotic spindle forms; Sister chromatids are visible; Nuclear envelope starts to breakdown.
Prometaphase- Nuclear envelope breaks down and microtubules contact chromosomes at kinetochores
Spindle fibers reach chromosomes and contact kinetochores.
Metaphase- Chromosomes complete migration to the metaphase plate
Chromosomes line up at the middle.
Anaphase- Sister chromatids separate into daughter chromosomes and are pulled to opposite poles of the spindle apparatus
Spindle fibers shorten
Telophase- Nuclear envelope re-forms and chromosomes elongate
Spindle disappears; nuclear envelope reforms and chromosomes begin to unwind.
150. What is cytokinesis?
Division of the cytoplasm and cell membrane.
Splitting of the cell membrane to form two new cells.
Plant cells form a cell plate while animal cells exhibit a cleavage furrow to do so.
151. Chromosomes that code for the same traits are said to be___________ chromosomes.
Homologous
152. Cells that contain a complete set of chromosomes from Q151 are said to be _____________ whereas cells that only contain one set of chromosomes are said to be __________________.
Diploid
Haploid
153. What occurs in prophase I of meiosis, and how is it important?
Chromosomes condense, bivalents form (homologous chromosome pairs joined together at chiasmata). It is important because the chiasmata mark the site of crossing over which promotes genetic diversity.
Homologous chromosomes come together (synapsis) and form a tetrad. Crossing over at chiasmata- homologous chromosomes exchanges segments.
154. Do homologous chromosomes separate in meiosis II or I?
Meiosis I
155. Mitosis produces ___________ (#) daughter cells that are ______________(chromosome #) and genetically ____________ whereas meiois produces ____________(#) daughter cells that are ____________________(chromosome #) and genetically __________________.
2 (46)
Diploid
Identical
4 (23)
Haploid
Different
156. What is nondisjunction?
When chromosomes fail to separate completely, or correctly during M phase of meiosis. (If both homologs in meiosis I or both sister chromatids in meiosis II move to the same pole of the parent cell.)
Failure of one or more pairs of homologous chromosomes to separate normally during nuclear division, usually resulting in an abnormal product of meiosis.
157. Describe the following chromosomal alterations: deletion, duplication, and inversion.
Deletion- Mutation in which during replication, part of the sequence of DNA is missing.
Loss of one or more nucleotides from a gene by mutation (the loss of a fragment of a chromosome)
Duplication- Mutation in which during replication, part of the sequence of DNA is repeated.
Repetition of part of a chromosome resulting from fusion with a fragment from a homologous chromosome, resulting from reattachment of a chromosome fragment to the original chromosome, but in a reverse direction.
Inversion- Mutation in which during replication, part of the sequence of DNA is reversed.
158. How does meiosis lead to genetic variation and why is genetic variation often advantageous?
Meiosis leads to genetic variation through RANDOM crossing over of homologous chromosomes from each parent cell. Advantageous because the more variety, the higher chance a species has to adapt to a changing environment
It leads to genetic variation, because you get 23 chromosomes from each your mother and your father. So there is some variation. That way, people are not exactly the same as their family members.
159.What enzyme builds new strands of DNA? Onto what end 5’ or 3’ can it add new nucleotides?
DNA polymerase III builds new strands of DNA
5’- 3’
160. Describe how DNA replication is semi-conservative.
Produces two copies that each contain one original strand of DNA and one new strand of DNA
When two strands become four strands after replication, then each double helix has a new strand and one old strand. This means that the newly formed double helix is half new and half old.
161. What are origins of replication/replication bubbles?
Specific sequence of bases. Bacterial chromosomes have one origin while eukaryotes have several.
Bacterial chromosomes have a single location where the replication process begins and a single bubble forms. Eukaryotes have multiple sites where each DNA synthesis begins, so it has multiple origins for replication bubbles.
162. What must first be placed so that the enzyme in Q159 can build a new DNA strand? What enzyme catalyzes this?
A primer must be added (DNA/RNA fragment)
163. What enzyme catalyzes the opening of DNA during replication?
DNA helicase
164. What is the leading strand? Lagging strand?
Leading- The strand being synthesized in the 5>3 direction towards the replication fork
In DNA replication, the strand of new DNA that is synthesized in one continuous piece, with nucleotides added to the 3’ end of the growing molecule (continuous strand)
Lagging- The strand being synthesized in the 5>3 direction away from the replication fork
In DNA replication, the strand of new DNA that is synthesized discontinuously in a series of short pieces that are later joined together (discontinuous strand)
165. What are Okasaki fragments?
Segments of synthesized DNA on the lagging strand made because the lagging strand must be synthesized backwards. Are later joined together to form a complete strand of newly synthesized DNA.
Short fragments of DNA synthesized on the lagging strand during DNA replicaion
166. What enzyme catalyzes the joining of fragments from Q165 together?
DNA ligase
167. What enzyme catalyzes the removal of primers and synthesis of DNA in place of the primers?
DNA polymerase
168. Contrast the starting of prokaryotic and eukaryotic DNA replication.
Location: In prokaryotes- occurs in the cytoplasm; in eukaryotes- occurs in the nucleus
Prokaryotic DNA is organized into circular chromosomes while eukaryotic DNA is organized into linear chromosomes
Prokaryotic have one replication bubble while eukaryotes have several
Prokaryotes have a single termination site
Prokaryotic- DNA is arranged in a circular shape and there is only one replication origin when replication starts. Eukaryotic chromosomes have multiple origins of replication.
169. What are some causes of DNA damage?
Chemicals in tobacco, cell divides when not ready, high levels of proto-oncogenes or mitogens, defective cyclins and CDK.
170. Describe the excision repair system.
Four steps in the nucleotide excision repair:
1.Error detection- enzymes detect an irregularity in DNA structure and cut the damaged strand.
2.Nucleotide excision- an enzyme excises a stretch of nucleotides that includes the damage.
3.Nucleotide replacement- DNA polymerase fills in the gap in the 5’3’ direction.
4.Nucleotide linkage- DNA ligase links the new and old nucleotides.
171. What molecule brings information on how to construct a protein from the nucleus to ribosomes in the cytoplasm? mRNA 172. What is the process of making the molecule from Q171 called?
Transcription
173. What is the process of synthesizing a protein by reading the molecule from Q171 called?
Translation
174. What is the central dogma of molecular biology? What are two exceptions?
Central dogma summarizes the flow of information in cells
DNA codes for RNA, which codes for proteins.
Information in cells flows in one direction: DNA (info storage)RNA (info carrier)Proteins (active cell machinery)
Exceptions:
Many genes code for RNA molecules that do not function as mRNA, they are not translated into proteins
In some cases, information flows in reverse – RNA back to DNA
175. What is the genetic code? Is it universal or different between different species?
Genetic code is different between species
Region of DNA that carries information for a discrete hereditary characteristic.
176. Why is the genetic code said to be redundant yet specific?
Because there are several different codons for only a few proteins
1 protein can code for multiple things
Ratio- 61 codons: 20 amino acids
177. What are codons?
Short sequences of DNA that code for a specific amino acid
3 base sequence
Each code for a specific amino acid
178. What is a mutation?
A change in the normal base sequence of DNA
179. Describe the following types of mutations and how they would affect a protein: silent, substitution, nonsense, frameshift.
Silent- does not affect final protein (often in 3rd base of codon)
Missense- changes sequence of amino acid (replacement)
Nonsense- results in a STOP codon (shortened- truncated protein)
Frameshift- insertion or deletion of a base shifts the reading frame of the codons which changes the sequence of amino acids
180. What enzyme catalyzes the building of RNA from a DNA template?
RNA polymerase
181. What is a gene? Promoter? Terminator?
Gene- region of DNA that carries hereditary information
Promoter- starts transcription
Terminator- ends transcription (causes everything to disassociate and translation stops)
182. What is the function of the -35 and -10 boxes of a prokaryotic promoter?
It is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand.
183. What is the job of sigma in prokaryotic transcription?
Binds to the promoter and opens the double helix
184. What is RNA processing? Does it occur in prokaryotics, eukaryotics or both?
The processing or post-transcriptional mods of mRNA before entering cytoplasm.
In eukaryotes- in the nucleus; after the pre-mRNA is processed, it exits the nucleus and is translated
185. What is removed during in the process of RNA processing?
Introns
186. What is added onto the ends of RNA during RNA processing? Why?
5’ caps and 3’ poly A tails in order to keep enzymes from chewing it up
187. What is alternative splicing and how does it contribute to the diversity of proteins within a cell?
Producing several proteins from a single gene
Splicing- removal of introns
188. What organelle is central to the process of translation? What is composed of?
Ribosome- large subunit and small subunit
189. What are tRNA? What is their main function?
Transfer RNA, bring amino acids to ribosomes in the cytoplasm for protein synthesis
190. What is an anticodon?
A specific three-base nucleotide sequence on tRNA that is complementary to a mRNA codon
Pairs to codon
On tRNA
191. There are more codons than tRNAs – how does the wobble hypothesis account for this.
61 codons; 40 tRNAs
Wobbling occurs at the 3rd position of the codon
A third base in each sequence is interchangeable (redundant but specific)
192. What are the roles of the E, P and A sites within the large ribosomal subunit?
E- holds a tRNA that will exit
P- holds the tRNA with growing polypeptide attached
A- holds an aminoacyl tRNA
193. Describe what occurs during translation in (1) initiation; (2) elongation and (3) termination.
Initiation- mRNA binds to small subunit, tRNA binds to AUG codon, large subunit binds to complete assemble
Elongation- 2nd tRNA binds to A site, peptide bond forms between 1st and 2nd amino acids, ribosome moves in 3’ direction, tRNA that was in P site no longer has an attached amino acid and enters E site, new tRNA moves into A site, peptide bond forms between amino acid in A site and the growing chain in the P site, chain is transferred by the formation of bond to the A site, ribosome moves in the 3’ direction, tRNA in E site exits and empty tRNA in P site is transferred to E site
Termination- ribosome reaches a stop codon, protein is released, ribosomal subunits separate and mRNA is released
194. When in the cell cycle does a cell undergo replication? Transcription? Translation?
Replication- during interphase or s phase
Transcription and translation- G1 and G2
195. What is a tumor? What is the difference between a benign and malignant tumor? Which have differences in cell division, cell differentiation? Both?
A tumor is a region of uncontrolled cell growth
Benign is not cancerous, malignant is
Benign tumors have not metastasized
Malignant tumors have spread to other regions in the body
Malignant tumors have problems in both cell differentiation and cell division
Benign tumors are well differentiated but have no problems with cell division
196.What is the role of checkpoints throughout the cell cycle?
To make sure that the damaged DNA does not replicate
Also to check that the cell is big enough, that organelles within the cell have matured enough before and after replication, or that DNA is replicated properly
197.What class of proteins promotes the cell cycle? Sets breaks to the cell cycle?
P class proteins
Proto-oncogenes
Lac I gene and repressor protein
Sets breaks- P53
198. What are oncogenes?
Genes that when mutated or expressed at high levels helps turn a normal cell into a tumor cell
Various genes that control cell growth that are inappropriately activated
Tumor inducing genes
Gene that when mutated or expressed at abnormally high levels contributes to converting a normal cell into a cancer cell
199. What is the maturation-promoting factor (MPF) comprised of? When is it highest? What is its function?
Made of cyclin B and cyclin-dependent kinase (CDK). MPF promotes the entrance into mitosis (the M phase) from the G2 phase by phosphorylating multiple proteins needed during mitosis. MPF is activated at the end of G2 by a phosphate, which removes an inhibitory phosphate group added earlier.
The MPF is also called the M phase kinase because of its ability to phosphorylate target proteins at a specific point in the cell cycle and thus control their ability to function
200. How does cyclin dependent kinase (cdk) become activated? How does MPF become inactivated after mitosis?
When CDKs and cyclin form a complex and activate CDK, it is called an MPF or maturation-promoting factor.
The presence of enough MPFs will cause the cell to move from the G phase into the mitotic of M phase.
Towards the end of mitosis, the MPF deactivates itself by promoting the degradation of cyclin.
The CDKs remain for later use but are now inactive because of the lack of cyclin
201. How do growth factors induce the cell cycle (ie. Cause mitosis)?
MPF-induces mitosis in all eukaryotes
MPF is a dimer consisting of a cyclin and a cyclin-dependent kinase (CDK)
CDK catalyzes phosphorylation of other proteins to start mitosis
202. What types of proteins are mutated in familial cancer syndromes (ie. Breast-ovarian; colo-rectal)?
Breast-ovarian-tumor suppressors that help in DNA repair
Colo-rectal- mutations in denes for mismatch repair system
203. What is the role of p53?
“Breaks” pushes cell into cycle arrest
Tumor suppressor
Prevents uncontrolled cell growth
Inhibit cell cycling by induction of p21 transcription
Detect DNA damage, telomere shortening, hypoxia, hyperproliferative signals
Initiate apoptosis
203. What makes cells different from other cells?
Structure
Function
204. What is a stem cell?
Eukaryote
An undifferentiated cell that can differentiate into any cell type
A cell capable of self renewal
Can produce daughter cells that can differentiate
205. What are the three levels of control of protein expression/function in prokaryotes?
Transcriptional, translational, and post-translational
206. What is the role of transcription factors? How are they regulated?
Inhibit or initiate gene expression
We do not know the mechanism for it (biggest problem with DNA)
They are nuclear proteins that, when activated, bind specific DNA regions (response elements) near a gene’s promoter and activate or repress the transcription of that gene, leading to increased OR decreased synthesis of the encoded protein
Regulated:
Phosphorylation of a kinase
Concentration
Activity
207. Under what environmental conditions is transcription of the lac operon at low levels? What occurs at the lac operon to account for this?
Lactose present/ glucose absent
Under low glucose levels, transcription of lac operon increases
Needed for transcription- lactose, empty o-site (lactose inhibits repressor protein), full capsite (glucose not there to inhibit CAP protein)
Presence of cAMP increases the transcription of lac operon
Activator- CRP
208. Under what environmental conditions is transcription of the lac operon turned off? What occurs at the lac operon to account for this?
No glucose/ lactose/ cap bond
In the lac operon with the presence of lactose, transcription is turned on
Off- repressor protein is locked to operator to prevent production of enzymes that would be used for breaking down abundant nutrients
209. Under what environmental conditions is transcription of the lac operon at its highest? What signaling system accounts for this and what is occurring at the lac operon?
High lactose/ low glucose (glucose absent/ lactose present)
If lactose is absent, LacR blocks access to the promoter
If glucose levels are high, cAMP levels will be low
Lactose removes repressor
Low glucose activates adenylyl cyclase and increases cAMP cAMP binds to catabolite activator protein (CAP)
CAP-cAMP binds to a specific promoter sequence and facilitates binding of RNA pol to activate transcription
210. What is a riboswitch?
Single stranded RNA that regulates gene translation
Causes molecules to bind and affect secondary structure
An mRNA that controls gene expression in response to concentration of small molecules. The gene controlled is involved in the synthesis of the metabolite which regulates the riboswitch
Found in un-translated parts of a bacteria mRNA
211. Give examples of post-translational modifications of proteins that can affect protein activity.
Phosphorylation- Ser, Thr, Tyr (the Hydroxyl groups)
Hydroxylation- Pro, Lys (the N groups)
Glycosylation- Ser, Thr, Asn for membrane or secreted proteins
Carboxylation- In clot formation
Prenylation- Addition of hydrophobic groups
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Which of the following is a theory? There is molecular and biochemical evidence that all organisms are related.…
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The first two steps of the scientific method involve observation and description of a phenomenon or group of phenomena and then formulating a question. The description must be reliable, replicable and valid (Wikipedia.org). Scientists will try and find a cause and effect relationship and that will lead to the development of theories. Scientists observe the phenomenon and will try to explain it with a hypothesis. A hypothesis is "an attempt to explain an observation, or…
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As Watson stated in "The Value of Theories", a scientific theory is a systematic explanation that unifies various observed phenomena and facts. Based on observations we make, science operates under theories which are constantly revised and checked by experiment. A scientific theory also possesses many vital qualities for true understanding.…
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Learning Goal: To understand how the scientific method can be used to search for explanations of nature. The scientific method is a procedure used to search for explanations of nature. The scientific method consists of making observations, formulating hypotheses, designing and carrying out experiments, and repeating this cycle. Observations can be either quantitative or qualitative. Quantitative observations are measurements consisting of both numbers and units, such as the observation that ice melts at . In contrast, qualitative observations are observations that do not rely on numbers or units, such as the observation that water is clear. A hypothesis is a tentative explanation of the observations. The hypothesis is not necessarily correct, but it puts the scientist's understanding of the observations into a form that can be tested through experimentation. Experiments are then performed to test the validity of the hypothesis. Experiments are observations preferably made under conditions in which the variable of interest is clearly distinguishable from any others. If the experiment shows that the hypothesis is incorrect, the hypothesis can be modified, and further experiments can be carried out to test the modified hypothesis. This cycle is repeated, continually refining the hypothesis. If a large set of observations follow a reproducible pattern, this pattern can be summarized in a law—a verbal or mathematical generalization of a phenomenon. For example, over the years people observed that every morning the sun rises in the east, and every night the sun sets in the west. These observations can be described in a law stating, "The sun always rises in the east and sets in the west." After a great deal of refinement, a hypothesis can lead to a theory. A theory is an explanation of why something happens. For example, Newton's theory of gravitation explains why objects tend to fall toward the Earth (as well as explaining the interactions between the Earth and the other…
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The Scientific Method is a system devised to allow scientists to gain insight, or knowledge, on a wide range of questions about one’s behavior and other points of interest. The first step in this process is to identify a question that deserves an explanation or answer to. For example, a good indentifying question that one could use would be why did the chicken cross the road? This is a specific behavior that can be addressed and quantified. Once the individual has the question at hand, the formation of a theory is next. A theory is the best guess that one has as to why the action took place. In the example of the chicken crossing the road, a theory would be because there was food over there. Another theory would be just to get to the other side in general. Once you have the theory down, you need to create a hypothesis to test it. A hypothesis is a best guess stated in a way that you can measure the results of the claim. Referring back to the example of the chicken crossing the road, a hypothesis would be because it was hungry. A hypothesis must be restated as an Operational Definition (testable procedures that can be quantified) before testing can take place. The example of this would be: If food were visible on the other side, the chicken will cross the road to eat it.…
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