BIO 201 Study Guide

BIO Chapter 2 Study Guide

1-Know the difference between an atom, an element and a compound.
-Atom-The basic unit of a chemical element.
-Element-A unique molecule that makes up all matter and cannot be broken down any further.
-Compound- Two or more elements together

2-Understand and be able to apply the concept of the Atomic number and the Atomic mass of an element.
-Atomic Number- The number of protons an element has.
-Atomic Mass-The number of Protons + Neutrons.
*the number of neutrons = the number of electrons

3- Understand the concepts of ions and isotopes.
-Ions-An atom or molecule that has lost or gained a charge.
-Isotopes-When two forms of the same element have the same number of protons but differ in the number of neutrons.

4-Be able to draw the electron shell diagram of an atom based on the atomic number and to predict the number of covalent and or ionic bonds that the atom will form based on the atomic number.
-electron shells-3 shells (2-8-18)
-Electron Orbital-2 electrons can fit into an orbital

5- Be able to distinguish covalent, ionic, hydrogen and hydrophobic bonds on the basis of structure and strength.
-Covalent-When unpaired electrons are shared by elements. Creates a Strong bond.
-Ionic-When electrons are transferred from one atom to another.
-Hydrogen-Weak electrical attractions between molecules that have opposite charges. They are formed and broken millions of times a second.

6-Be able to explain the difference between polar and non-polar covalent bonds.
-Polar covalent bonds-When there is an unequal sharing of electrons.
-Non polar covalent bonds- When there is an equal sharing of electrons.
*they are shown with the electrons pulled to one side of the bond if there is an un equal sharing.

7-Be able to draw the structural formula of a simple compound based on its chemical formula and the number of bonds each element typically forms.

8-Know the key properties of carbon that make it an ideal element to form the basis of organic chemistry.
-Carbon has 4 valance electrons that allow it to form long complex chains with other carbons or other molecules.

9-Be able to explain and apply the concepts of Ph, acids, bases, and buffers.
-pH- -log [H+]
-Acids-1 Low on the pH chart and increases the hydrogen ion composition of a solution.
-Bases-14 High on the pH chart and decreases the hydrogen ion composition in a solution.
-Buffers- Compounds that minimize changes in pH
*On the pH scale each step up is 10x more acidic

10-Be able to explain how molecules dissolve in water and predict solubility in different compounds given their structural formula.
-Molecules that are polar are water soluble. Waters uneven bonds pull atoms apart. Molecules that are not polar are hydrophobic and do not react to water. Hydrogen bonds make these reactions possible.

11-Explain the difference.
-Kinetic Energy- Thermal energy or the energy of movement. Something is hot its molecules are moving very fast. If something is cold its molecules are moving very slowly. It is measured by temperature.
-Potential Energy- Energy that is stored.

12- Expaign the difference.
-1st Law of Thermodynamics- Energy is never created or destroyed, just converted from one kind to another.
-2nd Law of Thermodynamics- Energy conversions increase entropy in the environment.

13- Gibbs free energy.
-

BIO Chapter 3 study guide

1- Be able to identify protein functions.
-Signaling- Can send various signals between cells
-Structure- Can help define cell shape
-Transport- Can carry materials in and out of a cell
-Catalysis- Help speed up reactions
-Defense- Antibodies and complement proteins attack pathogens
-Movement- Help move the cell or molecules within the cell

2-Be able to identify a molecule as an amino acid based on its structural formula and be able to predict whether the R- Group of an amino acid will be non-polar, polar or charged based on that structure.
-Amino Acids have and Amino Group (Nh2) and a Carboxyl group (COOH) and have a side group that can affect their reactivity and help the acids stay in solution

-Non-Ionized- have an NH2 amino group
-Ionized- have an H3N amino group

-Non-Polar-The R-Group has no electrical charge (Hydrophobic)
-Polar- have side groups that have atrial charges and can form hydrogen bonds (Hydrophilic)
-Charged- Have charged side groups that can form ionic and hydrogen bonds (Hydrophilic)

-They are acidic if they have a –O
-They are basic if they have a +NH

3- Know the hierarchy of organization of a protein starting with the individual atoms through the complex multi-subunit proteins.
-Single amino acid is called a monomer.
-Multiple amino acids joined together are called a polymer.

-Condensation Reaction- Monomer in, Water molecule out.
-Hydrolysis Reaction- Water molecule in, Monomer out.

4- 4 Levels of protein structure.

-Peptide bond-Condensation reaction. When a water molecule is removed and a monomer is added.

-The N terminus is the end that has the amino group exposed.
-The C terminus is the end that has the Carboxyl group exposed.
*The N terminus is the start of the chain and amino acids are added to the C terminus.

-Primary Structure- The unique sequence of amino acids. 20 amino acids.
-Secondary Structure- is formed by hydrogen bonds that occure between the carboxyl group of one amino acid and the amino group of another. They form beta pleated sheets or alpha helices
-Tertiary Structure- Bending and folding due to interactions between R-Groups and the shape of the polypeptide. Hydrogen bonding, Hydrophobic interactions, van der walls, covalent bonding, ionic bonding
-Quaternary Structure- The bonding between 2 distinct polypeptide subunits.

5- Be able to explain which levels of structure are involved when a protein is denatured.
-The secondary structure and up are affected when a protein is denatured. Hydrogen bonds and disulfide bonds are disrupted.
-Molecular Chaperones- help proteins within cells fold correctly
-Prions- improperly folded proteins. They can induce normal protein molecules to change their shape

6-Be able to explain what enzymes are and how they speed up chemical reactions.
-Enzymes- They speed up a chemical reaction. They decrease the amount of energy required for the reaction to proceed. And orient the substrate in a way that they can interact.

7- Be able to explain how substrate concentrations affects the enzymes activity, including the limiting factor at different substrate concentrations.
-One enzyme is specific for only one reaction.

8- Be able to explain the difference between competitive and non-competitive enzyme regulators.
-Competitive Regulators-When a non- reactive molecule fills the substrate and prevents catalysis.
-Non-Competitive Regulators- When more than one substrate is competing for the active site.

9-Be able to explain how temperature and pH affect enzyme activity, including how those factors decrease activity below and above the pH or temperature optimum.
-Higher temperature can increase reaction speed. Optimal around 60 deg C
-pH affects the enzymes shape and reactivity optimal around 7

CHAPTER 4
1- Explain the functions of DNA and RNA
-DNA-
- Is replicated to RNA
-Can store and transmit biological information that is required for growth and reproduction of all cells and organisms.

-RNA-
- Codes for proteins
-RNA contains a Hydroxyl group on the 2 prime carbon
-Can self replicate

2-Understand how DNA stores genetic information.
-Contains information for nucleotide synthesis.

3-Know the components of a nucleotide, be able to recognize the structural formula of one and be able to distinguish between an RNA nucleotide and a DNA nucleotide.
-RNA uses U instead of T

4-Know the hierarchy of organization of DNA molecule starting with individual atoms through to the double helix.
-DNA contains a phosphate group on the 5 prime carbon
-on the 2 prime carbon there is a hydrogen atom
-uses purines G and A and pyrimidine’s C and T (Nitrogenous bases)

5-Be able to explain the type and strength of bond that holds nucleotides together within a single strand of nucleic acid and between two complementary strands.
-A-T can form 2 hydrogen bonds
-C-G can form 3 hydrogen bonds

6- Be able to describe the basic structure of double stranded DNA
-Contains dioxyribose 2 prime carbon has a hydrogen and is less reactive

7- Be able to explain the interactions and bonds defining RNA structures.
-Formed by phosphodiester linkages- where the 5 prime and 3 prime attach by condensation reactions
-Can form hydrogen bonds with complementary bases on the same strand
-The hydroxyl group makes it more reactive and less stable

8-Be able to explain and apply the mechanism of DNA replication.
-DNA contains the information required for a copy of itself to be made. DNA itself serves as the template for the new molecule.

9- Be able to explain the concept of a ribozyme and give examples.
-An RNA molecule that can catalyze a number of chemical reactions.
-Tetrahymena it catalyzes both hydrolysis and condensation of phosphodiester linkages in RNA

BIO Chapter 5 Study guide
1-Be able to discriminate between the terms Carbohydrate, monosaccharide, disaccharide, oligosaccharide and polysaccharide.

-Carbohydrate-Carbs have diverse functions in cells.
-They can provide structure
-Indicate cell identity
-Store chemical energy

-Monosaccharide-Simple sugars.

-Disaccharide-When two monosaccharaides join they become a disaccharide and are created through a condensation reaction.
-Different orientations of the bonds can serve different purposes.

-Oligosaccharide-Can be used for identification of a cell.

-Polysaccharide-A long chain of monosaccharides.

2-Be able to recognize monosaccharaides given a structural formula in either the linear or ring form.
-Glucose

3-Be able to recognize and explain the difference between monosaccharaides of the same number of carbons.
-Aldose-Carbonyl group at the end of the carbon chain
-Ketose-Carbonyl group in the middle of the chain

4-Be able to explain the bond that joins monosaccharaides in polysaccharides including their structure and strength.
-Glycosidic Linkages- Form between hydroxal groups beta linkages are stronger
-Aplha-down
-beta-Up
-They are broken by hydrolysis

5-Understand the role of glycoproteins on cell surfaces.
-help identify identify itself they are found on the cell wall

6-Be able to explain the function of the five major polysaccharides listed in your text.
-Starch-Used for energy storage in plant cells.
-Glycogen-Used for energy storage in animal cells
-Cellulose-Used for structure in the cell walls of plants
-Chitin-Used for structure in fungi
-Peptidoglycan-Used for structure within a bacteria cell wall

7-Be able to explain HOW a polysaccharide can play a structural role.
-They provide fibrous structural support with hydrogen bonds.

8-Be able to explain the relative stability of a polysaccharides involved in energy storage vs. those involved in structure.
-Carbohydrates- offer short term energy storage due to unequal charges
-Cells use carbohydrates to create ATP excergonicly
-C-H bonds have high free energy and carbs have less bonds than fatty acids

-Fats- can offer more long term energy storage because there is equal sharing of electrons so they are not water soluble.
-have a large amount of C-H bonds

Chapter 6 study guide

1- Be able to define and identify (based on structural or molecular formulas) lipids.
-Lipids are mostly hydrophobic, carbon containing compounds.
-They have a Carboxyl group (-COOH) at the top and a long chain of hydrocarbons (H2C or CH2) following.
-The C-C and C-H bonds make lipids hydrophobic
-Easter linkages attach the glycerol heads and the fatty acid tails and are formed by a dehydration reaction.

2- Be able to recognize the structural formula of a steroid.
-It has a hydrophobic four ring structure with an attached side group.
-And a Hydrophilic OH

3-Be able to explain the function of steroid hormones and cholesterol.
-The amount of cholesterol in a lipid membrane affects its permeability. The more cholesterol the less permeable the membrane is.

4- Be able to explain two main functions of fats.
-Energy Storage
-They are a key component of animal cell membranes

5-Understand how molecules store energy and be able to compare energy storage potential based on chemical or structural formulas.
-alpha-glycosidic linkages are easily hydrolyzed for energy

6- Be able to explain the difference between saturated and unsaturated fats and explain the consequences of the degree of saturation in dietary fats on cardiovascular health in humans.
-Saturated Fat- No double bonds are present. And cell membranes are less permeable. Are solid at room temperature.
-Unsaturated Fat- Have one or more double bonds in the hydrocarbon tail, and membranes are much more permeable. They are also liquid at room temperature.

7- Be able to explain the difference between cis and trans fats, and the relevant health implications.
-Cis-Contains at least one double bond in the fatty acid chain
-Trans-when hydrogen’s alternate sides after a double bond. They act saturated but are unsaturated.

8-Be able to describe the structure of a phospholipid and how phospholipid structure varies.
-They have a polar hydrophilic head that contains a [polar group + phosphate + Glycerol]
-And a nonpolar hydrophobic fatty acid tail.
-Phospholipids can vary between the size of their tail and the number of double bonds between carbons in the fatty acid tail the longer the tail the membrane becomes less permeable
9- Be able to explain the concept of an amphipathic molecule, how such molecules arrange themselves in an aqueous solution and how that is related to the biological membranes.
-Amphipathic- A molecule that contains both hydrophobic and hydrophilic regions.
-They line up with hydrophobic tails facing each other and the hydrophilic heads outwards in the direction of water.

10- Be able to explain the factors that determine the permeability of solutes through a phospholipid bilayer. Be able to predict the relative permeability of two or more solutes molecules through a phospholipid bilayer based on their structural formulas.
-Membranes are selectively permeable
-High-Small non-polar molecules---Oxygen, Carbon Dioxide, Nitrogen
-Medium-Small uncharged polar molecules, large, uncharged polar molecules.
-Low-Ions

11- Be able to explain the fluid mosaic model of biological membranes. This includes knowing where each component is, what each does and how each moves.
-Phospholipids can move laterally within the membrane.
-The membrane also contains various macromolecules such as proteins and cholesterol.

12- Be able to explain the factors that affect the fluidity and permeability of a membrane.
-Temperature- The colder the temp the membrane becomes less permeable
-The structure of the Hydrocarbon Tails- If there are more saturated hydrocarbon tails the membrane will be less permeable
-The amount of Cholesterol- The more cholesterol the less permeable the membrane is.

13- Be able to explain and apply the concept of the electrochemical gradient of a solute across a membrane and how that gradient influences whether transport across the membrane in ant given direction will be passive or active.
-When there are unequal charges along a cell membrane
-

14- Be able to compare and contrast the two passive transport mechanisms we studied (channels vs. facilitated diffusion transport carriers). Know the range of molecules transported by each
-Passive transport-Does not require energy.
-Diffusion-Movement that results from a molecules kinetic energy.
-Osmosis-The movement of water to the higher solute concentration.
-Channel Proteins-Only allows a single type of ion to pass through. (FD)
-Gated Proteins-Channels that open and close in response to a signal. (FD)
-Active transport-Requires energy.

15- Be able to explain and give examples of primary active transporters (Pumps). Know the range of molecules transported.
-They can transport ions and other molecules against their gradient. Making the environment inside the cell much different from that outside the cell.
-sodium potassium pump- uses 3 sodium molecules and atp to send out the 3 sodium and bring in 2 potassium molecules

16- Be able to explain secondary active transport. Know the range of molecules transported.
-When a gradient of one molecule creates the energy to transport another molecule against its concentration.

17- Understand the relationship between primary and secondary active transport.
-Primary active transport creates the gradient for secondary active transport.