First Midterm Notes

Finalized Notes
Cells are small membrane bound units filled with concentrated aqueous solution of chemicals and given the ability of reproducing itself by dividing. Thus for this purpose the cells are the fundamental unit of life.
If cells are modified to specific specialization they cause the cell to lose its ability to reproduce, as a result they end up depending on other cells for the basic needs.
In all living things genes are stored in the DNA molecule, encoded in the same chemical code, constructed out of the same chemical compounds, interpreted by the same chemical machinery and reproduce in the same way.
DNA, RNA and proteins are the three main group of macromolecules which are important for the function of the cell.
Cell can function properly only if it has the correct set of proteins within the cell.
Genetic continuity is the ability of the cell to renew it self and cont. living through the next generation.
Central Dogma states that the DNA is transcribed into RNA which gets translated into proteins. Proteins dominates the behavior of the cell. This is the one idea which unifies all the cells, let it be prokaryotic or eukaryotic.
Proteins are made up of amino acid which are attached to each other in different sequence giving the proteins its unique 3D structure (conformation).
DNA polymerase not only synthesis the DNA, but it also checks to make sure that it is reading it correctly. It proof reads what it makes, to ensure that there are minimal mistakes in the copying of DNA during DNA replication.
The characteristics of life includes: ability to grow, the process of metabolism, the reproduce, to respond to stimuli, and the ability of movement (only possible in certain species).
The cell theory states that the cell is the smallest unit of life, all the living things are made up of cells and new cell arise only from pre-existing cells.
The first cell was created long time ago based on the Earth’s condition which allowed the chemical compounds to create an organism that is able to reproduce itself.
Mutation can create offspring in which they change for worse, better or neutral. After mutation they go through different pressures exerted by natural selection where the genes of the next generation will be of those of that survived.
The cells have the ability to transform the environment they live in. Ex. Cyanobacteria transformed the earth’s atmosphere by carrying out oxygenic photosynthesis which resulted in oxidizing environment from reducing environment. This cell allowed for the evolution of the anaerobic life.
To estimate relatedness one method is to compare the nucleotide sequence encoding the 16s or 18srRNA (if these RNA are defective then the organism will die) – the more diff the sequence the more distantly related the organisms.
Since the recent technology allows for the genome to be analyzed, we compare more than one genes to estimate relatedness.
The nucleotide sequence of chips and human is greater than 99% in terms of similarity.
Using the method of relatedness, we can organize the organisms into tree of life which is based on relatedness. It states that all the organisms we see today arose from one ancestral specie.
The diversity in organism results from difference in pattern of expression of genes temporally and spatially.
Evolution is the process by which the cells are modified and adapted to suit their environment better. Evolutionary process is random, it doesn’t have a purpose and goal. This is based on selection pressure in the environment which selects certain traits that benefits the organism to be passed down.
During the evolution, in addition to vertical gene transmission, there is large scale horizontal gene transmission. Ex. The mitochondria is an archaea which was eaten by ancestral eukaryotic cell and started to live within the cell. This transfer of genes from that bacteria resulted in horizontal gene transmission. Another example of horizontal gene transfer is the evolution of chloroplast. Modern day example can be seen in bacteria that is capable of transferring genes which are capable of fighting antibiotics.
Genome is all the information stored in the DNA of the cell.
DNA is the structure which holds the genetic information of the cell. It codes for proteins and occasionally codes for RNA. It has 4 main properties to it:
Complementarity
Polarity – DNA is directional
Fidelity – the ability to be passed down to next generation in almost perfect sequence identity (accuracy)
Stability – needs to be stable, structured. Must be able to resist the rapidly changing environments in the cell.
Cells can be classified into 2 types:
Prokaryotes: cells with no defined nucleus - No nuclei, lack membrane-bound organelles, and smaller than eukaryotes.
Eubacteria (Bacteria) – include many photosynthetic organism.
Archaebacteria (Archea) – grow in unusual environment.
Eukaryotes: cell with a true nucleus. - They are complex, have nuclei, abundant and diverse organelles that compartmentalize biochemical reactions (separate compartment for different set of reaction), larger than prokaryotes.
Includes protista, fungi, animals, plants
Cytoplasm is a transparent substance crammed with concentrated chemicals.
Mitochondria is thought to be evolved from aerobic bacteria that started to live inside the eukaryotic cell. Similarly, chloroplast is thought to have evolved from photosynthetic bacteria which started to live inside plant cell.
Nucleus is the essential structure in the eukaryotic cell. It holds the DNA which are separated from the rest of the cell by surrounding it with Nuclear Membrane. . This is the place where DNA are replicated and separated, and transcription occurs. It houses the chromosome (condensed DNA strands) during the cell division.
Nucleoplasm contains DNA (genetic info) and chromatin (DNA + histones complex)
Nucleolus has condensed DNA and genetic info for synthesis of ribosome.
Mitochondria are present in all the eukaryotic cell, they are the powerhouse of the cell. They have double membranes. Each has its own DNA and they reproduce by dividing in half.
Chloroplast are the large green organelles found in the plant cells. They are responsible for conversion of sunlight into food for the cells to use. They are like mitochondria in sense that they have their own set of DNA and reproduce by dividing in half and also that they have double layered membranes.
Plant cells are autotrophic, meaning they can capture sunlight and use it to produce its own food. However, animal cells are heterotrophic, meaning they need to have constant input of food and nutrients for survival.
Endoplasmic Reticulum is an irregular maze flattened membranes which houses the space for production of materials which are destined to exported from the cell.
Golgi apparatus receives the modified materials and are responsible for the transportation to the specific location inside or the outside the cell.
Lysosomes are small irregular structure which are responsible for breaking down of the unwanted molecules.
Peroxisomes are closed space for very dangerous reactions to take place within the cell.
Endocytosis is the process of engulfing large molecules, while exocytosis is the fusion of vesicle inside the cell to the external cell membrane.

Ribosomes are the machines required during the process of protein synthesis. They are found in cytoplasm, RER, chloroplast and mitochondria.
Cytoskeleton is the fine filaments of proteins which are anchored from the cell membrane to the nuclear membrane. Their main function is to provide cell with structural support and assist the cell in transportation of materials inside the cell and transportation of the cell itself. Consist of thee filaments:
Thinnest are the actin filaments, which are associated with production of contractile forces.
Thickest are the microtubules, which plays a role in cell division when the chromosomes needs to be separated.
Intermediate filaments serve to strengthen the cell.
The proteins that are formed must be maturated and processed (post-transcriptional modifications) before they can be used and targeted to final destination.
Structure of DNA predicts the function. This structure allows us to predict how it can be replicated.
Structure of proteins allows to predict the function of protein, such as which it binds to, what does it do.
DNA and RNA are polymers which are synthesized from a small set of repeatedly utilized monomers.
Nucleotide are involved in more than just being a structural component. They provide genetic info (DNA) and protein synthesis info (RNA), they are used in signaling (cAMP) and also function as coenzymes (NADH).

Chemical of life is based on 4 points:
Based a lot on carbon compounds
Chemical reaction that take place in aqueous solution with taking in the earths atmospheric temperature into consideration
Very complex
Dominated and coordinated by collection of polymeric molecules which controls the growth and the reproduction of cells.
Atom is the smallest particle of an element which still retains its chemical properties.
Atom is made up of electrons (negatively charged) revolving around nucleus (dense center of the atom) which consist of protons (positively charged) and neutrons (neutral).
The electrons in the outermost shell determines how the atom behaves during chemical bonding.
There are two types of chemical bonds:
Covalent bonds: formed when electrons are being shared by equally strong atoms. The sharing of electrons result because none of the atoms are strong enough to pull the electron away from the other.
Ionic bonds: formed when there is an exchange of electrons between a strong and weak atom. This type of bonding results in generally between metal and non-metal. It results in formation of ions. This type of bond is held together by electrostatic attraction between the positively and negatively charged atoms.
Bonds vary in strength depending on the type of bonds. The strength of the bond is determined by the amount of energy required to break that bond.
70% of the cells weight consist of water. Without water life as we know it would not exist. Water is held together in the liquid state by hydrogen bonding (when H binds to O or N of other molecule). Hydrogen bonding in water results in waters boiling point and freezing point.
Substances that give hydronium ion when dissolved in water is known to be acid. The stronger the acid the greater the number of hydronium ions produced.
Base is a substance that gives hydroxide ion when dissolved in water. The stronger the base the greater the number of hydroxide ions produced.
Buffers are usually substances that are weak acids and bases. Their function is to maintain the pH of the solution within the cell / extracellular liquid between specific ranges for the cells to function.
Simplest sugars are called monosaccharides which can be linked together by covalent bonds (glycosidic bonds) to form larger carbohydrates. The covalent bond is formed between the –OH of two diff monosaccharides, in this process a water molecule is produced, thus this reaction is known as condensation reaction.
The complex carbohydrates can be broken down into smaller sugar by breaking the covalent bonds through a reaction known as hydrolysis, in which water molecule is consumed.
Fatty acids are long molecules which has 2 distinct regions. The long hydrophobic chain made up of hydrocarbon and the small hydrophilic head. This type of molecules is known as amphipathic since it contains both hydrophobic / hydrophilic properties.
Amino acids are varied class of molecules with one defining property: they have central C atom which has H, amino group and carboxylic acid attached to it. These are the building blocks of the proteins. AA has isomers but only the L-form are found in the proteins.
Nucleotides are the building blocks of DNA and RNA. They can be grouped into two type purines are (guanine and adenine) and pyrimidine (cytosine, thymine and uracil).
ATP provides the energy for most of the cellular activities. It has 3 phosphate groups attached to it, and when those phosphate bonds are broken they release large amount of energy to power the cell. The phosphates are linked by phosphoanhydride bonds.
Macromolecules are formed by linking simple organic molecules via covalent bond.
DNA
RNA
Double stranded and in form of helical structure due to H bonds between nucleotides
Made using Deoxyriboses sugar, contains one less oxygen than ribose
It consist of A, T, G and C
More stable, doesn’t react often.
Stores genetic information and remains within the nucleus all the time.
Single stranded, has no helical structure, however nucleotides bind to itself.
Made from ribose sugar, which contains 6 oxygen.
Made up of A, U, G, C
Due to its structure, it reacts very often.
It codes for proteins. They are found within nucleus and cytoplasm.
Lecture 3
DNA has 4 main themes:
Complementarity: knowing how one set of nucleotide binds to other set.
Polarity: this is based on the chemical polarity (5’ and 3’ end). It has a direction.
Fidelity: it has ability to accurately copy DNA from one generation to other.
Stability: has to have long term chemical stability. It should be able to last in variety of environment.
DNA is made from repeating sequences of nucleotides. They play many different role in cell: protein synthesis, energy, signaling and coenzymes.
A single nucleotide is composed of pentose sugar (5C – deoxyribose) + nitrogenous base (A, G, C, T) + phosphate.
The nitrogenous base is linked to pentose sugar by a N-glycosidic bond on the C1’ and the phosphate group on C5’ and on the C1 for pyrimidine and C9 for purine.
Purine are the nitrogenous base that have 2 ringed structure includes (A and G), while pyrimidine are nitrogenous base with single ringed structure (C and T).
N to N – 4 describes where the double bonds are found.
The ribose differ from deoxy in sense that on the second carbon ribose has OH while deoxy has H. Thus, the second carbon on ribose is chiral and the one on deoxy is achiral.
The prime ‘, indicates that the carbon is part of the sugar.
Nucleoside differ from nucleotide in sense that nucleoside doesn’t have a phosphate group and nucleotides have phosphate group.
The phosphate in ATP have a property, the one attached to C is alpha, the one second further down C is beta and the one furthest from C is theta. Note that the phosphate groups are always attached to the 5’C.
Nucleoside structure:
Pentose sugar (ribose or deoxyribose) + nitrogenous base (A,C, G, T/U) – phosphate
1909-1929
Levene
DNA consist of equal proportions of Deoxyribose, nitrogenous base, phosphate
1950s
Chargaff
Number of A = T and G = C
Early 1950s
Franklin and Wilkins
X-ray diffraction shows DNA structure is double helix
1953
Watson and Crick
Deduced the double helical structure of DNA
The two numbers that caught the eye was:
0.34nm – thickness of one of the nucleotide incorporated into the DNA
3.4 – the distance the helix travel one complete rotation.
The polymerization of two nucleotides to form dinucleotide cost 2 ATP molecules. The polymerization starts at the 5’ and goes towards the 3’ end. As the polymerization conts, it form 3’-5’ phosphodiaster bonds.
By convention the DNA is written in format where it starts at 5’  3’, and only given one strand.
The native structure of DNA is cell is two antiparallel polynucleotide chains. Look diagram below.
For DNA is a double strand of nucleotides twisted into helical form at every 10 nucleotides (3.4nm), groves, hydrogen bonds between nitrogenous bases.
Complementary base pairing in DNA simplifies that one purine bonds to one pyrimidine. G-C base pairs are stabilized by 3 H bonds and A-T base pair by 2 H bonds. Thus, when trying to break the structure, more energy is required when breaking G-C bonds, as breaking A-T bonds. (apx temp at 90 can separate the strands apart). It is hard to break apart since, there are hydrophobic area which are stacked on top of each other.
Watson Crick predicted how the DNA could be replicated, based on the complementary pairing.

A-DNA (associated with chromatin that isn’t transcribed)
B-DNA (what is believed to be in cell)
Z-DNA (note known)
Right handed
Short and broad