Intro
What is the theory of evolution by natural selection?
All species descended from a common ancestor, species have diverged over time due to the pressure of natural selection
What four parts make up an amino acid?
R Group
carboxylic acid
amine
hydrogen
What does DNA polymerase need to replicate DNA?
DNA template, 3’ OH primer , dNTPs
What are the four parts of the Cell Theory? Explain each.
1) Cells are the Structural Unit of Life -Single-celled or multicellular, all organisms are composed of cells
2) Cells are the functional unit of life-cells are the smallest entities that have all the properties of life. Each cell is/can generate an entire organism
3) All cells are fundamentally similar in terms of metabolic strategies, structure and organization, and hereditary information. However, specific cell functions can vary due to specialization
4) All cells come from preexisting cells via cell growth and division
What is primary, secondary, teritiary, and quaternary structure?
It is a linear sequence of amino acids held together by covalent bonds (peptide bonds) that release water when formed.
Folding of the polypeptide that results from hydrogen bonds between the carbonyl group of one amino acid and the amino group of another. Forms alpha helices and beta pleated sheets.
Overall 3-D shape of polypeptide -held together by interactions between atoms in R groups that may be Hydrophobic interactions •Hydrogen bonds •Ionic bonds •Covalent (disulfide bonds).
When multiple polypeptide chains (subunits) come together in a single complex. Covalent, ionic, hydrogen, hydrophobic interactions.
Where does the energy to create phosphodiester bonds come from?
The three phosphate groups in the nucleotides repel each other, so it is favorable to break that bound
Based on the tree of life, are archaea more closely related to bacteria or eukaryotes?
Eukaryotes! (It might help to have them draw the tree).
How does the polar or nonpolar character of R-groups influence tertiary structure?
Usually hydrophobic R-group fold to the inside of the protein a hydrophilic R groups fold to the outside of the protein
When DNA is opened, unwound, and primed, which enzymes are used?
Helicase: breaks H bonds and opens up template Topoisomerase: relieves twisting forces/ supercoiling by clipping DNA strands
SSBPs: prevent DNA from reannealing/ reforming hydrogen bonds(***stress that you need to keep DNA open for replication to occur***)
Primase: adds RNA primer to ssDNA in 5’à 3’ direction (this is 3 à 5 relative to DNA) (how many times is the leading strand primed? The lagging strand?)
Rank covalent, ionic, hydrogen and Van der Waals in order of strongest to weakest.
And tell me what each of them are.
Covalent, ionic, hydrogen, Van der Waals (covalent>ionic because exists in biological system)
Hyrdrogen: A weak interaction between a partially positive H and a partially negative atom such as O, N
van der waals: Electrons are constantly moving around the positively charged nucleus. By chance, more electrons may be on one side of the atom than the other. This will cause the side with more electrons to have a partial negative charge and the side with fewer electrons to have a partial positive charge.
How do factors like temperature, pH, and salt concentration affect chemical bonds, and thus, protein structure?
Temperature -interrupts hydrogen bonds
pH-increase in number of free H+ ions. Ionization of amino acids
salt concentration -interrupts ionic bonds
Enzymes used when synthesis of leading strand begins
DNA Polymerase III: in 5’ to 3’ direction
Sliding clamp: holds DNA polymerase in place
Why don’t nonpolar molecules interact with water?
They don’t form hydrogen bonds and are neutral, water would rather H bond with itself to maximize the partial positive/negative interactions than associate with neutral molecules
What are chaperone proteins?
Proteins that shelter proteins and help them in their original folding or renaturation.
How is the very end of each chromosome replicated? Is this the same for leading and lagging strands?
Lagging strand-Telomerase extends the 3’ ends of linear parental DNA sequence using an RNA template to form telomeres that provide a place to put RNA primer and are shortened every time the DNA is replicated, but are long enough that no important genetic information is lost
Leading strand-DNA polymerase continues replicating DNA until it falls off the end of the chromosome