Module 2 - nucleic acids, amino acids, and peptides

Question 1

Describe the visible structural features of a DNA helix

Answer 1

right-handed, minor groove and major groove

Question 2

What is a nucleoside vs. a nucleotide?

Answer 2

base + sugar = nucleoside
nucleoside + phosphate groups = nucleotide

Question 3

What is different about the bases in DNA and RNA? Why?

Answer 3

DNA has thymine, RNA has uracil.
Uracil deaminates to cytosine. Any one of these changes that is not repaired in DNA leads to a C–>T mutation and eventually the base pair changes from originally being a C-G pair to a A-T pair.
Enzymes correct the deaminations so that only true uracils become thymine, not also the mutated cytosines.

Question 4

What is the difference in function between H bonds between bases and the base stacking interactions? What is the evidence for the importance of base stacking?

Answer 4

H bonds provide specificity, not stability
Base stacking provides stability through the hydrophobic effect. Evidence: H bonds also form between single strands and water, but that is less stable than double strands. G:C/C:G has different strength than C:G/G:C.

Question 5

What are the three forms of DNA double helix?

Answer 5

A form - right handed, but compressed
B form - right-handed, normal
Z form - left-handed and lots of G:C pairs

Question 6

How are some nucleosides modified and why?

Answer 6

they have a methyl in place of a hydrogen so prevent hydrogen bonding
allows certain structures to form and not others (allows the tRNA shape)

Question 7

What effect does OH instead of H have on RNA vs. DNA?

Answer 7

hydroxyl group allows autocleavage, meaning the RNA backbone spontaneously breaks and degrades

Question 8

What is unique about RNA from DNA as far as reaction activity?

Answer 8

Some RNA molecules called ribozymes are catalytic. Since they are single stranded, they can make weird shapes that allow them to act as catalysts.

Question 9

What is inosine?

Answer 9

a precursor base that can base pair with uridine, cytidine, and adenosine

Question 10

What is the G-quadruplex structure?

Answer 10

the interactions of 4 guanine bases within one of the strands of DNA

antibodies specific for the G-quadruplex have shown to bind to DNA in the telomere region of mitotic chromosomes

Question 11

What are histones and SSBs?

Answer 11

histones: bind to DNA in a sequence-independent manner, DNA wrapped around a histone forms a nucleosome, comprised of 8 subunits (H2A, H2B, H3 and H4)

SSBs: single-stranded binding proteins, preferentially bind to single-stranded DNA to keep the strand from pairing in that region (preserved single strands)

Question 12

What is the lac repressor?

Answer 12

a negative transcriptional regulatory protein that binds to a specific region of the bacterial genome, controls the lac operon and stops the enzyme from being produced when not needed

Question 13

How many possible protein sequences are there for a oligopeptide (10 amino acids)?

Answer 13

20^10 (20 possibilities at 10 positions)

Question 14

What is a heterotrimeric protein complex vs. a homodimeric protein complex?

Answer 14

heterotrimeric: three different protein subunits with different structures and properties
homodimeric: two of the same protein subunit

Question 15

What is the geometry of the carbon of an amino acid?

Answer 15

tetrahedral

Question 16

What is the pI of an amino acid? How can you determine it based on the given pKas of the amino, carboxyl, and R groups? Where it is located on the titration curve?

Answer 16

pI is the mean of the pKas, it represents the point at which the amino acid is in its Zwitterionic state (has no net charge)

for neutral AAs: avg the two pKas given
acidic AAs: the two lowest pKas
based AAs: the two highest pKas

can be located in the center of the slope between the two pKas used to calculate it

Question 17

All of the 20 amino acids found in nature are…

Answer 17

L amino acids, with S configuration (except cysteine which is R)

Question 18

What are the 4 categories of amino acids?

Answer 18

charged, hydrophilic, hydrophobic, and aromatic

Question 19

What are the charged amino acids?

Answer 19

aspartate, glutamate, lysine, arginine, and histidine

Question 20

What are the hydrophilic amino acids?

Answer 20

serine, threonine, cysteine, asparagine, and glutamine

Question 21

What are the hydrophobic amino acids?

Answer 21

glycine, alanine, proline, valine, leucine, isoleucine, and methionine

Question 22

What are the aromatic amino acids?

Answer 22

phenylalanine, tyrosine, and tryptophan

Question 23

When does an amino acid side group become protonated vs. deprotonated?

Answer 23

when pH>pKa, deprotonated
when pH<pKa, protonated

in other words, the group deprotonates when the pH goes above the pKa

Question 24

What do kinases do?

Answer 24

replace a OH with a phosphate group

Question 25

What do phosphatases do?

Answer 25

replace a phosphate group with an OH

Question 26

What amino acid can form a disulfide bond with another one of the same amino acid?

Answer 26

cysteine

Question 27

What is unique about aromatic amino acids?

Answer 27

they absorb ultraviolet light in the range of 250-280 nm

Question 28

How does GFP fluorescence work?

Answer 28

- absorption of blue light by a tripeptide chromophore of the protein - the chromophore forms spontaneously in the protein by a cyclization and oxidation reaction of 3 amino acids

Question 29

What is special about the peptide bond? Describe its rotational movement.

Answer 29

it is a partial double bond with restricted rotation so that all 6 atoms lie within the same plane rotation can occur around the two bonds flanking Ca, called the psi and phi angles

Question 30

How do peptide bonds form and break?

Answer 30

form: a condensation reaction catalyzed by RNA of ribosomes break: hydrolysis reaction catalyzed by enzymes called proteases

Question 31

Where are the phi and psi angles?

Answer 31

On each side of Ca, which is the carbon right after the nitrogen. Left of that carbon is phi, and right of that carbon is psi.

Question 32

What does a Ramachandran plot show?

Answer 32

the allowable and most common combinations of phi and psi angles for amino acids

Question 33

When given an amino acid sequence and three frames, how do you know which is most likely?

Answer 33

the one that does not have a stop codon (or has the latest stop codon)

Question 34

What are the type of amino acid mutations?

Answer 34

silent: change does not change the amino acid missense: change alters one amino acid nonsense: change creates a stop codon frameshift: adding or removing a protein causes many changes to the rest of the frame