Module 2 - nucleic acids, amino acids, and peptides Flashcards
Describe the visible structural features of a DNA helix
right-handed, minor groove and major groove
What is a nucleoside vs. a nucleotide?
base + sugar = nucleoside
nucleoside + phosphate groups = nucleotide
What is different about the bases in DNA and RNA? Why?
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.
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?
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.
What are the three forms of DNA double helix?
A form - right handed, but compressed
B form - right-handed, normal
Z form - left-handed and lots of G:C pairs
How are some nucleosides modified and why?
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)
What effect does OH instead of H have on RNA vs. DNA?
hydroxyl group allows autocleavage, meaning the RNA backbone spontaneously breaks and degrades
What is unique about RNA from DNA as far as reaction activity?
Some RNA molecules called ribozymes are catalytic. Since they are single stranded, they can make weird shapes that allow them to act as catalysts.
What is inosine?
a precursor base that can base pair with uridine, cytidine, and adenosine
What is the G-quadruplex structure?
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
What are histones and SSBs?
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)
What is the lac repressor?
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
How many possible protein sequences are there for a oligopeptide (10 amino acids)?
20^10 (20 possibilities at 10 positions)
What is a heterotrimeric protein complex vs. a homodimeric protein complex?
heterotrimeric: three different protein subunits with different structures and properties
homodimeric: two of the same protein subunit
What is the geometry of the carbon of an amino acid?
tetrahedral
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?
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
All of the 20 amino acids found in nature are…
L amino acids, with S configuration (except cysteine which is R)
What are the 4 categories of amino acids?
charged, hydrophilic, hydrophobic, and aromatic
What are the charged amino acids?
aspartate, glutamate, lysine, arginine, and histidine
What are the hydrophilic amino acids?
serine, threonine, cysteine, asparagine, and glutamine
What are the hydrophobic amino acids?
glycine, alanine, proline, valine, leucine, isoleucine, and methionine
What are the aromatic amino acids?
phenylalanine, tyrosine, and tryptophan
When does an amino acid side group become protonated vs. deprotonated?
when pH>pKa, deprotonated
when pH<pKa, protonated
in other words, the group deprotonates when the pH goes above the pKa
What do kinases do?
replace a OH with a phosphate group
What do phosphatases do?
replace a phosphate group with an OH
What amino acid can form a disulfide bond with another one of the same amino acid?
cysteine
What is unique about aromatic amino acids?
they absorb ultraviolet light in the range of 250-280 nm
How does GFP fluorescence work?
- 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
What is special about the peptide bond? Describe its rotational movement.
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
How do peptide bonds form and break?
form: a condensation reaction catalyzed by RNA of ribosomes
break: hydrolysis reaction catalyzed by enzymes called proteases
Where are the phi and psi angles?
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.
What does a Ramachandran plot show?
the allowable and most common combinations of phi and psi angles for amino acids
When given an amino acid sequence and three frames, how do you know which is most likely?
the one that does not have a stop codon (or has the latest stop codon)
What are the type of amino acid mutations?
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
