BioChem Exam 4

what is the general central dogma of biology? is it accurate?

DNA →RNA → Protein via transcription and translation

not entirely accurate, there are some exceptions - still a useful principle but not really “central dogma” anymore

what are the basic descriptors of a strand of DNA?

made by two complementary strands, the two strands are anti-parallel, and it has a right-handed helix structure

the backbone of a strand of DNA is made of _______ and ________

sugar and phosphate

the two strands of DNA interact with eachother via __________

H-bonds

a base + a ribose sugar = ___________

nucleoside

a base + a deoxyribose sugar = _______

deoxynucleoside

a nucleoside is a ______ and a ________

base and a (deoxy) ribose sugar

name the four RNA nucleosides

adenosine, guanosine, cytidine, uridine

name the four DNA nucleosides

deoxyadenosine, deoxyguanosine, deoxycytidine, (deoxy)thymidine

what is this

deoxyadenosine

in purines, which nitrogen is attached to C_ of the sugar. what about pyrimidines?

N9 for purines, N1 for pyrimidines, attach to C1’ of sugar

the bond between the N1-C1’ in pyrimidines and the N9-C1’ in purines is known as ________

β-glycosidic bond (linkage)

what is this

ribose sugar

what is this

deoxyribose sugar

the sugars in both RNA and DNA are called _______ (general term)

pentose sugars

how are the carbons on a pentose sugar labeled?

1’ - 5’, starting with the carbon bonded to the OH group that is on the ring

what is the difference between a ribose sugar and a deoxyribose sugar

ribose has an OH at the 2’C, while deoxyribose has an H

what is a nucleotide?

nucleoside + phosphate

a nucleotide is a _____ + _______

nucleoside + phosphate(s)

what is this (generally)

purine

what is this

adenine

which of these have a 𝛿- and which have a 𝛿+ (not all will have a charge)

𝛿- ~ 7

𝛿+ ~ 1

what is this

guanine

which of these have a 𝛿- and which have a 𝛿+ (not all will have a charge)

𝛿- ~ 1

𝛿+ ~ 6, 7

what is this (generally)

pyrimidine

what is this?

cytosine

which of these have a 𝛿- and which have a 𝛿+ (not all will have a charge)

𝛿- ~ 1

𝛿+ ~ 5, 6

what is this

uracil

which of these have a 𝛿- and which have a 𝛿+ (not all will have a charge)

𝛿- ~ 1, 5

𝛿+ ~ 6

what is this

thymine

which of these have a 𝛿- and which have a 𝛿+ (not all will have a charge)

𝛿- ~ 1, 5

𝛿+ ~ 6

in watson-crick base-pairing, a GC pair has ____ H-bonds and an AT pair has _____ H-bonds

GC - 3

AT - 2

what is base stacking / pi stacking

where when bases layer on top of eachother, van der Waals interactions contributes stabiity of base pairing

where is the glycosidic bond in DNA / RNA

between N1-C1’ in pyrimidines, and between N9-C1’ in purines

the majority of dsDNA in vivo is in what form

B-form

in the B-form of dsDNA, the sugar takes …?

C2’ endo

when in dehydrated conditions, dsDNA in vitro will take what form?

A-form

in vivo, dsRNA and RNA-DNA hybrids will take what form?

A-form

in the A form, the sugar takes the …?

C3’ endo

what is the Z form of dsDNA?

a left-handed helix with sequence specific (GC repeat)

which is more stable, B-form DNA or A-form DNA?

B-form

which is thinner, A-form DNA or B-form DNA?

B-form

which takes C-2’ endo puckering, A-form DNA or B-form DNA?

B-form

only ___________ allows B form structure (What kind of sugar puckering?)

C2’-endo

in C3’-endo puckering, is the sugar on the same side or the opposite side of the 5’ carbon?

opposite

what is the rise per base pair of the A-DNA structure?

a. 2.3Å

b. 3.4Å

c. 3.8Å

d. 4.2Å

a. 2.3Å

what is the rise per base pair of the B-DNA form?

a. 3.8Å

b. 4.2Å

c. 3.4Å

d. 2.3Å

c. 3.4Å

what is the rise per base pair of the Z-DNA form?

a. 3.8Å

b. 4.2Å

c. 3.4Å

d. 2.3Å

a. 3.8Å

what is the helix diameter of DNA in the A-form?

a. 18Å

b. 20Å

c. 26Å

d. 28Å

c. 26Å

what is the helix diameter of DNA in the B-form?

a. 18Å

b. 20Å

c. 26Å

d. 28Å

b. 20Å

what is the helix diameter of DNA in the Z-form?

a. 18Å

b. 20Å

c. 26Å

d. 28Å

a. 18Å

what is the screw sense of each form of DNA? (A, B, and Z)

A and B - right handed

Z - left handed

how many base pairs are there per turn of helix in A-form?

a. 10

b. 10.4

c. 11

d. 11.4

e. 12

c. 11

how many base pairs are there per turn of helix in B-form?

a. 10

b. 10.4

c. 11

d. 11.4

e. 12

b. 10.4

how many base pairs are there per turn of helix in Z-form?

a. 10

b. 10.4

c. 11

d. 11.4

e. 12

12

what is the pitch per turn of helix in A-form DNA?

a. 25.3Å

b. 35.4Å

c. 45.6Å

a. 25.3

what is the pitch per turn of helix in B-form DNA?

a. 25.3Å

b. 35.4Å

c. 45.6Å

b. 35.4

what is the pitch per turn of helix in Z-form DNA?

a. 25.3Å

b. 35.4Å

c. 45.6Å

c. 45.6

what is the ΔGº for the conversion of A-form DNA → B-form DNA?

~-0.5 kcal/mol(bp) - not much

which form does dsRNA take? why?

A-form, RNA has a bulky oxygen on 2’ carbon which interfere C’-2 endo by steric hinderance

what are the three typical motifs of DNA binding proteins?

helix-turn-helix, leucine zipper, and zinc finger

majority of DNA binding proteins recognize __________ with their ɑ-helices

major grooves

what structure is this?

helix-turn-helix

what structure is this?

leucine zipper

what structure is this?

zinc finger motif

what structure is this?

zinc finger

what is the approximate size of the major groove of DNA?

22Å

what is the approximate size of the minor groove in DNA?

12Å

why is protein binding to the major groove of DNA easier?

size fits well to an ɑ-helix and polar groups in major groove are well exposed

DNA binding proteins can read DNA sequence without unwinding dsDNA up to ______ base pairs

3 to 4

(1 rise = 3.4Å, 10-14Å)

because DNA is twisted, what is the MAXIMUM number of base pairs that a single protein can recognize?

5

a sequence of 5 amino acids will be seen once every how many base pairs?

1024 (4^5)

about how many proteins would it take to recognize a TRULY unique sequence of DNA

3

true or false: histone recognize specific sequences of DNA?

false

how do histone operate?

interact with polynucleotide backbone of DNA by positively charged amino acids

what amino acids do histones typically interact with?

R and K (Argenine and Lysine)

what form is the core of a histone?

octamer

the outside of the histone core (octamer) has lots of __________

positive charges

sequence specific proteins often bind to _________, typically as _________

symmetrical (inverted) DNA sequences, dimers

non-sequence specific proteins bind to DNA based on _____________ rather than a repeating or mirrored sequence pattern

general structural features (i.e. polynucleotide backbone)

____________________ of ɑ-helix allow sequence-specific DNA binding

amino acid-side chains

many recognition sequences are _______________ that are recognized by ________________ of proteins

inverted repeats, symmetric dimer (tetramer)

what kind(s) of protein(s) can recognize non-palindromic sequences

heterodimeric proteins and Zn-finger proteins

non-specific DNA binding proteins often contain _____ side chains to interact with polynucleotide backbone

basic (+)

what are the main functions of DNA polymerase?

nucleotide incorporation mechanism - elongate DNA sequence by adding nucleotides

proofreading

what are the main functions of the sliding clamp/the loader

processivity of DNA synthesis - how efficient a polymerase is and how well it duplicates DNA - high processivity = running a bunch without stopping

what are the main functions of helicase?

opens the replication fork and allows both strands of DNA to be duplicated at the same time

what are the main functions of primase?

start DNA replication by synthesising an RNA primer

what are the main functions of topoisomerase

twists unzipped DNA to prevent supercoiling/untwists to release tension

what are the main functions of telomerase

remakes the buffers (telomeres) on the end of chromosomes that are shortened in each replication of DNA, without them actual genetic material would be lost instead of just the telomeres

what is the approximate speed of DNA replication by polymerase?

500 nt/sec/catalytic subunit

what is the definition of “fidelity” in reference to replicative DNA polymerase?

chance of mistake per synthesis

does replicative DNA polymerase have higher fidellity with or without proof reading?

higher without - high chance of making mistakes becuase it is going so fast

match the following levels of fidelity with their respective DNA polymerase method

a. 10^-3 - 10^-4

b. 10^-6 - 10^-7

c. 10^-9 - 10^-10

1. with proofreading

2. without proofreading

3. in vivo (including mismatch repair)

a-2 ~ 10^-3 - 10^-4 without proofreading

b-1 ~ 10^-6 - 10^-7 with proofreading

c-3 ~ 10^-9 - 10^-10 in vivo (including mismatch repair)

what are three things DNA polymerase ALWAYS needs to function?

• needs template (DNA)

• needs primer (RNA or DNA)

• extends pre-existing 3’OH (cant start from nothing and can’t extend if OH end is blocked)

what does pyrophosphotase do in DNA replication?

enzyme that takes phosphates off the 3’ end to allow the next base to bond

makes it so the polymerase reaction is irriversible, which is GOOD for the formation of DNA

what is the core reaction of DNA synthesis?

(DNA)n + dNTP ←→ (DNA)n+1 + PPi

ΔGº’ = -3.5 kcal/mole

when two bases bind while forming DNA, what kind of bond is formed?

phosphodiester

the reaction: (DNA)n + dNTP ←→ (DNA)n+1 + PPi (ΔGº’ = -3.5 kcal/mole) is done by ________, while the reaction (DNA)n + dNTP ←→ (DNA)n+1 + 2 Pi (ΔGº’ = -7 kcal/mole) is done by ___________

DNA polymerase, Pyrophosphatase

what is the name for this structure? what is it a part of?

Klenow fragment of DNA polymerase I