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Biochemistry MCAT > DNA > Flashcards

DNA Flashcards

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MCAT flashcards
1
Q

What is the difference between a nucleoside and a nucleotide

A

Nucleoside - contain a five carbon sugar and nitrogenous base

Nucleotide is a nucleoside + one to three phosphate groups

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2
Q

What is the base-pairing rules according to Watson-Crick

A

A-T or A-U 2 H bonds

C-G 3 H bonds

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3
Q

What are the three major structural differences between DNA and RNA

A
  • T instead of U
  • double stranded and single stranded
  • sugar backbone is difference, deoxyribose and ribose
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4
Q

How does the aromaticity of purines and pyrimidines underscore their genetic function

A
  • the aromatciity makes the structure very stable and unreactive
  • stability is important for storing genetic information and avoiding spontaneous mutations
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5
Q

If a strand of RNA contained 15% C, 15% A, 35% G and 35% U, would this violate Chargaff’s rules. Why or why not

A

No, because RNA is single stranded, so the complementary strand rule for DNA does not hold true

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6
Q

Where is DNA found

A
  • bulk is found in chromosomes in the nucleus of eukaryotic cells
  • some DNA is found in mitochondria and chloroplasts
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7
Q

What is the structural difference between deoxyribose and ribose

A

both are five carbon sugars

  • the C2 position in deoxyribose is a H
  • the C2 position in ribose is a OH
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8
Q

What is the backbone of DNA composed of

A
  • alternating sugar and phosphate

- nucleotides are joined by 3’ to 5’ phosphodiester bonds

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9
Q

What is the charge of DNA and why

A
  • negative charge because phosphates carry a negative charge
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10
Q

The 5’ end of DNA will contain a ___ group and the 3’ end of DNA will contain a ___ group

A

5’ end has OH or phosphate group bonded to C5

3’ end has free OH on C3

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11
Q

DNA goes in which direction

A

5’ to 3’

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12
Q

What does CUT the PY stand for, how many rings

A

Cytosine, Uracil, and Thymine are all pyrimidines

one ring

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13
Q

What does PUR As Gold stand for, how many rings

A

Adenine and Guanine are all purines

two rings

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14
Q

What are the four rules for aromatic compounds

A
  • cyclic
  • planar
  • conjugated - alternating single and double bonds or lone pairs
  • 4n+2 - Hückel’s Rule
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15
Q

DNA strands are ____ to one another

A

antiparallel

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16
Q

The sugar phosphate backbone is on the _____ of the double helix and the nitrogenous bases are on the ____ of the double helix

A

outside

inside

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17
Q

What is Chargaffs rule

A

the amount of A = T
the amount of C = G
the total amount = 100

Total purines = Total pyrimidines

This does not apply to RNA, because it is single stranded

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18
Q

What is the complementary strand for 5’ ATCG 3’

A

5’ CGAT 3’

must be complementary and antiparallel

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19
Q

How many H bonds are between A and T, C and G

A

2 H bonds
3 H bonds

  • this is why a molecule with more C and G will have a higher melting point - because it takes more heat to break all the bonds compared to A T bonds
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20
Q

What is B and Z DNA

A

B DNA is a right handed helix - most common and stable

Z DNA is a left handed helix - less common, less stable

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21
Q

The major and minor groves in DNA provide _____

A

binding sites for regulatory proteins

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22
Q

Where do regularly proteins bind to DNA

A

on the major and minor groves of the double helix

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23
Q

What bases are pyrimidines and what bases are purines

A

pyrimidines are CUT - one ring

purines are AG - two rings

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24
Q

How does DNA become denatured

What are commonly used methods to denature DNA

A

by being placed in conditions that disrupt hydrogen bonding and base - pairing

heat, alkaline pH, chemicals (formaldehyde, urea)

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25
Q

What is reannelaing of DNA

A

brining the DNA strands back together usually accomplished if the denaturing agent is slowly removed

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26
Q

Compare Heterochromatin and Euchromatin

  • Where located
  • Density
  • Color under light microscopy
  • Expression
  • During which cell stage
A

Heterochromatin - nucleus, dense, dark, unexpressed, interphase

Euchromatin - nucleus, uncondensed, light, expressed, interphase

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27
Q

What prevents DNA replication from extending to the end of a chromosome and losing sequence

A

telomeres

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28
Q

Telomeres are

  • located
  • prevent DNA unraveling by
  • during replication
  • can be reversed by (partially)
  • type of DNA sequences
A
  • at the end of chromosomes - in the nucleus 5’ end
  • high GC content prevent the DNA from unraveling
  • shorten during replication
  • can partially be reversed by enzyme telomerase
  • contain repetitive sequences of noncoding DNA
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29
Q

Centromeres are

  • located
  • separated
  • contain strong bonds because of
A
  • in the middle of chromosomes, holding sister chromatids together
  • separated during anaphase of mitosis
  • high GC content to maintain strong bond between chromatids
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30
Q

How many chromosomes do human cells have

A

46

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31
Q

What forms a nucleosome

A
  • when DNA is wrapped around histone proteins (H2A, H2B, H3, H4) and stabilized by H1
32
Q

As a whole DNA and its associated histones make up ____ in the nucleus

A

chromatin

33
Q

As a whole DNA and its associated histones make up ____ in the nucleus

A

chromatin

34
Q

What does telomerase do

A
  • an enzyme that partially reverses the action of telomeres
35
Q

What is a similarity between telomeres and centromeres

A

both contain a high GC content
in telomeres this prevents DNA unwinding
in centromeres helps with strong bond between chromatids

36
Q

What is the function of helicase

A
  • unwinds the DNA
  • in eukaryotes and prokaryotes
  • during replication
37
Q

What enzymes main role is to unwind the DNA

A
  • Helicase

- in eukaryotes and prokaryotes

38
Q

What is the function of single-stranded DNA- binding protein

A
  • prevents reannelaing of DNA double helix during replication
  • in eukaryotes and prokaryotes
39
Q

What is the function of DNA topoisomerases

A
  • knick the DNA strand to reduce torsional strain and then reseals
  • reduces torsional strain from positive supercoils by introducing nicks in the DNA strand
  • in eukaryotes and prokaryotes
40
Q

What is the function of primase

A
  • places an RNA primer on DNA to to begin replication

- in eukaryotes and prokaryotes

41
Q

What is the function of DNA polymerase III and DNA polymerase alpha

A
  • adds nucleotides to growing daughter strand
  • in prokaryotes (III)
  • in eukaryotes (alpha)
42
Q

What is the function of DNA polymerase I

A
  • fills in gaps left behind after RNA primer is remvoed

- in prokaryotes

43
Q

What is the function of RNase H

A
  • removes RNA primer

- in eukaryotes

44
Q

What is the function of DNA ligase

A
  • joins DNA strands - specifically between Okazaki fragments
  • in eukaryotes and prokaryotes
45
Q

What enzyme unwinds the DNA in eukaryotes and prokaryotes

A

helicase

- both

46
Q

What enzyme prevents the reannealing of DNA in the double helix during replication in eukaryotes and prokaryotes

A

single stranded DNA-bining protein

- both

47
Q

What enzyme places the RNA primer in eukaryotes and prokaryotes

A

primase

- both

48
Q

What enzyme adds nucleotides to the growing daughter strand in eukaryotes and prokaryotes

A

Pro - DNA polymerase III

Eukaryote - DNA polymerase alpha

49
Q

What enzyme fills in the gaps left behind after RNA primer is removed in eukaryotes and prokaryotes

A

DNA polymerase I

- prokaryotes

50
Q

What enzyme removes the RNA primer in eukaryotes and prokaryotes

A

RNase H

- eukaryote

51
Q

What enzyme joins DNA strands in eukaryotes and prokaryotes

A

DNA ligase

- both

52
Q

What enzyme reduces torsional strain from possible supercoils by introducing nicks in the DNA strand in eukaryotes and prokaryotes

A

DNA topoisomerases

- both

53
Q

Is the leading or lagging strand more prone to mutations, why

A

lagging strand,

  • more chances of mutation because of the stop and go process of DNA replication
  • contains more RNA primers, so there will be more fill ins increasing the change of mutations

leading strand is a continuous process

54
Q

What is the replisome

A

aka replication complex

set of specialized proteins that assist the DNA polymerases during the process of DNA replication

55
Q

What is the origin of replication

A
  • DNA unwinds to this point and replication begins
56
Q

The direction of new DNA is in which direction and what does this cause

A
  • both directions

- causing a replication fork - with a leading and lagging strand

57
Q

Compare and contrast the leading and lagging strands

A

leading strand

  • continuous
  • needs one RNA primer in theory

lagging strand

  • stop and go process
  • needs multiple RNA primers
58
Q

Write out the DNA replication process in eukaryotes (prokaryotes)

A
  1. Helicase unwinds DNA into two strands – There is supercoiling while the NDA is unwinding so DNA topoisomerases add negative supercoils ahead of helicase and nick the strand to reduce this torsional strain
  2. Single strand DNA-binding proteins prevent the DNA strands from coming back together and prevents degradation by nucleases
  3. Primase adds an RNA primer to allow replication to begin on the strands
  4. DNA polymerase alpha (DNA polymerase III) reads the parent strand and starts to add nucleotides to synthesize the daughter strand - can only synthesis 5’ to 3’
  5. Leading and lagging strands

Leading strand is continuously copied, read from 3’ to 5’ and synthesized from 5’ to 3’, in theory only one RNA primer is needed

Lagging strand is not oriented in the correct direction, Okazaki fragments are produced, DNA polymerase completes one Okazaki fragment and then moves to the next, needs multiple RNA primers (one is needed to synthesize each Okazaki fragment) - DNA ligases helps to join Okazaki fragments

  1. RNA primer is removed by RNase (Polymerase I) - exonuclease
  2. DNA polymerase delta (DNA polymerase I) adds DNA nucleotides where the RNA primer was
  3. DNA ligases seals the end of DNA molecules making one continuous strand - joins DNA strands
59
Q

Is DNA replication faster in eukaryotes or prokaryotes

A
  • Slower in eukaryotes and faster in prokaryotes
60
Q

Compare contrast between prokaryotes and eukaryotes

  • origin of replication
  • unwinding of DNA
  • stabilization of unwound template strands
  • synthesis of RNA primers
  • synthesis of DNA
  • removal of RNA primers
  • replacement of RNA primer location with DNA
  • joining of Okazaki fragments
  • removal of positive supercoils ahead of advancing replication forks
  • synthesis of telomeres
A
  • one vs multiple per chromosome
  • helicase
  • single strand DNA binding proteins
  • primase
  • DNA polymerase III and DNA polymerase alpha
  • DNA polymerase I and RNase H
  • DNA polymerase I and DNA polymerase delta
  • DNA ligase
  • DNA topoisomerases
  • do not have, telomerase
61
Q

What are oncogenes

A
  • develop from mutations of porto-oncogenes and promote rapid cell cycling
62
Q

What is cancer

A
  • unchecked cell proliferation with the ability to spread by local invasion or metastasize (migrate to other parts of the body via lymphatic or circulatory system)
63
Q

What are tumor suppressor genes

A
  • code for proteins that reduce cell cycling or DNA repair
64
Q

What can happen if there is a mutation in the tumor suppressor genes

A
  • can cause cancer, because the gene is no longer producing proteins that reduce cell cycling or repair DNA
65
Q

What enzyme proofreads the DNA

A
  • DNA polymerase - proofreads its work and excesses incorrectly matched bases
  • daughter strand is identified by its lack of methylation and corrected accordingly
66
Q

Durning proofreading how does DNA polymerase tell the difference between the parent and daughter strand

A
  • the parent strand is more methylated

- the daughter strand lacks methylation

67
Q

Compare the four DNA repair mechanisms

  • Proofreading by DNA polymerase
  • Mismatch Repair
  • Nucleotide Excision Repair
  • Base Excision Repair
  • Phase of the cell cycle it occurs
  • key enzymes or genes
A

Proofreading by DNA polymerase

  • S
  • DNA polymerase

Mismatch Repair

  • G2
  • MSH2 and MLH1 (eukaryote) MutS and MutL(prokaryotes)

Nucleotide Excision Repair

  • G1/G2
  • excision endonuclease

Base Excision Repair

  • G1/G2
  • glycosylase, AP endonuclease
68
Q

What are key structural differences between the types of lesions corrected by nucleotide excision repair and those corrected by base excision repair

A

Nucleotide excision repair corrects lesions large enough to distort the double helix and base excision repairs small lesions that do not distort the double helix shape

69
Q

Explain DNA repair by proofreading

A
  • occurs during S phase
  • DNA polymerase
  • proofreads its work and excesses incorrectly matched bases
  • parent strand is more methylated
70
Q

Explain DNA repair by Mismatch repair

A
  • occurs during G2
  • MSH2 and MLH1 (eukaryote) and MutL and MutS (prokaryotes)
  • enzymes above detect the errors that happened during the S phase and removes them
71
Q

Explain DNA repair by Nucleotide Excision Repair

A
  • occurs during G1 and G2
  • excision endonuclease
  • Thymine dimers (as result of UV light) form in the double helix of the DNA, distorting the shape, this repair mechanism via excision endonucleases remove the dimer and then DNA polymerase can fill in the gap the dimer causes using the undamaged strand as the template and then DNA ligase seals the strand
72
Q

Explain DNA repair by base excision repair

A
  • occurs during G1 and G2
  • glycosylase and AP endonuclease
  • wrong base is detected and the base is recognized by glycoslyase enzyme and removed, this leaves an AP site (Apurinic/Apyrimidinic), the AP endonuclease recognizes this site and removes the damaged sequences, then DNA polymerase can fill in the gaps and DNA ligase can seal the strand
73
Q

When creating a DNA library, what are some of the advantages of genome libraries? What about cDNA libraries?

A

Genomic DNA libraries include all of the DNA of an organism’s genome, including non coding regions, this is useful for studying DNA introns, centromeres, or telomeres

cDNA libraries only include expressed genes from a given tissue, used to express recombinant proteins or to perform gene therapy

74
Q

What does PCR accomplish for the researchers? What does Southern Blotting accomplish?

A

PCR increases the number of copies of a given DNA sequence and can be used for a sample containing few copies of a given DNA sequence

Southern Blotting is useful when searching for a particular DNA sequence because it separates DNA fragments by length and then probes for a sequence of interest

75
Q

During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?

A

Dideoxyribonucleotide lacks the 3’ OH group that is required for DNA strands to elongate. When this is added to a growing stand, no more molecules can attach, they can’t form a bond

76
Q

What is the difference between a transgenic and a knockout mouse?

A

Transgenic mice have a gene introduced into their germ line or embryonic stem cells to look at the effects of that gene, best suited to study dominate genes

Knockout mice are those in which a gene of interest has been removed.

Biochemistry MCAT (7 decks)

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