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MCAT Content Review > BIO1: DNA REPLICATION&REPAIR/EUKARYOTIC CHROMOSOMES > Flashcards

BIO1: DNA REPLICATION&REPAIR/EUKARYOTIC CHROMOSOMES Flashcards

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MCAT flashcards
1
Q

Define nucleic acid

A

Macromolecule composed of nucleotide monomers

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2
Q

Define nucleotide

A

Nitrogenous base + sugar + 1-3 phosphates

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3
Q

Define nucleoside

A

Nitrogeneous base + sugar

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4
Q

Nucleotides are joined by what type of bonds?

A

Phosphodiester bonds

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5
Q

What does the nucleic acid “backbone” refer to?

A

Sugar and phosphate groups of each nucleotide linked by phosphodiester bonds

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6
Q

What type of bond links nitrogenous bases on double stranded DNA?

A

Hydrogen bonds

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7
Q

What type of bonds are used within nucleosides?

A

Glycosidic bonds between sugar and nitrogenous base

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8
Q

How do DNA and RNA differ in nucleotide structure?

A

DNA (deoxyribose) has an H on the 2’ carbon while RNA (ribose) has an OH on the 2’ carbon

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9
Q

Where does the nitrogenous base link on sugar?

A

1’ carbon

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10
Q

Where does the phosphate group(s) link on the sugar?

A

5’ carbon

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11
Q

Identify the purine bases

A

Adenine and Guanine

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12
Q

Define the structure of purines

A

Double ring structure

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13
Q

Identify the pyrimidines

A

Cytosine, Uracil (RNA), and Thymine (DNA) “pyramids CUT”

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14
Q

Define the structure of pyrimidines

A

Single ring structure

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15
Q

How do the nitrogenous bases of DNA and RNA differ?

A

DNA uses thymine and RNA uses uracil

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16
Q

What is the difference in structure between DNA and RNA nitrogenous bases?

A

Thymine has a methyl group and Uracil just has a H

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17
Q

What nitrogenous base is Adenine paired with?

A

Thymine /Uracil (RNA)

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18
Q

What nitrogenous base is Guanine paired with?

A

Cytosine

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19
Q

Which nitrogenous base pair is stronger?

A

Cytosine/Guanine because it has 3 H-bonds and is a stronger base pair

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20
Q

What does the double helix refer to?

A

DNA structure of linking of 2 nucleic acid strands by H-bonds between the nitrogenous bases in a right-handed helix

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21
Q

How are nucleic acid strands arranged?

A

Anti-parallel

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22
Q

What group is linked to the 5’ end of the nucleic acid strand?

A

Phosphate group

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23
Q

What group is linked to the 3’ end of the nucleic acid?

A

OH group

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24
Q

How are DNA sequences read/written?

A

5’ -> 3’ for both strands

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25
Q

How is the polynucleotide built?

A

5’ end of the nucleotide (phosphate containing) is added to the 3’ OH of existing strand using pyrophosphate to drive reaction

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26
Q

Define pyrophosphate

A

Two phosphates

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27
Q

When does DNA replication occur during the cell cycle?

A

S phase (synthesis phase)

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28
Q

What is the outcome of DNA replication?

A

One DNA molecule is replicated into two identical copies

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29
Q

What cellular process is DNA replication a part of?

A

Cell division

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30
Q

Define the general process for DNA replication

A

Parent DNA strand serves as a template and replication is iniatiated by an RNA primer and free floating nucleotides are added to the new daughter strand

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31
Q

What is the function of DNA helicase?

A

Unwinds the parent DNA strand

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32
Q

How does DNA helicase function?

A

Breaks H-bonds between nitrogenous bases

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33
Q

What is the function of topoisomerase

A

Relaxes DNA supercoils that accumulate due to the unwinding of DNA

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34
Q

Define DNA gyrase

A

A type of topoisomerase (relaxes DNA supercoils that accumulate due to the unwinding of DNA)

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35
Q

What is the function of SSB proteins?

A

Single strand binding proteins stabilize the single parent strands of DNA once unwound

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36
Q

What is the function of primase?

A

A type of RNA polymerase that lays down the RNA primer to initiate transcription

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37
Q

What is the function of DNA polymerase?

A
  1. Builds the daughter strand of DNA
  2. Proofreads and corrects errors
  3. Replaces the RNA primer
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38
Q

What is the function of ligase?

A

Links the Okazaki fragments of DNA daughter strand

39
Q

Define the step-by-step process for DNA replication

A
  1. Helicase binds to the ORI and begins to unwind forming a replication bubble
  2. Topoisomerase relaxes the supercoils upstream of the replication bubble
  3. SSBPs stabilize the newly separated parent strands
  4. Primase lays down the primer (later removed by DNA polymerase)
  5. DNA polymerase adds nucleotides one by one using parent strand as template
40
Q

Define annealing

A

Recombination of DNA when double-stranded DNA are separated

41
Q

What is the structure of free floating nucleotides?

A

Nucleoside triphosphates (dNTPs) containing 3 phosphates; pyrophosphate is eventually released to provide energy for nucleotide linkages

42
Q

How are new nucleotides added to the new daughter strand?

A

3’ OH on the last nucleotide of the daughter strand nucleophilically attacks the 5’ end of the phosphate of the incoming nucleotide

43
Q

What is the nucleophile in the DNA replication process?

A

The 3’ OH on the daughter strand is the nucleophile (e- rich species) that nucleophilically attacks the electrophile which is the 5’ phosphate group (e- deficient)

44
Q

Define the leading strand

A

The leading strand is synthesized in the same direction as the extending replication fork and is a single continuous strand

45
Q

Define the lagging strand

A

The lagging strand is not continuous and made up of multiple Okazaki fragments that are joined together by DNA ligase

46
Q

Define the bidirectional synthesis of DNA

A

Because double stranded DNA is unwound and creates a replication bubble, the leading strand (3’ -> 5’) is replicated continuously (5’ -> 3’) whereas the lagging strand (5’ -> 3’) is replicated backwards as the DNA is unwound/DNA polymerase is laid reverse of how DNA is usually read/written (5’ -> 3’)

47
Q

Describe the differences between DNA replication in eukaryotes and prokaryotes

A
  1. Location
  2. # of ORIs
  3. DNA polymerases
  4. Only eukaryotes have telomeres
48
Q

Describe DNA replication in eukaryotes

A

DNA replication in eukaryotes occurs in the nucleus and has many ORIs/DNA molecule which enables fast replication. Eukaryotes have 5 DNA polymerases and telomeres

49
Q

Describe DNA replication in prokaryotes

A

DNA replication in prokaryotes occurs in the cytosol and only has 1 ORI/DNA and has 3 DNA polymerases

50
Q

List the 2 main DNA polymerases used in prokaryotic DNA replication

A

DNA Pol III and DNA Pol I

51
Q

Describe the function of DNA Pol III

A

Main DNA pol that extends the daughter strand

52
Q

Describe the function of DNA Pol I

A

Slower than Pol III
Exonuclease activity enables it to remove RNA primer and replace with DNA
DNA error repair

53
Q

Define theta replication

A

In prokaryotic DNA replication due to the circular DNA of prokaryotes and singularity of ORI, the DNA creates 2 replication forks similar to the theta

54
Q

Define telomeres

A

Non-coding repeats added to the ends of the lagging strand of DNA that protect DNA and shorten with each round of replication

55
Q

Define senscence

A

Biological aging due to telomere shortening; if telomere is too short, the cell will stop dividing and fnctioning properly

56
Q

What is the function of telomerase?

A

Telomerase is an RNA-dependent DNA polymerase that catalyzes the lengthening of telomeres to reverse telomere shortening; a DNA polymerase then backfills the nucleotides on the lagging strand

57
Q

Where is telomerase found?

A

Germ line, stem cells, and cancerous cells

58
Q

Define RNA-dependent DNA polymerase

A

An enzyme that can make DNA using RNA as a template

59
Q

Define the types of DNA mutations

A
  1. Point mutations

2. Insertions and deletions

60
Q

Define point mutations and the types

A

Point mutations are substitution errors and described by their effect

  1. Silent mutations
  2. Missense mutations
  3. Nonsense mutations
61
Q

Define silent mutations

A

Silent mutations occur when a different base pair is added but the same amino acid is translated

62
Q

Define missense mutations

A

Missense mutations occur when a differen base pair is added resulting in a different amino acid that is translated; missense mutations are conservative when the new AA has similar biochemical properties to the old one

63
Q

Define nonsense mutations

A

Nonsense mutations occur when a base pair change causes the DNA and transcribed mRNA to encode a stop signal so that transcription and translation terminate prematurely

64
Q

Define insertion and deletion mutations

A

Insertions occur when one or more additional base pairs are inserted and deletions occur when one or more base pairs are deleted; may result in a frameshift

65
Q

Define frameshift

A

When insertion/deletion does not occur in a multiple of 3 base pairs so that the reading frame of the gene is changed so that all of the downstream regions of the gene will also be affected

66
Q

Define transposon

A

Transposon/transposable elements are regions of DNA that can move around in the genome and often cause structural changes/mutations in the DNA

67
Q

Where are transposons found?

A

Transposons are found in both prokaryotes and eukaryotes

68
Q

Define transposase

A

Parts of the transposon that encodes for enzymes that copy/cut and paste DNA segment into a different place in the genome

69
Q

List the mechnisms of DNA repair

A
  1. DNA polymerase
  2. DNA MMR
  3. Nucleotide and Base Excision Repair
  4. Homologous End Joining
  5. Non-Homologous End Joining
  6. Homologous End Joining
70
Q

What happens if the mutation cannot be fixed?

A

The cell undergoes apoptosis

71
Q

What activity acts as a backspace button for incorrect base pairs?

A

Nuclease activity

72
Q

Define the DNA MMR pathway

A

The mismatch repair pathway occurs when a base mismatch (A/C, G/T) is identified on the daughter strand, removed, and replaced

73
Q

Define the Nucleotide and Base Excision Repair

A

Removes a section of DNA surrounding errors caused by mutagens; DNA polymerase replaces the region, DNA ligase joins the fragments

74
Q

Describe Homologous Recombination and Non-Homologous End Joining

A

Fixes double strand breaks and removals of DNA regions; HR must be done after DNA replication and creates an exact copy; NHEJ occurs when homologous DNA is not available where cleaved ends are ligated together (mutagenic)

75
Q

How are sister chromatids linked?

A

Centromere

76
Q

Define sister chromatids

A

Sister chromatids are identical copies of dsDNA

77
Q

Describe how human chromosomes are ordered

A

There are 46 total chromosomes that represent 23 pairs (22 autosomal and 1 sex) chromosomes that are each composed of one maternal chromosome and one paternal chromosome

78
Q

Define p and q arms of the chromosome

A

When the centromere is off-center, it creates a shorter arm (p arm) and longer arm (q arm)

79
Q

Define nucleosome

A

Regions of DNA wrapped around a histone octamer (8 histone proteins)

80
Q

What charge do histones have and why?

A

Histones are positively charged to attract negatively charged DNA

81
Q

Define chromatin

A

Chromatin are combination of DNA and histone proteins (beads on a string) which bundles and condenses

82
Q

What are centromeres composed of?

A

Binding proteins and specific DNA sequences to link DNA molecules on the sister chromatids

83
Q

What are the types of chromatin?

A
  1. Heterochromatin

2. Euchromatin

84
Q

Define heterochromatin

A

Densely packed chromatin that tis not accessible to enzymes of transcription (transcriptionaly “silent”)

85
Q

Define euchromatin

A

Loosely packed chromatin that is accessible to transcriptional enzymes (transcriptionally active)

86
Q

Describe aneuploidy

A

Aneuploidy occurs when an organism has an abnormal number of chromosomes (+/- 46)

87
Q

Describe polysomy

A

Polysomy occurs when an organism has one or more additional copies of a chromosome (e.g. trisomy 21/down syndrome, triple X, kleifelter’s syndrome, turner syndrome)

88
Q

Describe post-translational protein modification

A

When proteins require support to fold into their native conformation after translation

89
Q

List the types of post-translational protein modification

A
  1. Chaperone protein helps fold into native conformation
  2. Cleavage of a region of the polypeptide (zymogen)
  3. Glycosylation
  4. Lipidation
  5. Acetylation and methylation
  6. Formation of disulfide bonds
90
Q

Define zymogens

A

An inactive precursor of an enzyme that requires a biochemical change to activate it (e.g. conformational change)

91
Q

Describe glycosylation

A

The addition of sugars to help a protein fold and stabilize

92
Q

Describe lipidation

A

The addition of lipids that regulates protein function

93
Q

Describe acetylation

A

An organic esterification reaction with acetic acid by introducing an acetyl functional group into a chemical compound

94
Q

Describe DNA methylation

A

Adding methyl groups to regulate gene expression

MCAT Content Review (13 decks)

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