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MCAT Bio > Molecular Bio (Chp 4) > Flashcards

Molecular Bio (Chp 4) Flashcards

1
Q

Purine bases

A

A and G
two rings

(mnemonic: silver (AG) is pure)

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2
Q

Pyrimidine bases

A

C, U, and T
single ring

(mnemonic: pyramids are sharp and CUT you)

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3
Q

phosphodiester bond

A

covalently links nucleotides in DNA chain

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4
Q

H bonds in DNA

A

(Purine-pyrimidine)
A-T (2 H bonds)
G-C (3 H bonds)

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5
Q

DNA structure characteristics

A
  • double stranded
  • antiparallel (5’ on one end paired with 3’ of other)
  • coiled
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6
Q

of chromosomes in humans

A

46 (23 inherited from each parent)

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7
Q

prokaryote (bacterial) genome

A

single circular chromosome

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8
Q

viral genome

A

linear or circular DNA or RNA

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9
Q

DNA gyrase

A

(prokaryote)

uses ATP E to twist DNA

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10
Q

Packing/condensing of human DNA

A
  • wrapped around histones
  • nucleosomes (resemble ball on a string) = wrapped around 8 histones
  • chromatin - wrapped nucleosomes
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11
Q

centromere

A

region of chromosome where spindle fibers attach during cell division (attach via kinetochores)

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12
Q

transcription

A

DNA (T) > RNA (U)

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13
Q

translation

A

RNA > proteins

accomplished by the ribosome

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14
Q

Central Dogma

A

DNA > RNA > protein

information DNA is used to create actual products (proteins - ex: enzymes, structural proteins, etc.)

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15
Q

codon

A

nucleic acid word (3 nucleotide letters)

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16
Q

stop codons

A

also called nonsense codon
UAA - your are annoying
UGA - you go away
UAG - you are gone

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17
Q

DNA code

no ambiguity vs degenerate

A

no ambiguity - DNA code can only be read one way

degenerate - two or more codons coding for the same amino acid

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18
Q

replication

A

duplication of DNA - occurs during synthesis phase of cell cycle
- semiconservative

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19
Q

helicase

A

enzyme that unwinds and separates double helix at origin of replication

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20
Q

topoisomerase

A

enzymes that cut one or both strands and unwrap DNA helix > releases excess tension caused by helicase

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21
Q

single strand binding protein (SSBPs)

A

protects DNA that has been unpackaged in prep for replication and keeps separated

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22
Q

DNA polymerase

A

catalyzes elongation of daughter strand using parental template

  • checks each new nucleotide to make sure it forms correct base pair
  • polymerization occurs in 5’ to 3’ ALWAYS
  • requires a template and primer
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23
Q

okazaki fragments

A

small chunks of DNA comprising lagging strand

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24
Q

DNA pol III

A

v fast, v accurate elongation of leading strand

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25
Q

DNA pol I

A

adds nucleotides at the RNA primer but more slowly than DNA pol III
- important for excision repair

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26
Q

germline mutations

A

mutations that can be passed onto offspring

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27
Q

somatic mutations

A

mutations in nongametic cells > not passed on to offspring

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28
Q

point mutation

A

single base pair substitutions (ex A in place of G)
can be:
-transitions - sub pyrimidine for another pyrimidine
-transversions - sub pyrimidine for purine

types:
- missence, nonsense, and silent

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29
Q

missence mutation

A

a point mutation that causes one amino acid to be replaced with a different amino acid

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30
Q

nonsense mutation

A

a point mutation that causes a regular codon to be replaced by a stop codon
> prematurely shortens the protein

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31
Q

silent mutation

A

a point mutation where a codon is changed into a new codon that codes for the same amino acid
> no change in amino acid sequence

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32
Q

Insertion mutation

A

addition of one or more extra nucleotides into the DNA sequence

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33
Q

Deletion mutation

A

removal of nucleotides from DNA sequence

34
Q

frameshift mutation

A

mutations that change the reading frame

35
Q

inversion mutation

A

section of DNA sequence is flipped (inversed) from end to end

36
Q

amplification mutation

A

segment of chromosome is duplicated

37
Q

translocation

A

recombination occurs between nonhomologous chromosomes

38
Q

Types of DNA repair

A

direct reversal
homology dependent repair - excision repair
post-replication reapir
double strand break repair - homologous recombination, nonhomologous end joining

39
Q

Direct reversal

A

direct reversal of DNA damage (example: repair of UV induced pyrimidine photodimers using visible light)

40
Q

homology dependent reapir

A

because DNA is double stranded, mutations on one strand can be fixed using undamaged, complimentary info on the other

41
Q

excision repair

A

removing defective bases or nucleotides and replacing them

42
Q

post replication repair

A

mismatch repair pathway targets mismatched watson-crick base pairs that weren’t repaired by DNA pol proofreading during replication

43
Q

double strand break repair

A

(double strand breaks can be caused by: reactive oxygen species, ionizing radiation, UV light or chemical agents)

(2) pathways to help fix
1. homologous recombination - one sister chromatid can help repair a DSB in the other
2. nonhomologous end joining - nonspecific end joining

44
Q

How is RNA distinct from DNA

A

(3) ways:
1. single stranded (except in some viruses)
2. contains uracil instead of thyamine
3. pentose ring in RNA is ribose rather than 2’ deoxyribose
4. several types: (are empty - R M T)
- rRNA - ribosomal
- mRNA - messenger
- tRNA - transfer

45
Q

mRNA

A

carries genetic info to the ribosome where it can be translated into a protein

46
Q

tRNA

A

responsible for translating the genetic code - carries amino acids from cytoplasm to the ribosome to be added to growing polypeptide

47
Q

rRNA

A

serve as components of the ribosome

48
Q

transcription

A

synthesis of RNA using DNA as the template

-proceeds 5’ to 3’

49
Q

introns vs extrons

A

introns - INtervening sequences of RNA

extrons - RNA that gets EXpressed

50
Q

spliceosome

A

mediates splicing (removing introns from RNA seq)

51
Q

modification of hnRNA before translation

mRNA processing

A
  1. 5’ cap added to end of molecule
  2. 3’ poly A tail
  3. splicing - remove introns
    mnemonic: introns in nucleus, exons exit nucleus
52
Q

RNA pol products for:
RNA pol I
RNA pol II
RNA pol III

A

RNA pol I = most rRNA

RNA pol II = hnRNA (ultimately mRNA)

RNA pol III = tRNA

Are empty (R M T)

53
Q

translation

A

synthesis of polypeptides according to aa sequence dictated by sequence of codons in mRNA

54
Q

tRNA (transfer RNA)

A

stem and loop structure stabilized by H bonds
each tRNA is specific to one amino acid (while each amino acid can have several tRNAs)
regions:
-anticodon region recognizes mRNA codon to be translated
-amino acid acceptor site - where amino acid attaches to tRNA

55
Q

wobble hypothesis

A

first 2 anticodon-codon pairs in tRNA follow normal base pairing rules BUT the third position is more flexible
> allows for less tRNAs than would be predicted

56
Q

ribosome

A 
prokaryote = 70s ribosome
eukaryote = 80s ribosome

float around in cytoplasm, each has a small and large subunit
binding sites:
- A site - where tRNA delivers aa
- P site - where growing peptide chain is and aa is added
-E site - where now empty tRNA exits ribosom

57
Q

prokaryotic translation occurs ___

A

while mRNA is being made ribosome attaches and begins translating it

58
Q

translation stages

A

(3)

  1. initiation - small ribosomal unit binds 2 initiation proteins (IF1 and IF3), then binds the mRNA transcript, then tRNA along with IF3, then 50S subunit completes complex
  2. elongation - A > P > E
  3. termination - a stop codon appears in A site (UAA, UAG, and UAA)

total E required to make = # amino acids * 4

59
Q

diff btw prokaryotic translation and eukaryotic translation

A
  • eukaryote = larger ribosome (80S > 70S)
  • eukaryote mRNA must be processed before translated (spliced, poly A tail, 5’ cap)
  • N- terminal amino acid is diff (Met instead of fMET)
  • eukaryote mRNA must be transported from nucleus to cytoplasm (>transcription and translation can’t occur at the same time in eukaryotic)
60
Q

Controlling gene expression at DNA level

A
  • DNA methylation and chromatin remodeling
  • Gene dose
  • Gene imprinting
  • X chromosome inactivation
61
Q

Controlling gene expression at DNA level

- DNA methylation and chromatin remodeling

A

DNA methylation turns off eukaryotic gene exp by:

  1. blocks the gene from transcriptional proteins
  2. certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change winding of DNA around histones
62
Q

Controlling gene expression at DNA level - Gene Dose

A

increase copy number > increase quantities of corresponding protein
gene deletion > decrease in gene expression

63
Q

Lac Operon

A

components
P region - promoter site on DNA
O region - operator site to which Lac represser binds
Z gene - codes for enzyme beta-galactosidase, cleaves lactose into glucose and galactose
Y gene - codes for permease, protein that transports lactose into the cell
A gene - codes for trancetylase - transfer an acetyl group from AcetylCoA to beta-galactosidase

regulatory sequences
crp - located at distant site, codes for catobolite activator protein
I gene - located at distant site, codes for Lac repressor protein

64
Q

nucleoside characteristics

A

sugar
base (1’)
no phosphates

65
Q

nucleotide characteristics

A

sugar
base (1’)
phosphates (5’)

66
Q

deoxyribose

A

used in DNA

no O on 2’

67
Q

ribose

A

used in RNA

68
Q

DNA synthesis direction

A

5’ > 3’

69
Q

DNA packing in prokaryotes

A
  1. methylation - protection from restriction enzymes

2. supercoiling - via DNA gyrase

70
Q

telomere

A

short sequence repeats at end of chromosome - stabilizes end of chromosome

71
Q

start codone

A

AUG - methionine

72
Q

polymerase errors

A
  1. point mutations
  2. small repeats
  3. insertion/deletion

repaired by:
mismatch repair pathway - only during or shortly after replication
nucleotide excision repair

73
Q

endogenous damage

A
  1. oxidized DNA
  2. cross-linked bases
  3. double or single strand breaks

fixed by:
homology directed repair
non-homology directed repair (often results in mutations)

74
Q

exogenous damage

A
  1. UV radiation > pyrimidine dimers - forms base pairs on same strand
    - repaired by: direct reversal with white light (doesnt work for humans though)
  2. X rays > double stranded breaks
  3. chemicals > physical damage, intercalation
75
Q

DNA replication

(4) general rules

A
  1. semiconservative - retains 1 parent strande
  2. 5’ -> 3’ synthesis
  3. requires a primer (RNA dimer)
  4. requires a template
76
Q

primase

A

synthisizes RNA primer at origin of replication

77
Q

ligase

A

connects okazaki fragments (lagging strands)

78
Q

Prokaryotic DNA replication

A

theta replication
- 1 origin of replication
- (5) DNA pol - only need to know III and I
III - high processivity, fast, add at 400 bp, no known function of DNA repair
I - low processivity, slow, DNA excision repair

79
Q

eukaryotic replication

A

replication bubbles

  • multiple origins of replication
  • multiple RNA pol (not asked about)
80
Q

Prokaryotic mRNA is polycistonic or monocistonic

A

polycistonic - many different proteins from single mRNA

81
Q

eukaryotic mRNA is polycistonic or monocistonic

A

monocistonic - one mRNA = 1 protein

82
Q

Translation E requirement

ribosome

A

formula = # amino acids * 4

MCAT Bio (6 decks)

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