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Molecular Biology Flashcards

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Biology 101 flashcards
1
Q

Nucleotide

A
  • sugar
  • base
  • phosphate
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2
Q

deoxyribose

A
  • DNA
  • missing 2’ OH
  • less apt to nucleophilic attack
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3
Q

nucleic acid polymerization

A
  • 5’ to 3’ synthesis and base sequence
  • antiparallel and complementary
  • phosphodiester bond
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4
Q

phosphodiester bond

A
  • covalently links nucleotides between 3’ OH and 5’ Phosphate
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5
Q

bases

A
  • purines

- pyrimidines

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6
Q

purines

A
  • 2 rings
  • adenine
  • guanine
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7
Q

pyrimidines

A
  • 1 ring
  • cytosine
  • thymine
  • uracil
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8
Q

genome

A
  • all the DNA in an organisms
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9
Q

prokaryotes

A
  • single circular DNA genome
  • methylation
  • supercoiling
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10
Q

methylation

A
  • protection from their own restriction enzymes (endonucleases)
  • no longer fits into the active site of the enzyme
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11
Q

endonucleases

A
  • chop off DNA

- restrict the growth of viruses whose DNA is not methylated

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12
Q

supercoiling done by the enzyme

A
  • gyrase - uses ATP by breaking the DNA and twisting the two sides of the circle into supercoils.
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13
Q

eukaryotes

A
  • several linear chromosomes
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14
Q

packing of eukaryotes

A
  • DNA packaged with histone octomer to form nucleosomes
  • forms the bead on a string
  • packed further into chromatin
  • packed into the eukaryotic cell as a chromosome
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15
Q

heterochromatin

A
  • tight packing inactive DNA
  • dense, dark regions on a stain
  • rich in repeats
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16
Q

euchromatin

A
  • less tightly packaged
  • active DNA
  • higher transcription rates and gene activity because DNA more accessible to enzymes and proteins
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17
Q

histones

A
  • basic to attract acidic DNA backbone

- two of each: H2A, H2B, H3, H4

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18
Q

centromere

A
  • region on the chromosome where
    • mitotic spindle attaches via kinetochores during cell division
    • where two pieces of DNA are held together after replication
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19
Q

centromere position

A
  • position defines ratio between long and short arms
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20
Q

equal size arms

A
  • metacentric
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21
Q

really short P arms

A
  • acrocentric
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22
Q

no P arm

A
  • telocentric
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23
Q

short P arms

A
  • submetacentric
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24
Q

telomeres

A
  • ends of linear chromosomes
  • “caps” linear chromosomes to prevent degradation
  • many repeats of a short sequence
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25
Q

ends of linear chromosomes

A
  • loops of ssDNA to protect ends of chromosomes
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26
Q

telomere caps

A
  • prevents activation of repair pathways

- prevent fusion with neighboring chromosomes

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27
Q

do prokaryotes have telomeres?

A
  • NO!

- they only have a circular chromosome

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28
Q

start codon

A
  • AUG - methionine
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29
Q

stop codons

A
  • UAA - U Are Annoying
  • UGA - U Go Away
  • UAG - U Are Gone
  • specify no amino acids
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30
Q

degenerate

A
  • multiple codons for the same amino aicd
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31
Q

intergenic regions

A
  • never transcribed nor translated
  • no genes
  • inherit the same intergenic regions from our parents.
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32
Q

polymerase errors

A
  • point mutations
  • small repeats - DNA pol falls off DNA strand then rejoins.
  • insertions/deletions (small, frameshift)
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33
Q

endogenous damage types

- inside the cell

A
  • reactive oxygen species

- physical damage

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34
Q

endogenous damage effect on DNA

- inside the cell

A
  • oxidized DNA - bases look different so they can’t base pair.
  • crosslinked bases - physically linked together. not just hydrogen bonded. can’t separate strand easily for replication. could crosslink to different strands.
  • physical damage - DNA broken or bases missing. sheer stresses.
  • these can lead to polymerase errors
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35
Q

exogenous damage types

- outside of the cell

A
  • radiation

- chemicals

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36
Q

exogenous damage effect on DNA

A
  • UV rad - pyrimidine dimers. pair with each other. (typically T=T)
  • X rays or gamma rays - double stranded breaks and translocations
  • chemicals - can lead to physical damage or to intercalation and polymerase will stick in something random and cause errors.
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37
Q

transposons

A
  • insertions/deletions
  • inversions
  • duplications
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38
Q

point mutations

A
  • single base pair change
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39
Q

missense mutations

A
  • codon for aa becomes a new codon for new aa

- changes aa

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40
Q

nonsense mutation

A
  • codon for aa becomes STOP codon

- shortened protein

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41
Q

silent mutation

A
  • codon for aa becomes new codon for same aa

- no effect

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42
Q

frameshift mutations

A
  • insertions and deletions

- changes the reading frame

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43
Q

transposase

A
  • cut and paste enzyme

- allows for mobility

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44
Q

IS element (inverted sequence)

A
  • transposase only
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45
Q

Complex transposon

A
  • transposase with genes
46
Q

composite transposon

A
  • two transposase flanking a central region
47
Q

how transposons contribute to genomic variation

A
  • code for the cut and paste transposase enzyme
  • transposase cuts the transposon out
  • transposase pastes transposon somewhere else.
48
Q

if a transposon is inserted into the intergenic region

A
  • no effect
49
Q

if a transposon is inserted into the coding region

A
  • can result in a big mutagenic effect
50
Q

if two transposons are in the same direction

A
  • pair up
  • big deletions and possible insertions
  • chromosomal rearrangements, possibly on a different chromsome
51
Q

if two transposons are in different directions

A
  • pair up to form U-loop
  • flipped and lead to inversion
  • chromosomal rearrangement on same chromosome
52
Q

inversion

A
  • a reversal of the gene sequence
53
Q

amplifications

A
  • doubling of the gene
54
Q

mismatch repair pathway

A
  • repairs bases due to DNA polymerase errors
  • detected after replication is complete
  • fix DNA based on polymerase errors
  • methylate the parent strand
  • cut out incorrect bases that are unmethylated
  • polymerize again
55
Q

base/nucleotide excision repair

A
  • occurs prior to replication because defective bases will lead to polymerase errors
  • incorrect base excised and replaced
56
Q

homologous end joining

A
  • repairs double stranded DNA breaks
  • occurs after replication
  • sister chromatid used as a template for repair broken strand
  • crossover of the sister chromatid
  • may lose an allele
  • best way to repair double stranded breaks
57
Q

non-homologous end joining

A
  • no sister chromatid for template (cell is not going through division and thus not replicating DNA).
  • clear out damaged regions
  • blunt ends of DNA
  • join the broken 2 strands together
  • mutagenic because losing some bases or could result in a translocation
58
Q

translocations

A
  • due to recombination between non-homologous chromosomes or faulty DNA repair (non-homologous end joining)
  • causes gene fusion if the joining point is in the middle of the gene.
59
Q

direct reversal

A
  • white light reverses damage

- pop pyrimidine dimers back into place to fix DNA

60
Q

rules for carrying out DNA replication

A
  • semiconservative - half of original DNA molecule will be saved in new DNA molecule
  • 5’ to 3’
  • requires an RNA primer
  • requires a template
61
Q

helicase

A
  • unwinds DNA
62
Q

topoisomerase

A
  • cuts DNA

- relaxes supercoiling by passing strands through each other.

63
Q

primase

A
  • puts down the RNA primer
64
Q

DNA polymerase

A
  • replicates DNA, proofreads, removes primer
65
Q

ligase

A
  • links Okazaki fragments
66
Q

prokaryotic replication

A
  • theta replication
  • 1 origin
  • 5 DNA polymerases
67
Q

DNA pol III

A
  • high processivity
  • fast 5’ to 3’ polymerase and 3’ to 5’ exonuclease activity
  • main replicating enzyme
  • no known function in DNA repair
68
Q

DNA pol I

A
  • low processivity
  • adds nucleotides to RNA primer then DNA pol III takes over
  • slow 5’ to 3’ polymerase and 3’ to 5’ exonuclease
  • 5’ to 3’ exonuclease to remove primer
  • DNA excision repair
69
Q

DNA pol II

A
  • 5’ to 3’ polymerase and 3’ to 5’ exonuclease
  • back up for DNA pol III
  • DNA repair
70
Q

DNA pol IV and V

A
  • error prone 5’ to 3’ polymerase activity

- DNA repair

71
Q

eukaryotic replication

A
  • multiple origins of replication
  • replication bubbles
  • several DNA pols, complex multisubunit enzymes
72
Q

end replication problem

A
  • primers add at lagging strand
  • RNA primers removed
  • shorter telomeres
73
Q

telomerase

A
  • lengthens the telomeres by adding bases
74
Q

telomerase characteristics

A
  • carries his own internal RNA primer to lengthen telomeres

- reverse transcriptase activity

75
Q

hnRNA

A
  • heterogenous nuclear RNA
  • unprocessed RNA in euk
  • precursor to mRNA
76
Q

miRNA

A
  • microRNA

- helps regulate gene expression

77
Q

siRNA

A
  • small interfering RNA
  • used for regulating gene expression
  • forms ds RNA molecule helix and ribosome will fall off.
78
Q

coding strand

A
  • sense strand

- same code but T instead of U

79
Q

template strand

A
  • anti-sense strand
  • complementary
  • the strand being transcribed
80
Q

regulation of transcription

A
  • promoter - binding site for RNA polymerase
81
Q

strong promoter

A
  • high affinity for RNA pol
  • get a a lot of RNA
  • high rates of transcription
82
Q

weak promoter

A
  • low affinity for RNA pol

- low rates of transcription

83
Q

DNA binding proteins

A
  • repressors - gene on must be turned off. bind to DNA to stop transcription.
  • enhancers - gene off must be turned on. Bind to promoter.
84
Q

prokaryotic transcription

A
  • transcription and translation happen in the cytosol at the same time
  • no mRNA processing
  • polycistronic - code for several different proteins from same mRNA
  • 1 RNA polymerase
85
Q

eukaryotic transcription

A
  • transcription (nucleus) and translation (cytosol) in different places
  • mRNA processing
  • monocistronic - one mRNA one protein
  • 3 RNA polymerases
86
Q

mRNA processing

A
  • 5’ G cap
  • 3’ poly A tail
  • splicing - remove introns. keep exons.
87
Q

RNA polymerases

A
  • RNA pol I - rRNA
  • RNA pol II - mRNA
  • RNA Pol III - tRNA

are empty - rmt

88
Q

aminoacyl tRNA synthetase

A
  • attaches AA to correct tRNA

- individual for all codoons

89
Q

wobble hypothesis

A
  • first two anticodons on tRNA bind normally
  • third anticodon is more loosely bound
  • adenine on tRNA can get converted to idenosine
  • happens when there are G, U, I at 5’ end of anticodon
90
Q

prokaryote ribosome subunit

eukaryote ribosome subunit

A
  • 50S + 30S = 70S

- 40S + 60S = 80S

91
Q

P site

A
  • growing protein held here

- first tRNA binds here

92
Q

A site

A
  • new amino acid added here
93
Q

initiation of translation

A
  • ribosome subunits assemble over the mRNA with met and tRNA in the P site
94
Q

elongation of translation

A
  • add new AA in A site
  • costs 1 GTP
  • form peptide bond between 2 AA
  • ribosome moves forward one codon
95
Q

termination of translation

A
  • stop codon in A site
  • bind release factors
  • break bond between final tRNA and final AA releasing the completed protein
96
Q

tRNA loading costs how many ATP

A
  • 2 ATP per tRNA
97
Q

initiation costs how many ATP

A
  • 1 ATP
98
Q

A site binding costs how many ATP

A
  • 1 ATP per tRNA

- 1 less than number of AA

99
Q

translocation costs how many ATP

A
  • 1 ATP each time

- 1 less than number of AA

100
Q

termination costs how many ATP

A
  • 1 ATP
101
Q

how to calculate the number of ATP needed

A

amino acids x 4

102
Q

post translational modifications

A
  • protein folding
  • covalent modification
  • processing
103
Q

protein folding

A
  • helped by chaperones
  • H bonds
  • hydrophobic/philic interactions
104
Q

covalent modification

A
  • disulfide bridges
  • glycosylation
  • phosphorylation
  • methylation
105
Q

processing

A
  • remove some parts of a protein to make it active

- zymogens

106
Q

zymogens

A
  • inactive enzymes

- pro/ - ogen

107
Q

areas of the DNA that are easily unwound for replication are composed of what bases?

A

-A-T rich

108
Q

stop site

A
  • usually a polyadenylation signal

- different in prokaryotes

109
Q

operator region

A
  • where repressors bind
110
Q

repressor

A
  • prevents RNA polymerase from binding to protein
111
Q

amino acyl tRNA synthase

A
  • attaches amino acids to correct tRNA.

- need as many unique ones as we have unique tRNAs.

Princeton Bio (14 decks)

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