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Molecular Biology 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
ends of linear chromosomes
- loops of ssDNA to protect ends of chromosomes
26
telomere caps
- prevents activation of repair pathways | - prevent fusion with neighboring chromosomes
27
do prokaryotes have telomeres?
- NO! | - they only have a circular chromosome
28
start codon
- AUG - methionine
29
stop codons
- UAA - U Are Annoying - UGA - U Go Away - UAG - U Are Gone - specify no amino acids
30
degenerate
- multiple codons for the same amino aicd
31
intergenic regions
- never transcribed nor translated - no genes - inherit the same intergenic regions from our parents.
32
polymerase errors
- point mutations - small repeats - DNA pol falls off DNA strand then rejoins. - insertions/deletions (small, frameshift)
33
endogenous damage types | - inside the cell
- reactive oxygen species | - physical damage
34
endogenous damage effect on DNA | - inside the cell
- 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
35
exogenous damage types | - outside of the cell
- radiation | - chemicals
36
exogenous damage effect on DNA
- 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.
37
transposons
- insertions/deletions - inversions - duplications
38
point mutations
- single base pair change
39
missense mutations
- codon for aa becomes a new codon for new aa | - changes aa
40
nonsense mutation
- codon for aa becomes STOP codon | - shortened protein
41
silent mutation
- codon for aa becomes new codon for same aa | - no effect
42
frameshift mutations
- insertions and deletions | - changes the reading frame
43
transposase
- cut and paste enzyme | - allows for mobility
44
IS element (inverted sequence)
- transposase only
45
Complex transposon
- transposase with genes
46
composite transposon
- two transposase flanking a central region
47
how transposons contribute to genomic variation
- code for the cut and paste transposase enzyme - transposase cuts the transposon out - transposase pastes transposon somewhere else.
48
if a transposon is inserted into the intergenic region
- no effect
49
if a transposon is inserted into the coding region
- can result in a big mutagenic effect
50
if two transposons are in the same direction
- pair up - big deletions and possible insertions - chromosomal rearrangements, possibly on a different chromsome
51
if two transposons are in different directions
- pair up to form U-loop - flipped and lead to inversion - chromosomal rearrangement on same chromosome
52
inversion
- a reversal of the gene sequence
53
amplifications
- doubling of the gene
54
mismatch repair pathway
- 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
base/nucleotide excision repair
- occurs prior to replication because defective bases will lead to polymerase errors - incorrect base excised and replaced
56
homologous end joining
- 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
non-homologous end joining
- 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
translocations
- 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
direct reversal
- white light reverses damage | - pop pyrimidine dimers back into place to fix DNA
60
rules for carrying out DNA replication
- semiconservative - half of original DNA molecule will be saved in new DNA molecule - 5' to 3' - requires an RNA primer - requires a template
61
helicase
- unwinds DNA
62
topoisomerase
- cuts DNA | - relaxes supercoiling by passing strands through each other.
63
primase
- puts down the RNA primer
64
DNA polymerase
- replicates DNA, proofreads, removes primer
65
ligase
- links Okazaki fragments
66
prokaryotic replication
- theta replication - 1 origin - 5 DNA polymerases
67
DNA pol III
- high processivity - fast 5' to 3' polymerase and 3' to 5' exonuclease activity - main replicating enzyme - no known function in DNA repair
68
DNA pol I
- 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
DNA pol II
- 5' to 3' polymerase and 3' to 5' exonuclease - back up for DNA pol III - DNA repair
70
DNA pol IV and V
- error prone 5' to 3' polymerase activity | - DNA repair
71
eukaryotic replication
- multiple origins of replication - replication bubbles - several DNA pols, complex multisubunit enzymes
72
end replication problem
- primers add at lagging strand - RNA primers removed - shorter telomeres
73
telomerase
- lengthens the telomeres by adding bases
74
telomerase characteristics
- carries his own internal RNA primer to lengthen telomeres | - reverse transcriptase activity
75
hnRNA
- heterogenous nuclear RNA - unprocessed RNA in euk - precursor to mRNA
76
miRNA
- microRNA | - helps regulate gene expression
77
siRNA
- small interfering RNA - used for regulating gene expression - forms ds RNA molecule helix and ribosome will fall off.
78
coding strand
- sense strand | - same code but T instead of U
79
template strand
- anti-sense strand - complementary - the strand being transcribed
80
regulation of transcription
- promoter - binding site for RNA polymerase
81
strong promoter
- high affinity for RNA pol - get a a lot of RNA - high rates of transcription
82
weak promoter
- low affinity for RNA pol | - low rates of transcription
83
DNA binding proteins
- repressors - gene on must be turned off. bind to DNA to stop transcription. - enhancers - gene off must be turned on. Bind to promoter.
84
prokaryotic transcription
- 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
eukaryotic transcription
- transcription (nucleus) and translation (cytosol) in different places - mRNA processing - monocistronic - one mRNA one protein - 3 RNA polymerases
86
mRNA processing
- 5' G cap - 3' poly A tail - splicing - remove introns. keep exons.
87
RNA polymerases
- RNA pol I - rRNA - RNA pol II - mRNA - RNA Pol III - tRNA are empty - rmt
88
aminoacyl tRNA synthetase
- attaches AA to correct tRNA | - individual for all codoons
89
wobble hypothesis
- 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
prokaryote ribosome subunit eukaryote ribosome subunit
- 50S + 30S = 70S | - 40S + 60S = 80S
91
P site
- growing protein held here | - first tRNA binds here
92
A site
- new amino acid added here
93
initiation of translation
- ribosome subunits assemble over the mRNA with met and tRNA in the P site
94
elongation of translation
- add new AA in A site - costs 1 GTP - form peptide bond between 2 AA - ribosome moves forward one codon
95
termination of translation
- stop codon in A site - bind release factors - break bond between final tRNA and final AA releasing the completed protein
96
tRNA loading costs how many ATP
- 2 ATP per tRNA
97
initiation costs how many ATP
- 1 ATP
98
A site binding costs how many ATP
- 1 ATP per tRNA | - 1 less than number of AA
99
translocation costs how many ATP
- 1 ATP each time | - 1 less than number of AA
100
termination costs how many ATP
- 1 ATP
101
how to calculate the number of ATP needed
amino acids x 4
102
post translational modifications
- protein folding - covalent modification - processing
103
protein folding
- helped by chaperones - H bonds - hydrophobic/philic interactions
104
covalent modification
- disulfide bridges - glycosylation - phosphorylation - methylation
105
processing
- remove some parts of a protein to make it active | - zymogens
106
zymogens
- inactive enzymes | - pro/ - ogen
107
areas of the DNA that are easily unwound for replication are composed of what bases?
-A-T rich
108
stop site
- usually a polyadenylation signal | - different in prokaryotes
109
operator region
- where repressors bind
110
repressor
- prevents RNA polymerase from binding to protein
111
amino acyl tRNA synthase
- attaches amino acids to correct tRNA. | - need as many unique ones as we have unique tRNAs.

Princeton Bio (14 decks)

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