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MCAT Biology & Biochemistry > Ch. 4: Molecular Biology > Flashcards

Ch. 4: Molecular Biology Flashcards

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1
Q

function of

DNA polymerase

A

replicates DNA, proofreads, removes primer

DNA replication

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2
Q

function of

helicase

A

unwinds DNA

DNA replication

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3
Q

function of

ligase

A

links Okazaki fragments

DNA replication

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4
Q

function of

primase

A

synthesizes RNA primer

DNA replication

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5
Q

function of

topoisomerase

A

cuts DNA, relaxes supercoiling

DNA replication

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6
Q

4 rules for DNA replication

A
  1. DNA replication is semiconservative
  2. Polymerization occurs in the 5’ to 3’ direction
  3. DNA polymerase requires a template
  4. DNA polymerase requires a primer
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7
Q

methods to fix

bad bases (mutation repair)

A

mismatched, oxidized, cross-linked, dimers, etc.
1. mismatch repair pathway
2. nucleotide excision repair

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8
Q

base pairing

A

purine + pyrimidine
A & T (2 H bonds)
G & C (3 H bonds)

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9
Q

when & what is the

base/nucleotide excision repair

A
  • any time in cell cycle (ideally before replication)
  • remove the bad base, replace with a good base
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10
Q

methods to fix

broken chromosomes (mutation repair)

A

physical damage, X-rays
1. homology-directed repair (HDR)
2. non-homologous end-joining (NHEJ)

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11
Q

central dogma

special information transfers

A

DNA –transcription–> RNA –translation–> proteins

special transfers
1. DNA from DNA (DNA replication)
2. RNA from RNA (RNA replication)
3. DNA from RNA (reverse transcription)

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12
Q

centromere

two functions & arms

A

heterochromatin region of chromosome where
1. sister chromatids are held together
2. mitotic spindle attaches (via kinetochores)

short arms (p) & long arms (q)

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13
Q

DNA polymerase I (prokaryotes)

processivity, enzymes, function

A
  • low processivity
  • slow 5’-3’ polymerase & 3’-5’ exonuclease
  • also 5’-3’ exonuclease to remove primer
  • adds nucleotides at RNA primer
  • DNA excision repair
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14
Q

DNA polymerase III (prokaryotes)

processivity, enzymes, function

A
  • high processivity
  • fast 5’-3’ polymerase & 3’-5’ exonuclease
  • adds nucleotides ~400 bp downstream of ORI
  • main replicating enzyme
  • no known function in DNA repair
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15
Q

methods to fix

DNA rearrangement (mutation repair)

A

transposons: generally don’t lead to repair mechanisms

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16
Q

name the 5

DNA replication enzymes

A
  1. helicase
  2. topoisomerase
  3. primase
  4. DNA polymerase
  5. ligase
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17
Q

DNA vs RNA

strandedness, components, shapes, types

A

DNA
- double-stranded
- thymine (T)
- deoxyribose
- double helix
- one type

RNA
- single-stranded
- uracil (U)
- ribose
- lots of different 3D shapes
- several types (rRNA, mRNA, tRNA, hnRNA, miRNA, siRNA)

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18
Q

sources & effects of

endogenous damage (mutations)

A

SPONTANEOUS

source: ROS, physical damage

effects
1. oxidized DNA
2. cross-linked bases
3. ss or ds breaks
*all can lead to polymerase errors

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19
Q

equation for

energy requirements of translation

A

amino acids x 4 = # ATP needed

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20
Q

eukaryotic DNA packaging

structure, euchromatin vs heterochromatin

A
  • several linear chromosomes
  • euchromatin: loose packing, higher activity, light staining
  • heterochromatin, tightly wound, inactive, dark staining, rich in repeats
21
Q

eukaryotic DNA replication

origins, DNA polymerases, phase

A
  • multiple origins, form replication bubbles
  • several DNA polymerases, complex multisubunit enzymes
  • occurs during S phase of cell cycle
22
Q

sources & effects of

exogenous damage (mutations)

A

ENVIRONMENTAL

effects
1. UV radiation (pyrimidine dimers)
2. X-rays (ds breaks & translocations)
3. chemicals (physical damage/intercalation, polymerase errors)

23
Q

when & what is

homology-directed repair (HDR)

A
  • must happen after replication (when sister chromatid is present)
  • use (identical) sister chromatid as template to fix broken chromosome
  • includes homologous recombination (HR)
24
Q

how are nucleotides linked to each other in the DNA chain?

A

phosphodiester bonds (covalent)

between 3’ hydroxy group of one deoxyribose & 5’ phosphate group of next

25
Q

intergenic regions

4 bullet points

A
  • massive expanses of noncoding DNA between genes
  • can direct chromatin assembly & regulate nearby genes
  • includes tandem repeats & transposons
  • can accumulate mutations
26
Q

when & what is the

mismatch repair pathway

A
  • during or shortly after replication
  • parent strand is methylated while daughter strand isn’t, can identify daughter/parent
27
Q

when & what is

non-homologous end-joining (NHEJ)

A
  • any time in cell cycle
  • ligate broken ends together
  • mutagenic because usually lose some bases
  • can also result in translocations
28
Q

nucleoside vs nucleotide

2 bullet points

A

nucleoside
- building block of nucleotide
- base & pentose

nucleotide
- monomer of polymeric RNA & DNA
- base, pentose, & phosphate(s)

29
Q

polymerase errors (mutations)

A

point mutations (single base pair change)
- missense: AA codon becomes new codon for new AA
- nonsense: AA codon becomes STOP codon
- silent: AA codon becomes new codon for same AA

frameshift mutations
insertions & deletions of nucleotides that change reading frame (not in multiples of 3)

30
Q

three types of

post-translational modification

A
  1. protein folding (aided by chaperonins)
  2. covalent modification (disulfide bridges, glycosylation, phosphorylation, etc.)
  3. processing (cleavage to form active protein, zymogens)
31
Q

prokaryotic DNA packaging

structure, two phenomenons

A
  • single circular DNA genome
  • methylation (protection from own restriction enzymes)
  • supercoiling (done by DNA gyrase)
32
Q

purines

A

guanine (G) & adenine (A)

33
Q

pyrimidines

A

cytosine (C), uracil (U), thymine (T)

*pyramids have sharp edges so they CUT

34
Q

regulation of transcription

2 methods

A

primary point of regulation for translation

(1) promoter
- strong: high RNA pol affinity, get lots of RNA
- weak: low RNA pol affinity, get less RNA

(2) DNA binding proteins
- repressors
- enhancers

35
Q

replication vs transcription

3 similarities & 2 differences

A

both
- have beginning point (origin vs START site)
- run in 5’ to 3’ direction
- use DNA template

transcription
- doesn’t use primer
- RNA polymerase can’t correct its errors (lower fidelity)

36
Q

ribosomes (prokaryotes vs eukaryotes)

subunits, intiation

A

prokaryotes (odd #)
large subunit: 50 S
small subunit: 30 S
total: 70 S

eukaryotes (even #)
large subunit: 60 S
small subunit: 40 S
total: 80 S

initiation (1 ATP)
prokaryotes: mRNA binds small, first tRNA binds, recruit large
eukaryotes: mRNA binds first tRNA, small binds, recruit large

37
Q

start codon & stop codons

1 start, 3 stop

A

start: AUG, codes for Met

stop: UAA, UGA, UAG
- don’t code for AAs
- “U Are Annoying, U Go Away, U Are Gone”

38
Q

telomere extension

why are telomeres shortened in the first place? what extends them & how?

A

when RNA primers on 3’ end of parent strand are removed, telomeres are shortened

telomerase: elongates telomeres on parent strand of DNA
1. built-in RNA template
2. reverse transcriptase activity (DNA from RNA)

39
Q

telomeres

4 characteristics

A
  1. ends of eukaryotic linear chromosomes
  2. contains both ss- & ds-DNA
  3. short sequence repeats (5’-TTAGGG-3’)
  4. stabilize ends of chromosome
40
Q

transcription (prokaryotes vs eukaryotes)

time/place, mRNA, cistron, RNA pol

A

prokaryotes
- transcription & translation at same time & place
- no mRNA processing
- polycistronic (many proteins from one mRNA)
- 1 RNA polymerase

eukaryotes
- transcription & translation at different times & places
- mRNA processing (5’ G-cap, 3’ poly-A tail, splicing)
- monocistronic (one mRNA for one protein)
- 3 RNA polymerases

“Names of RNA Pol a(R)e e(M)p(T)y”
1 2 3

41
Q

translation

sites, enzyme, termination

A

P site: growing Protein held here
A site: new Amino Acid added here

peptidyl transferase: catalyzes addition of AA to chain with peptide bond

termination (1 ATP)
1. no tRNA recognizes STOP codon in A site
2. instead, bind release factor which breaks bond between final tRNA & AA (i.e. releases completed protein)

42
Q

transposons (mutations)

A

mobile genetic elements
1. insertions/deletions (large)
2. inversions
3. duplications

43
Q

tRNA

nomenclature, enzyme, ATP requirements

A

Met-tRNA means tRNA is loaded with Met

Different aminoacyl tRNA synthetase for each AA

Requires 2 ATP to load AA (tRNA loading for AA activation)

44
Q

Watson-Crick model

A

cellular DNA is
- right-handed, antiparallel double helix
- held together by H bonds between bases
- bases on interior
- sugar-phosphate backbone on exterior
- double helix stabilized by VDW between stacked bases

45
Q

three components of nucleotides

A
  1. sugar (deoxyribose for DNA, ribose for RNA)
  2. aromatic, nitrogenous base
  3. 1-3 phosphate groups
46
Q

building block of DNA

abbreviation & full name

A

dNTP, where N = nucleotide

deoxyribonucleoside 5’ triphosphate

47
Q

wobble hypothesis

when does wobble base pairing happen?

A
  • first two codon-anticodon pairs bind normally (Watson-Crick)
  • third anticodon is more flexible
  • also, an adenine on tRNA can get converted to inosine for even more flexibility
  • cells can make do when running low on certain tRNA molecules

wobble base pairing happens when there is G, U, or I at the 5’ end of the anticodon

48
Q

exonuclease

A

an enzyme which removes nucleotides from the end (exo) of a polynucleotide by hydrolyzing their phosphodiester bonds

49
Q

endonuclease

A

an enzyme which removes nucleotides from the middle (endo) of a polynucleotide by hydrolyzing their phosphodiester bonds

MCAT Biology & Biochemistry (2 decks)

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