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biochem 2288 > 3 > Flashcards

3 Flashcards

1
Q

DNA: where is 5’ to 3’ and opp?

A

Top:L 5’ to 3’
Bottom: 3’ to 5’

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2
Q

composition of a nucleic acid

A

nucleic acid is composed of many nucleotide (5’ to 3’):
a pentose sugar linked to a N base via glycosidic bond @C1 + PO4 group
each nucleotide is linked tgt via phosphodiester bond

Each nucleotide is linked tgt via PO4 bond

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3
Q

purines vs pyrimidies

A

nitrogenous base can be purines (A G) or pyrimidines ( C T U)
flat surface, hydrophobic, inpt when stacked; has H bond (A T has 2 while GC has 3)

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4
Q

what is DNA 2x helix shape comes from?

A

Chargaff’s rule: in any org, lvl of ATCG will alwyas be consistent (AT > CG)
X-ray diffraction pattern
correct structural (tautomeric) forms of bases: suggested Keto forms

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5
Q

DNA 2x helix (B-DNA): ___ antiparallel, ____ stabilised by hydrophobic interactions
is __ n, in diameter, w/ a rise of ___ nm per bp
plane is ___ to ___ while sugar-PO4 ___ wraps around the __ in a __-___ coil

Stabilises through base stacking and base pairing: H bonds

A

righthanded, double steranded
is 2, 34
perpedincular / axis / backbone / axis / right handed

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6
Q

A-T has __ H bonds while G-C has ___

A

2, 3

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7
Q

5 points of comparison btw DNA vs RNA

A
  1. DNA has -H @ C2 while RNA has C2s hydroxyl
  2. thymine vs uracil
  3. long vs short
  4. 2x in double hexlix vs 3 stem loop strucrure
  5. few base modifications vs many
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8
Q

describe RNA structure

A

short, 2x helix regions that are antiparallel BT singple stranded
is sequence dependent-> irreguar, creates this complex 3D structure
allows rRNA to interact w/ multiple partners in ribosome

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9
Q

Human DNA must be condensed into ____ = DNA plus assoiciated ___ ___
red part is ___ aka tightly packed DNA not ___ )__)_
yellow part is _____ aka one regularly —-

A

chromatic, pckaging proteins
heterochromatin / regularly / expressed
euchromatin / expresssed

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10
Q

describe ribonucleoside

A

= pentose sguar w. N base (cytidine has cytosine for N base)

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11
Q

describe deoxyribonucleotide

A

in sugar, replace -OH @ C2 w. -H

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12
Q

describe ribonucleotide

A

= pentose sugar + N base + phosphate
has O H- for C2

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13
Q

length
%GC (< ___ interactions & ___ bonds)
more/ less complementary
more ___ (neutralize repel __ charges)
organic ____ </> 9affect hydrophobic interactions)
urea/formamide&raquo_space; (___ affect __ bonds)

extreme pH lowers it

A

factors affecting primer melting temp < when

hydrophobic / H
more
salt / PO4
solvent >
denat / H

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14
Q

ROs in bacteria vs eukaryotes

A

in bacteria you nee d1 w/ circular DNA
in eukaryotes, maybe 30-50k ROs

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15
Q

describe initiation of DNA replication

A

Replication Origin tends tb richer in A-T

@ RO, initiator protein binds to DNA and pulls them apart
helicase splits them apart creating a replication fork and estends the bubble
old DNA used as templates to create new ones = semi conservative

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16
Q

priming- DNA replication

A

need primase (a type of RNA polymerase) = creates a short RNA strand complementary to DNA called primer
bcs top DNA is 5’ to 3’ (L to R), primase creates from 5’ to 3’ (R to L)

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17
Q

DNA synthesis (overall_

A

primase dissociates, leaving behidnt he primer
=> DNA polym picks up from 3’ end, initiates 2nd strand DNA synthesis, adds bases
DNA polym catalyze the addition of dNTP by linking its alpha PO4 to DNA’s chain’s C3 OH
=> pyroPO4 PPi is released

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18
Q

how is DNA polym stringent?

A

DNA polym is stringent– tolerates v lil variation- picky with base it links

select dNATPis dictated by template strand
- if base comes w/ correct geometry, polym-mediated action occurs; if not, no rxn

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19
Q

describes proofreading

A

in case of mismatch / extra base / delete base
use a nuclease = enzyme that degrades nucleic acid (exo from outside, endo from inside)
=> DNA polym has a 2nd activity site w/ exonuclease activity

20
Q

describes ligation

RNA primase must be removed, DNA ____ joines 2 strands @ ___

in prokaryotes/eukaryotes
- ___ ___ (a nuclease) degrades primer, DNA polym ____ fills in gap (nick remains)
- DNA polym III kicks off primer, it __ ___, _____ ___

A

ligase, nick
Rnase H / IIII
broken down / nick remaisn

21
Q

describes copying mistkae

A

DNA polym faults every 10^7 nucleotides: mismatch , insertion, deletion
=> if unrepaired, duaghter cell swill cotnains the altered genome, call it a mutation

22
Q

list other DNA damamges

  1. can be __ ___ or __ ___: polyaromatic HC
  2. suga-____ ___:, mechanical stress
A
  1. depurination
  2. demamination
  3. pyrimidine dimers: most common dmaage cased by UV radiation
  4. base modifications: ionizing radiation or chemical mutagens like charred meats
  5. sugar phosphate break: ionization readiation, reactive O species, mechanical stress
23
Q

DNA repari system includes reviewing and mutation repair. T OR F

A

F. proofreading (DNA synthesis) and mismatch repair

24
Q

describes others of DNA repair ssystems

  • nucleotide excision repair: heals __ ___ & dmage that disrupt __ ___
    for eample xeroderma ___ caused by mutation when NER is ineffective
    => SKIN CANCER
    => is _____, tumour

non-___ end __ & homologous ____ reparis 2x stranded break

A

pyrimidine dimers / 2x helix
pigmentosum
ohotosensitive

homologous joining / recomb

25
Q

describe transcription

A

first, core promotor sequence must be present

RNA polym slides along DNA template and creates complemen. bp
-> mRNA -> dissociates
- transcription factor binds and recruits RNA polym @ promotor region while regulatory protein binds @ enhancer region

26
Q

combination control

A

group of protein tht works tgt to control gene expression

27
Q

differential splicing

A

splice DNA to create similar bt distinct protein, which may have diff function

28
Q

how to process mRNA in eukaryotes

A

add 5’ cap w/ specific protein, done by methylated G
3’ polyadenylation tail
splicing

29
Q

what is splicing? why slice?

A

to < coding capacity of gene

in eukaryotic cells, coding exons are interrupted by noncoding introns
cut out introns to give mature mRNA

30
Q

when does things happen?

A

transcription happen in nucleus, translation cytoplasm. after mRNA processed, exxits nucleus

31
Q

how does mRNA exit nucleus?

A

exits nucleus via nuclear pore complex (large protein complex)
replace cytosol-specific, RNA-binding protein with nucleus rNA-binding protein

32
Q

silent mutation

A

DNA sequence change bt not in protein sequence

33
Q

redundancy

A

more than 1 codon may code for the same am.a bt 1 codon can’t code for 2 ama

34
Q

framshift mutation

A

an insertion or deletion of base

35
Q

missense mutation

A

if in the exon, a single base change in translated protein

36
Q

nonsense mutation

A

change a base tht now becomes stop codon– prematurely terminates protein

37
Q

lose a function
- ____ in impt ama residue
- ____ or frmashift shoften ____
- lose structual intergrity (can’t ___)

gain a function:
- permanent __ of ____
- toxic to cell

A
  • missense
  • nonsense / protein
  • fold
  • ON// oncogene
38
Q

what is tRNA

A

adaptor molec

have similar structures to fit into the ribosome
have distinct features to fit codon and am.a
3’ CCA is in all tRNA– where amino acids attached
multiple base pair, H bodn stabilizes

39
Q

features of tRNA

A

all have a similar structure to fit into ribosome
have distinct feature tb truplet & am.a specific
3/ end CCA is concerved in all tRNA- a site for attachmnt of am.a

40
Q

synthesis of all protein chains in prokary + eukary begins with ________

A

Methionine

41
Q

specifity comes from:
- _____tRNA synthetase = enzyme that adds _____ to tRNA
correct matching of ____ of ___-______ w/ codon in ___ ___ site

A

aminoacyl / am.a
anticodon aminoacyl tRNA / ribosome

42
Q

features of genetic code

A

is universal, bt have evolved once
non-overlaping
every codon codes for something: an ama or stop codon

43
Q

DESCRIBES tRNA

A

transfer; adapter molec

  • have similar structure to fit into the ribosome
    have distinct features to bt codon & ama specific
    3’ CCA is in all tRNA – where ama attaches
    multple bp- H bond stabilizes
44
Q

describes translation

A

mRNA binds to ribosome
from 5’ to 3’-> tRNA makes protein from N to C terminus (alpha amino to alpha carboxyl)
as mRNA reads a codon @ time, tRNA delivers corresponding ama
energy for peptide bond synthesis comes from aa-tRNA ester bond– indirectly from aTP

45
Q

specifty comes from
_____ tRNA ___ = enzyme that adds am.a to ____
correct matching of aminoacyl’s ___) to _____’s codon

A

aminoacyl synthetase / tRNA
anticodon / ribosome

biochem 2288 (8 decks)

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