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Biochemistry > Molecular > Flashcards

Molecular Flashcards

0
Q

Heterochromatin

A

condensed, transcriptionally inactive, sterically inaccesible
- HeteroChromatin = Highly Condensed

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1
Q

Chromatin structure

A

DNA exists in condensed, chromatin form to fit in nucleus. Form nucleosome bead (bead on a string). Histones all inside, except H1 binds to nucleosome + DNA to stablize

  • In mitosis, DNA condenses to chromosomes
  • DNA/histones made in S phase
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2
Q

Euchromatin

A

Less condensed; transcriptionally active + sterically accessible
- Eu = true; “truly transcribed”

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3
Q

DNA methylation

A

Methylate cytosine/adenosine in DNA replication so mismatch repair enzymes know what is old/new prokaryote strands
- DNA methylation at CpG islands represses transcription (CpG Methylation Makes DNA Mute)

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4
Q

Histone methylation

A

Usually represses DNA transcription, but can sometimes activate
- Histone methylation mostly makes DNA mute

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5
Q

Histone acetylation

A

Acetylation makes DNA Active

- Relaxes DNA coiling –> can do transcription

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6
Q

Nucleotides

A

Nucleotide = base + deoxyribose + phosphate

  • Purines (PURe As Gold) - A, G
  • Pyrimadines (CUT the PY) - C, U/T
  • THYmine has a meTHYl
  • Uracil in RNA; thymine in DNA
  • G-C bond (3 bonds) stronger than AT cond (2 bonds) –> so higher melt temp
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7
Q

Nucleoside

A

NucleoSide = base + deoxyriboes (Sugar)

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8
Q

Synthesis of purine

A

Sugar + phosphate (PRPP) + base

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9
Q

Synthesis of pyrimadine

A
  • Temporary base (orotic acid) + sugar + phosphate (PRPP)
  • Modify base
  • RNA synth first –> then converted to DNA via ribonucleotide reductase
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10
Q

Purine salvage

A

ADENOSINE -> adenosine deaminase -> HYPOXANTHINE ->xanthine oxidase -> URIC ACID
- Deficiencies lead to purine salvage problems

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11
Q

Adenosine deaminase deficiency

A

Cause of autosomal recessive SCID
- Excess ATP + dATP, imbalanced nucleotide pool bc feedback inhibits ribonucleotide reductase -> prevent DNA synthesis -> decr lymphocyte count

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12
Q

Lesch-Nyhan syndrome

A

Absent HGPRT -> defective purine salvage

  • HGPRT converts hypoxantheine to IMP and GMP
  • Excess uric acid production and de novo purine synthesis (bc can’t salvage)
  • X-linked recessive
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13
Q

Lesch-Nyhan sxs

A

Signs - intellectual disability, self-mutilation, aggression, hyperuricemia, gout, dystonia
- HGPRT: hyperuricemia, gout, pissed off (aggression, self-mutilation), retardation (intellect disability), dysTonia

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14
Q

Lesch-Nyhan tx

A

allopurinol or febuxostat (2nd line)

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15
Q

Genetic code features

A
  • Unambiguous - each codon specifies only 1 AA
  • Degenerate/redundant - most AAs coded by multiple codons (except AUG, UGG)
  • Commaless, nonoverlapping - read from fixed start as continuous sequence (except some viruses)
  • Universal - genetic code conserved throughout evolution (except mitochondria)
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16
Q

DNA replication

A

Eukaryotic more complex than prokaryotic

- Both have semiconservative replication, and use continuous and discontinuous (Okazaki) fragments

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17
Q

Origin of replication

A

Certain sequence of base pairs where DNA replication starts

  • single in prokaryotes
  • multiple in eukaryotes
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18
Q

Replication fork

A

Y-shaped antigen along DNA template where leading/lagging strands are made

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19
Q

Helicase

A

Unwinds DNA at replication fork

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20
Q

ssBP (single stranded binding proteins)

A

prevents strands from reannealing

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21
Q

DNA topoisomerases

A

Create ss or ds break in DNA to remove supercoils

- Fluoroquinolones inhibits this

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22
Q

Primase

A

Makes RNA primer on which DNA polymerase III can start replication

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23
Q

DNA polymerase III

A

only in prokaryotes

- 5–>3 synthesis on leading strand and 3–> 5 exonuclease proofreading

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24
Q

DNA polymerase I

A

only in prokaryotes

  • Degrades DNA primer –> replace w/ DNA
  • Same fxn as polym III but also excises RNA primer
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25
Q

DNA ligase

A

Seals by catalysing formation of phosphodiester bonds between dsDNA (i.e. joins Okazaki frags)

26
Q

Mutations in DNA

A

Severity: silent &laquo_space;missence < nonsense <frameshift

  • Transition = purine to purine or pyrimadine to pyrimidine
  • Transversion = purine to pyrimadine (or vice versa)
27
Q

Telomerase

A

RNA dependent DNA polymerase –> adds to 3’ chrom end to avoid loss of genetic material (telomere shortening) w/ duplication
- Find these in stem cells and cancer cells (elongate telomeres so don’t get death)

29
Q

Silent DNA mutation

A

NT changes, but still codes for same AA (often 3rd position change)
- Same size, fxnal

30
Q

Missense mutation

A

NT substitution –> changes AA

i. e. Sickle cell
- Same size, nonfxnal

31
Q

Frameshift mutation

A

Deletion/insertion of # NT not divisible by 3 –> misreading of all those downstream
- Get shorter, non-fxnal proteins

32
Q

Splice-site mutation

A

Produces larger protein with altered function but preserved immune reactivity

33
Q

Nonsense mutation

A

NT substitution –> early stop codon
- Shorter nonfxnal protein
“Stop the nonsense”

34
Q

DNA repair

A

Single strand - NT excision repair, base excision repair, mismatch repair

Double strand - nonhomologous end joining

35
Q

NT excision repair

A
  • In single strand
  • Endonucleases release damaged bases –> DNA polymerase + ligase fill/reseal gap
  • Removes bulky DNA damage
  • Defective in xeroderma pigmentosum –> can’t heal pyrimidine dimers from UV light damage
36
Q

Base excision repair

A
  • In single strand
  • Base-specific glycosylase recognizes altered bases (makes AP site; no purine or pyrimidine)
  • DNA polymerase B fills gap, DNA ligase seals
  • Important for repairing spontaneous/toxic deamination
37
Q

Mismatch repair

A
  • In single strand
  • Finds mismatches in newly synthesized strands; gap filled/resealed
  • Defective in HNPCC (hereditary nonpolyposis colorectal cancer)
38
Q

Nonhomologous end joining repair

A
  • In double stranded
  • Brings together 2 ends of DNA fragments to repair ds bond; dont need homology
  • Defective in ataxia talangectasia
39
Q

RNA/DNA/protein synthesis direction

A

RNA/DNA both synthesized 5’ –> 3’

  • 5’ has triphosphate, where 3’ hydroxyl attaches
  • Drugs to prevent this have modified 3’ OH (prevent addition of next NT)

Protein - synthesized N-terminus to C-terminus

40
Q

Start codons

A

AUG inAUGurates protein synthesis

41
Q

Stop codons

A

UGA - U Go Away
UAA - U Are Away
UAG - U Are Gone

42
Q

Organization of eukaryotic gene

A

Sense/coding strand, enhancer, promotor (TATA box), start of transcription, transcribed region (introns + exons), terination signals

43
Q

Promotor

A

RNA polymerase + TFs bind to DNA upstream from gene locus (TATA box)
- Mutation here = decr gene transcription

44
Q

Enhancer

A

DNA stretch that alters gene expression by binding TFs

- Can be close to/far from or in intron of expression it regulates

45
Q

Silencer

A

Negative regulators bind here (repress)

- Can be close to/far from or in intron of expression it regulates

46
Q

RNA polymerase (eukaryotes)

A
  • RNA poly I –> rRNA (most numerous; r = rampant)
  • RNA poly II –> mRNA (largest RNA, m = massive)
  • a-amanitin = death cap mushrooms, inhibit RNA poly II –> hepatotoxicity
  • RNA poly III –> tRNA (smallest RNA, t = tiny)
47
Q

RNA polymerase (prokaryotes)

A

1 RNA polymerase makes all 3 kinds of RNA (r, m, t)

48
Q

Proofreading

A

RNA polymerase lack 3’–>5’ exonuclease proofreading!

- RNA viruses have more genetic variability, bc more mistakes (mutations) made

49
Q

Processing of RNA

A

hnRNA –> mRNA
In nucleus: capping 5’ end, polyadenylation of 3’ end (HO-AAAAx), splicing out introns –> now is mRNA
Cytosol: mRNA transported here from nucleus, translated
- Quality control at cytoplasmic P-bodies

50
Q

Splicing pre-mRNA

A

1) Transcript + snRNPs –> spliceosome
2) Lariat-shaped (looped) intermediate formed
3) Lariat released, primary removes intron + join 2 exons
- Anti snRNPs = anti-Sm, specific for SLE
- Anti-U1 RNP = MCTD (mixed connective tissue disease)

51
Q

Exons and Introns

A
  • Exons - contain genetic info coding for proteins
  • Introns - intervening noncodon segments of DNA
  • Exons often combined bc splicing to make more unique proteins
  • “introns are intervening sequences + stay in nucleus; exons exit nucleus and are expressed”
52
Q

tRNA

A

Carries AA to ribosome because of codon in mRNA

  • Needed for protein translation (make new proteins)
  • Proteins made on ribosome (APE)

75-90 NT long, 2/2 structure, cloverleaf form

  • CCA at 3’ end –> binds/carries AAs
  • T-arm - for tRNA-ribosome binding
  • D-arm - for tRNA recogn by correct tRNA synthetase (dihydrouracil residues)
  • Need tRNA synthetase to match tRNA with correct AA
  • *tRNA is only RNA with thymidine**
53
Q

tRNA wobble

A

Accurate base pairing only needed in 1st 2 NT positions of mRNA codon
- So codons w/ diff 3rd “wobble” position code for same tRNA/AA (bc degeneracy of genetic code)

54
Q

Protein synthesis

A
  • Occurs in ribosome
  • Steps: initiation, elongation and termination
  • Going “APE”
    A site = incoming Aminoacyl-tRNA
    P site = accomodates growing Peptide
    E site = holds empty tRNA as it Exits
55
Q

Eukaryotic initiation of protein synthesis

A
  • Initiated by GTP hydrolysis (“GTP - tRNA Gripping and Going places”)
  • Initiation factors assemble 40S ribosome subunit w/ initiator of tRNA
  • Initiation factors released when mRNA and ribosomal 60S subunit assemble w/ complex

Eukaryocytes: 40S + 60S –> 80S (Even)
PrOkaryotes: 30S + 50S –> 70S (Odd)

56
Q

Prokaryotic initiation of protein synthesis

A

Initiated by 30S subunit with initiator of tRNA

  • 50S subunit and GTP join
  • 30S + 50S = 70S
57
Q

Streptomycin

A

Binds and distorts 30S subunit of prokaryotes (need for translation initiation) –> can’t synthesize proteins
- Selectively inhibits prokaryotes, not eukaryotes (has 40S, not 30S)

58
Q

Elongation of protein synthesis

A
  • Aminoacetyl-tRNA binds A site
  • rRNA (“ribozyme”) catalyses peptide bone formation –> transfers growing peptide to AA in A site
  • Ribosome advances 3 NTs toward 3’ end of mRNA (translocation); peptidyltransferase of 50S moves peptidyl-tRNA to P site
  • AA cleaved from tRNA, empty tRNA goes to E site
59
Q

Tetrcycline

A

Inhibit aminoacyl-tRNA from binding to A site

60
Q

Clindamycin/erythromycin

A

Inhibits translocation (moving of ribosome 5’ to 3’)

61
Q

Chloramphenicol

A

Inhibits peptidyltransferase (moving from A –> P)

62
Q

Termination of protein synthesis

A

Stop codon recognized by release factor + polypeptide released from ribosome

63
Q

Posttranslational modifications

A
  • Trimming - remove N or C terminal from zymogen to make mature protein
  • Covalent alterations - phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquinination
63
Q

Chaperone protein

A
  • Intracellular protein –> helps/maintains protein folding

In yeast, are some heat-shock proteins, Hsp60, only expressed at high temps to prevent denaturing/misfolding protein

Biochemistry (6 decks)

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