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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
DNA polymerase I
only in prokaryotes - Degrades DNA primer --> replace w/ DNA - Same fxn as polym III but also excises RNA primer
25
DNA ligase
Seals by catalysing formation of phosphodiester bonds between dsDNA (i.e. joins Okazaki frags)
26
Mutations in DNA
Severity: silent << missence < nonsense
27
Telomerase
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
Silent DNA mutation
NT changes, but still codes for same AA (often 3rd position change) - Same size, fxnal
30
Missense mutation
NT substitution --> changes AA i. e. Sickle cell - Same size, nonfxnal
31
Frameshift mutation
Deletion/insertion of # NT not divisible by 3 --> misreading of all those downstream - Get shorter, non-fxnal proteins
32
Splice-site mutation
Produces larger protein with altered function but preserved immune reactivity
33
Nonsense mutation
NT substitution --> early stop codon - Shorter nonfxnal protein "Stop the nonsense"
34
DNA repair
Single strand - NT excision repair, base excision repair, mismatch repair Double strand - nonhomologous end joining
35
NT excision repair
- 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
Base excision repair
- 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
Mismatch repair
- In single strand - Finds mismatches in newly synthesized strands; gap filled/resealed - Defective in HNPCC (hereditary nonpolyposis colorectal cancer)
38
Nonhomologous end joining repair
- In double stranded - Brings together 2 ends of DNA fragments to repair ds bond; dont need homology - Defective in ataxia talangectasia
39
RNA/DNA/protein synthesis direction
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
Start codons
AUG inAUGurates protein synthesis
41
Stop codons
UGA - U Go Away UAA - U Are Away UAG - U Are Gone
42
Organization of eukaryotic gene
Sense/coding strand, enhancer, promotor (TATA box), start of transcription, transcribed region (introns + exons), terination signals
43
Promotor
RNA polymerase + TFs bind to DNA upstream from gene locus (TATA box) - Mutation here = decr gene transcription
44
Enhancer
DNA stretch that alters gene expression by binding TFs | - Can be close to/far from or in intron of expression it regulates
45
Silencer
Negative regulators bind here (repress) | - Can be close to/far from or in intron of expression it regulates
46
RNA polymerase (eukaryotes)
- 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
RNA polymerase (prokaryotes)
1 RNA polymerase makes all 3 kinds of RNA (r, m, t)
48
Proofreading
RNA polymerase lack 3'-->5' exonuclease proofreading! | - RNA viruses have more genetic variability, bc more mistakes (mutations) made
49
Processing of RNA
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
Splicing pre-mRNA
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
Exons and Introns
- 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
tRNA
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
tRNA wobble
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
Protein synthesis
- 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
Eukaryotic initiation of protein synthesis
- 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
Prokaryotic initiation of protein synthesis
Initiated by 30S subunit with initiator of tRNA - 50S subunit and GTP join - 30S + 50S = 70S
57
Streptomycin
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
Elongation of protein synthesis
- 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
Tetrcycline
Inhibit aminoacyl-tRNA from binding to A site
60
Clindamycin/erythromycin
Inhibits translocation (moving of ribosome 5' to 3')
61
Chloramphenicol
Inhibits peptidyltransferase (moving from A --> P)
62
Termination of protein synthesis
Stop codon recognized by release factor + polypeptide released from ribosome
63
Posttranslational modifications
- Trimming - remove N or C terminal from zymogen to make mature protein - Covalent alterations - phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquinination
63
Chaperone protein
- 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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