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Foundations I SM > DNA, Replication, Transcription, Translation > Flashcards

DNA, Replication, Transcription, Translation Flashcards

1
Q

Helicase

A

Binds to ssDNA at replication forks and moves two strands apart, requires ATP as energy source

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2
Q

Type 1 DNA topoisomerase; Type 2 DNA topoisomerase

A

Reversibly cuts 1 strand and passes intact strand through break, relieves negative supercoiling in prokaryotes and both typesof supercoilingin eukaryotes

Makes transient breaks in both strands, uses ATP as energy source, relieves positive supercoiling in both eukaryotes and prokaryotes (DNA gyrase)

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3
Q

DNA Polymerase for replication

Alpha

Beta

Gamma

Delta

Epsilon

A

Priming

DNA repair

mitochondrial

lagging strand sythesis, displaces RNA primer

leading strand synthesis

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4
Q

Types of DNA damage

BER

NER

Mismatch Repair

NHEJ/NR

A

oxidation, alkylation, hydrolsis, deamination

helix-distorting lesions such as thymine dimers

Errors in DNA replication and recombination

ionizing radiation, free radicals

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5
Q

BER Enzymes

A

DNA glycosylase

AP endonuclease

deoxyribose phosphate lyase

DNA polyermase

DNA ligase

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6
Q

Diseases due to DNA repair defects

A

Xeroderma pigmentosum (no NER)

Bloom’s Syndrome (DNA helicase)

Werner syndrome (DNA helicase involved in repair)

Hereitary nonpolyposis colorectal cancer (DNA mismatch repair)

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7
Q

Eukaryotic RNA polymerase

A

Pol I- Ribosomal RNA

Pol II- protein encoding, most snRNA

Pol III- tRNA, some snRNA and rRNA

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8
Q

tRNA

A

tRNA DNA has promoters downstream of start site, ACC at 3’ end is amino acid attachment site, small intron at anticodon loop is excised, extensive base modification

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9
Q

Transcription Factors

General TF”s bind to the core promoter

A

TFIIB- Basal Response Element

TFIID- TATA box and Downstream Promoter Element

TFIIF- recruits the polyermase

TFIIH- helicase, and is a protein kinase that phosphorylates the polymerase

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10
Q

Aminoacyl tRNA

A

Catalyzed by synthase

Requires 2 ATP hydrolysis

methionyl tRNA’s recognize start codons

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11
Q

Initation of Eukaryotic Translation

A

Met tRNA binds EIF2 (GTP) and that complex binds to the small 40s ribosomal subunit at the P site

5’ cap of mRNA binds to CBP and EIF4E

Both complexes associate, and helicase unwinds secondary structure of mRNA and searches for start codon embedded in Kozak sequence

GTP dissociates off EIF2 and 60s binds to the met TRNA at the P site of 40, iniation factors released

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12
Q

Elongation of Eukaryotic Translation

A

met tRNA is at P site

EF1alpha bound to next aminoacyl tRNA and is released upon binding to A site

peptide bond formed catalzyed by ribozyme

EF2 moves mRNA and releases empty tRNA on the P site and shifts peptide over one site

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13
Q

Termination of eukaryotic translation

A

Stop codon enters the A site

no tRNAs bind to stop codon and release factors cause hydrolysis of the peptide chain

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14
Q

Post-translational modification

A

Proteolytic trimming- iniator methionine is removed, removal of signal sequences, activation of precursor protein, and cleavage of polyproteins

Modification of AA side chains- acetylation, methylation, ADP-ribosylation, phophorylation, hydroxylation, glycosylation, carboxylation, palmitoylation

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15
Q

Cases of Protein Aggregation

A
  1. mutations in proteinsor in the quality control system
  2. defects in translation
  3. environmental stress: heat,oxidative stress
  4. Aging, increased oxidative stress and reduced capacity to remove misfolded proteins
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16
Q

Methods of Protein Breakdown

A

Chaperone mediated autophagy

Autophagy by autophagosome

Vesicle autophagy within lysosome

Macroautophagy of organelles

Ubiquitin-Proteosome complex

17
Q

Gene availability for transcription

A

Chromatin remodeling

Methylation of DNA

Gene arrangment (VDJ)

Gene amplication (double minutes)

Gene deletions

18
Q

Transcriptional Regulation

A

Coactivators, corepressors, and TATA binding protein associated factors that bind to the basla transcription complex

Steroid hormone recpetors

TF regulation through nuclear entry and exit and post translational modification ex. Creb and NFkB

19
Q

Post transcriptional processing of RNA

A

Alternative splicing- exon skipping, mutually exclusive exons, alternative donor and acceptor sites, and intron retention

Alternative poly-A adenylation sites

RNA editing- change the base to introduce stop sequence

Recyling of Processing factors on polymerase tail

20
Q

Translational Regulation

A

Heme inhibits the inhibitory control of eIF2a

Insulin removes 4E-BP inhibition of eIF4E

Under high Fe conditions, IRE-BP binds Fe instead of the 5’UTR IRE on Ferritin (intracellular iron storage) and transferrin (iron transport)–> Ferritin translated transferrin degraded

Internal Ribosome Entry sites bypass the requirement for CBP

Frameshifting of ribosome on mRNA

Exosome complex- degrades aged mRNA’s and ncRNA’s

SLBP and histone mRNA stability

21
Q

Histone/Nucleosome Assembly

A

Formation of H3-H4 dimers then tetramers, add onto H2A and H2B dimers. N-tail will get modified

Linker DNA bound/neutralized by Histone H1

22
Q

TrxG/PcG

A

TrxG promotes gene expression

PRC1 methylates histones, PRC2 binds at promoter to silence gene

23
Q

DNA methylation

A

Cytosine is always methylated, Dnmt 3a does de novo methylation of anything but centromeric DNA, and Dnmt 3b does de novo methylation of centromeric DNA, Dnmt 1 participates in maintenance methylation

CpG islands are popular targets

24
Q

Genomic Imprinting

A

All epigenetic changes in sperm DNA inherited by the maternal gamete are erased vice versa

ex. IGF2 actively transcribed and H19 methylated in one chromosome and IGF2 not transcribed and H19 hypomethylated in the other

25
Q

Histone Modification

A

Acetylation- HAT’s and HDAC’s

Methylation

Ubiquination

Sumoylation

Phosphorylation

26
Q

Transmembrane Protein Classifications

And peripheral proteins

A

Structure- alpha helix, beta barrel

Topology- Type I (C terminal in cytoplasm), Type II (N terminal in cytoplasm), Type III (???), and Type IV (multi-pass protein)

Monolayer attached, lipid linked and protein linked

27
Q

Protein Modifications

Where and What

A

Where: ER Lumen

What: N-linked glycosylation (dolichol-linked 14 sugar chain)

Some type I transmembrane proteins exchange carboxy terminal to GPI anchor

Where: Golgi Apparatus

What: Modification of N-linked oligosaccharides, O-linked glycosylation (serine and threonine)

Proteolytic cleavage of protein precursors

Mannose trimming

28
Q

Folding of proteins in ER

UPR

A

Bip- ATP dependent chaperones

Calnexin binds to oligosaccaharide senses correct/incorrect folding

Mannosidases

Protein disulfide isomerases

Conditions that lead to UPR- oxidative stress, glucose deprivation, aberrant calcium regulation, viral infection

29
Q

Vesicular Traffic

A

ER to Golgi- Cop II

Golgi to ER- Cop I (KDEL sequence)

TGN to anywhere else dicated by M-6-P receptors, clathrin coated vesicles

Endosomes are for sorting and recycling

Foundations I SM (10 decks)

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