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Biochemistry > Exam #4 First Aid USMLE > Flashcards

Exam #4 First Aid USMLE Flashcards

1
Q

H1

A
  • Histone that binds to the nucleosome & linker DNA

- Only Histone not in the nucleosome core

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2
Q

When does DNA & Histone synthesis occur in the cell cycle?

A

S-phase

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3
Q

Nucleosome Core Histones

A
  • H2A
  • H2B
  • H3
  • H4
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4
Q

Heterochromatin

A
  • Highly Condensed & Inactive

- Think HeteroChromatin, Highly Condensed

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5
Q

Euchromatin

A
  • Less condensed, transcriptionally active, sterically accessible
  • Think Eu= True, truly transcribed
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6
Q

DNA Methylation

A
  • Methylation at CpG islands represses transcription

- Think Methylation Makes DNA Mute

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7
Q

Histone Acetylation

A
  • Relaxes DNA coiling, allowing for transcription

- Think Acetylation makes DNA Active

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8
Q

What is the production of cytosine deamination?

A

Uracil

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9
Q

DNA Replication Characteristics

A
  • Semiconservative

- Involves BOTH continuous & discontinuous synthesis

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10
Q

Origin of Replication

A
  • Consensus sequence in genome where DNA replication begins

- Single in prokaryotes, Multiple in eukaryotes

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11
Q

Replication Fork

A
  • Y-shaped region along DNA template where leading & lagging strands are synthesized
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12
Q

Helicase

A

Unwinds DNA

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13
Q

Single-stranded binding proteins

A

Prevents strands from reannealing

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14
Q

Topoisomerases

A

Create single or double strand break in helix to relieve supercoiling

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15
Q

Fluoroquinolones

A

Inhibit DNA gyrase i.e. prokaryotic topoisomerase II

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16
Q

Primase

A

Makes an RNA primer on which DNA polymerase III can initiate replication

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17
Q

DNA Ligase

A
  • Catalyzes the formation of phosphodiester bonds within ds-DNA
  • Seals or joins Okazaki fragments
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18
Q

Telomerase

A

RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material during replication

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19
Q

Silent Mutation

A

Nucleotide substitution codes for the same amino acid

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20
Q

Missense Mutation

A
  • Nucleotide substitution results in different amino acid

- Sickle Cell Disease

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21
Q

Nonsense Mutation

A
  • Nucleotide substitution results in an early STOP codon

- Think STOP the Nonsense

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22
Q

Frameshift Mutation

A
  • Insertion or deletion of nucleotides not divisible by 3 causing a misreading of DNA downstream
  • Duchenne Muscular Dystrophy
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23
Q

Nucleotide Excision Repair

A
  • Repairs bulky helex distorting lesions e.g. pyrimidine dimers from UV exposure
  • Endonucleases release an oligonucleotide containing damaged bases
  • DNA polymerase & ligase fill and reseal the gap
24
Q

Xeroderma Pigementosum

A

Defective Nucleotide Excision Repair

25
Q

Base Excision Repair

A
  • Important repair for spontaneous/ toxic deamination
  • Base-specific glyocsylase recognizes altered base & creates AP site
  • AP-endonuclease & Lyase cleave
  • DNA polymerase fills in the gap & Ligase seals it
26
Q

Mismatch Repair

A
  • Newly synthesized DNA strand is recognized
  • Mismatched nucleotides are removed
  • Gap is filled & resealed
27
Q

HNPCC

A

Defective Mismatch Repair

28
Q

Nonhomologous End Joining

A
  • Brings together 2 ends of DNA fragments to repair ds-DNA breaks
29
Q

Ataxia Telangiectasia

A

Nonhomologous End Joining

30
Q

DNA & RNA Synthesis

A
  • 5’–>3’

- 5’ end of incoming nucleotide bears triphosphate energy source

31
Q

Protein Synthesis

A

N-terminus to C-terminus

32
Q

mRNA START Codon

A
  • AUG
  • Think AUG inAUGurates protein synthesis
  • Codes for methionine, which may be removed before translation is completed
33
Q

mRNA STOP Codons

A
  • UGA= U Go Away
  • UAA= U Are Away
  • UAG= U Are Gone
34
Q

Promoter

A
  • Site where RNA polymerase & other transcription factors bind to DNA
  • TATA box, CAAT box, GC rich regions
35
Q

Enhancer

A

Stretch of DNA that alters gene expression by binding transcription factors distant from START site

36
Q

Silencer

A

Site where negative regulators bind

37
Q

Pol I

A

rRNA

38
Q

Pol II

A

mRNA

39
Q

alpha-amanatin

A
  • Found is death cap mushrooms
  • inhibits Pol II
  • Causes hepatotoxicity
40
Q

Pol III

A

tRNA

41
Q

Characteristics of RNA polymerase

A
  • No proofreading function

- No primers

42
Q

pre-mRNA or hnRNA

A

initial transcript that will become mature mRNA

43
Q

RNA processing steps

A

1) Capping 5’ end (methylguanosine)
2) Polyadenylation of 3’ end
3) Splicing out introns

  • ALL occurs in the NUCLEUS
44
Q

Introns vs. Exons

A
  • Exons contain actual genetic information
  • Introns are intervening noncoding segments

Think:

  • INtrons are INtervening sequences and stay IN the nucleus
  • EXons EXit the nucleus and are EXpressed
45
Q

Aminoacyl-tRNA synthetase

A
  • Charges tRNA

- Responsible for accuracy of amino acid selection

46
Q

tRNA Wobble

A
  • Accurate base pairing is only required in the first two nucleotide positions of an mRNA codon
  • Codons differing in 3rd “wobble” position may code for the same tRNA
  • Insoine
47
Q

Translation Initiation

A
  • GTP hydrolysis
  • eIFs (eukaryotic Initiation Factors) help assemble 40S ribosomal subunit (small) with initiator tRNA & are released when mRNA & 60S subunit (large) assemble the complex

Think:

  • ATP= tRNA Activation
  • GTP= tRNA Gripping & Going places
48
Q

Translation Elongation

A

1) Aminoacyl-tRNA binds to A-site (EXCEPT initiator methionine tRNA)
2) rRNA, “ribozyme” catalyzes peptide bond formation & transfers growing polypeptide to amino acid in A site
3) Ribosome advances 3 nucleotides, moving peptidyl tRNA to the P site

Think: APE

  • A= incoming Aminoacyl-tRNA
  • P= accommodates growing Peptide
  • E= holds Empty tRNA as it Exits
49
Q

Termination

A
  • STOP codon recognized by release factor in A site

- Completed polypeptide is released from ribosome

50
Q

Post-translational Modifications

A
  • Trimming: Removal of N or C terminal propeptides

- Covalent Alterations: Phosphorylation, Glycosylation, Hydroxylation, Methylation, Acetylation, Ubiquitination

51
Q

Chaperone Protein

A
  • Intracellular protein involved in facilitating and/or maintaining folding
  • Heat Shock Proteins e.g. Hsp60
52
Q

Cyclins

A
  • Regulatory proteins that control cell cycle events
  • Phase specific
  • Activate CDKs
53
Q

Rough Endoplasmic Reticulum

A
  • Site of synthesis of secretory (exported) proteins

- Site of N-linked oligosaccharide addition to many proteins

54
Q

Golgi Apparatus

A
  • Distribution center for protein & lipids from the ER to vesicles & plasma membrane
  • Modifies N-oligosaccharides on asparagine
  • Adds O-oligosaccharides on serine & threonine
  • Adds mannose 6-phosphate to proteins for trafficking to lysosomes
55
Q

I-cell Disease

A
  • Inclusion Cell Disease
  • Inherited lysosomal storage disorder
  • Caused by defect in phosphotransferase (failure of Golgi to phosphorylate mannose)
56
Q

SRP

A
  • Signal Recognition Peptide

- Cytosolic Ribonucleoprotein that traffics proteins from the ribosome to the RER

57
Q

Proteaseome

A

Barrel-shaped protein complex that degrades damaged or polyubiquitinated proteins

Biochemistry (17 decks)

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