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Comprehensive Review > Molecular Review (Bittel) > Flashcards

Molecular Review (Bittel) Flashcards

1
Q

Histone Tail Modifications (Acetylation and Methylation)

A

acetylation = ACTIVE (open up histone)

methylation = INACTIVE (histone tightly closed)

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2
Q

Okazaki Fragment

A

discontinuous strands of DNA formed on the lagging strand by DNA polymerase

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3
Q

Base Excision Repair

A
  • remove single base and sugar (AP endonuclease and phosphodiesterase)
  • DNA polymerase adds nucleotide, DNA ligase seals nick
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4
Q

Nucleotide Excision Repair

A
  • excision nuclease removes small DNA strand with dimer in it
  • DNA polyermerase synthesizes new portion of strand, DNA ligase repairs nick
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5
Q

RecA

A
  • allows single-stranded DNA pairing with homologous double helix
  • protein binds to single DNA strand and searches duplex 3 nucleotides at time and invades DS once sequence is found (heteroduplex)
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6
Q

DNA-only transposons

A
  • short inverted repeats at each end
  • enzyme: transposase
  • moves as DNA (cut-and-paste or replicative pathways)
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7
Q

Retroviral-like retrotransposons

A
  • directly repeated long terminal repeats (LTRs) at each end
  • enzymes: reverse transcriptase and integrase
  • moves via RNA intermediate whose production is driven by a promoter in the LTR
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8
Q

Nonretroviral retrotransposons

A
  • poly A at 3’ end of RNA transcript; 5’ is often truncated
  • enzymes: reverse transcriptase and endonuclease
  • moves via RNA intermediate that is often synthesized from a neighboring promoter
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9
Q

Sry gene

A
  • in somatic cells causes primordial germ cell (PGC) to differentiate into Sertoli cells instead of follice cells
  • cause differentiation into male rather than female
  • PDC becomes a sperm cell instead of an egg
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10
Q

Sertoli and Leydig cells

A
  • Sertoli = secretes anti-Mullerian hormone (suppress female development)
  • Leydig = secretes testosterone
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11
Q

Meiosis

A
  • gametes are HAPLOID

- arise from MEIOSIS; two rounds of cell division but one round produces half the number of chromosomes

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12
Q

Process of Fertilization (5 steps)

A
  1. binding of sperm to zona pellucida
  2. acrosome reaction (helps sperm tunnel through zona pellucida, alters sperm for binding)
  3. penetration through zona pellucida
  4. fusion of plasma membranes (first by tip of sperm then side)
  5. sperm contents enter eggs cytoplasm
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13
Q

Zona Pellucida membrane proteins (3)

A

ZP1 - cross-links filaments of ZP 2 and 3

ZP2/3 - form long filaments

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14
Q

What is the central dogma of biology?

A

DNA is transcribed to messenger RNAs which act as templates for protein synthesis in translation

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15
Q

Translation Process (3 steps)

A
  1. Initiation: ribosome assembles around target mRNA, first tRNA is attached at START codon
  2. Elongation: tRNA transfers AA corresponding to next codon. Ribosome moves to next mRNA codon, creating polypeptide
  3. Termination: when stop codon reached, ribosome releases the polypeptide
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16
Q

Short Telomere Syndrome (STS)

A
  • accelerated aging syndromes often caused by inheritable gene mutations resulting in decreased telomere lengths
  • organs with high turnover (bone marrow, liver, lungs, and immune system) are commonly affected
  • treatment requires multidisciplinary approach
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17
Q

Telomerase

A
  • builds new telomere sequences onto the ends of chromosomes
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18
Q

Translesion DNA polymerase

A
  • allows polymerases to skip over distortions/dimers but often result in mutations
  • replicative DNA polymerase dissociates from sliding clamp, allowing translesion DNA polymerase to attach and bridge damage
19
Q

Homologous Recombination and Non-homologous End Joining

A
  • both repair double stranded breaks

- HR is more accurate that NHEJ because it uses a template for repair of damaged/broken fragment

20
Q

Thymine Dimers

A
  • induced via free radicals caused by UV light
  • blocks replication and kill the cell unless its broken; if dimer repaired, often leads to mutations
  • repaired w/nucleotide excision repair (cut out surrounding nucleotides and fill space back in)
21
Q

mRNA

A

messenger RNAs, code for proteins

22
Q

rRNA

A

ribosomal RNAs, form basic structure of the ribosome and catalyze protein synthesis

23
Q

tRNA

A

transfer RNA, central to protein synthesis as adaptors between mRNA and AA

24
Q

snRNA

A

small nuclear RNA, variety of nuclear functions

  • splicing of pre-mRNA
25
Q

snoRNA

A

small nucleolar RNA, help to process and chemically modify rRNA

26
Q

miRNA

A

micro RNA, regulate gene expression by blocking translation of specific mRNA and cause degradation

27
Q

siRNA

A

small interfering RNA, turn off gene expression by directing degradation of selective mRNAs and establishment of compact chromatin structures

28
Q

piRNA

A

Piwi-interacting RNA, bind piwi proteins and protect the germ line from transposable elements

29
Q

IncRNA

A

long non-coding RNA, many serve as scaffolds

  • regulate diverse cell processes (X-chromosome inactivation)
30
Q

TATA box

A
  • 25 nucleotides from the transcription initiation site
  • TBP binding is initial step to being transcription
  • additional proteins are added until complex is assembled –> TRANSCRIPTION START
31
Q

Activator protein

A
  • help initiate transcription
  • coordinate acquisition of multiple different proteins needed for transcription initialization
  • play role in modifying DNA shape –> affects transcription rate
32
Q

5’ mRNA cap

A

allows mRNA to be distinguished from noncoding RNAs and is also important for establishing translation

33
Q

Consensus Sequences in mRNA spicing

A
  • 5’ end: AG (exon) and GURAGU (intron)
  • intron center: YURAC
  • 3’ end poly YNCAG (intron) and G (exon)
34
Q

exosome

A
  • protein complex that cleans up damaged RNAs before they leave the nucleus
  • rich in RNAses and chops up RNAs for recycling
35
Q

miRNA and RISC

A
  • Drosha cleaves pri-miRNA into pre-miRNA
  • pre-miRNA cleaved by Dicer to produce miRNA
  • miRNA leads to mRNA degradation (high homology) and mRNA translation repression (partial homology)
  • RISC complex: Dicer, AGO
36
Q

SnoRNA and modifications

A
  • cause biochemical modification of noncoding RNAs
  • most common modifications = pseudouridylation and 2’O methylation
  • splicesomal RNAs are also modified
37
Q

Nucleolus

A
  • site where rRNA is processed and assembled into ribosome subunits
38
Q

wobble position

A

3rd position in mRNA codon that can associate with different anticodon bases in the 3rd position of tRNA

U - A, G, I
C - G, I
A - U, I
G - C, U

39
Q

aminoacyl-tRNA synthetase

A
  • helps ensure correct amino acid is coupled to the tRNA
40
Q

4 steps of protein synthesis

A
  1. new tRNA binds to A site
  2. tRNA in P site releases peptide bond. Peptide bond forms between AA in P site to AA in A site
  3. large subunit moves along mRNA, shifting tRNAs to P and E sites
  4. small subunit moves along mRNA,ejects tRNA in E site
41
Q

Fungi and antibacterial compounds

A
  • fungi produce antibacterial compounds that exploit differences in ribosomal subunits
  • inactivate bacterial translation
42
Q

Nonsense mediated decay

A
  • eliminates mRNAs with premature stop codons
  • premature stop codons generated through incorrect splicing
  • system may help prevent translation of mutated genes with premature stop codons that could cause severe damage
43
Q

What usually indicates that a protein is misfolded?

A
  • an exposed section of hydrophobic amino acids
  • if not corrected, can result in accumulation of protein aggregates that can be harmful
  • hsp70 –> helps correctly fold protein as it is translated
44
Q

proteasome

A

searches for misfolded proteins in nucleus and cytoplasm, ingests them, and degrades them so that the AAs can be recycled

  • recognizes ubiquitination (only marked proteins can enter, as to prevent destruction of correctly folded proteins)

Comprehensive Review (7 decks)

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