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intro cell + molec bio > tuesday week 3 > Flashcards

tuesday week 3 Flashcards

1
Q

constitutive genes

A

ALWAYS expressed

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2
Q

what are genes called that are always expressed

A

constitutive

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3
Q

regulated genes

A

genes only expressed in the cell types and conditions in which they are required

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4
Q

what are genes called that are not always expressed?

A

regulated gene

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5
Q

describe in situ hybridization

A

single stranded labeled DNA or RNA probes detect complimentary sequences (of RNA) within tissue, cells, or chromosomes

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6
Q

describe/explain what a northern blot is

A

using RNA not DNA or proteins.

  1. seperate strands by mass in agar using electrophoresis
  2. transfer RNA strands to nylon membraine
  3. add probes (DNA or RNA) which will bind to RNA strands using complementary base pairing
  4. probes visualized using x-ray film (dots/blobs we read)
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7
Q

cDNA

A

complementary DNA. DNA synthesized using RNA as a template

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8
Q

whatis reverse transcriptase PCR (RT-PCR)

A

a method of detecting mRNA transcripts using cDNA intermediate

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9
Q

steps of reverse transcriptase PCR

A
  1. make cDNA using poly-T prime and reverse transcriptase
  2. PCR for mRNA using gene-of-interest specific primers
  3. gel electrophoresis to detect gene of interest
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10
Q

operon

A

several genes expressed from a common promoter with a common regulatory DNA sequence (operator)

ONLY in bacteria

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11
Q

operator

A

common regulatory sequence in operon translation

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12
Q

polycistronic

A

a single transcript containing more than one coding sequence that is translated into more than one polypeptide/protein (many rhibosomes translating on the same strand of mRNA)

ONLY in bacteria

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13
Q

trp

A

triptophan

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14
Q

trp operon

A

trp operon is expressed when tryptophan levels are low and repressed when trp levels are high (negative rienforcement loop)

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15
Q

low trp

A

the repressor is not bound by trp and does not bind to DNA. RNA polymerase transcribes the trp operon genes

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16
Q

high trp

A

trp serves as a corepressor and binds to a repressor which has a high afinity for the operator sequence in this state. tryptophan is in repressor which causes conformational change and blocks RNA polymerase from transcribing

17
Q

promoters

A

general transcription factors + RNA polymerase bind to promoter, this initiates transcription.

promoter is always adjacent and upstream of the coding sequence

promoter activity is directional; and inverted promoter will not function

18
Q

enhancers + silencers

A

transcription factors (activators or repressors) bind to enhancers and silences and influence the rate of transcription

19
Q

how to enhancers + silencers regulate gene expression

A

enhancers + silencers regulate transcription through the binding of activators and repressors to their respective enhancer or silencer

enhancers + silencers can regulate at a distance, upstream/downstream, within an intron, even on another chromosome.

enhancer + silencer activity is orientation independent (can face/go any way)

20
Q

mediator protein

A

connects (physically) enhancers + silencers to protein complex + RNA polymerase

a bridge between transcriptional activators/repressors and RNA polymerase II

21
Q

how the body can modify gene expression during: DNA packing

A
  1. histone tail modifications
  2. histone modifying enzymes
  3. chromatin remodeling complex
22
Q

histone tail modifications

A

histone tail modifications: tail modifications can alter afinity of nucleosome to the chromatin fiber or can be bound by regulatory proteins.

  • modified using phosphorilation, methylation, etc
  • effects tightness/loosness of DNA around nucleosome (histone octomer)
23
Q

histone modifying enzymes

A
  • histone acytl transferase (HATs) increase transcription
  • histone deacetylaces (HDACs) reduce transcription
24
Q

chromatin remodeling complex

A

ATP dependent restructing of DNA relitive to histones (complexes loosen + tighten and/or shift DNA position around nucleosomes (longer shorter ligand DNA))

25
Q

ways gene expression effected by regulation during transcription

A
  1. transcription of a single gene can be regulated by many proteins - lots of things brought together + binded together to regulate a gene
  2. a single protein can regulate many genes (sort of like operon in bacteria) - set of different (seperate) genes share a regulatory sequence so one environmental factor (ex. increase in cortosol) will turn on all of these genes at once
26
Q

epigenetic inheritance

A

the transmission of gene expression from parent to daughter cell(s) WITHOUT altering the DNA sequence

27
Q

how does epigenetic inheritance play into gene expression/why is it important to know about?

A

if a TRANSCRIPTION FACTOR is part of a positive feedback loop (it activates itself), it can establish ‘memory’ of cell identity and pass that on without modifying DNA

28
Q

gene expression/regulation during mRNA processing

A

happens specifically during splicing (usualy).

alternative splicing: different combinations of exons are spliced together to produce alternate mRNA’s that will produce different protein sequences through splicing of exon(s) or keeping of introns

29
Q

alternative splicing

A

method of gene regulation.

different combinations of exons are spliced together to produce alternate mRNA’s that will produce different protein sequences through splicing of exon(s) or keeping of introns

30
Q

how can gene expression be regulated during mRNA stability/degradation steps of transcription

A

sequences within 3’ UTR control the rate of mRNA degradation. the longer the AAAA sequence (tail) the longer it takes to degrade (more stable)

31
Q

how can gene expression be regulated during translation

A

translation repressor proteins can bind to prevent translation (on mRNA post transcription ofc)

32
Q

micro RNAs (miRNAs)

A

control mRNA stability and translation

33
Q

RISC

A

RNA induced silencing complex

a single miRNA can inhibit translation of many mRNAs

34
Q

how can gene expression be regulated during protein modification and degradation

A

proteasome is a protease (enzyme that degrades proteins) (26S)

ubiquitin (76aa protein) attaches to side chains of a target protein using ubiquitin ligases

35
Q

what does 26s degrade

A
  • misfolded proteins
  • proteins that are regulated
  • unneeded proteins
  • cleaved protein fragments
36
Q

ubiquitin

A

76aa protein that attaches to lysine side chains of a target protein using ubiquitin ligases

ubiquiting can be thought of as a way cells ‘tag’ a certain protein for recycling

poly-ubiquitinated proteins are unfolded and cleaved by the proteasome

intro cell + molec bio (14 decks)

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