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Biology 101 flashcards
1
Q

Coding strand

A

Strand of DNA that RNA strand ends up essentially being the same as
Also called sense strand

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2
Q

Template

A

Strand of DNA that RNA is synthesized off of

Also called antisense strand

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3
Q

Time and place of transcription and translation in prokaryotes versus eukaryotes

A

Proks: coupled transcription and translation
Euks: transcription and translation separated spatially and temporally

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4
Q

Splicing in prokaryotes vs. eukaryotes

A

Proks: no splicing
Euks: splicing

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5
Q

of RNA polymerases in eukaryotes versus prokaryotes

A

Proks: 1 polymerase
Euks: 3 polymerases

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6
Q

of genes per RNA in prokaryotes versus eukaryotes

A

Proks: polycistronic RNA (many genes per RNA)
Euks: monocistronic RNA (1 gene per mRNA)

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7
Q

What directs polymerase to the correct spot in prokaryotes versus eukaryotes?

A

Proks: sigma
Euks: general transcription factors

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8
Q

Polymerase I

A

Class of promoter: I
Transcripts: rRNA precursor
Location: nucleolus

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9
Q

Polymerase II

A

Class of promoter: II
Transcripts: mRNA, miRNA, snRNA
Location: nucleoplasm

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10
Q

Polymerase III

A

Class of promoter: III
Transcripts: tRNA and specialized rRNA
Location: nucleoplasm

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11
Q

DNA footprinting

A

Can be used to determine where on DNA polymerase binds
2 samples of DNA: treat 1 sample of DNA with protein of interest
Nuclease chops up DNA samples
Gel electrophoresis: no fragments shown where protein was bound to DNA sample (protein protects DNA from nuclease)

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12
Q

Filter binding assay

A

Way to measure polymerase affinity for DNA
1. Label promoter region
2. Incubate DNA with polymerase
3. Apply DNA/polymerase sample to filter that binds proteins tightly
If polymerase is bound to DNA, radioactivity is seen on filter (free DNA flows through)
Increased radioactivity=increased binding

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13
Q

Class I promoter

A

Made up of core promoter and UCE (upstream control element)

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14
Q

Transcript of pol I to rRNA

A

Transcript contains rRNA linked by external and internal transcript spacers
Cleaved to make rRNA
Processing is done to maintain stoichiometry of transcripts (all under the same promoter)

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15
Q

Class III promoter

A

Made up of Box A and Box B (separated by a short element)

Located downstream of +1 site

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16
Q

Class II core promoter

A

Contains:
1. TATA box or DCE (downstream core element)
2. BRE (transcription factor II B response element)
3. Inr (initiator; contains +1 site)
Sequences are recognized by proteins that recruit polymerase

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17
Q

Reporter assay

A

Way to determine which sequences in a promoter are necessary for transcription
Make plasmid clone and put promoter of interest upstream of reporter gene (ex- luciferase)
If promoter is being used, reporter gene is also transcribed
Luciferase: measure light production

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18
Q

Linker scanning

A

Changing big chunks of DNA and seeing results of change via qPCR
Done by cutting piece of DNA and ligating in linker (doesn’t contain sequence of interest)
If linker is where key sequence in promoter used to be, then transcription is lessened
Not just removing sequences: also reversing sequences or moving them around

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19
Q

TATA box

A

Contained in promoter regions of specialized genes
Bound by TATA binding protein
Responsible for recruitment of other general transcription factors

20
Q

TATA binding protein binding to TATA box

A 
TBP (saddle-shaped protein) forces open the minor groove
Bent conformation (80 degree angle) is recognized by other transcription factors
21
Q

Transcription factor that can take over the role of TBP in TATA-less genes

A

TFIID

22
Q

Housekeeping gene

A

Always on (always transcribed)

23
Q

Conditionally expressed gene

A

Used (transcribed) only when needed

More likely to have TATA boxes

24
Q

Transcription initiation steps

A
  1. TATA binding protein and transcription factor II D (TFIID) bind to and bend DNA
  2. TFIIA and TFIIB recognize bent DNA and recruit RNA pol II and TFIIF
  3. TFIIE and TFIIH come in and TFIIH opens promoter
  4. TFIIH phosphorylates tail of pol II, causing tail to dissociate from pre-initiation complex (promoter escape)
25
Q

Transcription elongation factors

A

Add phosphates to RNA pol II when it stalls during transcription initiation

26
Q

Abortive transcripts

A

Transcripts that are 10 nucleotides long or less and are degraded during promoter escape

27
Q

Mediator

A

Mediates interaction between the activator and RNA pol II

Multi-subunit complex that is required for transcription

28
Q

Components of preinitiation complex

A

Activators (bound to enhancer sequences as well as mediator)
Mediator complex (bound to some activators and RNA pol II)
RNA pol II
Chromatin remodelers and HATs (bound to other activators)

29
Q

Cis regulatory elements

A

Sequences that are on the same strand as the encoded gene of interest

30
Q

Trans acting factors

A

Come from elsewhere (not near or on the gene) to bind to regulatory elements

31
Q

Places where regulatory promoters can exist relative to the gene of interst

A

Can be either upstream or downstream of gene of interest

32
Q

2 domains of activators

A

Activation domain

DNA-binding domain

33
Q

Leucine zipper

A

Form of DNA binding domain of activators
Dimer (like pair of tongs picking up DNA)
Stretches of leucines interacting with each other (tong handles; coiled coil domain)

34
Q

Helix-loop-helix

A

Form of DNA binding domain of activators
Dimer
Basic amino acids interact with DNA
Flexibility of loop allows for tight packing

35
Q

Homeodomain

A

Form of DNA binding domain of activators
3 alpha helices
Amino acids in 3rd helix interact with DNA
Helix-turn-helix

36
Q

Zinc finger

A

Form of DNA binding domain of activators
“Finger”: alpha helix
Zn stabilizes structure
Inserts into minor groove

37
Q

Combinatorial control advantages

A 
Energy conservation (can activate multiple genes simultaneously with the same transcription factors)
Tighter gene control (specificity of response to cell signals)
38
Q

2 roles of activators

A

Bind to pre-initiation complex

Enhance chromatin remodeling

39
Q

Insulators

A

Big, bulky proteins that can be used to selectively block activators

40
Q

4 ways that repressors decrease gene expression

A
  1. Physically block activators
  2. Block activation domain
  3. Block RNA pol escape
  4. Recruit HDAC
41
Q

Phosphorylation of RNA pol II tail

A

Recruits RNA processing enzymes
Which ones depend on stage of transcription (promoter escape- capping factors recruited; elongation- splicing factors recruited)

42
Q

Type of linkage that m7G cap undergoes

A

5’-5’ linkage (5’ end of RNA to 5’ end of cap)

43
Q

How m7G cap is added onto RNA

A

Beta phosphate of transcript (gamma phosphate is cleaved by RNA pol II) attacks alpha phosphate of m7G

44
Q

3 purposes of 5’ cap

A
  1. Protect RNA from degradation
  2. Ribosome can recognize cap
  3. Encourage splicing of 1st intron
45
Q

Transcription termination and polyadenylation

A
  1. Poly A signal sequence in RNA is recognized by splicing factors
  2. RNA is cleaved
  3. Poly A polymerase adds adenine nucleotides to RNA
  4. Poly A binding proteins bind to adenines
46
Q

4 purposes of polyadenylation

A
  1. Protect 3’ end of RNA
  2. Extend RNA half life
  3. Encourage splicing of last intron
  4. Enabling translation
47
Q

Torpedo model of transcription termination

A

Torpedo protein chews up excess transcript

When torpedo catches up to RNA pol (chews up all of excess transcript), RNA pol is released

Molecular Bio (10 decks)

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