BFCP1 S05 + S06

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S05: Transcription; S06: Translation

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68 Terms

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T/F: DNA → RNA is more common than DNA → RNA → protein

T

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The most common type of RNA is _____, making up __% of total RNA

rRNA

80%

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mRNA accounts for __% of all RNA

5%

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What are discreet regions of DNA?

Specific, identifiable DNA sequences

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Consensus sequences

Highly conserved sequences of DNA that are usually bound by regulatory proteins

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Promoter sequences and splice sites (5’ and 3’ splice sites) are examples of ______.

consensus (conserved) sequences

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T/F: the 3’ and 5’ noncoding regions (UTRs) are transcribed and translated

F: UTR (untranslated regions) are transcribed but not translated

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Organize the following from 5’ → 3’ on a DNA strand: polyadenylation signal, promoter sequence, coding sequence, 5’ UTR’, 3’ UTR, transcription start site (+1)

5’ - promoter - transcription start site - 5’ UTR - coding sequence - 3’ UTR (including polyadenylation signal) - 3’

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Are the following sequences found on DNA or mRNA strands?:

  1. Promoter

  2. 3’ poly-A tail

  3. 5’ cap

  1. Promoter: DNA only

  2. 3’ poly-A tail: mRNA only

  3. 5’ cap: mRNA only

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TATA box

The site where the TATA binding protein (TBP) binds to ensure proper placement of RNA polymerase

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What are common promoters and where are they found?

TATA box: proximal to coding region

CAAT box, GC box/GC-rich regions: distal to coding region

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What is the main difference in function between the TATA box and the CAAT/GC boxes?

TATA box: ensures high fidelity

CAAT/GC box: determines frequency of transcription

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Transcription factors

PROTEINS that control how much transcription occur, acting as on/off switches

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Pre-initiation complex (PIC)

A group of transcription factor proteins (including that TATA binding protein (TBP)) that assembles at the promoter region to tell RNA polymerase where to bind

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Explain the basal transcription complex formation

TBP (TATA binding protein) binds that TATA box, which recruits other transcription factors such as TFIID and RNA polymerase

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T/F: the basal transcription complex travels with RNA polymerase throughout transcription

F: the complex stays behind as RNA polymerase transcribes

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Where are enhancers/silencers found, and what do they do?

Found at any point in the DNA sequence

Influence levels of transcription

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Function of activators/repressors

PROTEINS that bind to enhancers/silencers to influence frequency of transcription

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Functions of RNA polymerase I, II, and III

I: creates rRNA

II: creates mRNA and miRNA

III: creates tRNA

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Do DNA and RNA polymerase require a primer to start replication/transcription?

DNA polymerase: yes, needs the 3’ OH group present

RNA polymerase: no

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4 steps of transcription

  1. Pre-initiation: formation of basal transcription complex

  2. Initiation

  3. Elongation

  4. Termination

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Purpose of the 5’ cap

Protects mRNA from degradation

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T/F: all hnRNA get a 5’ cap

F: only those transcribed by RNA polymerase II get the cap

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The poly (A) tail is added (upstream/downstream) of the polyadenylation signal on the ___ end of the mRNA sequence. This is done after the enzyme _____ cleaves nucleotides (upstream/downstream) of the signal.

The poly (A) tail is added downstream of the polyadenylation signal on the 3’ end of the mRNA sequence. This is done after the enzyme endonuclease cleaves nucleotides downstream of the signal.

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AAUAA

Polyadenylation signal on the 3’ end of mRNA

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Function of poly(A) tail

Protects the mRNA to help with nuclear transport

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The 5’ end of an intron has the sequence ___ and the 3’ end has the sequence ___.

5’ end: GU

3’ end: AG

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snRNPs = ______ + proteins

snRNAs (small nuclear RNAs)

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Branch site

A specific adenine on an intron that attacks the 5’ splice site

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During splicing, the _____ site will attack the __’ splice site with the help of snRNPs, creating a ___ that will then be liberated.

During splicing, the branch site will attack the 5’ splice site with the help of snRNPs, creating a lariat that will then be liberated.

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What are 3 things that happen to go from hnRNA → mRNA?

  1. Splicing

  2. Addition of 5’ cap

  3. Addition of 3’ poly(A) tail

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Function of sigma factors

In prokaryotes, they bind with RNA polymerase to recognize the promoter sequence

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Explain how the growing RNA strand and DNA strands stay together/separate in eukaryotes vs prokaryotes.

Prokaryotes: growing RNA liberates from DNA as its being built

Eukaryotes: RNA is tightly bound to DNA throughout

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Polycistronic vs monocistronic

Polycistronic: one mRNA strand codes for multiple proteins, in prokaryotes

Monocistronic: one mRNA strand codes for one protein, in eukaryotes

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What is the significance of mRNA’s ½ life?

-Shorter ½ life for transiently needed protein

-Longer ½ life for proteins that are needed all the time

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T/F: prokaryotic mRNA undergo splicing

F

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The start codon is _ _ _ and encodes _____.

AUG

Met

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The stop codons are _ _ _, _ _ _, and _ _ _ and they encode ______.

UAA, UAG, UGA

they don’t encode anything

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What does it mean for genetic code to be degenerate?

Redundant - most AAs have multiple codons

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Silent mutation

Codon is changed but codes for the same AA

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Missense mutation

Codon change leads to AA change

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Nonsense mutation

Codon change leads to a stop codon instead

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Trinucleotide repeat expansion mutation

Excessive repetition of a trinucleotide

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Splice site mutation

Mutation affecting the consensus sites in introns (GU and AG), causing improper splicing

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Frameshift mutation

Adding or removing 1-2 bases to affect the reading frame of mRNA

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T/F: there is exactly 1 tRNA for every AA

F - 50 tRNAs, but only 20 AAs. More than 1 tRNA for each AA.

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Specify what the terms “charged” and “activated” mean in translation.

Charged: the name for tRNA when the appropriate AA is added to it

Activated: the name for the AA once its bound

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EVERY tRNA has a conserved sequence 5’ _ _ _ 3’ on its 3’ end that is bound to its appropriate _____.

EVERY tRNA has a conserved sequence 5’ CCA 3’ on its 3’ end that is bound to its appropriate AA.

<p>EVERY tRNA has a conserved sequence 5’ CCA 3’ on its 3’ end that is bound to its appropriate AA.</p>
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Aminoacyl-tRNA synthetase

Enzyme responsible for binding AAs to their appropriate tRNA

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T/F: aminoacyl-tRNA synthetases have the ability to remove mischarged AAs from the tRNA

T

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What is the function of the large and small subunit of the ribosome in translation?

Large unit: catalyzes peptide bonds between AAs in the growing polypeptide

Small unit: ensures fidelity

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Aminoacyl-tRNA vs peptidyl-tRNA and which ribosomal site they are found in

Aminoacyl-tRNA: an incoming tRNA carrying a single AA, found in A site

Peptidyl-tRNA: the tRNA carrying the growing polypeptide chain, found in P site

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3 ribosomal sites of translation

A: holds the incoming aminoacyl-tRNA

P: holds the peptidyl-tRNA with the bound polypeptide chain

E: holds the empty tRNA after the polypeptide chain is transferred

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Where does translation take place?

On ribosomes that are free in the cytoplasm or in the rough ER

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What is the role of ATP and GTP in translation?

ATP: required for aminoacyl-tRNA synthetase (to attach AA to tRNA)

GTP: required for binding aminoacyl tRNA to the A site and for translocation

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What direction is DNA read in transcription?

What direction is mRNA read in translation?

DNA: READ 3’ to 5’

mRNA: read 5’ to 3’

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Wobble hypothesis

The base at the 3’ end of the anticodon can be non-traditional because it isn’t as important for fidelity

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3 steps in protein translation

  1. Initiation

  2. Elongation

  3. Termination

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Initiation of translation:

  1. Small subunit meets the _____ codon of mRNA

  2. tRNA carrying ____ (___-tRNA) is bound to the small subunit

  3. ________ subunit joins

  4. ____ plays a role in combining the subunits

  5. the tRNA goes to the ___ site

  1. Small subunit meets the start codon of mRNA

  2. tRNA carrying Met (Met-tRNA) is bound to the small subunit

  3. Large ribosomal subunit joins

  4. GTP plays a role in combining the subunits

  5. the tRNA goes to the P site

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Elongation of translation:

  1. Peptide bonds between AAs are catalyzed by _______

  2. Translocation is the process of _______ and requires ____ to power it.

  3. _________ factors play a role in delivering the correct aminoacyl-tRNA to the ___ site and also require ___.

  1. Peptide bonds between AAs are catalyzed by peptidyl transferases.

  2. Translocation is the process of moving the ribosomal subunit to the next codon and requires GTP to power it.

  3. Eukaryotic elongation factors play a role in delivering the correct aminoacyl-tRNA to the A site and also require GTP.

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Peptidyl transferase is the _____ of the large ribosomal unit and functions to _______.

rRNA

catalyze peptide bond formation in the growing polypeptide chain

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Termination of translation:

  1. ______ factors recognize the ___ codon and release the polypeptide

  1. Eukaryotic release factors recognize the stop codon and release the polypeptide

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Polysomes/polyribosomes

Multiple ribosomes reading different parts of the same mRNA to make copies of the protein quickly

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<p>Identify the oldest and newest ribosome (aka the direction of translation)</p>

Identify the oldest and newest ribosome (aka the direction of translation)

The leftmost ribosome is the newest one and will continue to move right, in the 5’ to 3’ direction

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Translational trimming

Post-translational modification where the protein is cleaved to make a functional protein

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Zymogens

Pre-cursors to functional proteins that require trimming

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What is the generic term for post-translational additions to proteins?

Covalent modifications (ex: phosphorylation, hydroxylation, etc)

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Streptomycin, tetracyclien, erythromycin, cycloheximide, puromycin

Drugs that inhibit translation