Cycle 7 BMP Workshop Flashcards
What are the basis of the central dogma of genetics?
Transcription and translation
Transcription and translation are the two fundamental steps in what?
Protein synthesis
Why are proteins important?
Proteins are the functional units of the cell, used for every biological process in the cell
What can be transcribed off DNA
All RNAs
* tRNA
* rRNA
* mRNA
* miRNA
* Many others…
What is the only RNA that is translated into protein?
mRNA
Define:
Noncoding RNA
RNA that don’t get translated into a protein
Define and give examples of:
Housekeeping RNA
Always there/active, involved in transcription and translation of all genes
(rRNA, tRNA, snRNA)
Define and give examples of:
Regulatory RNA
Regulate gene expression or other processes in the cell
(miRNA and siRNA)
Define:
Non-template/coding/sense strand
Sequence of transcript matches this sequence
Define:
Template/anticoding/antisense strand
Sequence of transcript is complementary to this sequence
True or False:
mRNA is synthesized 3’ to 5’
WRONG, mRNA is synthesized 5’ to 3’
True or False:
In translation groups of 3 bases (codons) are read 5’ to 3’
True
What do each codon specify for?
An amino acid
True or False:
Codons appear in all RNAs
False, codons are unique to mRNAs, non-coding RNAs are not read as having codons
What does it mean that genetic code is “redundant”?
More than one group of 3 nucleobases codes for one amino acid
Define:
Silent Mutations
Base pair change that results in no change in amino acid encoded
Define:
Missense Mutation
Change in base pair results in change in amino acid encoded
Define:
Nonsense Mutation
Change in base pair causes premature truncation of protein in translation due to stop codon being formed instead
Define:
Frameshift mutation
An insertion or deletion in the sequence that shifts the entire reading frame
List:
The 4 types of gene mutations
- Silent
- Missense
- Nonsense
- Frameshift
List:
Differences between prokaryotes and eukaryotes in transcription and translation
Timing and location
* Prokaryotes: Simultaneous transcription and translation occurs in cytoplasm
* Eukaryotes: Transcription occurs in nucleus, translation occurs in cytoplasm
RNA
* Prokaryotes: mRNA is directly transcribed
* Eukaryotes: pre-mRNA is first produced, must be processed into mature mRNA before translation eukaryotes
In a prokaryote:
- Which way does polymerase move?
- Which way does polymerase read?
- Which way does transcription occur?
- Polymerase moves towards whichever side has the longest strand of mRNA
- RNA polymerase reads 3’-5’
- Transcription occurs from 5’-3’, as the polymerase is reading from 3’-5’
In prokaryotes:
- What is the chain of multiple ribosomes known as?
- Which ribosome on the chain is the oldest?
- Polyribosome
- The one closest to the DNA (3’ end of the mRNA
True or False:
RNA complementary base pairs with itself
True
RNA can complementary base pair with itself. What does this allow it to do?
Form secondary structures
Define:
rRNA
Catalytic component of ribosome, which is made up of rRNA and protein
What is snRNA?
A type of housekeeping RNA, involved in snRNPs
What do snRNPs comprise of? What is their function?
Protein + RNA
Responsible for alternative splicing
Describe:
How snRNPs function
- Bind to regulatory sequences in the intron (at intron-exon junctions)
- Cuts out (splice out) the introns
True or False:
Chloroplasts and Mitochondria have their own transcription machinery but not translation machinery
False, chloroplasts and mitochondria have their own transcription and translation machinery
What are chloroplasts and mitochondria genome like?
Genome is greatly reduced
True or False:
Chloroplasts and mitochondria are prokaryote-like
True
What are the 3 key components of a transcription unit?
- Promoter
- Coding sequence
- Terminator
In a transcription unit:
What is the purpose of a promoter?
Regulates where, when and to what level a gene is expressed
In a transcription unit:
What is the function of a coding sequence?
Encodes the RNA product (tRNA, mRNA, rRNA, …)
In a transcription unit:
What is the function of a terminator?
Sequence that must be transcribed into RNA before it can be interpreted
In a transcription unit:
Where does RNA polymerase bind?
Promoter
In a transcription unit:
What is the coding sequence also known as?
Open reading frame
In a transcription unit:
What is the usual structure of the terminator?
Usually an inverted repeat
True or False:
The structure of a prokaryote and eukaryote transcription unit are different
Somewhat true; both prokaryotes and eukaryotes have a promoter, coding sequence, and terminator, they just may be structurally and mechanically different
In the transcription unit, where is the site that transcription starts? What is it known as?
- On the 3’ end of the promoter
- Known as the 1+ start site
What is between the promoter and coding sequence? What is between the coding sequence and terminator?
- The 5’ UTR
- The 3’ UTR
(UTR stands for Untranslated region)
List:
The components of the transcription unit that are transcribed
- 5’ and 3’ UTRs
- Coding sequence
- Terminator
True or False:
The promoter is transcribed
False
What is a regulatory sequence? Do 5’ and 3’ UTRs have regulatory sequences?
Regulatory sequences are sequences of capable of increasing/decreasing the expression of a specific gene
Yes, 5’ and 3’ UTRs have their own regulatory sequences
How do coding sequences always start and end?
- Always start with a start codon (AUG for methionine)
- Always end with stop codon (UGA, UAA, UAG)
What is the function of a promoter?
Site that initiates transcription
In a prokaryotic promoter:
What are the sites that RNA polymerase binds to? Describe them
-35 and -10 regions
* Rich in adenine and thymine (as two hydrogen bonds between AT are easier to split than three hydrogen bonds between CG)
* Sequences at these sites are consensus sequences
What do consensus sequences do? What happens when they are mutated?
- The closer a given promoter matches the consensus sequence, the stronger it is
- Could lead to decreased or increased gene expression
In a prokaryotic promoter:
What is the SD box?
Shine-Dalgarno box
* Complementary base pairs with the RNA in a ribosome
* Tells the ribosome that the start codon is nearby
How does prokaryotic transcription termination work?
An inverted repeat
* Terminator sequence transcribed into RNA and produces a hairpin loop
* The loop is recognized by RNA polymerase as a sign to stop transcribing
In prokaryotic transcription, what helps RNA polymerase dissociate from DNA?
A series of adenine molecules found after the terminator sequence
True or False:
Eukaryotic transcription directly produces mRNA
False, eukaryotic transcription produces pre-mRNA which must be processed
List:
Reasons why pre-mRNA has to be processed
- Eukaryotic genes contains a lot of extra nucleobases that don’t need to be expressed
- Due to physical separation between transcription and translation, there is a need to increase the stability of mRNA so that it does not degrade
What are the extra nucleobases that don’t get expressed in eukaryote genes called?
Introns
List:
Modification made in mRNA processing
- Addition of a 5’ guanine cap
- Addition of a poly(A) tail
- Splicing out introns and joining together of exons
What do eukaryotes have in their promoter instead of -35 and -10 regions?
TATA box (consists of thymines and adenines)
True or False:
RNA polymerase can directly bind to the TATA box in eukaryotes
False, this is a big difference bewteen prokaryotes and eukaryotes:
* RNA polymerase is able to directly recognize the DNA at the promoter and bind in prokayotes
* Transcription factors recognize the promoter at TATA box first in eukaryotes, and RNA polymerase recognizes the transcription factors
In eukaryotic promoters, what is the function of promoter proximal regions?
Along with distant regulatory sequences, they can either enhance or repress expression
What are transcription factors
- Proteins
- Able to bind to other promoters, alter the way that RNA polymerase is able to bind
- Encoded by genes (distant regulatory sites)
Give the result when:
- RNA polymerase binding is enhanced
- RNA polymerase is blocked from binding
- Expression of the gene product is increased
- Expression of the gene product is decreased
True or False:
In prokaryotes, all regulation occurs on the promoter
True
How does eukaryotic transcription termination work?
- Contains cleavage site in 3’UTR
- Cleavage site is transcribed by RNA polymerase
- Recognized by RNAses, cleaving the RNA
- Stops RNA polymerase
True or False:
The cleavage site in eukaryotes is not transcribed
False, it is transcribed
True or False:
The poly(A) tail is transcribed
False, it is not transcribed
In eukaryotic transcription termination:
How is the poly(A) tail added on? What is it’s purpose?
By an enzyme (poly(A) polymerase), to improve stability of the mature mRNA
What does the addition of 5’ cap and poly(A) tail in eukaryotic pre-mRNA do?
- Improves stability of mRNA and protect it from degradation by RNases in the cytosol
- Aids in export through the nuclear envelope
True or False:
5’ cap is involved in initiating translation
(Explain why)
True, since it can be recognized by the ribosome
What is splicing carried out by?
snRNPs
How does splicing work?
- RNA within snRNPs complementary base pair with 3’ and 5’ splice sites
- Forms cuts at those sites, allows for high specificity
What is the purpose of alternative splicing?
Allows for massive protein diversity using a limited number of genes (get variants of mRNA from the same coding DNA (gene))
True or False:
One gene can code for various different proteins
True
In alternative splicing, how is a variant of the mRNA created?
Changing introns and exons based on demands of the cell
What is the difference between constitutive splicing and alternative splicing?
- Constitutive splicing: All exons are included
- Alternative splicing: Some exons are cut out
True or False:
Alternative splicing is not normal
False, it is a normal process
How does translation start in an eukaryote?
The ribosome recognizes 5’ cap of mRNA and scans until it reaches AUG (start codon)
Where does the end of translation occur in eukaryotes? How is this achieved?
Stop codons (UAA, UAG, UGA)
Release factors (proteins) eject the polypeptide from ribosome
True or False:
Stop codons do not code for anything
True
In what direction does translation occur?
5’ to 3’
Identify if the following is “understood as” DNA or RNA:
Promoter
N/A (not transcribed)
Identify if the following is “understood as” DNA or RNA:
-10/-35 regions
DNA (only in prokaryotes)
Identify if the following is “understood as” DNA or RNA:
TATA Box
DNA (only in eukaryotes)
Identify if the following is “understood as” DNA or RNA:
ATG & TAG/TAA/TGA (Translation start/stop)
RNA (mRNA)
Identify if the following is “understood as” DNA or RNA:
Terminator
RNA (mRNA - hairpin loop)
Identify if the following is “understood as” DNA or RNA:
PolyA signal
RNA (pre-mRNA)
Identify if the following is “understood as” DNA or RNA:
Cleavage site
RNA (pre-mRNA)
Identify if the following is “understood as” DNA or RNA:
Intronic splice sites
RNA (pre-mRNA)
Identify if the following is “understood as” DNA or RNA:
SD box
RNA (mRNA)
Identify if the following is “understood as” DNA or RNA:
Exons
RNA (mRNA)
State the molecule associated with the site in DNA:
-10/-35 regions
RNA polymerase
State the molecule associated with the site in DNA:
TATA box
Transcription factors
State the molecule associated with the site in DNA:
ATG & TAG/TAA/TGA (translation start/stop)
tRNA (with its anticodon) and release factor
State the molecule associated with the site in DNA:
Terminator
RNA polymerase
State the molecule associated with the site in DNA:
PolyA signal
PolyA polymerase protein
State the molecule associated with the site in DNA:
Cleavage site
RNase protein
State the molecule associated with the site in DNA:
Intronic splice sites
snRNPS
State the molecule associated with the site in DNA:
SD box
rRNA in ribosome
State the molecule associated with the site in DNA:
Exons
tRNA (with its anticodon)
What does the following complementary base pair with:
DNA
- Self (alpha helix)
- DNA (DNA replication)
- mRNA
- rRNA
- tRNA
- snRNA (all during transcription)
What does the following complementary base pair with:
mRNA
- Self
- DNA (transcription)
- snRNA (splicing of pre-mRNA in eukaryotes)
- rRNA (SD box - translation initiation in prokaryotes)
- tRNA (translation)
What does the following complementary base pair with:
rRNA
- Self
- DNA (transcription)
- mRNA (SD box - translation intiation in prokaryotes)
What does the following complementary base pair with:
tRNA
- Self
- DNA (transcription)
- mRNA (translation)
What does the following complementary base pair with:
snRNA
- Self
- DNA (transcription)
- Pre-mRNA (splicing in eukaryotes)
What does the following complementary base pair with:
Proteins
Does not complementary base pair (no nucleotides)
