Gene Expression & Regulation Flashcards
Ch. 17, 18
3 differences between RNA and DNA
RNA is:
1. single stranded
2. has a uracil base
3. has a ribose sugar
DNA is:
1. double stranded
2. has a thymine base
3. has a deoxyribose sugar
What is transcription
What is the first product of transcription
The synthesis of RNA using DNA information.
The first product of transcription is the primary transcript or pre-mRNA
What is translation
The synthesis of a polypeptide using mRNA
What is a triplet code
The genetic instructions for a polypeptide chain written in DNA as 3-letter words
True or False:
During transcription, for each gene, only 1 strand acts as the template strand
True. Only one strand can be the template to code for a protein
True or False:
The same strand will always be used for any specific gene. The opposite strand may, however, become the template strand for a different gene
True. This is determined by enzymes that transcribe the gene
True or False:
RNA synthesis is in antiparallel direction
True
What is a codon
An mRNA triplet code
One codon codes for one amino acid
What is the coding strand also known as
The non-template DNA strand
What is the sense strand also known as
The template DNA strand
What is the reading frame
The frame in which triplet codes are read together properly so that they produce the proper amino acid
What is RNA polymerase
An enzyme that unwindes the DNA double helix and synthesizes the pre-mRNA, and finally closing the DNA strands back together
What is a promoter
Sequence of non-coding DNA where RNA pol. and other transcription factors bind to DNA and begin transcription
What is a transcription unit
DNA sequence downstream from the promoter to the terminator
What is the start point
The nucleotide pair where RNA pol. begins mRNA synthesis
Describe initiaion of transcription in 3 parts
- Eukaryotic promoter includes TATA box ~25 nucleotide pairs upstream from the start point
- Transcription factors bind to DNA (some recognize TATA box) before
- Additional transcription factors along with RNA polymerase bind and for Transcription Initiation Complex
Describe transcription in terms of
1. Initiation
2. Elongation
3. Termination
- After RNA polymerase binds to DNA, it unwinds strands and begins mRNA synthesis at start point on template strand
- RNA pol. moves downstream, building mRNA. DNA reforms double helix
- pre-mRNA transcript is removed and RNA pol. detaches
What is a transcription factor
A protein that mediates the binding of RNA pol. to DNA
What is the TATA box
DNA sequence in promoter of As and Ts that helps binding of transcription factors
What is polyadenylation
The addition of the poly-A tail to the pre-mRNA
What is RNA processing
both ends of the primary transcript are altered and some interior parts are cut out
What are the benefits of the 5’ cap and poly-A tail
F. acilitates exportation out of nucleus
A. ttachment to ribosomes is easier
P. rotectes mRNA from degradation
What changes are made during RNA processing
Introns and cut out by spliceosomes and a 5’ GTP end cap as well as a poly-A tail are added
What is alternative RNA splicing
The different splicing sequences of one gene
(this is determined by enhancers and inhibitors)
What is tRNA
An RNA molecule that transfters an amino acid from the cytoplasm to a growing polypeptide chain at a ribosome
What is an anticodon
A specific nucleotide triplet sequence that base pairs with an mRNA codon
What is an aminoacyl-tRNA synthetase
An enzyme that catalyzes the bonding of a specific tRNA to its specific amino acid (this results in a charged tRNA because the reaction requires an ATP)
There is a specific aminoacyl-tRNA synthetase for each amino acid
Explain the E, P, A sites of a ribosome
A. The aminoacyl tRNA binding site is where the next tRNA comes into the ribosome
P. The peptidyl tRNA binding site is where the amino acid chain grows
E. The exit site is where uncharged tRNAs leave the ribosome
Describe translation initiation
A small ribosome subunit binds to mRNA
An initiator tRNA (Methionine) will bind to 5’ cap and read along until it finds START codon.
tRNA anticodon hydrogen-bonds to start codon
Big subunit will bond
Describe translation elongation
tRNA molecules enter at the A site
Amino acids are added one-by-one to the chain (at the C-terminus) on the previous amino acid
(This requires GTP)
Describe translation termination
When a STOP codon is reached, a release factor comes into the A site instead of a tRNA molecule.
This causes hydrolysis between amino acid chain and tRNA.
Chain leaves and remaining complex dissociates.
What is a signal recognition particle (SRP)
A particle that escorts the ribosome to the ER during protein synthesis
What is a polyribosome (polysome)
A string of ribosomes all translating the same mRNA strand
What is a mutation
What is a pointshift mutation
A mutation is a change to the genetic info. (DNA) of the cell
A pointshift mutation occurs on only 1 nucleotide base pair
What is a substitution mutation
What are the 3 types
The changing of 1 nucleotide base pair
The 3 types are:
1. Silent - no change to protein being coded
2. Missense - change to amino acid but order of amino acids is not important in nonsense proteins
3. Nonsense - changed mutation now produces STOP codon ; protein may not function
What is a frameshift mutation
What are the 2 types
A frameshift mutation is a deletion or addition of one nucleotide base pair
The 2 types are:
1. Insertion - the addition of a base pair
2. Deletion - the removal of a base pair
What is a control element
A non-coding DNA strand that serves as binding sites for transcriptions factors
What are the two ways in which metabolic pathways are controlled
- Cells can adjust activity of enzymes in the cell
- Cells can adjust production of enzymes
In the tryptophan repressor metabolic pathway, describe the feedback inhibition
Activity of the 1st enzyme in the pathway will be inhibited by the end product
Tryptophan is an amino acid that must be produced by cell enzymes if there is none in the environment. When there is enough tryptophan in the cell, it will inhibit the production of new tryptophan-synthesizing enzymes so the cell cannot produce a surplus of the amino acid that will go to waste
Describe the operon model of the tryptophan repressor metabolic pathway
Cells can regulate the expression of the genes coding for the necessary enzymes
If the environment provides all the necessary tryptophan, the cell will cease production of the enzymes that catalyze tryptophan synthesis
We would see a decrease in mRNA synthesis coding for these enzymes
What are coordinately controlled genes
In prokaryotic cells, these are grouped genes of related function that will be transcribed into 1 transcription unit, but still become multiple proteins
Coordinately controlled genes have 1 operator for the transcription unit
What is an operator
The “on/off” switch segment of DNA in prokaryotic cells
Found within promoter or between promoter and regulatory genes
Controls RNA pol. access to genes
What is an operon
A segment of DNA including the operator, the promoter, and the genes in the transcription unit
What is a repressor protein
A protein that can bind to an operator, inhibiting RNA synthesis (in both repressible and inducer operons)
Repressors are specific to the operator of each operon
What is a regulatory gene
A gene located upstream from the operon that codes for repressor proteins
A regulatory gene is continuously expressed, usually at low rates
Most repressor proteins (inducer/repressor) are allosteric. What does this mean
The shape change of a protein due to activation through the binding of a molecule at a specific site
What is a corepressor molecule
What is an inducer molecule
Corepressor = A molecule that binds to a repressor protein causing activation
Inducer = A molecule that binds to a repressor protein causing deactivation
Describe in short the repressible tryptophan operon when the operon is on and off
On
1. Tryptophan is absent in the cell, so
2. The operon is on, coding for tyrptophan-synthesising enzymes therefore
3. The repressor is inactive and unbound
Off
1. Tryptophan is present in the cell, so
2. The operon is off, not producing enzymes, therefore
3. The repressor protein is active with help from the corepressor (tryptophan molecule) and is bound to the operator
Negative Control Operon
Describe in short the inducible lac operon when the operon is on and off
Off
1. Lactose is absent, so
2. The repressor is active and bound to operator but unbound by inducer, therfore
3. The operon is off, not producing enzymes for lactose digestion
On
1. Lactose is present, so
2. The repressor protein is deactivated by inducer molecule (allolactose) and unbinds from operator, therefore
3. Operon turns on, and lactose-digesting enzymes are synthesized
Negative Control Operon
Describe the difference between a “Negative Control” operon and a “Positive Control” operon
Negative control = An operon that is turned off by an active repressor protein
Positive control = An operon that is enhanced by an active activator protein
Opposites if you think
What is an activator protein
A protein that binds to DNA that stimulates gene transcription
Ex. cAMP receptor protein (CRP)
Describe in short the positive gene regulation seen in the lac operon
On
1. Lactose is present and glucose is scarce, so cAMP levels increase, meaning that
2. cAMP will bind to CRP, causing it to activate and bind to promoter, leading to
3. Increase in RNA’s affinity to bind to and transcribe lactose-digesting enzymes
Off
1. Lactose and glucose are present, so cAMP levels decrease, meaning that
2. cAMP will not be bound to CRP and will not bind to promoter
3. Lactose-digesting enzyme synthesis is not enhanced, but is still happening
Lac repressor is inactive in both senarios
What is differential gene expression in eukaryotic cells
The different expression of genes by cells within the same genome (they have the same DNA)
In what 3 ways is gene transcription affected
- Location of a gene’s promoter
- Histone modification and DNA methylation
- Epigenetic inheritance
Describe histone acetylation
The N-terminus of each histone protein sticks out where the addition of an acetyl group (-COCH3) can be added
This promotes transcription by opening the chromatin strucure into euchromatin
Describe DNA methylation
The addition of methyl groups to certain nucleotide bases in the DNA
This leads to condensed chromatin in the form of heterochromatin that is hard to transcribe
Genes are more mythylated in cells where they are not transcribed
Daughter DNA strands are methylated with each new replication
Describe epigenetic inheritance
The inheritance of traits past down to daughter cells that are not DNA-sequence based
Ex. Methylation/acetylation, DNA scaffolding, positive operon function
In eukaryotic cells, what are the 4 ways in which initial transcription is regulated
- General transcription factors (GTFs) at the promoter
- Enhancers and specific transcription factors (STFs)
- Combinatorial control of gene activity
- Nuclear architecture
Describe how GTFs at the promoter affect initial gene transcription
GTFs must bind to/around the promoter before RNA polymerase can bind to DNA and begin synthesis of mRNA
GTFs act as glue between DNA and RNA polymerase
Describe how STFs and enhancers affect initial gene transcription
Gene expression can be increased or decreased by the binding of STFs to enhancers
STFs here are activators / repressors
Enhancers are control elements
Describe how enhancers can still affect a gene even if they are 1000s of nucelotides away
- Activator proteins bind to enhancers
- DNA bending protein bends DNA to bring enhancers close to promoter
- Activators bind to mediator proteins and GTFs which relay the message - This is an Active Transcription Initiation Complex
Describe how combinatorial control of gene activity affects initial gene transcription
Eukaryotic genes that are co-expressed are typically scattered over chromosomes
Coordinate gene expression relys on genes having the same sequence of enhancers
Activator proteins in the nucleus bind simultaneously, causing transcription at the same time
Describe how nuclear architecture affects initial gene transcription
Transcription factors, RNA polymerase, proteins, etc. are most common in the middle of the nucleus
Chromosomes are also positioned so that the most commonly expressed genes are facing the middle of the nucleus
What are the 3 ways in which post-transcription mRNA and proteins are regulated
- RNA processing
- Initiation of translation / mRNA degradation
- Protein processing / degradation
How does RNA processing regulate post-transcription mRNA
Alternative RNA splicing allows different mRNA molecules to be produced from 1 primary transcript
How does initial translation and mRNA degradation regulate post-transcription mRNA and proteins
During translation initiation, some mRNA can be blocked by regulatory proteins that bind to UTR sequences, preventing ribosomal attachment and leading to degradation
How does protein processing and degradation regulate post-transcription proteins
Protein processing includes assembly, activation, packing, shipping, etc. (what happens in golgi)
Proteins can be marked for destruction by cell by adding molecules (ubiquitin) to the protein
Big protein complexes (proteasomes) recognize ubiquitin and destroy protein
What are some examples of mutagens
- Chemical carcinogens
- X / UV rays
- radiation
- some pathogens
What is a proto-oncogene
What is an oncogene
Proto-oncogene = A normal gene that codes for cell division
Oncogene = A mutated proto-oncogene that codes for rapid cell division
Mutations can lead to 2 problems. What are they
- Increase in the amount of proto-oncogene protein production
- An increase in activity of these proteins
The 3 main ways proto-oncogenes become oncogenes:
- Movement of DNA within the genome
- Amplification of proto-oncogenes
- Point mutation in the control element / gene itself
How does DNA movement within the genome contribute to cancer formation
Cancer cells may have broken / incorrectly joined chromosomes. If a proto-oncogene is accidentally placed next to a hyperactive promoter, more cell dividing proteins will be produced
How does amplification of proto-oncogenes contribute to cancer formation
Amplification of a proto-oncogene can lead to an increase in the amount of cell-dividing proteins in the cell
How do point mutations contribute to cancer formation
A mutation in the control element can lead to an increase in transcription factors and RNA pol. binding to DNA and thus increase in cell-division proteins
A mutation in the gene itself can code for hyperactive cell-division proteins, causing increased cell division
What is a tumor-suppressor gene
A normal gene that codes for proteins to inhibit cell division
Proteins from proto-oncogenes and tumor-supressor genes are usually part of the…
Cell signalling pathway
What happens when a Ras G-protein is mutated in a signal transduction pathway
Although growth factors are not present to transmit a signal to divide, the mutated Ras protein overexcessively issues the signal to other kinases into the nucleus that the cell must divide. Activators enhance the transcription of proteins that are now overexpressed and the cell divides too much.
What happens when a P53 gene is mutated in the cell cycle-inhibiting pathway
P53 codes for STFs that synthesize cell-cycle-inhibitor proteins.
If damaged DNA is found, this will be relayed through kinases to the cell-cycle-inhibitor proteins. If the P53 is mutated and cannot make these proteins, there is nothing to stop the damaged DNA from being reproduced during cell division. This can lead to cell division with damaged DNA.
