MCAT BIO CH. 4 PART 3 Flashcards
When does termination of elongation in translation occur?
When a stop codon appears in the A site
What happens when a stop codon appears in the A site?
The A release factor enters the A site
What does the release factor cause to happen?
The peptidyl transferase to hydrolyze the bond between the last tRNA dn the completed polypeptide
How many release factors do prokaryotes have?
Three release factors
What are the purpose of the first two release factors, RF1and RF2?
RF1: Recognize termination codons UAA and UAF
RF2: Recognizes UAA and UGA
What is the purpose of RF3?
RF3 is a GTP-binding protein that leads to dissociation of RF1RF2 after peptide release
RF3 recognizes a stop codon T/F
False
How is the N-terminal amino acid different from prokaryotes and eukaryotes?
Euk: Met
Prok: fMet
What do eukaryotes used during translation instead of the Shine-Dalgarno?
There are 5’ UTR sequences in eukaryotes that function in starting translation
What is a common eukaryotes sequences that start translation?
Kozak sequence
What does eukaryotic translation begins with?
Eukaryotic translation begins with formation of the initiation complex
What complex forms in the beginning on eukaryotic translation?
43S pre-initiaion complex forms
What is the 43S pre-initiation complex composed of?
Composed of the 40S small ribosomal subunit, Met-tRNAMet and proteins called eIFs
What are eIFs?
Eukaryotic initiation factors
What happens once the 43S pre-initiation complex is assembled?
Complex recruited to the 5’ capped end of the transcript by an initiation complex of proteins (with eIFs)
What does the initiation complex do to the mRNA?
Scans the mRNA from the 5’ end to find the start codon
What happens once the initiation complex finds the start codon on the mRNA?
The large ribosomal subunit (60S) is recruited and translation can begin
What eIFs proteins are essential?
- eIF3
2. eIF4A, eIF4E and eIF4G
What is the purpose of the eIF3 protein?
Binds the small ribosomal subunit and prevents it from prematurely associating with the 60S subunit
What is the purpose of eIF4A?
A helicase and unwinds mRNA
What is the purpose of eIF4E?
Binds to the 5’ cap of the mRNA
What is the purpose of eIF4G?
A scaffold protein
What is the importance of the levels of the eIFs proteins?
Their levels are a rate-limiting step for translation
Higher amount of the three eIFs proteins means……? A lower amount means…?
Higher: Cell can perform more translation
Lower: Decreases translation
The activity of eIF proteins is controlled by what?
- Post-translational modification such as phosphorylation
What factors do eukaryotes have for the elongation step of translation?
eEF-1 and eEF2
What is eEF-1 composed of?
Has two subunits
What is the function of both subunits in the eEF-1 eukaryotic prokaryotes?
- Helps with entropies of an aminoacyl-tRNA into the A site
2. Guanine nucleotide exchange factor that catalyses the release of GDP
What is the function of the eEF-2 eukaryotic prokaryotes?
The eukaryotic translocase
What does eukaryotic translation termination include?
Two release factors: 1. eRF1 and 2. eRF3
What is the purpose of the eRF1 in eukaryotic translation termination?
eRF1 recognizes all three termination codons
What is the purpose of the eRF3 in eukaryotic translation termination?
eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed polypeptide
What is cap-dependent translation?
The major role of 5’ mRNA cap recognition for translation
What is cap-independent translation?
Eukaryotes can sometimes start translation in the middle of an mRNA molecule
If cap-independent translation means that translation can begin anywhere on the mRNA molecule, what is not required?
Doesn’t require the 5’ cap of the mRNA
In order to be able to start translation anywhere on the eukaryotic mRNA, what must be included in the transcription?
Internal ribosome entry site
What is the internal ribosome entry site (IRES)?
Specialized nucleotide sequence
What is the purpose of IRES in most cells?
Code for proteins that help the cell deal with stress or help activate apoptosis
What does the IRES makes sure?
Makes sure the cell can make essential proteins when under sub-optimal growth conditions
What happens when a cell is under stress?
Cells under stress generally inhibit translation (via inhibiting translation initiation)
What does cap-independent translation allow based on cell stress?
Allows the cell to make proteins wending so is crucial for survival or programmed cell death
Activation of translation using an IREs requires what that is different?
Requires different proteins than normal initiation
What are the six ways gene expression can be controlled
- Transcriptional control
- RNA processing control
- RNA transport and localization control
- mRNA degradation control
- Translation control
- Protein activity control
What is the principle site gene expression control in both eukaryotes and prokaryotes?
Transcription
What is epigenetic?
Change gene expression due to heritable or have a long term effect, not due to DNA sequence
What are the three most studied areas in epigenetic?
- DNA methylation
- Chromatin re-modelling
- DNA interference
What are the four ways we can control gene expression at the DNA level?
- DNA Methylation and Chromatin Remodeling
- Gene dose
- Imprinting
- Chromosome inactivation
How can the DNA of eukaryotic and prokaryotic cells be modified?
Covalently modified by adding a methyl group
What do bacteria do to DNA after DNA synthesis and why is it important?
Bacteria methylate new DNA shortly after synthesis, and the brief delay is useful in mismatch repair pathway
How can methylation control one expression in prokaryotes?
By promoting or inhibiting transcription
What does DNA methylation do to gene expression in eukaryotic cells?
Turns off eukaryotic gene expression
What are the two ways gene expression is turned off by methylation in eukaryotes?
- Blocking
2. Change DNA
Based on methylation turning off gene expression in eukaryotes, what is the “blocking” reasoning of how it turns it off?
Methylation physically blocks the gene from transcriptional proteins
Based on methylation turning off gene expression in eukaryotes, what is the “blocking” reasoning of how it turns it off?
Methylation physically blocks the gene from transcriptional proteins
Based on methylation turning off gene expression in eukaryotes, what is the “Change DNA” reasoning of how it turns it off?
Certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change the winding of DNA around histones
What is the gene dose way of increasing gene expression?
Increase the copy of number of gene by amplification
When increasing the number of gene copy, why does that increase gene expression?
Allows a cell to make large quantities of the corresponding protein
What is genomic imprinting?
When only one allele of a gene is expressed
What is imprinting considered?
An epigenetic process
Silencing of certain gene involves….?
DNA methylation, histone modifications and binding of long ncRNAs
When epigenetic marks are there, how long does it stay for genomic imprinting?
Established in the germ-line and maintained throughout life
At which stage does X-inactivation occur?
At the blastocyst stage of early development
What is X-inactivation?
Each cell in the inner cell mass randomly inactivates an. X chromosome and the decision is irreversible
How is the X inactivated?
Condensed, packaged in heterochromatin and high levels of DNA methylation
What is a simple mechanism of transcriptional regulation that is also problematic?
Some promoters are simply stronger than others and don’t respond to changing conditions in the cell
What is anabolism? What is catabolism?
Anabolism: Biosynthesis
Catabolism: Degradative metabolism
What does repressible means?
Anabolic enzymes inhibited in the presence of excess amounts of products
What does inducible enzymes mean?
Catabolic enzymes who transcription can be stimulation by the abundance of a substrate
What are the two examples of repressible and inducible enzymes?
- Lac Operon
2. Trp Operon
The lac operon is….?
Inducible since the enzyme it codes for are part of lactose catabolism
The Trp Operon is….?
Repressible since the enzyme it codes for mediate tryptophan biosynthesis or anabolism
What are the components of an operon?
Coding sequence for enzymes and upstream regulator sequences (control sites)
What can operons also include but don’t usually?
Regulatory proteins such as repressors or activators
What are the five letters that explain the components of the Lac Operon?
- P region
- O region
- Z gene
- Y gene
- A gene
What is the purpose of the P region in the Lac Operon?
The promoter site on DNA to which RNA polymerase binds to initiate transcription of Y, Z and A genes
What is the purpose of the O region in the Lac Operon?
The operator site to which the Lac repressor binds
What is the purpose of the Z gene in the Lac Operon?
Codes for the enzyme β-galactosidase
What is the purpose of β-galactosidase?
Cleaves lactose into glucose and galactose
What is the purpose of the Y gene in the Lac Operon?
Codes for permease
What is the purpose of permease?
A protein which transports lactose into the cel
What is the default for repressible systems? What is the default for inducible systems?
On, Off
What is the purpose of the A gene in the Lac Operon?
Codes for transacetylase
What is the purpose of transacetylase?
Enzyme that transfers acetyl group from acetyl-CoA to β-galactosidase
Is the A gene required for lactose metabolism?
No
Based on the regulation of the lac operon, which genes have their own promoters?
- Crp gene
2. I gene
What is the purpose of the crp gene in lac operon? Where is it located?
- Codes for a catabolic activator protein (CAP) and helps couple the lac operon to glucose levels in the cell
- Located at a distant site
What is the purpose of the I gene in the Lac Operon? Where is it located?
Codes for Lac repressor protein; located at a distant site
The protein product of the crp and I gene control what?
Control gene expression of Z, Y and A
What does bacterial cells use as an energy source preferably?
Glucose
What happens in the bacteria cell in the presence of glucose?
Lac operon will be off or expressed at low amounts
What mediates the lac operon being off in the presence of glucose?
CAP and repressor proteins
What does the glucose level control in the lac operon?
Glucose levels control protein called adenyl cyclase
What is the purpose of adenyl cyclase in the lac operon?
Adenyl cyclase converts ATP to cyclic AMP (cAMP)
In high glucose levels, how is cAMP and adenyl cyclase?
Adenyl cyclase: Inactivated
cAMP: Levels are very low
In low glucose levels, how is cAMP and adenyl cyclase?
Adenyl cyclase: Activated
cAMP: levels are high
What happens at low glucose levels that aid in activating RNA polymerase?
CAP binds cAMP and complex binds the promoter of the lac operon
What does the repressor protein bind to when coded by the __ gene?
Binds to the operator when coded by the I gene
What does the lac repressor protein prevent from binding?
Prevents RNA poly from binding the promoter and transcribing Z, Y and A genes and blocking transcription of operon when lactose is absent
What can lactose do to the lac repressor protein?
Allosteric bind; change conformational and falls off DNA as it can no longer bind
What does high transcription of Z, Y and A gene occur?
When glucose is absent and lactose is present; digest lactose to produce glucose
When high levels of cAMP bind to Cap, what does that cause?
Helps activate RNA polymerase activity at the lac operon
What happens when lots of lactose start to go scarce?
Isn’t enough to bind to the repressor and most of the repressor proteins return to their original state
How many enzymes do bacteria use to make tryptophan from chromatic acid?
Five
What is the repressor protein to production of tryptophan?
trpR gene
What does the trpR gene product do?
Repressor binds to Trp and complex binds to operator, turning off transcription
What happens when no Trp is present?
Repressor protein cannot bind the operator
What happens when repressor protein cannot bind to the operator since Trp is not present?
RNA poly can transcribe the give genes and give gene products allows the making of Trp
What is Trp an example of?
Anabolic repressible transcription
What is usually conserved in protein coding genes?
- Upstream control elements
- Promoter with binding sites for basal transcription complex and RNA poly II
- TATA box at -25
What is the TATA box?
A highly conserved DNA recognition sequence for the TATA box binding protein (TBP)
What does the binding the TBP allow, based on the TATA box?
Initiates transcription complex assembly at the promoter
Where are activator proteins located?
Bound by enhancer sequences in DNA
Which cell has gene repressor proteins?
Eukaryotes
What do gene repressor proteins do?
Inhibit transcription
What do transcription factor have that is extremely important?
Transcription factors have DNA binding domain and are crucial in transcription regulation
What can transcription factors bind to?
Bind to promoters or other regulatory sequences
The binding of transcriptional machinery to DNA is controlled by?
Extracellular signals
What are the three most common methods of transcriptional regulation in eukaryotes?
- RNA Translocation
- mRNA Surveillance
- RNA Interference
What is RNA Translocation, based on methods of transcriptional regulation in eukaryotes?
mRNA transcripts aren’t translated into proteins until they are localized properly in the cell
What is mRNA Surveillance, based on methods of transcriptional regulation in eukaryotes?
Cells monitor mRNA molecules to ensure that only high-quality mRNA transcripts are read by ribosome
What is RNA Interference (RNAi) based on methods of transcriptional regulation in eukaryotes?
A way to silence gene expression after a transcript has been made; amount of transcripts in the cell decreases
What is RNAi mediated by?
miRNA and siRNA (Section 4.7)
What are the three types of post-transcriptional modification?
- Protein Folding
- Covalent Modification
- Processing
What are chaperons?
Function in assembly or folding of other macromolecular structures
If the protein is folded correctly, it is said to be in its…
Native conformation
For covalent modification during post-translational modification, adding a hydrophobic group would aid in what?
Facilitate membrane localization
What does it mean when a protein is acetylated?
Addition of an acetyl group (-C(O)CH3) usually at the N terminus of a protein or at a lysine
What does it mean when a protein is formylated?
Addition of a formyl group (-C(O)H)
What does it mean when a protein is alkylated? What AAs is it usually done to?
Addition of an alkyl group; usually done to lysine or arginine
What does it mean when a protein is glycosylated?
Addition of a glycosyl group; substitute for of a cyclic saccharide
What does it mean when a protein is phosphorylated?
Addition of a phosphate group (PO) to serine, threonine, tyrosine, or histidine amino acid
What does it mean when a protein is sulphated?
Addition of a sulphate group (SO4^-2) to a tyrosine
What can proteins do to other proteins that is considered a covalent modification?
Can link to other proteins
What do many proteins require in order to become mature or functional?
Cleavage
What are zymogens or proenzymes? What is their purpose?
Enzyme precursors; used when the mature protein may be dangerous to the organism
What is a well-known example of post-translation processing?
Insulin
What is insulin made from?
A prohormone - preproinsulin
What is preproinsulin?
The primary translation product of the human INS gene
What needs to be removed to have proinsulin formed?
N-terminus signal peptide is removed and sulphide bonds form, in the endoplasmic reticulum
How many cleavage events are necessary to process proinsulin?
Three
What are the events cleaved to process proinsulin?
- C peptide is removed
2. Dipeptide fragments
How is the C peptide removed to process proinsulin?
Removed by a family of enzymes called pro protein coneytases
How is the Dipeptide fragments removed to process proinsulin?
Removed from the C-terminus of the B chain peptide by carboxypeptidase
Where do the cleavage events occur, based on the cleavage events to process insulin?
Secretory vesicle
