Human Genetics Test 3
Describe 3 ways in which activators and repressors act to affect gene expression.
- Promote or inhibit the binding to TFIID to the promoter region. TFIID is the first GTF to bind to the promoter, and it then recruits other GTFs and RNA pol II. - Interact with Mediator to promote or inhibit phosphorylation of the carboxyl terminal domain (CTD) of RNA pol II. Phosphorylation allows RNA pol II to begin elongation. - Interact with proteins complexes that alter chromatin structure to make the DNA more or less accessible to GTFs and RNA pol (for example, ATP chromatin remodeling complexes).
Do all genes use the same DNA strand as the template strand?
Different genes located on the same chromosome may use a different DNA strand as the template strand, but any individual gene always uses the same DNA strand as the template strand.
5-methylcytosine is deaminated to thymine. What type of mutation could result after DNA replication (i.e., what is the base pair change, and is it a transition or a transversion)?
During DNA replication, A would be added opposite the T leading to a CG to TA transition.
It seems wasteful for organisms to use energy to transcribe introns only to remove them. What is an advantage of having genes that contain introns?
Genes can be alternatively spliced to produce different polypeptides by using different combinations of exons.
What is a germ line cell? Can mutations in germline cells be transmitted to offspring?
Germ-line cells are gametes and the lineage of cells that give rise to gametes. Mutations in germ-line cells can be transmitted to offspring.
What are induced mutations?
Mutations caused by environmental agents: either chemical agents, physical agents or viruses.
What happens during the process of transcription (in one sentence)?
The sequence of DNA nucleotides in a gene is copied (transcribed) to a sequence of RNA nucleotides.
What is the function of aminoacyl tRNA synthase enzymes?
They add the correct amino acid to the correct tRNA molecule. A different aminoacyl tRNA synthase enzyme is required for each amino acid.
According to the original wobble rules, what is the minimum number of tRNAs needed to recognize all of the codons for Leucine (Leu)?
Three: 3' - AAU - 5' could recognize UUA and UUG 3' - GAI - 5' could recognize CUU, CUC and CUA 3' - GAC - 5' or 3' - GAU - 5' could recognize CUG
What causes RNA polymerase to end transcription?
Transcription ends after RNA polymerase transcribes the polyA signal sequence. RNA is cleaved after this sequence and RNA polymerase dissociates a short way downstream.
Where does translation start and stop? Do the start and stop codons specify an amino acid?
Translation starts at a methionine (Met) codon, which specifies the amino acid methionine (Met). Translation stops at a Stop codon, which does not specify an amino acid.
What are the 3 RNA modifications that happen to mRNA molecules, and what is the purpose of each of the events?
- Addition of a 5' 7-methylguanosine cap: The 5' cap is required for export of the mRNA out of the nucleus, mRNA stability, and it is recognized by translation initiation factors that promote binding of the mRNA to the ribosome. - Addition of a 3' polyA tail (i.e., a string of ~200 A nucleotides): The polyA tail is required for export of the mRNA out of the nucleus and mRNA stability. It also interacts with translation initiation factors and promotes translation. - Splicing: Splicing removes non-coding introns and connects exons.
If a tRNA molecule carries glutamic acid, what are the two possible anticodon sequences that it could contain? Be specific about the 5' and 3' ends.
3' - CUU - 5' or 3' - CUC - 5' (however, 3' - CUU - 5' could take care of both codons due to wobble).
What is the amino acid sequence encoded by the following mRNA? 3'- ACC AGU AUG UUU ACU UUA AUU UGA CGG GUA CAU CCG -5'
3'- ACC AGU AUG UUU ACU UUA AUU UGA CGG GUA CAU CCG -5' This is the same amino acid sequence as in Q7 because codons are always read 5' - 3' and amino acid sequence is always given from N-terminus to C-terminus. Met-Gly-Ser-Leu-Ile-Ser-Phe-Val
If the DNA non-coding (template) strand is 5' - ACG TAG CCA GGT - 3' what is the mRNA sequence that would be transcribed from it?
5' - ACC UGG CUA CGU - 3' (This is exactly the same as 3' - UGC AUC GGU CCA - 5', but sequences are conventionally given from 5' - 3').
If the DNA coding (non-template) strand is 5' - ACG TAG CCA GGT - 3' what is the mRNA sequence that would be transcribed from it?
5' - ACG UAG CCA GGU - 3'
An mRNA codon has the sequence 5 - ACG - 3'. Which tRNA anticodon will bind to this codon, and which amino acid does the tRNA carry?
5' - CGU - 3' (same as 3' - UGC - 5') or 5' - UGU - 3' (same as 3' - UGU - 5') The tRNAs carry threonine (Thr) as specified by the codon.
What is the amino acid sequence encoded by the following mRNA? 5' - GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA - 3'
5' - GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA - 3' Met-Gly-Ser-Leu-Ile-Ser-Phe-Val
If a tRNA has the anticodon sequence 3' - CCI - 5' what codon(s) can it recognize?
5' - GGU - 3', 5' - GGC - 3' and 5' - GGA - 3', which all encode alanine.
A tRNA has the anticodon 5'-CCG-3'. Which mRNA codon does this tRNA recognize? Which amino acid does this tRNA carry?
5'- CGG - 3'(same as 3'- GGC - 5')The tRNA carries arginine (Arg) as specified by the codon
A polypeptide contains 200 amino acids. How many nucleotides are expected in the coding sequence of the gene?
600
Based on the gene and protein sequences that follow, what type of mutation has occurred? Normal gene DNA: ATG GCC GGC CCG AAA GAG ACC Mutated gene DNA : ATG GCC GGC CCG GAG ACC Normal protein: Met-Ala-Gly-Pro-Lys-Glu-Thr Mutated protein: Met-Ala-Gly-Pro-Glu-Asp
A 3 base pair deletion occurred between nucleotides 12 and 16 resulting in the deletion of a codon and the corresponding amino acid. The deletion did not cause a frameshift mutation.
Based on the gene and protein sequences that follow, what type of mutation has occurred? Normal gene DNA: ATG GCC GGC CCG AAA GAG ACC Mutated gene DNA : ATG GCC GGC ACC GAA AGA GAC C Normal protein: Met-Ala-Gly-Pro-Lys-Glu-Thr Mutated protein: Met-Ala-Gly-Thr-Glu-Arg-Asp
A base was inserted between nucleotides 9 and 10, which caused a frameshift mutation.
What is a benign tumor? What is a malignant tumor?
A benign tumor is an overgrowth of normal cells. In a benign tumor, the cells are still under normal cellular regulation and cannot invade other tissues in the body. If the cells acquire more mutations over time, the benign tumor can turn malignant. A malignant tumor is an overgrowth of abnormal cells that are no longer under normal cellular regulation and have the ability to proliferate out of control and invade other tissues.
What is a codon? Is a codon specified by DNA, mRNA or tRNA? Are codons read from 5' - 3' or 3' - 5'? How many nucleotides make up a codon?
A codon is a sequence of 3 nucleotides that specify an amino acid. A codon is specified by mRNA. mRNA codons are read from 5' - 3'.
What is a consensus sequence? In the sequences below, what is the consensus sequence? GGC ATT GAC T // GCC ATT GTC A // CGC ATA GTC A // GGA AAT GGG A // GGC TTT GTC A // GGC ATA GTC A
A consensus sequence lists the most common nucleotide at each position: GGC ATT GTC A
What is a frameshift mutation, and how does it occur? Does the mutation alter amino acid sequence? Does the mutation affect phenotype?
A frameshift mutation alters the reading frame, and it is caused by the addition or deletion of a number of amino acids not divisible by 3. A frameshift mutation usually has a detrimental effect on protein structure/function and resulting phenotype.
What is a mutation?
A heritable change in DNA sequence (i.e., a change in DNA sequence that is passed to daughter cells when a cell divides).
What are the base pairing rules between DNA and RNA during transcription?
A in DNA pairs with U in RNA, T in DNA pairs with A in RNA, G in DNA pairs with C in RNA and C in DNA pairs with G in RNA.
What is a missense mutation: i.e., does the mutation alter the codon sequence? Does the mutation alter the amino acid sequence? Does a missense mutation affect phenotype?
A missense mutation is caused by a base substitution that changes codon sequence, and the codon is a non-synonymous codon that encodes a different amino acid. The mutation usually affects phenotype depending on the location of the amino acid substitution in the protein and the identity of the new amino acid. If the new amino acid is chemically/structurally similar to the original amino acid, and/or if the substitution occurs in a region of the protein that is not highly critical for folding or function, then there is a better chance that the mutation will be neutral. If the mutation does affect phenotype, it is much more likely to be detrimental than beneficial to function (although in the right circumstances missense mutations can produce genetic variation for natural selection).
How can a mutation in the promoter region of a gene, or a regulatory region of a gene, affect the amount of functional protein produced?
A mutation in the promoter region may affect the ability of RNA polymerase and general transcription factors to bind and initiate transcription. A mutation in regulatory sequences may affect the ability of regulatory transcription factors (enhancers and repressors) to bind, thereby altering the rate of transcription.
What is a nonsense mutation: i.e., does the mutation alter the codon sequence? Does the mutation alter the amino acid sequence? Does a nonsense mutation affect phenotype?
A nonsense mutation is caused by a base substitution that changes codon sequence, and the new codon encodes a non-synonymous codon that specifies a stop codon. The mutation causes early termination of translation resulting in a shortened protein missing amino acids off the 3'-end. The mutation usually has a detrimental effect on protein structure/function and resulting phenotype.
What is a point mutation, and what causes point mutations?
A point mutation is a change in DNA sequence due to a single base pair substitution or the addition/deletion of a single base pair. (Often, the term point mutation is used to refer to any small change in DNA sequence resulting from a small number of base pairs).
What is a gene? What two types of functional product do genes encode?
A segment of DNA that encodes a functional product- either a polypeptide or a functional RNA molecule (such as rRNA, tRNA, snRNA, miRNA, for example).
What is a silent mutation: i.e., does the mutation alter the codon sequence? Does the mutation alter the amino acid sequence? Does a silent mutation affect phenotype?
A silent mutation is caused by a base substitution that changes codon sequence, but the new codon is a synonymous codon that encodes the same amino acid. The mutation does not usually affect phenotype because the amino acid sequence is unchanged. However, it could affect phenotype if it occurs at an exon/intron boundary region and changes the sequence of a splice site.
What is a trinucleotide repeat expansion? In Huntington disease, a TNRE occurs in the coding region. What is the result of a trinucleotide repeat expansion in the coding region of the gene? In Fragile X syndromes a TNRE occurs in the 5' untranslated region. How does this TNRE affect gene expression?
A three nucleotide (trinucleotide) sequence expands in copy number.A TNRE in the coding region results in additional amino acids in the resulting protein. In Huntington disease, an expansion of the repeat CAG causes additional glutamine amino acids to be included in the resulting protein. The long glutamine tract causes the proteins to form aggregates in the nucleus. In fragile X syndromes, expansion of the repeats CCG or CGG to a critical number introduces CpG islands in the 5' region of the gene. The DNA subsequently gets methylated resulting in gene silencing.
An oncogene is a gene that, when over-active, contributes to uncontrolled cell proliferation. Cancer promoting mutations in oncogenes are usually gain of function dominant mutations. Oncogenes encode proteins that promote cell division or prevent apoptosis. If a protein promotes cell division, then its over-activity may produce uncontrolled cell division. If a protein normally prevents apoptosis, then its over activity may inappropriately prevent mutated cells undergoing apoptosis, so the mutated cells will continue to survive and proliferate.
A tumor suppressor gene is a gene whose loss of activity contributes to uncontrolled cell proliferation. Cancer promoting mutations in tumor suppressor genes are usually loss of function, recessive mutations. Tumor suppressor genes encode proteins that prevent cell division, promote apoptosis or promote DNA repair. If a protein prevents cell division, then its loss of activity will enable cells to proliferate. If a protein usually promotes apoptosis, then its loss of activity means that mutated cells may not be programmed to die and mutated cells will continue to survive and proliferate. If a protein usually repairs DNA, then its loss of activity means that cancer promoting mutations will not be repaired.
What effect to activators have on gene expression? What sequence do activators bind to?
Activators promote gene transcription. Activators bind to enhancer sequences in DNA.
What is RNA editing? What is the result of RNA editing?
After transcription, one base is converted to a different base. RNA editing alters the structure and/or properties of the resulting polypeptide. For example, the apolipoprotein B protein transports fat molecules around the body. Editing of the apolipoprotein B mRNA in the small intestine (by changing a C to a U) introduces a premature stop codon resulting in a shortened polypeptide that plays a role in fat absorption in the small intestine. The glutamate receptor (binds to the neurotransmitter, glutamate) can also undergo editing by changing A to I in the receptor mRNA, which alters the properties of the receptor channel protein to fine- tune synaptic transmission.
What are intercalating agents, and what type of mutations do they typically cause?
Agents that insert in between bases. They can cause the insertion or deletion of bases from DNA.
Alkylating agents are chemicals that add alkyl groups to bases. How can this type of base modification cause a mutation?
Alkylated base do not base pair properly during DNA replication. For example alkylated guanine base pairs with thymine instead of cytosine.
Why is an inherited predisposition to developing a cancer usually due to inheriting a mutation in a tumor suppressor gene rather than in an oncogene?
An individual usually inherits a mutation in one copy of a tumor suppressor gene, which does not affect development. A mutation is acquired in the second copy later in life. If an individual inherited a mutation in an oncogene then it would probably be fatal during development or it would promote the very early development of a cancer, so the mutation is less likely to be transmitted over generations.
What is an oncogene? Do cancer promoting mutations in oncogenes usually cause gain of function or loss of function? How do oncogenes contribute to uncontrolled cell proliferation?
An oncogene is a gene that, when over-active, contributes to uncontrolled cell proliferation. Cancer promoting mutations in oncogenes are usually gain of function dominant mutations. Oncogenes encode proteins that promote cell division or prevent apoptosis. If a protein promotes cell division, then its over-activity may produce uncontrolled cell division. If a protein normally prevents apoptosis, then its over activity may inappropriately prevent mutated cells undergoing apoptosis, so the mutated cells will continue to survive and proliferate.
What are base analogs, and how do they cause mutation?
Base analogs are chemicals that are similar in structure to one of the bases and they become incorporated instead of the base during DNA replication. Base analogs can cause mutation because they do not follow complementary base pairing rules resulting in the wrong base being added opposite the base analog next time the DNA gets replicated.
What causes cancer?
Cancer is caused by the accumulation of mutations that promote uncontrolled cell proliferation.
An RNA transcript has the sequence below. What is the sequence of the template and coding strands of the DNA that encodes this RNA? On which side (5' or 3') of the template strand is the promoter located? mRNA sequence: 5' - GGC AUG CAU UAC GGC AUC ACA CUA GGG AUC - 3'
Coding strand: 5' - GGC ATG CAT TAC GGC ATC ACA CTA GGG ATC - 3' Template strand: 3' - CCG TAC GTA ATG CCG TAG TGT GAT CCC TAG - 5' The promoter is located at the 3' end of the template strand.
What are introns and exons? The spliceosome removes introns. What two types of molecules is the spliceosome composed of? How does the spliceosome recognize introns?
Exons are coding regions that encode amino acids (i.e., expressd regions). Introns are non-coding intervening regions that do not encode amino acids. The spliceosome is composed of multiple subunits that are each composed of proteins and a type of functional RNA called small nuclear RNA (snRNA). The spliceosome recognizes the conserved intron branch site in the center of the intron and conserved 5' and 3' splice sites, which are located at exon/intron boundaries.
What type of DNA damage is induced by UV radiation?
Formation of pyrimidine dimers between adjacent pyrimidine bases. Cytosine bases in a pyrimidine dimer are more prone to deamination to form uracil, ultimately leading to a transition mutation. Also, the normal DNA polymerases (delta and epsilon) cannot replicate over pyrimidine dimers, which cause a distortion of the DNA double helix. If the damage is not repaired prior to DNA replication, translesion bypass polymerases can be used to replicate over the lesion and some of the translesion bypass polymerases have a higher error rate.
What are general transcription factors (GTFs)? Do all genes transcribed by a particular RNA polymerase (e.g., RNA polymerase II) require the same set of GTFs, or do different genes use different GTFs?
GTFs are transcription factors that are required for transcription initiation by RNA polymerase. All genes transcribed by a particular RNA polymerase require the same set of general transcription factors, e.g., all genes transcribed by RNA pol II require the same set of GTFs for transcription initiation. The GTFs bind to the promoter region and recruit RNA pol to the promoter.
When would you expect a mutation in an intron sequence to affect the resulting protein?
If the mutation occurs in a splice site it may affect splicing of the mRNA resulting in exons inappropriately being spliced out or introns being left in.
What is a transition mutation? What is a transversion mutation?
In a transition mutation, a pyrimidine base is replaced by another pyrimidine base or a purine base is replaced by another purine base. In a transversion mutation, a pyrimidine base is replaced by a purine base or vice versa.
How do the spontaneous lesions we discussed (i.e., depurination, deamination, tautomeric shift) result in mutation? (i.e., does the structure of the base stay the same or is it altered, and does the base follow complimentary base pairing rules during DNA replication)?
In depurination, a purine base is lost from DNA. In deamination and tautomeric shift, the structure of the base is altered. The bases with altered structure (or the empty site with no base in the case of depurination) do not follow complimentary base pairing rules, so if the lesion is not repaired before DNA replication then the wrong base will be added opposite the lesion, ultimately resulting in a mutation.
Cytosine undergoes tautomeric shift just prior to DNA replication. It changes from the common amino form to the rare imino form, which pairs with adenine. What type of DNA mutation would result (i.e., what is the base pair change, and is it a transition or a transversion)?
In subsequent rounds of DNA replication the A will pair with T leading to a CG to TA transition.
Briefly describe the 3 stages of translation (a couple of sentences for each stage) mentioning the functional roles of the A, P and E sites.
Initiation: initiation factors bind to the 5' mRNA cap and facilitate binding of the mRNA to the 40S ribosomal subunit. The subunit then scans the mRNA for the start codon. After finding the start codon, the first tRNA carrying Met binds to the P site and the 60S ribosomal subunit associates with the small subunit. Elongation: a tRNA with an anticodon complementary to the codon in the A site binds to the A site. A peptide bond forms between the amino acid in the A site and the amino acid at the end of the polypeptide chain held by the tRNA in the P site. The growing polypeptide chain is then transferred to the tRNA in the A site and the ribosome translocates one codon in the 3' direction. The tRNA in the E site exits the ribosome and a new tRNA comes into the A site for the cycle to start again. Termination: translation ends when there is a stop codon in the A site. The stop codon is recognized by a release factor which promotes release of the completed polypeptide and dissociation of the mRNA and ribosome subunits.
What does it mean when we say that the genetic code is degenerate?
It means that the same amino acid can be specified by more than one codon. There are only 20 standard amino acids, but there are 61 different codons that specify amino acids.
What is the role of the Mediator complex?
Mediator interacts with the regulatory transcription factors, and it regulates phosphorylation of the carboxyl terminal domain (CTD) of RNA pol II, which is the switch between transcription initiation and elongation.
What is metastasis?
Metastasis occurs when malignant cancer cells enter the blood stream (or lymphatics) and spread to other locations in the body.
Methylation of DNA affects gene expression. Which base in DNA is methylated to affect gene expression? At what location in DNA does methylation of this base typically occur? What effect does methylation of DNA typically have on gene expression (although there are exceptions), and why does it have that effect?
Methyl groups can be added to cytosine (C) bases. Methylation of cytosine bases typically occurs at CpG dinucleotide sequences (i.e., where CG are located next to each other). Approximately 70% of promoters are associated with a CpG island (a long stretches of CpG dinucleotide repeats). Methylation is associated with gene silencing. Methyl groups may directly inhibit the binding of activators to enhancers, or methyl groups may attract methyl binding proteins that interact with other proteins that promote gene silencing, such as histone deacetylase.
Proteins have 3 or 4 levels of structure depending on whether the protein is composed on one or more than one polypeptide. Describe each of the 4 levels of protein structure (one or two sentences for each level will do).
Primary structure: Sequence of amino acids. Secondary structure: Folding of local regions of the polypeptide chain. Common secondary structures are the alpha helix and beta sheet. Tertiary structure: Overall 3D folded shape of a polypeptide. This is the final level of structure for a protein composed of a single polypeptide. Quaternary structure: The association of two or more polypeptides to form a multi-subunit protein.
Does RNA polymerase require a primer? In which direction does RNA polymerase synthesize a new strand (i.e., in the 3' - 5' direction or in the 5' - 3' direction)?
RNA polymerase does not require a primer. RNA polymerase synthesizes an RNA strand in the 5' - 3' direction (incoming nucleotides are added to the free 3' end of the growing strand).
Which enzyme transcribes DNA to RNA? How many different types of RNA polymerase are there in humans?
RNA polymerase transcribes DNA to RNA. Humans have 3 different RNA polymerase enzymes. RNA polymerase II transcribes all polypeptide encoding genes to mRNA. RNA pol I transcribes most rRNA genes, and RNA pol III transcribes tRNA genes and the 5S rRNA gene. Other functional RNA molecules are transcribed by one of the three polymerases just mentioned.
What are regulatory transcription factors (RTFs)? Do all genes transcribed by a particular RNA polymerase (e.g., RNA polymerase II) require the same set of RTFs, or do different genes use different RTFs?
Regulatory transcription factors control the rate of gene transcription. Genes transcribed by a particular RNA polymerase are controlled by different combinations of regulatory transcription factors. For example, all genes transcribed by RNA pol II require the same set of general transcription factors, but different genes are controlled by different sets of regulatory transcription factors because different genes are transcribed at different rates, and different sets of genes are expressed in different cell types, during different stages of development, and under different environmental conditions.
What effect do repressors have on gene expression? What sequence to repressors bind to?
Repressors inhibit gene transcription. Repressors bind to silencer sequences in DNA.
Briefly describe the composition of eukaryotic ribosomes (how many subunits does a ribosome have, and which two types of macromolecule are ribosomes composed of)?
Ribosomes have a small 40S subunit and a large 60S subunit. The subunits are composed of ribosomal RNA (rRNA) and proteins.
What is a somatic cell? Can mutations in somatic cells be transmitted to offspring?
Somatic cells are all of the other body cells that are not germ-line cells. Mutations in somatic cells cannot be transmitted to offspring because only DNA in sperm cells and egg cells is transmitted to offspring.
What are spontaneous mutations?
Spontaneous mutations occur naturally.
Which codons are synonymous with CUU (synonymous codons specify the same amino acid)?
Synonymous codons are those that specify the same amino acid. Non-synonymous codons specify different amino acids. UUA, UUG, CUC, CUA, CUG are all synonymous with CUU.
What are DNA base tautomers, and what is tautomeric shift?
Tautomers are different structural forms (isomers) of a base. The bases usually occur in the most common form, but when single stranded, they can undergo spontaneous tautomeric shift to the rare form. It can cause a mutation because the rare tautomeric forms do not pair according to complementary base pairing rules.
What are the 5' and 3' untranslated regions?
The 5' untranslated region (UTR) is a region upstream from the translation start site, and it does not get translated to amino acid. The 3' UTR is a region downstream from the stop codon, and it does not get translated to amino acid.
How can translocations and inversions produce mutations that may affect phenotype?
The breakpoint that initiates the event may occur in a coding region, which would disrupt the gene sequence, or a gene may be moved to a new location where it is under the control of different regulatory elements that alter the rate of gene transcription and therefore the amount of protein produced.
What is the histone code? What effect does acetylation of histone tails have on chromatin structure and gene expression? What effect does methylation of histone tails have on chromatin structure and gene expression?
The histone code refers to the pattern of histone tail modifications (acetylation, methylation and phosphorylation), which affects chromatin structure. Acetylation of histone tails by histone acetyltransferase is associated with an open chromatin structure, which promotes gene expression. Acetyl groups are added to lysine amino acids, which removes the positive charge on lysine and therefore decreases the association of the lysine residues with negatively charged DNA. Methylation of histone tails can be associated with gene expression or gene silencing depending on 1) the amino acids that are methylated and 2) the number of methyl groups attached at a particular position. The pattern of modifications (i.e., the histone code) is recognized by proteins that have binding sites specific for a particular pattern of methylation.
If the DNA template strand is 5' - TCA ACG TAG CCA GGT CAT- 3' what is the amino acid sequence of the polypeptide it encodes? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?
The mRNA is: 5' - AUG ACC UGG CUA CGU UGA - 3' The resulting polypeptide is therefore: Met-Thr-Trp-Leu-Arg Met is at the N-terminus and Arg is at the C-terminus
If the DNA coding strand is 5' - ATG ACG TCG CCA GGT TGA- 3' what is the amino acid sequence of the polypeptide it encodes? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?
The mRNA is: 5' - AUG ACG UCG CCA GGU UGA - 3' The resulting polypeptide is therefore: Met-Thr-Ser-Pro-Gly Met is at the N-terminus and Gly is at the C-terminus
Explain how the Ames test works. Explain why S. typhimurium His- mutants cannot grow in the absence of histidine, and what has to occur in order for them to be able to grow. Explain how we determine the spontaneous mutation rate, and how we determine whether a chemical agent is a likely mutagen.
The mutants have a mutation in a gene that is required for synthesis of the amino acid histidine. In order for the bacteria to grow in the absence of histidine, they have to develop a reversion mutation that converts the mutant gene back to its original form. The number of reversion colonies on the control plate represents the spontaneous mutation rate. A chemical is a suspected mutagen if it substantially increases the rate of reversion mutation above the background spontaneous mutation rate.
At which location of a gene do the GTFs and RNA polymerase bind to initiate transcription? What is the difference between a focused promoter (for example, a TATA box type promoter) and a dispersed promoter. Are the majority of human genes associated with a focused or dispersed promoter?
The promoter region. A focused promoter contains a consensus sequence, such as the TATA box consensus sequence, where the general transcription factors and RNA polymerase bind and then RNA polymerase initiates transcription from a defined transcriptional start site. Approximately 30% of human genes are associated with a focused promoter. The other 70% of genes are associated with a dispersed promoter, which does not contain a consensus sequence and contains several potential transcription initiation sites within a range of approximately 100 base pairs. It is currently not understood what determines the binding location of the general transcription factors and RNA polymerase.
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - ACT - 3' to 5' - ACA - 3?
The resulting codon changes from ACU (Thr) to ACA (Thr), so a silent mutation results.
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - ACT - 3' to 5' - CCT - 3'?
The resulting codon changes from ACU (Thr) to CCU (Pro), so a missense mutation results.
What type of mutation results if a base pair substitution changes the DNA coding strand from 5' - TAT - 3' to 5' - TAA - 3'?
The resulting codon changes from UAU (Tyr) to UAA (stop), so a nonsense mutation results.
What is translation (one sentence)?
The sequence of nucleotides in mRNA directs the linking together of amino acids in a precise order to form a polypeptide.
The diagram below depicts a gene and shows the positions that encode translational start and stop codons. Which strand (top or bottom) is the template strand for this gene? 3'------------TAC--------------------ATT------------5' 5'------------ATG--------------------TAA-------------3'
The top strand is the template strand because, when transcribed, it will give an mRNA with the start codon at the 5' end and the stop codon at the 3' end.
How many standard amino acids are there? What distinguishes the different amino acids?
There are 20 standard amino acids distinguished by the side group. The side group gives each amino acid its distinct properties.
What are transposable elements? Approximately how much off the human genome is composed of transposable element sequences? Are transposable elements still capable of moving about the human genome? How could a transposable element cause a mutation?
Transposable elements are mobile genetic elements that can move about the genome (i.e., jumping genes). Approximately 45% of the human genome is composed of transposable elements. Most transposable elements in the human genome are no longer capable of movement, and several that are capable are silenced by host regulatory mechanisms. However, some transposable elements (LINEs and SINEs) continue to be able to move about the human genome at a low rate.. A transposable element can cause mutation if it inserts into a gene or the regulatory sequences of the gene (the table in the handout shows disorders that are known to have resulted from transposable element insertions). Transposable elements can also promote structural changes to chromosomes (deletions/duplications, inversions and translocations) if there is recombination between identical transposable element sequences at different chromosomal locations.
A depurination event removes an adenine base from DNA. If the base is not replaced before DNA replication, what type of mutation could result (i.e., what is the base pair change and is it a transition or transversion)?
When it comes to DNA replication, DNA polymerase could add any of the 4 bases opposite the empty site. If it adds G then the result is an AT to CG transversion. If it adds C then the result is an AT to GC transition. If it adds A then the result is an AT to TA transversion.
What is wobble between the codon and anticodon? In which position of the codon and anticodon is the wobble base located?
Wobble means that the nucleotides located in the 3' position of the codon and the 5' position of the anticodon do not always base pair according to the complementary AU/GC base pairing rules. For example, G at the 5' end of the anticodon can pair with either C or U at the 3' end of the codon.
What is a carcinogen?
cancer causing agent
Consider the following mutations, and, for each, explain whether you expect it to be a) potentially cancer promoting b) dominant or recessive i) A mutation that destroys the active site of an enzyme necessary to promote cell cycle progression ii) A very premature STOP codon in a gene encoding a protein involved in DNA repair iii) A point mutation that renders one of the signaling proteins in the cell division pathway constitutively active iv) A null mutation in a gene encoding an apoptosis-promoting protein
i) The mutation would probably be recessive because it is loss of function. The mutation WOULD NOT be cancer promoting because it does not promote cell proliferation. ii) The mutation would probably be recessive because it is loss of function. The mutation WOULD be cancer promoting because any future cancer-promoting mutations may go unrepaired. iii) The mutation would probably be dominant because it is gain-of-function, and the mutation WOULD be cancer promoting because it promotes cell proliferation. iv) The mutation would probably be recessive because it is loss of function. The mutation WOULD be cancer promoting as it would allow cell proliferation in a cell that would normally undergo apoptosis.
The Ames test was performed to determine whether chemical X is a likely mutagen. i) On the control plate (where bacteria were not mixed with chemical X), there were 5 colonies. On the experimental plate (where bacteria were mixed with chemical X), there were 6 colonies. Do the results indicate that chemical X is a mutagen? ii) What about if there were 5 colonies on the control plate and 50 colonies on the experimental plate?
i) The results do not indicate that chemical X is a mutagen because there has been no substantial change in the rate of reversion mutation. ii) The results indicate that chemical X is a likely mutagen as there has been a substantial increase in the rate of reversion mutation (in an actual experiment it would be repeated several times and statistics would be applied to determine if the increased rate is significant).
Some genes are regulated post-transcriptionally. What is the role of micro RNA (miRNA)? How can one micro RNA control gene expression of many genes?
miRNAs are functional RNA molecules that bind to target mRNAs and repress translation. miRNAs are typically 22 nucleotides long, but it has been shown that perfect complementarity is often only observed between the target mRNA (commonly in the 3' UTR) and nucleotides 2 - 8 of the miRNA (which is known as the seed region). Therefore, one miRNA can have many target mRNAs that all share the same short nucleotide sequence in the 3' UTR that is complementary tothe seed region.
What is the name of the region where RNA polymerase binds to the DNA to initiate transcription?
promoter region