human genetics exam 3

How many types of RNA polymerase are there in humans?

- 3

what type of mutation has occurred? Normal gene DNA: ATG GCC GGC CCG AAA GAG ACC Mutated gene DNA : ATG GCC GGC CCA GAG ACC Normal protein: Met-Ala-Gly-Pro-Lys-Glu-Thr Mutated protein: Met-Ala-Gly-Pro-Glu-Thr

- 3 base pair deletion occurred between nucleotides 12 and 14 resulting in the deletion of three nucleotides, resulting in one codon being altered (but it encodes the same amino acid), and one codon being deleted - deletion did not cause a frameshift mutation

Does DNA polymerase add nucleotides to the 5'-3' direction or the 3'-5' direction?

- 3' end of a growing strand

If the DNA coding strand is 5' - ACG TAG CCA GGT - 3', what is the mRNA sequence transcribed?

- 5' - ACG UAG CCA GGU - 3'

In which direction does RNA polymerase synthesize a strand of mRNA (in 3'-5' or in 5'-3')?

- 5'-3' direction

How can a mutation in the promoter region of a gene, or a regulatory region of a gene, affect the amount of gene product 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 are the base pairing rules between DNA and RNA during transcription?

- A pairs with U in RNA - T pairs with A in RNA - G pairs with C in RNA - C pairs with G in RNA

what are the 3 RNA modifications that happen to mRNA molecules? #2

- 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

what are the 3 RNA modifications that happen to mRNA molecules? #1

- 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

below is a chromosome. which ends could not be replicated by DNA polymerase? Why not? 5' - A------------------B - 3' 3' - C -----------------D - 5'

- B & C - the 3' ends of the template strands

Why is RNA primer needed?

- DNA polymerase cannot add a nucleotide to a bare strand; it needs a 3' end on which to add an incoming nucleotide

after telomerase had added telomere repeats to the template DNA strand, how are telomere repeats added to the complimentary daughter strand?

- DNA primase, DNA polymerase, and DNA ligase then synthesize a complementary DNA sequence on the complimentary, daughter strand

how can depurination introduce a base substitution during DNA replication?

- If the empty site is not repaired prior to DNA replication, DNA polymerase can add any of the four bases opposite the empty site. If DNA polymerase adds a base that is not the original base (75% chance it will be a different one), then a base substitution event occurs

What does it mean to say that the genetic code is degenerate?

- It means 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

why does methylation of CpG islands have this effect?

- Methyl groups may directly inhibit the binding of activators to enhancers, or methyl groups may attract methyl binding proteins that interact with other proteins, which then promote gene silencing (such as histone deacetylase)

is the lagging strand made continuously or as a series of Okazaki fragments?

- Okazaki fragments

why is DNA ligase needed to form the final phosphodiester bond to link DNA fragments following removal of primers?

- Once the primer has been removed, the 5' DNA nucleotide that was linked to the primer only has one phosphate group, so there is no pyrophosphate to provide energy for DNA polymerase to form a phosphodiester bond to link it to the 3' nucleotide of the upstream DNA fragment that replaced the primer. - DNA ligase can make that phosphodiester bond to connect two adjacent DNA fragments.

Describe 3 ways in which activators and repressors 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 chromatin remodeling complexes that alter chromatin structure to make the DNA either more accessible or less accessible to GTFs and RNA pol

The GTFs bind to the promotor region and recruit...

- RNA pol to the promotor

Which enzyme transcribes DNA to RNA?

- RNA polymerase

what are the 3 RNA modifications that happen to mRNA molecules? #3

- Splicing: Splicing removes non-coding introns and connects exons

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?

- The sequence of nucleotides in mRNA directs the linking together of amino acids in a precise order to form a polypeptide

Where does translation stop?

- a Stop codon

DNA must be replicated every time.....

- a cell divides to produce new cells

what is a CpG island?

- a long stretches of CpG dinucleotide repeats, which is associated with approximately 70% of human promoters

What are the 3' untranslated regions?

- a region downstream from (after) the stop codon, and it does not get translated to amino acid

What are the 5' untranslated regions?

- a region upstream from (before) the translation start site, and it does not get translated to amino acid

What is a gene?

- a segment of DNA that encodes a functional product

What is a codon?

- a sequence of 3 consecutive nucleotides that corresponds to a specific amino acid or an end to translation (if a stop codon)

function of telomerase?

- adds telomeres repeats to the 3' end of a parental (template) DNA strand (telomere repeats then get added to the 5' end of the complimentary daughter strand by DNA primase and DNA polymerase)

when does the enzyme telomerase cease being active in most somatic cells?

- after birth

what is RNA editing?

- alters the structure and/or properties of the resulting polypeptide - 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)

Do most human genes contain a focused promotor or a dispersed promotor?

- approx. 30% of human genes are associated with a focused promotor and tend to be genes that are heavily regulated - other 70% genes are associated with a dispersed promotor, tend to be genes for which expression changes little

When synthesizing the lagging strand, does DNA polymerase move toward the replication fork or away from the replication fork?

- away from the replication fork (opposite direction along DNA strand)

does replication take place uni-directionally or bi-directionally from the origin?

- bi-directionally

function of single stranded binding proteins?

- bind to single stranded DNA to protect the DNA from degradation and to prevent the single strands reforming a double helix before replication has taken place

what effect does methylation and phosphorylation of histone tails have on chromatin structure and gene expression?

- both be associated with gene expression or gene silencing depending on 1) the amino acids that are modified and 2) the number of chemical groups attached at a particular position

How can translocations and inversions produce mutations that may affect phenotype?

- breakpoint that initiates the event may occur in a gene, or a gene may be moved to a new location where it is under the control of different regulatory elements that alter expression of the gene product

How is DNA replication initiated?

- by the sequential binding of several different proteins to the origin of replication

how can one micro RNA control the expression of many genes?

- can have many target mRNAs that all share the same short nucleotide sequence in the 3' UTR that is complementary to the seed region

what effect does acetylation of histone tails have on chromatin structure and gene expression?

- causes a more open chromatin structure, which promotes gene expression by making DNA more accessible - Acetyl groups are added to lysine amino acids, which removes the positive charge on lysine and decreases the association of lysine with negatively charged DNA. Deacetylation of histone tails by histone deacetylase makes the DNA more condensed again

What is senecence?

- cell division ceases

where does DNA polymerase get the energy for the formation of a phosphodiester bond?

- cleavage of pyrophosphate from an incoming nucleotide triphosphate supplies the energy for phosphodiester bond formation

what are exons?

- coding regions that are translated to produce an amino acid sequence

how does the spliceosome recognize introns?

- 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 is a focused promotor?

- contains a consensus sequence, such as the TATA box consensus sequence, where the transcription factors and RNA polymerase bind, then RNA polymerase initiates transcription from a defined transcriptional start site.

is the leading strand made continuously or as a series of Okazaki fragments?

- continuously agent

which base in DNA is methylated to affect gene expression?

- cytosine (C) bases

What are DNA base tautomers?

- different structural forms (isomers) of a base

DNA polymerase can detect...

- distortions of the DNA double helix and can digest DNA in the 3'-5' direction to remove the incorrect base

What is a dispersed promotor?

- does not contain a consensus sequence and contains several potential transcription initiation sites within a range of approx. 100 base pairs

when is the enzyme telomerase active?

- during embryonic and fetal development

what does it mean when we say DNA replication is semi-conservative?

- each strand (parent strands) serves as a template to produce a new strands (daughter strands) - after replication, the new DNA molecules are composed of one original (parental) strand and one new (daughter) strand

4th step of DNA replication

- following formation of the pre-replication complex, DNA polymerase and other components of the replication machinery are recruited to the origin

function of DNA ligase?

- forms the final covalent bond to link the 5' nucleotide of one DNA fragment to the 3' nucleotide of the upstream DNA fragment, which filled the gap after the primer was removed

what are telomeres?

- found at the ends of chromosomes and are composed of a short DNA sequence repeated many times

if the DNA strand below acts as a template during DNA replication, which way will DNA polymerase slide along the strand- from left to right or from right to left? 5' - ACTGGGCCTAGATTTAAC - 3'

- from right to left because the new strand is made from 5'-3' (incoming nucleotides added 3' end which is moving toward the left of the page)

RNA pol I and RNA pol III transcribes genes encoding...

- functional RNA molecules

What is a germ line cell?

- gametes and the lineage of cells that give rise to gametes

what effect does methylation of CpG islands have on gene expression?

- gene silencing

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

Is a codon located in DNA, mRNA or tRNA?

- in DNA and mRNA

1st step of DNA replication

- in GI of the cell cycle, the origin of recognition (ORC) binds to the origin of replication on the template DNA strand

3rd step of DNA replication

- in S phase, the pre-replication complex is activated to form the pre-initiation complex by the recruitment of additional factors including proteins that form the helicase complex

What is the role of the Mediator complex?

- interacts with regulatory transcription factors and it regulates phosphorylation of the carboxyl terminal domain of RNA pol II, which is the switch between transcription initiation and elongation

what is the result of RNA editing?

- introduces a premature stop codon resulting in a shortened polypeptide that plays a role in fat absorption in the small intestine

function of DNA primase?

- lays down an RNA primer to prime (begin) replication

function of DNA polymerase delta?

- links together incoming nucleotides to synthesize the lagging strand

function of DNA polymerase epsilon?

- links together incoming nucleotides to synthesize the leading strand

What is a consensus sequence?

- lists the most common nucleotide at each position

Define depurination

- loss of a purine base from DNA

Define the term deamination

- loss of an amine group from a base

RNA polymerase II transcribes all polypeptide encoding genes to....

- mRNA

Where does translation start?

- methionine (Met) codon

DNA replication has a high fidelity (addition of an incorrect nucleotide is rare) What accounts for the high fidelity?

- mismatched base pairing

hydrogen bonding is less stable between..

- mismatched base pairs, so mis-matched base pair is less likely added vs a complimentary base pair

if telomerase remained active in all somatic cells after birth, the consequence would be...

- much higher rates of cancer

Does RNA polymerase require a primer?

- no

Do all genes use the same DNA strand as a template?

- no - but the same gene always has the same strand as the template strand

The new strand is made 3' to 5'.

- no replication/ transcription

The template strand is RNA.

- no replication/transcription

Can mutations in somatic cells be transmitted to offspring?

- no, because only DNA in sperm cells and egg cells is transmitted to offspring.

what are introns?

- non-coding intervening regions that do not encode amino acids

at what location in DNA does methylation of this base typically occur?

- occurs at CpG dinucleotide sequences

why do cells reach senescence?

- occurs when telomere length becomes critically short; the cell must stop dividing so it doesn't lose germline DNA from the ends of chromosomes.

why is it necessary to make fragments on one strand?

- on lagging strand, DNA polymerase must synthesize new strand in 5'-3' direction, but replication fork is moving in opposite direction - DNA polymerase must make fragments and then move back towards the fork to make the next fragment once more template DNA has been separated

what is seed region?

- perfect complementarity need only be between the target mRNA (commonly in the 3' UTR) and nucleotides 2 - 8 of the miRNA

what is the function of spliceosome?

- performs splicing, in which introns are removed and exons are connected

What two types of functional product do genes encode?

- polypeptide or a functional RNA molecule (such as rRNA, tRNA, snRNA..)

function of DNA topoisomerase?

- prevents supercoiling (tangling) of the DNA ahead of the replication fork

To which region of a gene does RNA polymerase bind to initiate transcription?

- promotor region

if the wrong base is added, DNA polymerase has....

- proofreading activity

what two types of molecule is the spliceosome composed of?

- proteins and a type of functional RNA called small nuclear RNA (snRNA)

Are codons read from 5' - 3' or 3' - 5'?

- read from 5' - 3'

what is the histone code?

- refers to the pattern of histone tail modifications: acetyl, methyl, and phosphate groups can be added to amino acids in histone tails, and the specific pattern of chemical groups added (i.e., which groups and in which location) affects chromatin structure

function of flap endonuclease?

- removes RNA primers by cleaving off RNA nucleotides from the 5' end

An RNA primer is required to initiate synthesis

- replication

Synthesis of a new strand begins at an origin of replication

- replication

The process occurs only during the S-phase of the cell cycle.

- replication

The product is DNA.

- replication

The new strand is complementary to the template strand.

- replication and transcription

The template strand is DNA

- replication and transcription

after DNA replication takes place bi-directionally, there is a.....

- replication fork moving in each direction

Do all genes transcribed by the same RNA polymerase require the same set of GTFs, or do different genes use different GTFs?

- require same set of GTFs

function of DNA helicase complex?

- separates the two DNA strands at the replication fork

What is an RNA primer?

- short RNA sequence that is necessary to prime (begin) DNA replication

what is an origin of replication?

- site from which DNA replication is initiated

what does DNA replication take place?

- takes place during the S phase of the cell cycle

does telomerase add telomere repeats to the 3' end or the 5' end of the template strand?

- the 3' end of template

2nd step of DNA replication

- the ORC then recruits additional proteins to form the pre-replication complex

what defines the origin replication in higher eukaryotes, including humans?

- there is no defined consensus sequence

why are telomeres added?

- to prevent losing germline DNA from the ends of chromosomes during DNA replication

when synthesizing the leading strand, does DNA polymerase move toward the replication fork or away from the replication fork?

- toward the replication fork

What causes RNA polymerase to end transcription?

- transcribes the polyA signal sequence. - mRNA is cleaved shortly downstream of the polyA signal sequence.

Synthesis of a new strand begins at a promoter

- transcription

The new strand is identical to the coding strand, but with U's in place of T's

- transcription

The product is RNA.

- transcription

What are general transcription factors (GTFs)?

- transcription factors that are required for transcription initiation by RNA polymerase

what is the role of micro RNA (miRNA)?

- type of functional RNA molecule that binds to target mRNA and represses translation

function of DNA polymerase alpha?

- works with DNA primase to initiate DNA replication from a primer

Does the mutation alter the amino acid sequence? (silent mutation)

-no

Does a silent mutation typically affect phenotype?

-yes, if the base substitution occurs in a splice site (located at the exon/intron boundary regions) and subsequently causes aberrant splicing

How many standard amino acids are there?

20 standard amino acids distinguished by the side group

According to the original wobble rules, what is the minimum number of tRNAs needed to recognize all codons for Leucine (Leu)?

3 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

How many nucleotides make up a codon?

3 nucleotides

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)

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' Which DNA strand (top or bottom) is the coding strand (the coding strand will contain the sequence ATG when read from 5' - 3'

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' (template) 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' (coding) 5' - ACA GGG AUG AGG UCC CUU CUG ACC UAA AAC - 3' (mRNA)

If the DNA non-coding (template) strand is 5' - ACG TAG CCA GGT - 3' what is the mRNA sequence transcribed?

3' - UGC AUC GGU CCA - 5' (or 5' - ACC UGG CUA CGU - 3')

Approximately how much off the human genome is composed of transposable element sequences?

45%

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' which corresponds to the AUG start codon in mRNA?It will also contain a sequence that corresponds to a stop codon (i.e., TGA, TAA, or TAG)

5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' (coding) contains a 5' - ATG - 3' sequence and a 5' - TAA - 3' sequence, which correspond to start and stop codons in mRNA

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' What is a tRNA anticodon sequence that brings each amino acid to the ribosome? which amino acid does the tRNA carry?

5' - ACA GGG AUG AGG UCC CUU CUG ACC UAA AAC - 3' (mRNA) 3' - UAC UCC AGG GAA GAC UGG 5' (tRNA) Met -Arg - Ser - Leu - Leu - Thr

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' What is the mRNA sequence produced from this gene?

5' - AUG - 3' start codon and a 5' - UAA - 3' stop codon

A tRNA has the anticodon 5'-CCG-3'. Which mRNA codon(s) does this tRNA recognize?

5' - CGG - 3' (same as 3' - GGC - 5')

An mRNA codon has the sequence 5 - ACG - 3'. Which tRNA anticodon(s) will bind to this codon

5' - CGU - 3' (same as 3' - UGC - 5') or 5' - UGU - 3'

If a tRNA has the anticodon sequence 3' - CCI - 5' which codon(s) can it recognize?

5' - GGU - 3', 5' - GGC - 3' and 5' - GGA - 3', which all encode glycine

is the new DNA strand synthesized in the 5'-3' direction or the 3'-5' direction?

5'-3' direction

3' - TGT CCC TAC TCC AGG GAA GAC TGG ATT TTG - 5' 5' - ACA GGG ATG AGG TCC CTT CTG ACC TAA AAC - 3' How many amino acids are in the polypeptide encoded by this gene?

6

A polypeptide contains 200 amino acids. How many nucleotides are in the coding sequence of the gene?

600

How can a TNRE in the coding region of the Huntington gene cause the Huntington disease phenotype?

A CAG TNRE in the coding region of the Huntington gene results in additional glutamine amino acids in the resulting polypeptide. If the number of glutamine amino acids gets above a critical number, the long glutamine tract causes the protein to form aggregates, which disrupts the normal functioning of the protein

How does a TNRE in the 5' untranslated region of the FMR1 gene cause the Fragile-X syndrome phenotype?

A CCG TNRE in the 5' UTR of the FMR1 gene introduces a CpG island in the 5' region of the gene. The DNA subsequently gets methylated resulting in gene silencing

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 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 is a trinucleotide repeat expansion (TNRE)?

A three nucleotide sequence expands in copy number

What sequence do activators bind to?

Activators bind to enhancer sequences in DNA

What effect to activators have on gene expression?

Activators promote gene transcription.

what is the sequence of the template and coding DNA strands from which the transcription was produced? 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'

describe the 3 stages of translation #2 step

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

In these sequences, 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

GGC ATT GTC A

Explain in a couple of sentences how pyrimidine dimers can cause mutation during DNA replication

If the dimer is not repaired prior to DNA replication, translesion bypass polymerases can be used to replicate over the lesion and the translesion bypass polymerases have a higher error rate (i.e., are more likely to add an incorrect base during DNA replication)

How can a mutation in an intron sequence affect the resulting polypeptide?

If the mutation occurs in a splice site it may cause aberrant splicing of the mRNA resulting in exons inappropriately being spliced out or introns left in

describe the 3 stages of translation #1 step

Initiation: initiation factors bind to the 5' mRNA cap to facilitate binding of the mRNA to the 40S ribosomal subunit, and the first tRNA carrying Met binds to the P site. The complex then scans the mRNA for the start codon. After finding the start codon, the 60S ribosomal subunit associates with the small subunit

Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus? 5' - TCA ACG TAG CCA GGT CAT- 3'

Met is at the N-terminus and Arg is at the C-terminus

Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus? 5' - ATG ACG TCG CCA GGT TGA- 3'

Met is at the N-terminus and Gly is at the C-terminus

What is the amino acid sequence encoded by the following mRNA (only the coding sequence starting at the start codon gets translated)? 5' - GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA - 3'

Met-Gly-Ser-Leu-Ile-Ser-Phe-Val

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'

Met-Gly-Ser-Leu-Ile-Ser-Phe-Val

DNA coding strand is 5' - ATG ACG TCG CCA GGT TGA- 3' what is the amino acid sequence of the polypeptide produced by the gene?

Met-Thr-Ser-Pro-Gly

DNA template strand is 5' - TCA ACG TAG CCA GGT CAT- 3' what is the amino acid sequence of the polypeptide encoded by the gene?

Met-Thr-Trp-Leu-Arg

Are transposable elements still capable of moving about the human genome?

Most transposable elements in the human genome are no longer capable of transposition, and several that are capable are silenced by host regulatory mechanisms - some transposable elements (LINEs and SINEs) continue to be able to move about the human genome at a low rate

What are induced mutations?

Mutations caused by environmental agents: chemical agents or physical agents

Describe the 4 levels of protein structure #1

Primary structure: Sequence of amino acids in the polypeptide

Describe the 4 levels of protein structure #4

Quaternary structure: Refers to the association of two or more polypeptides to form a functional protein. Each polypeptide in the protein is referred to as a protein subunit

explain how ROS can react with DNA to introduce a base substitution event during DNA replication

ROS are produced during normal cellular processes in the body (such as aerobic cellular respiration, phagocytosis, and detoxifying reactions in peroxisomes), but ROS can also result from exposure to certain environmental agents. ROS can react with DNA to alter the structure of DNA bases, e.g., 8-oxo-guanine. The altered bases do not follow the same base pairing rules during DNA replication

what are regulatory transcription factors (RTFs)?

Regulatory transcription factors regulate transcription level. Genes transcribed by a particular RNA polymerase are controlled by different combinations of regulatory transcription factors.

what sequence to repressors bind to?

Repressors bind to silencer sequences in DNA

What effect do repressors have on gene expression?

Repressors inhibit gene transcription

Describe the 4 levels of protein structure #2

Secondary structure: Local regions of the polypeptide chain fold to form localized structures called secondary structures. Common secondary structures are the alpha helix and beta sheet. Secondary structures form due to hydrogen bonding between neighboring amino acids

describe the 3 stages of translation #3 step

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

Describe the 4 levels of protein structure #3

Tertiary structure: The overall 3D folded shape of a polypeptide is its tertiary structure. Chemical bonds and interactions between amino acid side chains (which is determined by the sequence of amino acids) drive folding of the polypeptide into its tertiary structure. This is the final level of structure for a protein composed of a single polypeptide

Explain how one determines the spontaneous mutation rate and how one determines if a chemical agent is a likely mutagen

The number of colonies on the control plate represents the spontaneous mutation rate because any colonies that grow on the control plate must have developed a reversion mutation. A chemical is a suspected mutagen if there are significantly more colonies on the experimental plate (i.e., where bacteria are grown in the presence of the chemical) versus the control plate (i.e., where the chemical is not present) because the chemical induced reversion mutations at a significantly higher rate than the spontaneous background rate.

on which side (5' or 3') of the template strand is the promotor located?

The promoter is located at the 3' end of the template strand.

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 happens during the process of transcription?

The sequence of DNA nucleotides in a gene is copied (transcribed) to a sequence of RNA nucleotides.

what type of mutations do intercalating agents cause?

They can cause the insertion of bases into DNA or the deletion of bases from DNA

What must occur for them to be able to grow in the absence of Histidine?

To grow in the absence of histidine, the bacteria must develop a reversion mutation that converts the mutant gene back to its original form.

Which codons are synonymous with CUU (synonymous codons specify the same amino acid)?

UUA, UUG, CUC, CUA, CUG

Which physical agent, encountered every day, causes pyrimidine dimers?

Ultra violet (UV)

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

Define tautomeric shift

a base changes structure to its other structural form

What is a point mutation

a mutation that affects a single base pair

What is a transversion mutation?

a pyrimidine base is replaced by a purine base or vice versa

What is a transition mutation?

a pyrimidine base is replaced by another pyrimidine base, or a purine base is replaced by another purine base

What is the function of aminoacyl tRNA synthase enzymes?

add the correct amino acid to the correct tRNA molecule A different aminoacyl tRNA synthase enzyme is required for each amino acid

Define intercalating agent

agents that have a planar structure, like the structure of DNA, and insert (i.e., intercalate) in between DNA bases.

explain how an alkylated base can result in a base substitution event during DNA replication

alkylated base does not follow the same base pairing rules as the original base during DNA replication, so a base substitution event will occur if the alkylated base is not repaired prior to DNA replication

Do all genes transcribed by the same RNA polymerase require the set of RTFs, or do different genes use different RTFs?

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

explain how deamination and tautomeric shift result in a base substitution event during DNA replication

altered base does not follow the same base pairing rules as the original base during DNA replication, so a base substitution event will occur if the altered base is not repaired prior to DNA replication

anticodon 5'-CCG-3' Which amino acid does this tRNA carry?

arginine (Arg)

explain how a base analog can result in a base substitution event during DNA replication

base analogs do not follow the same base pairing rules as the base that they mimic, which results in a base substitution event during DNA replication

Which strand (top or bottom) is the template strand for this gene? 3'------AAT---------GTA---------5' 5'------TTA---------CAT----------3'

bottom strand is the template strand because it will be transcribed to an mRNA with the start codon, AUG, at the 5' end and the stop codon, UAA, at the 3' end

What type of DNA damage does high-energy ionizing radiation (such as X-rays) cause?

cause DNA breaks, which can result in mutation during the repair process

What is a nonsense mutation: i.e., does the mutation alter the codon sequence?

caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon encodes a stop codon

What is a missense mutation: i.e., does the mutation alter the codon sequence?

caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon is a non-synonymous codon that encodes a different amino acid

What is a silent mutation: i.e., does the mutation alter the codon sequence?

caused by a DNA base substitution, which changes the mRNA codon sequence - The new codon is a synonymous codon that encodes the same amino acid as the original codon

what causes point mutations?

caused by a base substitution event

Define base analog

chemicals that are similar in structure to one of the DNA bases and can become incorporated instead of nucleotide during DNA replication

which two types of macromolecule are ribosomes composed of?

composed of ribosomal RNA (rRNA) molecules and proteins

Do the start and stop codons specify an amino acid?

does not specify an amino acid

Does such a mutation affect phenotype? (addition/deletion)

expected to have a neutral to detrimental effect on the structure and function of the polypeptide, but it does depend on the location of the mutation, the nature of the added/deleted amino acids, the number of amino acids added/deleted, and whether or not an existing codon was also disrupted

How could a transposable element cause a mutation?

if it inserts into a gene or the regulatory sequences of the gene. 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.

What is a frameshift mutation, and how does it occur?

is caused by the addition or deletion of a number of nucleotides not divisible by three - The added/deleted nucleotides alter the reading frame of the mRNA and change the codons that occur after the location of the addition/deletion

What are transposable elements?

mobile genetic elements that can move about the genome (i.e., jumping genes)

In the Ames test, explain why S. typhimurium His- mutants cannot grow in the absence of histidine

mutants have a mutation in a gene that is required for histidine synthesis.

What are spontaneous mutations?

occur due to natural causes

What is a somatic cell?

other body cells that are not germ-line cells

What are reactive oxygen species (ROS)?

oxygen containing molecules that are highly reactive towards other molecules, including DNA

Define pyrimidine dimer

refers to two adjacent pyrimidine bases that have are connected through chemical bonds (bases hydrogen bond with a base on the opposite strand, but they should not form a chemical bond with a base on the same strand

The UTR is a common location where...

regulatory proteins associate with the mRNA

new strand is made 5' to 3'

replication and transcription

How does the addition or deletion of a number of nucleotides divisible by three effect the resulting polypeptide?

results in the addition or deletion of an amino acid -does not alter the reading frame of the downstream codons. Depending on the location of the added/deleted nucleotides (i.e., if it doesn't occur nicely between existing codons), they may also disrupt an existing codon

What distinguishes the different amino acids?

side group gives each amino acid its distinct properties

How many subunits does a ribosome have?

small 40S subunit and a large 60S subunit

mRNA codon- 5 - ACG - 3' which amino acid does the tRNA carry?

threonine (Thr)

Can mutations in germline cells be transmitted to offspring?

yes

Does the mutation alter the amino acid sequence? (missense)

yes, a detrimental effect on the structure and function of the polypeptide

Does a missense mutation affect phenotype?

yes, but it does depend on the location of the amino acid substitution and the identity of the new amino acid. If the new amino acid is chemically/structurally like 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 the mutation will have a neutral rather than a detrimental effect

Does the mutation alter the amino acid sequence? (nonsense)

yes, causes early termination of translation resulting in a shortened polypeptide missing all amino acids encoded after the stop codon

Does the mutation affect phenotype? (frameshift)

yes, detrimental effect

Does the mutation alter amino acid sequence? (frameshift)

yes, detrimental effect

Does a nonsense mutation affect phenotype?

yes, expected to have a detrimental effect on polypeptide structure and function (and resulting phenotype)