Biochemistry unit 4

When comparing a normal and mutant gene sequence, how do you identify a frameshift mutation?

'The number of nucleotides between the normal and mutant gene sequences is different and the amino acid sequence is different.'

In the organization of DNA into chromosomes, DNA is wrapped around ______ to form nucleosomes. Nucleosomes are organized further to form ________.

histones; chromatin

Histone proteins can be chemically modified by the addition of a methyl group. If this causes nucleosomes to pack _______, the process of _______ is decreased at those DNA sites.

more tightly; transcription

Assuming there is one copy of the target DNA sequence before PCR, how many copies of DNA are thereafter 5 PCR cycles?

32

The following sequence is the coding DNA strand of the collagen gene: 5' ATG GCG TTC GAA 3' What is the sequence of the corresponding mRNA?

5' AUG GCG UUC GAA 3' The coding strand and the mRNA both go in the same direction, but the mRNA contains Us instead of Ts.

DNA polymerase can synthesize new DNA strands in which direction?

5' to 3'

Which of the following changes can NOT be detected using PCR?

A silent mutation is caused when a point mutation (single nucleotide change) occurs it changes the mRNA codon (triplet sequence that codes for amino acid), however, it doesn't affect the amino acid it codes for.

If the coding (non-template) DNA sequence of a normal gene is 5' GTC GCA TGG TGA 3', what kind of mutation would create the mutant gene sequence 5' GTC GAC ATG GTG A 3'?

An insertion mutation adds nucleotides to a gene and is a type of frameshift mutation, which changes the way the mRNA codons are read, changing the amino acid sequence.

mismatch repair

Fixes mistakes made by DNA polymerase during DNA replication

Nucleotide Excision Repair (NER)

Fixes multiple damaged nucleotides

Proteins that promote coiling of DNA and help prevent DNA strands from "tangling" are called?

Histones

What changes can occur to the DNA and to the histones that will impact gene expression?

Methylation

Which statement is true with respect to mismatch repair and nucleotide excision repair (NER)?

Mismatch repair follows the same steps as NER.

Which of the following components is NOT used in PCR?

RNA polymerase

What color is the primer in the following diagram?

Red

A nonsense mutation in a gene _____.

introduces a premature stop codon on mRNA

dNTPs are DNA nucleotides used in PCR.

True

DNA polymerase is used in DNA replication and in PCR.

True

What is the coding strand sequence if the non-template strand sequence is 5'-AGC CTT TAA CTA-3'?

5'-TCG GAA ATT GAT-3' is similar to the complementary sequence 3'-TCG GAA ATT GAT-5' for the original sequence (5'-AGC CTT TAA CTA-3'), but strand is not antiparallel (the 5' end is where the 3' would be for a complementary strand and vice versa). The sequence that is complementary to the non-template, coding strand of DNA is the non-coding, template strand. The question asks for the coding strand.

The LEP gene codes for an anorexigenic hormone. Interestingly, breastfeeding has been shown to alter methylation of the promoter of this gene, leading to increased LEP expression. What is likely happening in response to breastfeeding:

Breastfeeding decreases the methylation of the promoter of the LEP gene, increasing the spacing between nucleosomes.

Base Excision Repair (BER)

Corrects DNA containing a damaged single DNA base

Several components of cigarette smoke, including benzopyrene, insert themselves (intercalate) into the DNA between nucleotides and lead to several types of mutations such as frameshift mutations, including both insertions and deletions. Which of the following repair pathways would be used to repair this type of damage?

Nucleotide Excision Repair

What is the proper order of the steps involved in excision repair?

Recognize the damage, remove the damage, resynthesize the sequence, ligate the DNA backbone.

homologous recombination repair

Repairs a broken chromosome using genetic information from same chromosome inherited from other parent.

A thermocycler is a machine used for PCR that varies the temperature of a sample.

True

Frameshift mutations:

change the number of nucleotides in a mutant gene compared to the normal gene.

If the coding (non-template) DNA sequence of a normal gene is 5' GTC GCA TGG TGA 3', which DNA sequence would represent a nonsense mutation?

correct answer is "5' GTC GCA TAG TGA". A point mutation (single nucleotide change in a codon) that changed the G in the second position of the third codon (TGG) into an A (TAG) changed the amino acid tryptophan (Trp) into a premature stop codon - This is a point mutation in the DNA that would result in a nonsense mutation in the protein.

Which of the following is the correct tRNA anticodon for the mRNA codon 5' GCA 3'?

mRNA binding to tRNA is also complementary and antiparallel. Thus, the complementary sequence to 5' GCA 3' is 3' CGU 5'. Because the answers are presented with the 5' end on the left, we 'flip' the sequence to get 5' UGC 3'.

What would be the amino acid sequence that would result from this template sequence: 5'-TGC AAG CCA-3'?

this template would be 3'—ACG UUC GGU-5'. mRNA codons are read 5' --> 3' on the genetic code table. 'Flipping the sequence gives us 5'-UGG CUU GCA-3'. Using the genetic code table, we see that UGG encodes Trp; CUU encodes Leu; and GCA encodes Ala: Trp Leu Ala. enzyme

Which of the following is NOT a step in base excision repair?

Synthesis of an RNA primer

If one strand of chromosome 2 has a DNA sequence that consists of this: 5'AAG CGG TAC GTA 3' What will be the composition of the complementary DNA strand? A) 5' TTC GCC ATG CAT 3' B) 5' TAC GTA CCG CTT 3' C) 3' AAG CGG TAC GTA 5' D) 3' TTC GCC ATG CAT 5'

The correct answer is 'B and D'. All complementary base pairing must be antiparallel. The strand that is complementary to 5' AAG CGG TAC GTA 3' is 3' TTC GCC ATG CAT 5'. If we simply read the sequence backwards, from right to left, we get 5' TAC GTA CCG CTT 3'. Thus, both of these are the correct answers

Point mutations

The correct answer is 'change a single nucleotide in a mutant gene compared to the normal gene.

A missense mutation:

The correct answer is 'changes a single amino acid in a protein'. A single nucleotide change in the DNA (point mutation ) that changes a codon in the mRNA such that it codes for a different amino acid that it did before is called a missense mutation.

A patient with xeroderma pigmentosum is prone to developing multiple skin cancers starting in childhood. This occurs because of a mutation in a gene that codes for enzymes that help repair DNA damage through the nucleotide excision repair (NER) pathways. How does NER differ from other repair mechanisms? In NER:

The error in one strand of DNA is removed as well as several nucleotides on either side of the error. The gap that was removed is filled in by DNA polymerase

What would the amino acid sequence be from this coding strand sequence: 5'-GGA AGG CCC-3'?

The mRNA transcribed from the template strand is complementary and antiparallel to it. The coding strand of DNA (also called the non-template strand) is also complementary and antiparallel to the template strand. Thus, translating 5'-GGA AGG CCC-3' gives us Gly Arg Pro.

The LCT gene codes for Lactase, which is responsible for the breakdown of lactose. Which of the following statements could explain how Lactase activity is increased in the presence of lactose?

The presence of lactose causes nucleosomes to separate, exposing the LCT gene

What would be the resulting mRNA sequence from a template strand with this sequence: 5'-CAG CTC GTC-3'?

The sequence that is complementary to 5'-CAG CTC GTC-3' is 3'-GUC GAG CAG-5'. Since the possible answers in the list to choose from are presented with their 5' ends on the left, we simply reverse the sequence to get 5'-GAC GAG CUG-3'. 3'-GUG GAG GAG-5' results from pairing G with both C (correct) and G (incorrect).

If the coding (non-template) DNA sequence of a normal gene is 5' GTC GCA TGG TGA 3', which DNA sequence would represent a deletion mutation?

The sequence, '5' GTC GCA TGT GA 3" results from a mutation that removes a G from the third codon (TGG).

Which of the following would be considered a point mutation to a DNA strand that consists of a nucleotide sequence: 5' CTG ACG TAT CTT AAT 3'?

The sequence, 5' CTG ACG TAA CTT AAT 3', is correct because a point mutation changes a single nucleotide in a codon, in this case, changing the T in the third position of the third codon to a (TAT > TAA).

The following are steps involved in the polymerase chain reaction. Which is the correct order:

Denaturation, annealing, and elongation

When the wrong nucleotide is added to a newly forming DNA strand during DNA replication:

Distortion of the double helix structure occurs because of uncomplimentary pairing of the nucleotides

Some changes to the DNA do not modify the coding sequence of the DNA but do affect its winding and unwinding from nucleosomes. These changes can increase or decrease the availability of DNA and hence, the transcription of a gene. These are called ____________ changes.

Epigenetic

Which of the following changes can NOT be detected using PCR?

Epigenetic changes

Which of the following components are involved in the process of actively transcribing a gene?

Epigenetic modifications to nucleosomes, DNA Ligase, DNA polymerase

The polymerase chain reaction is a tool used to study protein structure.

False

Which of the following statements about epigenetics is false?

The DNA sequence is permanently altered.

Match the letters with the correct names of the processes of the central dogma (Replication; Transcription; Translation).

The central dogma starts with DNA, which is able to be replicated to prepare for cell division (A). DNA in the nucleus can also be accessed and transcribed to mRNA (B). The mRNA will leave the nucleus and enter the cytoplasm where it will be translated into a protein by the ribosome (C).

During DNA replication, which of the following sequences can be used as a primer for the following DNA sequence: 3' AGT GGA TCA CTA GGC TCT 5'?

The complementary RNA sequence for 3' AGT GGA TCA CTA GGC TCT 5'? is 5' UCA CCU AGU GAU CCG AGA 3'. Thus 5' UCA CCU AGU GAU 3', which is contained within the sequence above (beginning at the 5' end), could serve as a complementary primer for DNA synthesis.