molecular biology exam 2017, questions and answers PDF

Preview

Summary

Download molecular biology exam 2017, questions and answers PDF

Description

1) The earliest form of life so far identified on earth are known as: a) stromatolites b) prokaryotes c) haemaotites d) archaebacteria e) ribozymes 2) Panspermia is the theory that life on Earth originated outside our solar system. Which theory proposes that microscopic life can be propagated in space, propelled by radiation pressure from stars: a) Pseudo-panspermia b) Directed panspermia c) Accidental panspermia d) Lithopanspermia e) Radiopanspermia 3) The purine bases in DNA are: a) Adenine and Thymine b) Adenine and Cytosine c) Adenine and Guanine d) Thymine and Cytosine e) Thymine and Uracil 4) The difference between a nucleoside and a nucleotide is: a) The addition of a phosphate in a nucleoside b) The addition of a phosphate in a nucleotide c) The addition of a hydroxyl group in a nucleoside d) The addition of a sugar molecule in a nucleoside e) The addition of a base in a nucleotide 5) The origin of replication in bacteria is known as: a) Ori A b) Ori C c) dna A d) dna B e) ORC 6) Topoisomerases in eukaryotes are able to: a) Extend DNA in a 5’ to 3’ direction b) Separate double stranded DNA into two single strands c) Nick DNA to relieve supercoiling

d) Bind to the replication fork and stabilise polymerase e) Generate Okazaki fragments during DNA replication 7) Which of the following type of RNA has catalytic activity: a) Messenger RNA b) Transfer RNA c) Ribozymes d) Small nuclear RNA e) micro RNA 8) In transcription of mRNA, the DPE element stands for: a) Downstream promotor element b) Downstream product enhancer c) Drosophila promotor enhancer d) Driver of proximal enhancement e) Driver of promoter enhancement 9) The polyA tail on the 3’ end of mRNA is thought to function as: a) A transcriptional signal for RNA polymerase b) A degradation signal for RNase digestion c) An identification sequence for non-bacterial DNA d) A precursor sequence which is selectively removed after mRNA capping e) A stabilisation sequence during RNA translation 10) Cis regulatory elements are always: a) Located on a different chromosome to the transcribed gene b) Within 100kb of the promotor of the transcribed gene c) More than 100kb away from the promotor of the transcribed gene d) Located on the same chromosome to the transcribed gene e) Located on the homologous chromosome to the transcribed gene 11) The 3 stages of genomic DNA isolation in order are: a) Purification, lysis, precipitation b) Lysis, precipitation, purification c) Extraction, concentration, purification d) Extraction, purification, concentration e) Precipitation, lysis, concentration 12) A commonly used detergent in lysing of cells is: a) Triton X-100 b) NP-40 (Nonident-40)

c) ACK buffer (Ammonium, Chlorine, Potassium) d) Tris-HCl e) Chelex resin 13) The role of guanidinium thiocyanate in phenol chloroform extraction is to: a) Stabilise double stranded DNA b) Prevent ‘foaming’ of the sample under manual handling c) Isolate RNA from DNA d) Induce a neutral pH in the phenol-chloroform mix e) Denature proteins including RNases 14) Electrophoretic movement of DNA through an agarose gel is based on: a) The molecular weight of the DNA molecule b) The salt concentration of the DNA molecule c) The GC content of the DNA molecule d) The Tm (annealing temperature) of the DNA molecule e) The Purity of the DNA molecule 15) The technique used to separate DNA molecules based on their shape is known as: a) SSCP b) Comet assay c) Polyacrylamide gel electrophoresis d) RT-PCR e) Denaturing gradient gel electrophoresis 16) DMSO can be added to a PCR mix to: a) Stabilise primers in the PCR mix b) Destabilise template secondary structures c) Minimise the chance of mis-priming in annealing d) Bind unused MgCl2 in the PCR mix e) Alter the pH of the PCR mix to an optimal pH of 8.3 17) The initial phase of a PCR reaction is known as: a) The linear phase b) The plateau phase c) The lag phase d) The extension phase e) The annealing phase 18) In forensic genotyping, the abbreviation STR stands for: a) Short tangential repeat

b) Short tandem repeat c) Silent transcriptional repeat d) Single transcriptional reaction e) Silent tandem repeat 19) Southern blotting is a technique used to: a) Draw DNA from a gel onto a nitrocellulose membrane b) Draw RNA from a gel onto a nitrocellulose membrane c) Draw protein from a gel onto a nitrocellulose membrane d) Denature DNA prior to size based separation in a gel e) Denature protein prior to size based separation in a gel 20) Fluorescent in-situ hybridisation (FISH) is used to: a) Map the location of chromosomes undergoing metaphase b) Map DNA sequences from a specific parent in an individual c) Map DNA sequences and genes to a chromosomal position d) Map transcription factor binding sites on a chromosome e) Map actively transcribed genes in heterochromatin 21) Which of the following characteristics is a feature of Type IV restriction endonucleases: a) They have separate recognition and cleavage sites at least 100bp apart b) They have a random cleavage site distal to the recognition site c) They recognise non-palindromic sequences but cut 20-30 bases away from these d) The recognise and differentially cut methylated DNA e) Have a cleavage and recognition site which are co-located 22) The technique known as Restriction Fragment Length Polymorphism (RFLP) is used to: a) Determine DNA sequence of a full length PCR product b) Determine the DNA sequence of a PCR primer c) Determine the presence or absence of a single nucleotide polymorphism d) Determine the number of repeats in a microsatellite e) Determine parent of origin effects via methylation of DNA 23) The most commonly used radioactive label in DNA Sanger sequencing is: a) 32P b) 14C c) 13C d) 33P e) 12C 24) Which of the following is NOT an example of epigenetic change:

a) DNA methylation b) Transvection c) X-inactivation d) DNA mutation e) Bookmarking 25) In epigenetic regulation, 5-methylcytosine can be spontaneously deaminated to form: a) Cytosine b) Guanine c) Uracil d) Adenine e) Thymine 26) Pseudoautosomal regions are: a) Regions of autosomes inactivated by methylation in both males and females b) Regions of sex chromosomes able to undergo homologous recombination in females c) Regions of sex chromosomes devoid of histones to allow transcription in females d) Regions around the centromere devoid of gene expression e) Regions of compacted DNA leading to reduced gene expression 27) Genetic imprinting is a mechanism which allows: a) Genes to be expressed in a parent of origin manner b) Expression of dominant alleles in a recessive fashion c) Genes on the X-chromosome to show reduced expression in females d) Genes on the Y-chromosome to show enhanced expression in males e) Expression of methylated genes at reduced efficiency 28) The ‘rule of thumb’ method for calculating Tm of a 20 base pair primer with 50% GC content would give a temperature of: a) 58 degrees b) 72 degrees c) 55 degrees d) 40 degrees e) 60 degrees 29) Double stranded DNA molecules are unwound by: a) DNA topoisomerase enzymes b) DNA helicase enzymes c) DNA polymerase enzymes d) DNA restriction endonuclease enzymes e) DNA kinase enzymes

30) Which of the following is NOT a method of histone modification: a) Phosphorylation b) Methylation c) Acetylation d) Restriction digestion e) Citrullination Section B – 15 mark short answer questions Question 1 Describe how you would determine the presence or absence of a single nucleotide polymorphism in DNA sample using restriction endonucleases (15 marks) I would want you to describe an RFLP assay. Remember the feedback from the coursework question 5 – this is very similar. You could either give a step by step protocol (time consuming and a danger that you miss a vital step or get it in the wrong order) or a general answer but if general I would expect some detail on specifics still eg time and temp for the restriction digestion, what result you would expect for a particular variant and so on. You might bring in elements of how primers and enzyme are chosen (see restriction endonuclease workshop) but this should not be a major focus given the question. I would mark poorly an answer that talked about sequencing or SSCP. Given the question asks for an assay using restriction endonucleases, this is what you should focus on – sequencing would identify the SNP but that is not what you have been asked for. Question 2 Briefly describe each of the following groups of elements involved in eukaryotic transcription regulation: Cis regulatory elements (5 marks)  DNA sequence motifs o motifs recognised by the same trans-activator protein have very similar sequence o this motif is called the ‘consensus’  They are located on the same chromosome as the gene they regulate  But they can be anywhere (well, almost…) on that same chromosome: upstream downstream, even long distance away  They are orientation independent: work backward just as well as forward  DNA bending brings the cis elements close to the core promoter Trans-activating proteins (5 marks)  Of course, they can be suppressors as well  They are proteins  Bind to specific motifs in the cis regulatory elements at high specificity  Recruit further proteins, and eventually the transcription machinery  They are called ‘trans’, because the gene they are encoded by can be anywhere in the genome

Core promoter. If you feel you can better answer this question with a diagram, feel free to do so, but don’t forget to annotate your drawing and make notes as you feel fit. (5 marks)  The core promoter for protein-coding genes extends from 40bp upstream of the transcription start site to 40bp downstream from this site, and includes the following elements:  A consensus TATAXAX (where X is an A or T) is present 25 to 30 bases upstream of transcription start sites for RNA Pol II genes, known as the TATA box  Found primarily in highly expressed gene promoters  TATA-less promoters have other short sequences that replace the TATA box  Other components of the core promoter o Initiator (Inr) element flanks the start site o Downstream promoter element (DPE) o TFIIB recognition elements (BRE)  BREu and BREd flank the TATA box Question 3 Outline the ways in which the genome can undergo epigenetic regulation to alter gene expression. Your answer should focus on at least 4 different mechanisms or examples of regulation and the effects these have. I would be looking for any 4 of the following: DNA methylation, histone modification, x inactivation, maternal imprinting, stem cells, transvection or bookmarking. I would expect a general description of each (bearing in mind some of these little is known about, so 2 lines is not going to be sufficient) and possibly a short introduction on epigenetics in general – what it is, how it does not involve sequence changes etc If the examples were then related to real world relevance such as methylation in cancer, stem cells in cloning, microRNAs in gene regulation and disease incidence for example then that would score more highly as you have not only remembered the methodology, you have demonstrated its application in molecular biology. Question 4 The isolation of nucleic acids from cellular material is a fundamental process in molecular biology. Outline the steps required to isolate DNA and RNA from a tissue sample using at least 2 different methodologies (10 marks) The key thing to note here is that 2 examples are required. You would probably start with the main steps as lysis, precipitation and purification and then move on to some specific methods. This is a tricky question to get absolutely spot on, as there is so much you could write about. There are slides on tissue homogenisation, lysis buffers and chelex, ethanol precipitation etc and one could spend time on these without reaching the methods. For these I would be looking for any 2 from: phenol-chloroform, AGPC extraction, spin column DNA isolation or a mix of the individual lysis, precipitation and purification methods such as lysis with ACK buffer, sodium acetate precipitation and ethanol purification. So long as your answer makes sense and flows well I would be happy.

Explain the process of ethanol precipitation for concentration of nucleic acids and how this can be used to concentrate a dilute sample to a more concentrated one (5 marks) Precipitation with sodium acetate or ethanol would be the method, but I would expect to see the chemistry behind this (slide 11 of the lecture) that talks about the polar nature of DNA, removal of salt, possibly introduce spin columns and the chemistry behind the binding to silica and removal from silica into a smaller volume to concentrate your DNA sample....