MAR 220 Final Exam

The complement DNA sequence to AACTGGATT is

TTGACCTAA

If this sequence AACTGGATT is transcribed into RNA, the RNA sequence is

UUGACCUAA

Genomic DNA is ____________, resulting in the production of ______________.

transcribed, mRNA

These codons CCA, CCC, CCG, and CCU code for the amino acid?

Proline (Pro)

DNA exists in a double-stranded form whereas RNA is mainly a single stranded molecule. What is \n the likely reason for DNA being double stranded?

Double stranded DNA is a much more stable structure and less reactive than single stranded RNA and this helps to protect our genetic code. Having a second copy of our genetic code means that there is a reference for repair in the event of a mutation or damage.

Which organelle is the DNA found in?

Nucleus

Translation of mRNA into peptides happens in the

Ribosomes (in the cytoplasm)

Name this structure

Nucleotide (deoxyadenosine)

DNA codes for?

Proteins (genetic code)

What is not true about the genetic code?

a. It is unambiguous \n b. A codon in mRNA is read in a non-contiguous fashion \n c. It is nearly universal \n d. It is degenerate

a. It is unambiguous

What benchtop instrument is used to mix a molecular sample rigorously?

Vortexer (vortex mixer)

Centrifuge instruments rely on centrifugal forces to do what?

To separate the components of a mixture according to density and/or particle size

A ________________ is an instrument that can very rapidly increase or decrease temperature and \n is used to complete the polymerase chain reaction.

thermocycler

If you wanted to transfer exactly 4.3 microliters of a solution from one microcentrifuge tube to another using the micropipette in the image how would \n you set the dial?

0

4

3

When transferring very small volumes (0.1-10 microliters) using a micropipette it is helpful to:

Pipette up and down two to three times to mix/accurately and precisely transfer the liquid

Which of the following images represents the proper sterile technique when using single use supplies in a molecular laboratory?

D (but also B if multiple options)

A ____________________ is an instrument that measures the intensity of light absorbed or transmitted after it passes through a sample solution

spectrophotometer

When using hazardous chemicals in the laboratory setting you should:

wear proper PPE and follow safe lab protocols

Where should DNA, RNA or Protein samples be stored?

In a freezer/on ice (−80°C)

During the process of DNA extraction using a spin column, the silica filter

washes away particulates and inhibitors that are not bound to the silica filter

Which of the following is not a major step during a DNA extraction?

a. Precipitation of DNA

b. Using restriction enzymes to cut DNA strands

c. Protease enzymes

d. Lysis of cell membranes

b. Using restriction enzymes to cut DNA strands

What is the purpose of sodium dodecyl sulfate in a DNA extraction?

disruption of cell walls and dissociation of nucleic acid/protein complexes

What is remaining in the solution that travels through the spin column once the DNA is bound to the silica filter?

DNA bound to the silica filter

Why is alcohol used to precipitate nucleic acids from a solution in a DNA extraction?

Increases DNA concentration

What is the function of Proteinase-K in DNA or RNA extractions?

To digest/eat any contaminated proteins in the sample

When you want to design a new PCR primer pair for a gene, you start by searching GenBank for these sequences to align:

existing alignments of the gene in similar species

The GenBank accession number AY861684.1 \n belongs to the DNA sequence for:

Mytilus galloprovincialis (Mediterranean Mussel) HSP70 (HSP70) mRNA, complete cds

The TaqMan probe with the sequence GGT \n TCT GAT TAC TTC CTC CGT CTT TAA CCT will reveal in a BLAST search that it detects

Carcinus maenas (European Green Crab)

MAKTGPAIGIDLGTTYSCVGVFQHGKVEIIANDQ. This partial sequence comes from?

mytilus sp. HSP70

If you want to design a new degenerate primer pair for a gene based on an alignment of sequences of related species, where would you place the primer?

conserved and non-conserved region; forward primer is placed at begin of top strand, reverse primer is placed at the end of the bottom strand, and the target sequence is between them

Which of the following marine organisms would you be least likely to include in an alignment to design a degenerate primer for a gene of an Atlantic Blue Marlin?

organism of the same genus/species; similar larger fish with the protein present and coded

What would the reverse degenerate primer be for an amino acid sequence of MFHQYAW?

ACC CGU AUC GUU GUG AAA UAC

What would the forward degenerate primer be for an amino acid sequence of MEDAIRM?

AUG GAA GAC GCA AUA AGA AUG

To predict the length (number of bases) of a PCR product using 2 specific primers

By subtracting the lower sequence number value of the forward strand from the lower sequence number value of the reverse strand you can find out the PCR product length

During a polymerase chain reaction (PCR), the 3 steps DNA denaturing, primer annealing, and elongation are repeated 30 to 40 times. If you want to generate more PCR product, can you simply increase the number of PCR cycles (say, up to 50 or 60)?

No

How would someone calculate the approximate annealing temperature of a primer for a PCR \n reaction?

The annealing temperature is determined by calculating the melting temperature (Tm) of the selected primers for PCR amplification, generally begin with a temperature 3-5°C lower than the lowest Tm of the primers

What is the purpose of raising the temperature to 95°C in a PCR Reaction?

To completely denature the DNA

Quantitative real-time PCR is used to measure gene expression. The first step for a gene expression experiment is to

convert RNA to complementary DNA (cDNA); reverse transcription

When quantifying gene expression by qPCR a “housekeeping gene” is typically quantified in \n parallel to the gene(s) of interest. Why?

The reference genes or housekeeping genes are expressed in a wide variety of tissues and cell types and show no or only minimal changes in expression levels between the individual samples and experimental conditions

When separating DNA in an agarose gel electrophoresis

the DNA is loaded into pre-cast wells in the gel and a current applied- The phosphate backbone of the DNA (and RNA) molecule is negatively charged, so DNA fragments will migrate to the positively charged anode

If you observed more than one band in the gel electrophoresis image from the PCR product of a \n single sample what would your conclusion be?

There is DNA of varying fragment size and length present within the sample

If you observed no band in the gel electrophoresis image from the PCR product of a single sample \n what would your conclusion be?

There was insufficient quantity or concentration of DNA loaded on the gel

In gel electrophoresis how do scientists make the DNA migrate through the gel?

apply an electric current through the gel

What is the definition of a species?

a group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding

How does one mathematically test the reliability of a phylogenetic tree?

bootstrap probability (Pb) of interior branches of the tree, if the bootstrap probability is high for most branches, the tree is considered to be reliable

In CRISPR the CAS9 protein

is a 160 kilodalton protein which plays a vital role in the immunological defense of certain bacteria against DNA viruses and plasmids, and is heavily utilized in genetic engineering applications

The CAS9 enzyme was discovered from:

Bacteria found in the Richmond Mine hot springs

Protease inhibitors in the lysis buffer for protein extraction

One of the most important additives in lysis buffer is Protease inhibitors, can either be a chemical compound or a peptide

The SDS gel to separate proteins by size

SDS-PAGE separates proteins primarily by mass because the ionic detergent SDS denatures and binds to proteins to make them uniformly negatively charged. When a current is applied, all SDS-bound proteins in a sample will migrate through the gel toward the positively charged electrode.

A fluorescently labeled secondary antibody in a western blot directly binds to

aids in the detection, sorting or purification of target antigens by binding to the primary antibody, which directly binds to the target antigen

Jennifer Doudna, Emmanuelle Charpentier

CRISPR/CAS9

James Watson, Francis Crick, Rosalind Franklin

Structure of DNA

Kary Mullis

Polymerase chain reaction (PCR)

Frederick Sanger

first-generation DNA sequencing

Paul Hebert

DNA barcoding

Marion Bradford

Protein determination

Ulrich Laemmli

SDS buffer for electrophoresis

Thomas Brock

Taq DNA polymerase