Molecular Diagnostics Exam 1 Nucleic acid structure, analysis, and characterization

From which of the following samples would you expect the least likelihood of suitable DNA recovery

Formalin/ Mercury fixed tissue samples

The absorbance reading of a DNA sample at 260nm = 0.172 what is the concentration of DNA in the sample?

8.60 ug/mL
(0.172 x 50)

Durning electrophoresis DNA moves toward the

Anode

If the DNA sample 260 nm/ 280 nm ratio is less than___ it is contaminated

1.6

The absorbance reading of an RNA sample at 260 = 0.3087; what is the concentration of RNA in the sample

12.28 ug/mL
( 0.3087 x 40)

A RNA sample has the following absorbance readings:
A260 = 0.208 A280 = 0.096 This RNA is pure and is suitable for use.

True

The most abundant RNA in cells is

Ribosomal RNA

All of the following substances can be used for inactivating RNAse with the exception of

Chelex

Which of the following can be used to detect the location of DNA bands in a gel following electrophoresis

SYBR Green
Ethidium Bromide
Fast Blue

The most commonly used concentration of agarose for DNA separation

0.8%

A commonly used restriction endonuclease derived from Escherichia coli that produces a 5' overhang or sticky end:

Eco RI

The immobilized target for a Western Blot is

protein

A technique using a labeled probe to target a unique or specific DNA target often used in forensic testing

southern blot

The process of joining two complimentary strands of nucleic acid resulting in a hybrid double strand

hybridization

The disadvantage of using polyacrylamide gels over agarose is that polyacrylamide

Nerotoxic

The purpose of a buffer in an electrophoresis system is to

carry the electrical current
maintain the pH
protect the sample molecules during electrophoresis

Which of the following serves as a tracking dye for DNA electrophoresis

Bromphenol blue

The ability of a restriction endonuclease under nonstandard conditions bind and cut sequences other than there defined recognition sequence is known as

Star activity

In order to de-purinate DNA after electrophoresis, the gel should be soaked in which of the following?

Hydrochloric acid (HCL)

the absorbance reading of a DNA sample at 260 nm from a 1:100 dilution is 0.172. What is the DNA concentration in ug/mL?

860 ug/mL
(0.172 x 50 x 100) =

Primer dimers result from

Primer dimers occur when primers hybridize to each other at the 3' ends. (3' complementary in the primer sequences).

How many copies of target are made after 30 cycles of PCR?

2-30

Steps in PCR involving DNA

Denaturation
Annealing
Extension

This occurs when primers bind to sites other than the intended target

Misprimes

The type of PCR utilizing fluorescent detectors for measuring product

Real time

A PCR control containing Taq Polymerase, buffer, dNTPs, primers and no target DNA

contamination

A PCR control containing Taq polymerase, buffer, dNTPs, primers, and DNA of unrelated target sequence

amplification

In contrast to standard PCR real time PCR is

quantitative

A PCR product should NOT be expected in all of the following controls EXCEPT

amplification

PCR master mix

Taq polymerase
dNTPs
buffers
primers

Taq Polymerase is obtained from which of the following organisms?

Thermus aquaticus

Primer dimers result from:

3' complementarity in the primer sequences

Which of the following is used to aid in preventing misprimes before amplification begins?

Hot start

Which of the following is an appropriate way to avoid PCR contamination?

A separate room for PCR setups

A PCR control run to detect contamination

Reagent blank

All of the following nucleic acid amplification procedures are run at isothermal temperatures with the exception of

Real time PCR

A type of DNA amplification where a series of multiple labeled tags are attached to a target molecule

Branched DNA

A type of amplification where cDNA is made from mRNA

RT-PCR
(Reverse Transcriptase

All of the following are true of Transcription mediated Amplification with the exception of

Taq DNA polymerase is required

A final concentration of Taq polymerase required for a reaction is 0.01 units/uL in a 50 uL PCR. The enzyme is supplied in 5 units/uL. How many uL of enzyme would be need to add to the reaction?

1 uL of a 1:10 dilution of Taq

Which of the following best illustrates the flow of information in cells?

DNA>RNA>Protein
-central dogma

Organisms having two sets of chromosomes (one paternal the other maternal) are said to be:

diploid

If one strand of DNA has the sequence 5'-ATTGCA-3' the complementary strand would have the sequence:

3'-TAACGT-5'

The process whereby the information from the genetic code is converted into protein

translation

The process by which genetic information is transferred from DNA to RNA:

transcription

Different forms of a gene are known as:

alleles

DNA replication is said to be:

semiconservative

In the double helix structure of DNA, cytosine has hydrogen bonds to:

guanine

A gene that is always expressed is said to be:

dominant

Which of the following bases is unique to RNA?

uracil

A term applied to the visible expression of a trait or characteristic of an individual:

phenotype

Which of the following individuals is noted as the "father of genetics"?

mendel

Which of the following best fits the class of molecules called nucleotides?

Nitrogen base, phosphate group and a pentose sugar

The place on a chromosome where a given gene is located:

locus

All of the following enzymes are part of the DNA replisome with the exception of:

RNA polymerase

Which of the following nitrogen bases is NOT a pyrimidine?

adenine

The enzyme that unzips the DNA helix in preparation for replication is?

DNA helicase

The difference between the sugar in DNA and the sugar in RNA is that the sugar in DNA:

contains one less Oxygen atom

What feature allows DNA to replicate?

Complementary base pairing

The term used to describe an individual having different copies of a gene that govern the expression of a trait:

heterozygote

DNA is a polymer of ________

nucleotides, consisting of a nitrogenous base (1' C), a sugar, and a phosphate group

four common nitrogenous bases

adenine, guanine, thymine, cytosine

purine ring structure bases

adenine and guanine
-double ring structure

pyrimidine ring structure

thymine and cytosine
-single ring strutuctre

chargraff's rule

# of adenines = # thymines; # of guanines = # of cytosines

DNA exists as two polymers joined together by

hydrogen bonds
two H bonds form between A and T
three H bonds form between C and G

the two DNA polymers form the

double helix
-phosphates form backbone with deoxyribose sugars
-phosphates negatively charged so they repel each other
-DNA twists to repel like charges

DNA strands have polarity based on the __________ bond

phosphodiester

DNA strands have a 5' ________ end and a 3' _________ end

phosphate; hydroxyl

semiconservative DNA replication

one molecule will split in half; each half will act as a template strand to build its complimentary strand

a new DNA strand is polymerized from the _________ end to the _______ end, reading the parent strand from the ____ end to the ____ end

polymerized from the 5' to the 3'end
reading the parent strand from the 3' to the 5'

a group of proteins assembled for DNA replication

replisome

despite the antiparallel nature of the two strands, DNA synthesis proceeds along both strands in the ______ direction

same

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand. - discontinuous synthesis

DNA ligase

Joins Okazaki fragments of lagging strand; on leading strand,

the leading strand is copied __________, while the lagging strand is copied ______.

continuously, discontinuously

complimentary rule

single nucleic acid can bind to single strands that have complimentary bases
-each nucleotide added to new strand bonds with complementary nucleotide to parent strand
-allows for replication without loss of nucleotide order

medicine that disrupts DNA sequencing

anticancer, HIV, HSV, Varicella-Zoster

factors required for dna recombination

nucleases -cut dna into pieces
ligases- paste pieces together
plasmids - carry recombinant dna into cell

polymerases function

catalyze info of phosphodiester bond
adds bases and removes rna primers

helicase

unzips dna; creates replication fork

Primases

synthesizes short rna to prime dna synthesis

methylase

add methyl groups to nitrogen bases

deaminase

removes an amino group

exonuclease

removes bases from ends of dna strands

endonucleases

cut strand internally

recombinant dna technology

used in lab to modify dna in vitro

restriction endonucleases

cuts specific sequences in dna
serves as immune system for bacteria, degrading dna but not cutting their own
-Eco R I; E. coli strain R 1st enzyme G v A A T T C

Plasmids

responsible for horizontal gene transfers in bacteria
-circular extra-chromosomal DNA

DNA vs RNA

DNA double stranded, deoxyribose sugars, thymine
RNA single stranded, ribose sugars, uracil
-single strand allows rna to be small enough to leave nucleus and go to ribosomes
-rna is a nucleic acid without a complimentary partner

RNA replication

no priming
many more initiation sites
slower (50-100) bp per second
lower fidelity
more processive
copies segments rather than whole strands

amino acids

classified by chemical properties of side chains: polar vs non, pos or neg
-neutral at pH that is isoelectric point
-joined together by -C-C-N peptide bonds to make proteins

protein structure

primary amino acid sequence
secondary intrachain folding - beta sheets and alpha helix
tertiary interaction of peptides with one another to form multisubunit proteins
quaternary protein-protein interaction for function: monomers from multimers; dimers trimers tertramers

genetic code

translates nucleic acid sequence into amino acid sequence
3 nucleotides = one codon = 1 amino acid

gene

ordered sequence of nucleotides on a chromosome that encodes a specific functional product
-contain nucleotide sequences that will be transcribed or translated into protein

protein translation

takes place in ribosomes
-messenger mRNA - single stranded RNA molecule that carries instructions from DNA to ribosome in cytoplasm
-ribosomes - peptidyl transferase forms a peptide bond between growing peptide and incoming amino acids; makes proteins
-transfer tRNA carries amino acids from cytoplasm to ribosome during protein synthesis; charged tRNAs carry their amino acids and hybridize through their anticodon sequences to mRNA codons

charging tRNA

amino-acyl tRNA synthesis covalently attach amino acids to tRNAs, matching side chains and anticodons
1. amino acid + ATP --> aminoacyl-AMP + Ppi
2. aminoacyl-AMP + tRNA --> aminoacyl-tRNA + AMP

protein translation termination

termination signaled by stop codons UAA, UAG, UGA which are not charged with amino acid
stop codons trigger hydrolysis of the finished polypeptide from the final tRNA

DNA can be manipulated in vivo using ______

metabolizing enzymes
-restriction endonucleases, ligase, plasmids

RNA carries genetic information from ______ to the ______ for protein synthesis

DNA, ribosomes