2. Molecular and Cell Bio: Genomics

Question 1

Which statement is correct

a. Watson and Crick linked genes to proteins
b. Mendel identified that DNA in cells causes heredity
c. Beadle and Tatum discovered the molecular structure of DNA
d. Crick hypothesized that proteins cannot be transformed back into DNA

Answer 1

D.

Beadle and Tatum linked genes to proteins ​
Avery identified that DNA in cells causes heredity
Mendel: concept of heredity with recessive or dominant patterns​
Watson and Crick discovered the molecular structure of DNA

Question 2

How many autosomal chromosomes are present in the dog and in the cat, respectively.

a. 38; 19
b. 19; 38
c. 23; 54
d. 54; 23

Answer 2

a. 38; 19

c. 23; 54 ​(human; indian elephant)

Question 3

Which of the following is true?
a.Proteomics is the analysis of the total protein content of a cell, tissue, or organism
b.Bioinformatics is the study of the chemical fingerprints that specific cellular processes leave behind
c.Systems biology is a global term for the application of information to enable the capture, storage,
and interpretation of biologic data.
d.Metabolomics is the study of the complex interactions between molecules in biologic systems.

Answer 3

A is correct

(Metabolomics) is the study of the chemical fingerprints that specific cellular processes leave behind

c. (bioinformatics) is a global term for the application of information to enable the capture, storage, and interpretation of biologic data.
d. (systems biology) is the study of the complex interactions between molecules in biologic systems.

Question 4

Finish this sentence… For a biomarker to be appropriate for use as a measure of the joint’s response to the test treatment fo OA, it “must reliably _______”

Answer 4

i. predict the overall effect on the clinical outcome

ii. no OA biomarkers do this yet

Question 5

Which is false?
a.The glycosaminoglycan content of synovial fluid, serum, or tissue culture
medium increases as a result of inflammatory insult to the cartilage.
b.The major proteoglycan of articular cartilage is the large aggregating
proteoglycan, secrecan.
c.Proteoglycan biomarkers are non-specific for OA
d.The primary component of chondroitin sulfate is a repeating disaccharide
sequence

Answer 5

b.The major proteoglycan of articular cartilage is the large aggregating
proteoglycan, AGGREGAN

Question 6

Which is true concerning OA biomarkers?
a.7D4 and 3B3 are generally considered to be “catabolic” markers of
cartilage turnover in osteoarthritis.
b.3b3 recognizes an epitope that is expressed only weakly in normal adult
cartilage but is found in increased concentrations in the developmental
stages of cartilage growth, such as in the growth plates, in fetal cartilage,
and during attempted repair early in osteoarthritis.
c.The concentration of the 7D4 epitope, quantified by immunoassay of synovial fluid and stifle articular cartilage from sheep, dogs, and humans was significantly increased in animals with traumatic or
experimentally induced osteoarthritis compared with controls.
d.Synovial 3B3 levels are not elevated following meniscectomy.

Answer 6

C is correct

a. 7D4 and 3B3 =ANABOLIC
b. (7D4) recognizes an epitope etc

Question 7

What does the monoclonal antibody 5D4 recognize?

a. N-terminal sequence ARGSVIL (​OA-1​)
b. Oversulfated forms of keratan sulphate
c. Chondroitin sulfate
d. New N-terminus of aggrecan after aggrecanases (​BC-3 antibody​)

Answer 7

b.Oversulfated forms of keratan sulphate

Question 8

What is the correct sequence of steps for type II Collagen Synthesis?
a.Pre-propeptides are modified; tropocollagen is formed by removal of C- and N-terminal domains; formation of triple helix; products spontaneously aggregate
b.Tropocollagen is formed by removal of C- and N-terminal domains; Pre-propeptides are modified; formation of triple helix; products spontaneously aggregate
c.Pre-propeptides are modified;
formation of triple helix; tropocollagen is formed by removal of C- and N-terminal
domains​; products spontaneously aggregate
d.Pre-propeptides are modified; tropocollagen is formed by removal of C- and N-terminal domains; formation of triple helix; products spontaneously aggregate

Answer 8

C
Pre-propeptides are modified (​in the rough endoplasmic reticulum lumen​);
formation of triple helix;
tropocollagen is formed by removal of C- and N-terminal domains (​in the ECM)​;
products spontaneously aggregate
(​don’t want intracellular helix formation​)

Question 9

Which Matrix Metalloproteinases is NOT a known primary player in cartilage collagen 
destruction? 
a.MMP-8 
b.MMP-13 
c.MMP-7 
d.MMP-1

Answer 9

c.MMP-7 (​MMP-14​)

a. MMP-8
b. MMP-13 *​most important b/c preference for type II collagen
d. MMP-1

Question 10

Which collagen epitope is detectable in circulation?

a. ¼ length fragment
b. ⅓ length fragment
c. ½ length fragment
d. ¾ length fragment

Answer 10

d.¾ length fragment (​Col2-¾ epitope resulting from cleavage at Gly-Leu bond,
further degraded by MMP-9)

Question 11

Which adipokine decreases with increased body fat?

Answer 11

Adiponectin

Question 12

What are 2 biomarkers used for pyrexia, sepsis, and endotoxic shock?

​Which has the shorter half life?

Answer 12

TNF-a and IL-6

TNF-a

Question 13

Which is true?
A Codons are groups of three nucleotides that code for specific amino acids
B Introns contain genomic DNA
C Transcription of mRNA molecules to polypeptides occurs within ribosomes
D The term 5’ to 3’ indicates the directionality by naming the nitrogen atoms in the nucleotide ring

Answer 13

A is correct

(Exons) contain genomic DNA.
(Translation) of mRNA molecules to polypeptides occurs within ribosomes.
The term 5’ to 3’ indicates the directionality by naming the (Carbon atoms)

Question 14

2. What is reverse transcriptase?

Answer 14

Protein that generates DNA from RNA template

Question 15

What is telomerase?

What happens if you don’t have telomerase?

Answer 15

Retrotransposon
Adds specific DNA sequence repeat to 3’ end of DNA in the telomere region at the end of eukaryotic chromosomes

Cell is shortened quickly until it enters senescence

Question 16

What is the genome?

Answer 16

Genetic sequence on one set of chromosomes

Question 17

What is the term for a mutation that does not affect the fitness of the individual?

Answer 17

neutral mutation

Question 18

Which of the following is true?
A Minisatellites are ideal for use in linkage studies due to high herterogeneity
B Missense or nonsense mutations account for 59% of genetic mutations
C A missense mutation is a type of synonymous mutation
D Microsatelites are 10-60 bp in length

Answer 18

B is correct

MICROsatellites are ideal for use in linkage studies due to high herterogeneity
A missense mutation is a type of NONsynonymous mutation
MINIsatelites are 10-60 bp in length

Question 19

Which of the following is true?
A Linkage disequilibrium is the association of alleles at different loci that is higher than random chance
B Microsatellite marker sets do not yet exist for the canine genome
C Polygenic disorders are the best traits to elucidate using gene linkage approach
D Candidate gene association studies require pedigree information and screen larger numbers of polymophisms than linkage studies

Answer 19

A is correct

Microsatellite marker sets exist for the canine genome (using > 500 markers → resolution of rouhgly 5 centimorgans across the canine genome
MONOGENETIC disorders are the best traits to elucidate using gene linkage approach
Candidate gene association studies DO NOT require pedigree information and SCREEN SMALLER numbers of polymorphisms than linkage studies

Question 20

Which is true?
Genome-wide study of association does not require a prior hypothesis as to where a polymorphism is located
Including different breeds with the same trait in analysis takes advantage of low linkage disequilibrium between breeds
SINE insertions, duplication of FGF3, FGF- 4 and FGF - 19 with ORAOV1 have both been shown to be related from mapping canine traits
All of the above are true

Answer 20

All of the above

Question 21

True/False: Recombinant proteins are produced by molecular cloning?

Answer 21

TRUE
DNA Sequence is isolated by PCR, inserted into virus or plasmid, introduced into bacterial cells where large quantities of DNA, mRNA, protein are produced

Question 22

Which of the following is false regarding transcriptomics?
A The transcriptome is the set of mRNA molecules in a cell or population of cells which varies with the cell type and environment
B RNA is much less susceptible to degradation during PCR studies compared to DNA
C A single copy of the target sequence will produce 10^9 copies after 30 PCR cycles
D Deep sequencing involves the identification and quantification of the entire RNA content of a cell

Answer 22

RNA is MORE susceptible to degradation during PCR studies compared to DNA

Question 23

Can you name the steps of PCR?

Answer 23

Denatured: DNA is heated to separate into single strands (90-95 degrees C)
Annealing: sample is cooled to allow primers to bind target sequences (50-60 degrees C)
Extension or Elongation: DNA polymerase synthesizes a new DNA template (60-72 degrees C)

Question 24

True or false: Coombs test detects autoantibody binding on the surface of red blood cells through observation of cellular aggultination when incubated with anticanine immunoglobulin

Answer 24

TRUE

Question 25

Name 4 tests that are used to identify specific proteins in cells, tissue and fluid samples

Answer 25

Western blotting,
immunohistochemical staining,
enzyme-linked immunosorbent assay (ELISA),
mass spectrometry

Question 26

True or false: Western blot is used to detect specific proteins by taking the test sample separating it by gel electrophoresis before transfering onto the membrane that is incubated with an antibody to the target protein.

Answer 26

TRUE

Question 27

True or false: An ELISA detects antigens or antibodies by fixing them to the surface of a microtiter plate nonspecifically or specifically through their capture with the antibody or antigen

Answer 27

TRUE

Question 28

What type of mutation causes the MDR1 abnormality in dogs?
Missense mutation
Frameshift mutation
Nonsense mutation
Synonymous mutation

Answer 28

Frameshift mutation

It then results in the development of a stop codon that prematurely terminates MDR1 synthesis

Question 29

Which of the following is false in regards of Gene Therapy?
A The dog is seen as a good model for different phenotypes, for example cardiomyopathies, retinal disorders, and muscular dystrophies.
B Some of the challenges of gene therapy are problems with the physical aspects of delivery of nucleic acids, their specificity to target cells, maintenance of expression, and development of resistance.
C Genetic material may be transferred to cells using physical means, such as altering cell membrane permeability, by microinjecting into the cell nucleus, or by using liposomes, microencapsulation, or gold particle delivery systems.
D An advantage of retroviral vectors are that a target cell can be dividing before the retrovirus integrate, and that the site of integration is random.

Answer 29

D

An a disadvantages of retroviral vectors are that a target cell must be dividing before the retrovirus can integrate, and that the site of integration is random, which can result in deleterious effects such as activation of an oncogene or inactivation of a normal gene.

Question 30

What is molecular biology?

Answer 30

What is molecular biology?

Study of biological processes at a molecular level

Question 31

What is the central dogma of molecular biology?

Answer 31

What is the central dogma of molecular biology?

DNA can be copied to DNA and that can be copied to mRNA. Proteins can be synthesized using the information in mRNA as a template. Protein information cannot be reverted to nucleic acid or from RNA to DNA.

Question 32

When a client states his dog is part wolf and absolutely needs raw meat as a part of his diet, despite being a 14 pound obese chihuhua who would die in less than 24 hours if left in the wilderness, what smart answer could you retort that is related to genetics?

Answer 32

When a client states his dog is part wolf and absolutely needs raw meat as a part of his diet, despite being a 14 pound obese chihuhua who would die in less than 24 hours if left in the wilderness, what smart answer could you retort that is related to genetics?

Analysis of the canine genome, sequenced in full in 2005 from a boxer dog, has shown that modern dogs have developed adaptations in their genome around 10,000 years ago that may have allowed them to thrive on a diet rich in starch, rather than relying on meat-based diets.

Question 33

Name 2 diseases caused by insertion of sequences into functional DNA

Answer 33

Name 2 diseases caused by insertion of sequences into functional DNA

1. Lamellar icthyosis - Jack Russell terrier
2. Heredity Myopathy Labrador

Question 34

Interference of normal embryologic development by exogenous factors is called:

A. Epigenetics
B. Teratogenesis
C. Imprinting
D. Housekeeping

Answer 34

Interference of normal embryologic development by exogenous factors is called:

B. Teratogenesis

Question 35

Which of the following statements about genetic mutations is false:

A. They are changes to the nucleotide sequence of the genetic material of organisms
B. Develop only because of errors in copying genetic material during division
C. May be seen in the germ line, somatic cells, or both
D. Frequency of mutations can be reduced or increased by natural selection

Answer 35

Which of the following statements about genetic mutations is false:

B. Develop only because of errors in copying genetic material during division

True:
A. They are changes to the nucleotide sequence of the genetic material of organisms
C. May be seen in the germ line, somatic cells, or both
D. Frequency of mutations can be reduced or increased by natural selection

Question 36

A ______ mutation replaces the normal amino acid codon with a stop codon which leads to the termination of the protein sequence and the truncation of the protein sequence.

A. Nonsense mutation
B. Missense mutation
C. Point mutation
D. Frameshift mutation

Answer 36

A ______ mutation replaces the normal amino acid codon with a stop codon which leads to the termination of the protein sequence and the truncation of the protein sequence.

A. Nonsense mutation

Question 37

Linkage disequilibrium is defined as:

A. The inheritance of a trait controlled by a single genetic locus with two alleles
B. The non-random association of alleles at two or more loci in a general population
C. The physical distance between loci on a linkage map
D. Genetic distance between a marker allele and the mutation

Answer 37

Linkage disequilibrium is defined as:

B. The non-random association of alleles at two or more loci in a general population

Question 38

What is a transcriptome?

A. A technique whereby a specific segment of DNA or RNA can be amplified
B. A group of one or more housekeeping genes
C. The set of mRNA molecules present in a cell or population of cells which varies with the cellular environment and cell type
D. A DNA binding dye which fluoresces when it binds to double-stranded DNA

Answer 38

What is a transcriptome?

C. The set of mRNA molecules present in a cell or population of cells which varies with the cellular environment and cell type

Question 39

Proteomics is defined as …

A. The analysis of the total protein content of a cell, tissue, or organism.
B. The complete sequencing of proteins
C. The study of how proteins fold to create their function
D. This is a made up word with no definition

Answer 39

Proteomics is defined as …

A. The analysis of the total protein content of a cell, tissue, or organism.

Question 40

All of the following are examples of tests that using proteomics, EXCEPT:

A. Coombs test
B. Antibody clonality
C. Electrophoresis
D. Immunohistochemistry
E. ELISA
F. Western Blot
G. Mass spectrometry
H. None of the above, all are forms of proteomics

Answer 40

All of the following are examples of tests that using proteomics, EXCEPT:

H. None of the above, all are forms of proteomics

A. Coombs test
B. Antibody clonality
C. Electrophoresis
D. Immunohistochemistry
E. ELISA
F. Western Blot
G. Mass spectrometry

Question 41

Define each one:

A. The study of the chemical fingerprints that specific cellular processes leave behind, or, more specifically, their small-molecule metabolite profiles is ___________.
B. The application of information to enable the capture, storage, and interpretation of biologic data is __________.
C. The study of the interaction of genetic variation with response to a drug, be that efficacy or toxicity, is __________.
D. The treatment of disease through the transfer of genetic material (RNA or DNA) is __________.

Answer 41

Define each one:

A. The study of the chemical fingerprints that specific cellular processes leave behind, or, more specifically, their small-molecule metabolite profiles is METABOLOMICS.
B. The application of information to enable the capture, storage, and interpretation of biologic data is BIOINFORMATICS.
C. The study of the interaction of genetic variation with response to a drug, be that efficacy or toxicity, is PHARMACOGENOMICS.
D. The treatment of disease through the transfer of genetic material (RNA or DNA) is GENE THERAPY.

Question 42

A genome-wide study of association study of the genetic basis of cranial cruciate ligament rupture in a population of _____(what breed of dog)_____ has suggested that neurologic pathways may be involved in susceptibility to the disease.

Answer 42

A genome-wide study of association study of the genetic basis of cranial cruciate ligament rupture in a population of NEWFOUNDLAND DOGS has suggested that neurologic pathways may be involved in susceptibility to the disease.

Question 43

Which method is NOT a method of transferring genetic material?

A. Altering cell membrane permeability (by chemical or electrical means)
B. Microinjecting into the cell nucleus
C. Using liposomes, microencapsulation, or gold particle delivery systems
D. Viral vectors
E. Yeeting it into the cell

Answer 43

Which method is NOT a method of transferring genetic material?

E. Yeeting it into the cell

Real methods:
A. Altering cell membrane permeability (by chemical or electrical means)
B. Microinjecting into the cell nucleus
C. Using liposomes, microencapsulation, or gold particle delivery systems
D. Viral vectors