Genetics and Medicine Unit 2

What are some mechanisms that regulate gene expression?

-DNA packing -DNA or chromatin modifications - control sequences - transcription factors - circadian clock -alternative RNA splicing -non coding RNAs -CRISPR- Cas9

When and where was the first human case of the Zika virus?

1952 Brazil

E Coli

3 enzymes are synthesized in response to lactose

How long was the largest Ebola outbreak?

34.8 days

During DNA replication, one DNA strand is copied to make a new DNA molecule composed of two DNA strands. This new DNA molecules contains:

50% of the parent DNA.

What was significant about the 2018 Ebola outbreak in DRC?

60% reported in children, ring vaccination as strategy to control outbreaks

What early evidence prior to 1953 supported the hypothesis of Watson and Crick that DNA carried the information for genetic inheritance? a. Frederick Griffith's experiments when he was trying to develop a vaccine to pathogenic pneumonia. b. The Human Genome Project. c. The Vertebrate Genome Project. d. The Genome 10K Project. e. The Moonshot.

A

What is NOT a role of microRNAs in expression: a. encode proteins b. small, single stranded c. imperfect base pairing d. native to cell and normal regulatory processes e. block translation of mRNA or promotes degradation of mRNA

A.

The Hersey-Chase experiments in 1952 were important because they showed that: a. proteins were the hereditary molecules b. DNA was the hereditary material c. a nuclear extract was madeup of H,O,N and P with a unique ratio of N to P d. the X-ray diffraction data showed a double helix e. the concentrations of A=T and C=G

B. DNA was the hereditary material

defense system bacteria uses to protect against invading genetic elements

CRISPR-Cas9

What is transcription regulated by?

Circadian Clock

Which of the following is NOT true about the Dengue Virus? A. "backbone" fever B. 3-14 days for symptoms to develop C. fever, headache, joint pain, skin rash D. isn't life threatening E. caused by 1 of 4 different, but related viruses

D

DNA vs RNA

DNA: deoxyribose sugar, thymine, double strandRNA: ribose sugar, uracil, single strand

What is essential for generation miRNAs of mammals?

Dicer

What is the relationship between dominant and recessive traits?

Dominant traits mask recessive traits

infections that recently appeared or whose incidence or geographic range is rapidly increasing or threatens to increase in the future

EIDs

What is another word for the single stranded RNA hemorrhagic fever

Ebola

disease maintained in population, wide geographical distribution ex) common cold

Endemic

What did Francois Jacob and Jacques Monod model explain?

Enzyme Induction 1961

inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

Epigenetic Inheritance

modifications to DNA that DONT change DNA base sequence, but CAN affect gene expression

Epigenetic Regulation

When did Ebola begin?

February 2014 in Guinea

Who established the gene concept?

Gregor Mendel

Are epigenetic changes heritable or acquired traits?

Heritable traits

region on DNA near promoter, acts as switch for gene expression to be on and off, determines whether RNA polymerase can bind to promoter

Operator

protein binds operator and turns off gene expression

Repressor

disease occasionally in low numbers, Not geographically defined ex) Tegus, rabies, plague, measles

Sporadic

During which zoonotic stage is there no transmission to humans with the agent only in animals?

Stage 1

primary infection zoonotic stage with transmission from animals

Stage 2

What happens when lactose is NOT present in E coli?

The operon is off, repressor bound to operator, RNA polymerase cannot bind AND the repressor is constitutively expressed

What happens when lactose is present in E Coli?

The operon is on, lactose binds to the repressor(conformational change)

proteins that bind to specific DNA sequences and control transcription of DNA to mRNA

Transcription Factors

What were Watson and Crick known for?

Won nobel prize for DNA discoveries,

what is the infant brain disorder, microcephaly, Guillen barre syndrome?

Zika

A genome graph: a. is a network of DNA sequences typically from 1,000 or more individuals. b. relies on dideoxynucleoside triphosphates to lead to short fragments of DNA. c. is too confusing to be of use. d. is unethical because it shares the source of the DNA. e. is a reference genome based on a few individuals.

a

In many organisms including humans, chromosomes are found in homologous pairs. Homologous chromosomes a. are identical in the arrangement of their genes, but some versions of the genes (alleles) may differ between the chromosomes. b. are identical both in the arrangement of their genes and in every version of every gene. c. all of the choices stated. d. have roughly similar arrangements of their genes, but some versions of the genes may differ between the genes. e. are similar in size and shape, but this deceptive similarity has nothing to do with placement of gene arrangement or type.

a

Which of the following is true about double-stranded DNA? a. Its 3-D conformation is quite different from RNA's 3D conformation. b. The two strands are identical. c. It is shaped like a triple helix. d. Adenine and uracil are present in equal amounts. e. Adenine and cytosine are present in equal amounts.

a

gene

a heritable factor that controls a specific characteristic (i.e. flower color)

We have learned the following from Cancer Genomics Projects except for the following one statement that is incorrect. a. All breast cancer patients have the same oncogenic signature. b. Most cancers are caused by 2-8 sequential alterations over 20-30 years. c. Mary Claire King was the first to show that breast cancer can be inherited. d. A large percentage of epithelial cancers can result from whole chromosome shattering or chromothripsis. e. All cancer patients do not respond to the same chemotherapy or treatment plan.

a. All breast cancer patients have the same oncogenic signature.

Autism is a complicated genetic disorder. Identify the one false statement. b. There are somatic mutations that only appear in a small fraction of the cells of the body. c. Autism is typically not recognized until kids are 2-3 years old. d. The genetic profile was identified through deep sequencing techniques. a. Autism is a disease similar to cancer where mutations accumulate as a function of age. e. New predictive approaches have resulted through using systems biology to identify an increase in common metabolites in autism not seen in normal children.

a. Autism is a disease similar to cancer where mutations accumulate as a function of age

Scientists commonly choose white blood cells that are going through mitosis to prepare karyotypes. Why? a. During mitosis, chromosomes are more condensed than during interphase. b. Cells in mitosis contain the greatest number of chromosomes, thus providing more material for study. c. Karyotypes are based on chromatin and not chromosomes. d. Cells in mitosis have the fewest chromosomes, thus simplifying karyotype analysis. e. More cells are in mitosis than any other stage of the cell cycle, making it easier to obtain mitotic cells for study.

a. During mitosis, chromosomes are more condensed than during interphase.

A researcher treats cells with an inhibitor that prevents DNA synthesis from starting. This treatment would trap the cells in which stage of the cell cycle? a. G1 b. G2 c. mitosis d. G0 e. cytokinesis

a. G1

The ENCODE Project revealed new insights about the human genome. Identify the one correct answer. a. Recognition that evolutionary change occurs through sequences that alter gene regulation. b. ~80% of the genome encodes proteins. c. >80% of the human genome could not be explained; it had no biochemical function. d. The organization of the human genome is similar to the bacterial genome. e. The results do not require validation.

a. Recognition that evolutionary change occurs through sequences that alter gene regulation.

The latest update from the Human Genome Project in 2018 reports all of the following except one below. Identify the incorrect statement. a. There is one gene product for each gene. b. The definition of a gene now includes any interval along chromosomal DNA that is transcribed into functional RNA as well as RNA translated into protein. c. The number of genes identified keeps increasing. d. We actually do not know the total number of genes. e. There continues to be faster, more accurate, DNA sequencing and at lower costs.

a. There is one gene product for each gene.

The 3-D structure of RNA is very different from DNA because of the following EXCEPT: a. a series of deoxynucleotides connected by covalent bonds b. the nitrogenous base uracil c. the 2'-hydroxyl (-OH) makes RNA more chemically reactive d. the base pairing prevents formation of an anti-parallel double helix e. RNA molecules vary in length from 10s-10002 nucleotides yet DNA can be billions of base pairs

a. a series of deoxynucleotides connected by covalent bonds

Which of the following allows for a single gene to encode for more than one polypeptide? a. alternative mRNA splicing. b. mRNA degradation. c. CRISPR. d. DNA packing. e. Circadian clock regulation.

a. alternative mRNA splicing.

What does DNA packing prevent?

access to genes for transcription

small changes in viral genetic makeup

antigenic drift

large changes in genetic makeup

antigenic shift

What have been the successes from the Human Genome Project? Identify the one incorrect a. Launch of the 10K Genome Project. b. The shotgun approach was fast but not reliable. c. Development of new technologies for DNA sequencing and analysis that have enhanced the speed and decreased the cost. d. Development of new protocols based on DNA analysis such as testing for genetic diseases using blood from the pregnant woman rather than amniocentesis. e. Understanding cancer and rare genetic diseases.

b

The results of the Human Genome Project have changed how we view our DNA/genome. What were the major surprises? Identify the incorrect answer a. Gene control sequences (promoters, enhancers, microRNA) make up 24% of the human genome. b. A single individual's DNA was sequenced; therefore little was initially learned from it. c. Protein-encoding genes make up ~1.5% of our genome. 98.5% is noncoding DNA. d. There are millions of transposable elements that are repeated throughout the genome. e. There is repetitive DNA sequence between the genes.

b. A single individual's DNA was sequenced; therefore little was initially learned from it.

Over the past 10 years we have learned a great deal about cancer through genomics projects such as The Cancer Genome Atlas (TCGA) Project. Which one of the following is incorrect? a. Every individual tumor is distinct with regard to genetic alterations, but pathways affected in different tumors may be similar. b. All breast cancers show the same oncogenic signature. c. Chromothripsis can occur in >50% of soft-tissue cancer types. d. Most cancers are caused by 2-8 sequential alternations over 20-30 years. e. ~140 genes are known whose mutations drive cancer.

b. All breast cancers show the same oncogenic signature.

What was one major surprise from the Human Genome Project published in 2003? a. Protein-encoding genes make up ~98.5% of our genome. b. Protein-encoding genes make up ~1.5% of our genome. c. A single individual's DNA was sequenced so we did not learn much. d. The shotgun approach of sequencing was fast but not reliable. e. The Human Genome Project was expensive and mostly hype based on what resulted from the project.

b. Protein-encoding genes make up ~1.5% of our genome.

X-linked conditions are more common in men than in women because a. men acquire two copies of the defective gene during fertilization. b. men need to inherit only one copy of the recessive allele for the condition to be fully expressed. c. women simply do not develop the disease regardless of their genetic composition. d. the sex chromosomes are more active in men than women. e. the genes associated with the sex-linked conditions are linked to the Y-chromosome, which determines maleness.

b. men need to inherit only one copy of the recessive allele for the condition to be fully expressed.

When is RNA processed?

before leaving the nucleus

hemaglutinin (HA) H1-H16

binds cells receptors and critical fusion of viral and endosomal membranes

Amino Acids

building blocks of proteins (about 20 kinds)

Which of the following is NOT a factor that drives EID emergence? a. socio economic b. environmental c. cultural d. climate change e. ecological

c

What is CRISPR/Cas9? Identify the one incorrect answer. a. a defense system that bacteria use to protect against invading genetic elements. b. Clustered Regularly Interspaced Short Palindromic Repeats. c. A method of protein sequencing. d. A gene-editing tool. e. Offers exciting promise for curing human diseases, advancing agriculture, altering pests that carry disease.

c. A method of protein sequencing

There is the need for differential gene expression for the humans because of one of the following. Identify the one correct answer. a. Gene expression is very straight forward because the genes lie in tandem, and all are turned on at the same time. b. Cells differentiate by the action of enzymes. c. All cells contain the same genotype. d. There is one master homeotic gene that turns on all genes at one time in all cells. e. There is no need for differential gene expression.

c. All cells contain the same genotype.

Why is the inheritance of so many traits difficult to explain using only Mendel's view of genetics? a. Failures in the predictive power of Mendel's ideas about inheritance are artifacts that reflect our incomplete understanding of the organisms under study b. Mendel worked with peas, not humans, and the genetic principles that operate in a simple organism like a pea plant cannot be applied to an organism as complex as a human c. Mendel was correct for the traits he investigated, but his principles must be extended to explain more complex patterns of inheritance d. Mendel's laws of segregation and independent assortment apply only in a limited set of cases in sexually reproducing organisms. e. Because Mendel did not know about chromosomes, he could not have been expected to describe the laws of inheritance.

c. Mendel was correct for the traits he investigated, but his principles must be extended (not discarded) to explain more complex patterns of inheritance

Count Me In was established in 2018 as a nonprofit organization committed to advancing patient- partnered research with support from the Broad Institute, Emerson Collective, Dana-Farber Cancer Institute, and the Biden Cancer Initiative. The approach is based on the following statements except one. Choose the one incorrect answer. a. Each cancer has a specific oncogenic signature. b. Only through very large data sets can identification of mutations common to a particular cancer group be correlated with a specific treatment approach. c. There is not a need for this approach because our physicians have access to all of our medical results. d. The goal is not just to have a genome data base but to include saliva, blood, and stored tumor samples, clinical information to discover new and important patterns in cancer progression and response to treatment. e. The goal is that this become a freely accessible data base much like that of the Human Genome Project and the Cancer Atlas.

c. There is not a need for this approach because our physicians have access to all of our medical results.

We have learned a great deal about COVID-19 except one incorrect response below. Identify it. a. The COVID-19 virus is a single-stranded virus. b. Of the 7 known coronaviruses, COVID-19, SARS, and MERS are considered zoonotic. c. We now know that COVID-19 was engineered for biological warfare and escaped from a military laboratory. d. COVID-19 is presently considered a pandemic by the World Health Organization. e. Sheltering in place and social distancing do flatten the curve.

c. We now know that COVID-19 was engineered for biological warfare and escaped from a military laboratory.

The 3-D structure of RNA is very different from DNA because of the following: a. the 2'-hydroxyl (OH) makes RNA more chemically reactive b. the nitrogenous base uracil c. all of the choices d. the base pairing prevents formation of an antiparallel double helix e. a series of ribonucleotides connected by covalent bonds

c. all of the choices

James Allison and Tasuku Honjo were awarded the 2018 Nobel Prize in Physiology or Medicine because of which one of the following? A. They were responsible for the shotgun method of sequencing. b. They developed a new CRISPR strategy to fight cancer. c. They patented the BRCA1 and BRCA2 genes and developed a diagnostic test for breast cancer. d. They identified key proteins on T cells, called immune checkpoint proteins, that were normally responsible for turning off activated T cells. e. They identified key proteins on hemoglobin that are normally responsible for turning off sickle cell anemia.

d

Mary Claire King in 1990 identified the gene associated with increased risk of breast cancer. Based on her initial work, we now know the following except one incorrect statement. a. BRCA1 and/or BRCA2 mutations increase the risk for breast cancer. b. BRCA1 and BRCA2 encode for proteins involved in DNA repair. c. Dr. King developed the BROCA diagnostic test in 2015, which can screen for 50-60 genes in patients suspected of a predisposition to hereditary cancers. d. In 2015, Myriad Genetics argued before the Supreme Court that naturally occurring DNA should not be patent eligible. e. BRCA1 is localized to chromosome 17.

d

Which of the following is not true in regards to the encode project today? A. are long range signals for regulation b. evolutionary changes alter regulation c. noncoding regions harbor rich array of elements with diverse gene regulatory d. all the above are true e. evolutionary changes through protein coding sequences

d

Which of the following was a novel deduction that Watson and Crick were able to make about DNA based on Rosalind Franklin's X-ray diffraction data, i.e., Photo 51? a. They concluded that DNA was composed of nucleotides. b. The amounts of A = T and the amounts of C = G in all DNA molecules. c. None of the choices stated. d. The consistent width of DNA led them to conclude that purines must base-pair with pyrimidines. e. Chromosomes are the locations of our genes encoded by sequences of nucleotides.

d

During mitosis, the chromosomes move because _______________________________. a. they diffuse within the nucleus to areas where they are less concentrated. b. other chromosomes push them along. c. of the increased concentration of proteins and membrane vesicles in the cells. d. they attach to a dynamic, precisely regulated mitotic spindle. e. because of the electrostatic interactions with the cytoplasm

d. they attach to a dynamic, precisely regulated mitotic spindle.

Cells with two of each kind of chromosome are described by the term

diploid

the gene that can generate 17,500 proteins found in different nerve cells

drosophilia

A carrier of a genetic disorder who does not show symptoms is most likely to be____________ to transmit it to offspring. a. heterozygous for the trait and unlikely b. homozygous for the trait and able c. heterozygous for the trait and unable d. homozygous for the trait and unable e. heterozygous for the trait and able

e

A mouse that has the genotype AANnPpzz will have the same phenotype as a mouse with the genotype: (Note that the uppercase alleles A, N, P, and Z are dominant). a. AAnnPPZz b. AANnppZz c. AANNPPZZ d. AaNNPpZz e. AaNNPPzz

e

What is NOT a role of siRNA? (Small Interfering RNA) a. double stranded b. hybridizes with target c. silence gene expression d. defense mechanism e. does not cleave

e

Which of the following statements about genetic diversity over a few generations is false? a. Genetic diversity is enhanced by independent orientation of chromosomes at metaphase I during meiosis. b. Genetic diversity is enhanced by homologous chromosomes in meiosis that carry different versions of genes. c. Genetic diversity is enhanced by random fertilization. d. Genetic diversity is enhanced by crossing over during prophase I of meiosis. e. Genetic diversity is enhanced by mutations.

e

Vitamin D-resistant rickets is an X-linked dominant bone disorder. A man with this form of rickets marries a normal woman. What proportion of the couple's sons is expected to have vitamin D-resistant rickets? a. 100% b. 25% c. 50% d. 75% e. 0%

e. 0%

All are true of a genome graph except which one of the following. a. A network of DNA sequences typically from 1,000 or more individuals. b. More accurate because captures regions that were not identified previously because of insertions, duplications, and or deletions. c. May identify mutations missed by sequence comparison to a single genome. d. This universal genome approach could store information about from whom the genome(s) came. e. A reference genome based on a few individuals.

e. A reference genome based on a few individuals.

The structure of DNA is very stable because of the following. Choose the one statement that is true. a. Orientation of the strands is antiparallel. b. The two strands are held in register through precise hydrogen bonding between adenine & thymine and guanine & cytosine. c. Stability results because of a large number of noncovalent interactions including hydrogen bonds, hydrophobic interactions and van der Waals interactions. d. The absence of uracil. e. All of the above.

e. All of the above

James Allison was awarded the 2018 Nobel Prize in Physiology or Medicine for the following medical breakthroughs. Which statement below is false. a. He identified a key protein receptor that allows the immune system's T cells to recognize the antigens of infected or abnormal cells including cancer cells. b. He showed that the activated T-cells multiply, but turn off rather than continue to attack cancerous cells. c. He proposed that activated T-cells also had a second receptor that was a control switch or immune checkpoint that turned off activated T-cells. d. He developed antibodies to the checkpoint receptor that bound and inactivated the switch so that the T cells would continue to attack the cancer cells. e. He pioneered the use of immune checkpoint inhibitors to treat COVID-19.

e. He pioneered the use of immune checkpoint inhibitors to treat COVID-19.

new case of disease increasing rapidly and geographically confined ex) SARS

epidemic

What explains the differences in identical twins?

epigenetic variations

Most deadly pandemics have been caused by

influenza viral strains

X-linked conditions are more common in men than in women because

men need to inherit only one copy of the recessive allele for the condition to be fully expressed

functioning unit of DNA containing a cluster of genes under the control of a single regulatory promoter

operon

new case of disease increasing and spreading rapidly with wide global distribution ex) HIV/AIDS

pandemic

region of DNA that facilitates transcription of genes site for RNA polymerase to bind DNA

promoter

During which stage of meiosis does crossing over and formation of tetrads occur?

prophase 1

What was significant about the 2014 Ebola outbreak in Sierra Leone?

rapid accumulation of interhost and intrahost genetic variation with no evidence of additional zoonotic sources, sustained human-human transmission by contact bodily fluids

Most genetic disorders of humans are caused by

recessive alleles

Circadian clock regulates:

sleep, hormone release, rise and fall of blood pressure

the large RNA-protein complex that processes introns and exons is called

spliceosome

limited outbreak with transmission from animals or humans

stage 3

long outbreak with transmission from animals or humans

stage 4

exclusive human agent with transmission only from humans

stage 5

allele

variation of a gene

neuramidinase (NA) NA1-9

viral enzyme that facilitates virus release from infected cell

Why are so many EIDs linked to Viruses?

viruses have high rate of mutation

Is coordinated gene expression of genes not in tandem common?

yes