Genetics CRISPER and EPIGENETICS

c. non-homologous end joining

Cas nuclease makes a double-strand break. Which repair mechanism is the cell most likely to use? A. Homologous repair B. Direct repair C. Non-homologous end-joining D. Base-excision repair

CTCF

Cohesin control the size and location of chromatin loops in the nucleus, thus controlling which enhancers can affect which genes

chemical, do not alter

Epigenetic changes are ____ modifications to chromatin structure that ______ the DNA sequence.

differentiation

Epigenetic marks in cells play a role in ________, the process by which a cell becomes specialized in form and function. Even sperm and egg cells in the adult have epigenetic tags and are specialized.

chromatin

Epigentic changes are changes in ____ structure, which alters geen expression

methylation; each

Expression of an imprinting allele in the offspring depends on whether the allele came from the female or male parent. Imprinted _____ patterns are erased and re-written in the germ cells of ____ generation, regardless of which parent they originate from.

complementary, both

For homologous repair, you put a DNA into the cell along with the CRISPR/Cas. The DNA has to be ___________ to ________ sides of the site recognized by CRISPR plus, in the middle, include what you want to insert into the allele

d. decrease transcription.

High levels of methylation of DNA near a gene will a. decrease translation. b. decrease transcription. c. either increase or decrease transcription, depending on which base is methylated. d. increase transcription.

Two

How many RNAs is required to pair with the Cas protein in natural bacterial system?

b. late S phase.

If the only thing introduced into a cell is the CRISPR/Cas combination, when can the cell use homologous recombination to repair the damage? a. it depends on the target locus. b. late S phase. c. G1. d. only in meiosis.

A True

If your grandmother was exposed to a toxin when she was pregnant with your mother, you could be directly affected by the exposure, even if you are never directly exposed to that toxin. A) true B) false

anneal to the complementary target DNA.

In CRISPR/Cas gene editing, one function of the guide RNA is to

One (the two RNA needed in the bacterial system is combined and engineered into one RNA strand)

In biotech designed CRSPR/Cas systems that are created for gene editing, how many RNAs bind with the Cas protein

c. the sequence of the guide RNA.

In gene editing by CRISPR/Cas, the specific locus that will be targeted for editing is determined by a. the virus that was the original source of the CRISPR RNA. b. the DNA-binding domain of Cas. c. the sequence of the guide RNA. d. the homologous DNA introduced into the cell.

D. DNA taken from a virus.

In the CRISPR/Cas system in bacteria, the 'spacer' is A. non-functional DNA that allows the repeats to form a stem secondary structure. B. the region between the CRISPR locus and the Cas locus. C. the part of the CRISPR RNA that interacts with the Cas protein. D. DNA taken from a virus.

A. a nuclease that creates double-strand breaks.

In the CRISPR/Cas system, Cas is A. a nuclease that creates double-strand breaks. B. a nuclease that creates single-strand nicks. C. an RNA that matches a previously encountered viral DNA. D. an RNA that interacts with a nuclease protein.

e. pair with the target sequence.

In the CRISPR/Cas system, the role of the "seed sequence" is to a. direct homologous recombination. b. act as a primer for RNA synthesis. c. act as a primer for DNA synthesis. d. pair with the target sequence. e. pair with the target sequence.

a. DNA sequence in the target.

In the Crispr/Cas system, the PAM is a(n) a. DNA sequence in the target. b. RNA sequence in the guide RNA. c. separate RNA molecule required for d. correct positioning of CRISPR. e. DNA sequence in the CRISPR locus.

DNA methylation; histone proteins; RNA

Molecular mechanisms that alter chromatin structure 1) change patterns in ______ 2) chemical modification of _____ 3) ____ molecules that affect chromatin structure and gene expression

recessive; heterozygous

Overall, imprinting results in ______ alleles that may be expressed in a ____ individual.

FALSE (it is the sequence naturally found on the DNA of the virus or of your target)

PAM sequence is determined by the CRISPR RNA. True or false

b. false CRISPER originated from a mechanism that bacteria cells have to fight off virus by destroying viral DNA (location is the DNA itself before it even gets to gets to be used for transcription) miRNA are interference/destruction of mRNA that gets destroyed as soon as it goes into the cytoplasm AFTER being transcribed from DNA template in the nucleus

The CRISPR system shares an evolutionary history with miRNA / siRNA systems A. True B. False

a. given a mutation that inactivates its product.

The CRISPR/Cas system can be used to generate "gene knockouts". This means that the target gene is a. given a mutation that inactivates its product. b. replaced by a new gene. c. moved to a new location on the chromosome. d. completely removed from the genome.

True but they have totally different functions

The CRISPR/Cas system is a complex of a nuclease protein (Cas9) and a short targeting RNA (guide RNA) that are superficially similar to the siRNA+Argonaute RISC complex T/F

B. Target DNA only

The PAM sequence is located on the A. Guide RNA only B. Target DNA only C. Both the guide RNA and target DNA

D. The Cas9 protein

The PAM sequence is recognized by A. The guide RNA B. The RISC C. Argonaute D. The Cas9 protein

nucleosomes; accessed

The cell protects the DNA by wrapping it around histone proteins into packages called _____. The level of packing controls whether the DNA can be ______ by by replication, transcription, or repair proteins

Homologous repair & Non-homologous end-joining.

The two types of DNA repair that can be used on double-strand breaks are (choose both correct answers)

E

We can positively influence our epigenome by A) eating healthier B) refraining from smoking C) abstaining from drug use D) being more active E) all of the above

PAM

What guides the bacteria nuclease (Cas) to chop up the viral DNA and not to chop up the bacteria's own DNA?

Cas 9 protein starts to unwind the DNA

What happens when PAM sequence on the target DNA is recognized by Cas protein?

It gets transcribed into part of the guide RNA that binds to the bacteria CAS protein and serves as a RNA guided targeting of viral element/DNA that might infect the bacteria again

What is the 1 repeat + spacer DNA used for in bacteria?

a. target DNA

What is the DNA sequence that is destroyed by Cas 9 protein called? a. target DNA b. template DNA

PAM (eg. viral DNA has to have it to be recognized for bacteria Cas 9 to know it is the target to be destroyed)

What is the very short sequence that the target DNA must have?

PAM

What limits the available CRISPR targets?

CpG

What methylation pattern provides a mechanism for preserving the pattern through mitosis

seed

When used for gene editing, the spacer DNA is the equivalent of the _______ sequence.

B. replaced by RNA that is the reverse-complement to our intended target.

When we use the CRISPR/Cas system as a tool, the 'spacer' is A. eliminated. B. replaced by RNA that is the reverse-complement to our intended target. C. kept, and additional targeting RNA is added. D. RNA taken from a virus.

transcription

Where does epigenetics occur?

B

Which of the following accurately describes histone acetylation? A) only found in histone H1 B) loosens histones and allows access by other enzymes C) found only on proline residues D) caused by methyltransferases

a. cas d. guide RNA f. PAM g. seed sequence

Which of the following are components of the CRISPR/Cas system? A. Cas B. Pri-miRNA C. Dicer D. guide RNA E. Argonaute F. PAM G. Seed sequence

b. pri-miRNA c. dicer e. argaunaute g. seed sequence

Which of the following are components of the micro-RNA system? A. Cas B. Pri-miRNA C. Dicer D. guide RNA E. Argonaute F. PAM G. Seed sequence

B

Which of the following is NOT a chemical modification commonly found on core histone N-terminal tails? A) methylation B0 hydroxylation C) phosphoryaltion D) acetylation

guide RNA

includes the transcript from 1 repeat + spacer unit + a separate RNA that interacts with Cas9 (combined in biotech CRISPR systems)

imprinting

occurs when some cells escape reprogramming prior to fertilization

CTCF

one of the most important proteins in terms of controlling patterns of gene expression

reprogrammed; reprogramming; imprinting

A fertilized egg needs to have special epigenetic marks removed so that all cell types can develop in the next generation. Each generation is ______ during early development. A small portion of the cells escape this ______, and this escape is called. _____.

activated; inactivated; gene expression

Acetylated chromatin is ______, while methylated chromatin is _______. _______ is high in acetylated chromatin, but low in methylated chromatin.

C

An allele that is highly methylated cannot be accessed by transcription machinery. This allele is... A) expressed B) transcribed C) silenced D) active

Yes, even though they don't alter the DNA sequence, they can be passed down to generations

Are epigenetic changes inheritable?

transcription; transcription; transcription; transcribed; silenced

Before _____ can begin, the _____ enzymes and protein must physically access the DNA; if the ____-initiating proteins can't bind to the regulatory DNA, genes cannot be _____ and they are considered to be _____

immune

CRISPR/Cas in nature originated as a bacterial _______ system

repeats and spacer sequence

CRISPR/Cas starts with virus attacking and injecting its DNA into the bacteria. The bacteria chops up the virus DNA and incorporates it into the bacteria's own chromosome as a string of ______ and _____

d. Cas 9 is a nuclease (degrades DNA)

Cas (sometimes written as Cas9) is a(n) a. DNA sequence. b. nuclease. c. RNA. d. protease.

B. A random insertion or deletion is created

Cas nuclease makes a double-strand break. If CRISPR/Cas is targeted to a protein-coding region, what is the most likely outcomterm-21e? A. The cut ends are simply ligated back together B. A random insertion or deletion is created C. The end of the chromosome without a centromere will be lost D. A randomly chosen gene from a non-homologous chromosome will be used as a template

A. Homologous repair

Cas nuclease makes a double-strand break. If a piece of DNA that includes bits identical to the sequences flanking the break site are also introduced into the cell at the same time, what repair pathway could be used? A. Homologous repair B. Direct repair C. Non-homologous end-joining D. Base-excision repair

homologous repair

Cas nuclease makes a double-strand break. If a piece of DNA that includes bits identical to the sequences flanking the break site are also introduced into the cell at the same time, what repair pathway could be used?

E

Which of the following statements about histones and gene expression is CORRECT? A) acetylation involves the addition of acetyl groups to histone proteins, and it usually results in repression of transcription B) addition of methyl groups to the tails of histone proteins always results in activation of transcription C) histone code refers to the modification that takes place on the globular domain of the octamer histone core D) phosphorylation of cytosines generally leads to increase in transcription E) in a general sense, highly condensed DNA bound with histone proteins represses gene expression

B

Which of the following types of eukaryotic gene regulation takes place at the level of DNA? A) posttranslational modification B) alternation of chromatin structure C) mRNA processing D) RNA interference E) mRNA stability

epigenetic marks

_____ in cells play a role in differentiation, the process by which a cell becomes specialized in form and function. Even sperm and egg cells in the adult have epigenetic tags and are specialized.

histone (change to a protein, but gets copied when DNA replicates into another DNA)

_______ modifications are maintained during replication

Enhancer-Promoter interactions

control eukaryotic transcription; involve DNA looping; linked by a complex termed mediator

reprogramming

erases most epigenetic tags so that the fertilized egg can develop into any type of cell