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Innate Immunity

Response time: Immediate

Specificity: Non-specific

Memory: No memory

Cell involved: Phagocytes (neutrophils, macrophages), NK cells, dendritic cells

Evolutionary age: Ancient, in all organisms

Adaptive immunity

Response time: Delayed

Specificity: Highly specific to particular antigens

Memory: Forms memory; stronger & faster on re-exposure

Cells involved: T cells, B cells

Evolutionary age: More recent; found only in vertebrates

What are endonucleases (restriction enzymes)?

Endonucleases that cut DNA at specific recognition sequence and destroy foreign phage DNA

How do bacteria protect their own DNA from being cleaved by their endogenous restriction enzymes?

Methylation of the host DNA.

In the context of bacterial defense, what does CRISPR-Cas represent?

An adaptive immune system in bacteria that targets and destroys viral DNA

How do bacteria block phage absorption?

By preventing phages from attaching to the bacterial cell surface

How do bacteria block phage DNA insertion?

By preventing phage DNA from entering the bacterial cell after attachment

What is absorptive infection (cell suicide) in bacteria?

When an infected bacterial cell destroys itself to stop phage replication

How does CRSPR-Cas provide immunity?

It stores viral DNA sequences and uses them to recognize and cut future infections

What do the "spacer" sequences within a bacterial CRISPR locus do?

Allow bacteria and archaea to “remember” and defend against specific viruses or plasmids

What occurs during spacer acquisition? When new spacers are added to the CRISPR locus, what happens to the repeat sequences?

Invading phage DNA is cleaved into smaller fragments known as protospacers, which are then inserted into CRISPR loci to become new spacers

Repeat sequences are duplicated such that each spacer is flanked by repeats on each side

What is cRNA biogenesis?

The process of transcribing CRISPR loci into long RNA transcripts that are then processed into shorter unit

What are the three main stages of the CRISPR-Cas mechanism for destroying invading DNA?

Spacer acquisition, crRNA biogenesis, and target interference.

In the interference stage, what role do Cas nucleases play?

They cleave the viral DNA complementary to the crRNA and neutralize the infection

What do mature crRNAs do?

They associate with Case nucleases and guide them to matching viral DNA

What is the target interference in CRSPR-Case?

The process where CRISPR RNA guides Cas proteins to destroy invading viral DNA

What sequence must be adjacent to the target DNA for Cas9 to recognize and cleave it?

The PAM (protospacer adjacent motif).

What is a PAM sequence?

A protospacer adjacent motif found in invading viral or plasmid DNA that is required for Cas9 cutting

Why is the PAM important in CRISPR-Cas9 targeting?

It ensures Cas9 only targets foreign DNA and not the bacterial CRISPR array.

How does Cas9 distinguish foreign DNA from the bacterial CRISPR locus?

It only cuts DNA that is adjacent to a PAM sequence, which is found in foreign DNA but not in the bacterial genome

How does CRISPR avoid destroying its own spacer DNA?

Its own CRISPR sequences lack PAM sites, preventing Cas9 from cutting them.

In an engineered CRISPR-Cas9 system for genome editing, what two components are required for cleavage in vitro?

Cas9 and a Guide RNA (sgRNA).

The sgRNA (single guide RNA) is a combination of?

Customized crRNA and tracr RNA-derived sequences

What is nonhomologous end-joining (NHEJ)?

An error-prone eukaryotic DNA repair pathway that often results in small insertions or deletions to directly ligate broken DNA ends without using a template

What is homology-directed repair (HDR)?

A DNA repair pathway that uses an undamaged homologous chromosome or sister chromatid as a template

How can HDR be used in genetic engineering?

It can use an artificial donor DNA template to introduce specific changes

What is the main difference between NHEJ and HDR?

NHEJ is error-prone and template-free, while HDR is accurate and uses a DNA template.

What is chromosome rearrangements?

Mutations that alter the structure of chromosomes

How does aneuploidy differ from polyploidy?

Aneuploidy alters the number of individual chromosomes, while polyploidy adds complete sets of chromosomes.

What are the four basic types of chromosome rearrangements?

Duplications, deletions, inversions, and translocations.

What is this type of chromosome rearrangement: deletion?

A portion of the chromosome is missing or deleted

What is this type of chromosome rearrangement: duplications?

A portion of the chromosome is duplicated, resulting in extra genetic material

What is this type of chromosome rearrangement: inversions?

A portion of the chromosome has broken off, turned upside down, and reattached. As a result, the genetic material is inverted

What is this type of chromosome rearrangement: translocations?

Movement of chromosome segment to a nonhomologous chromosome or to another region of the same chromosome

What is pseudodominance?

When a recessive mutation appears to be dominant due to loss or inactivation of the normal (wild-type) allele

What is haploinsufficieny?

A condition where one functional copy of a gene is not enough to produce a normal (wild-type) phenotype.

What happens in haploinsufficiency?

A heterozygous individual shows a mutant phenotype even though one normal allele is present

What is the primary consequence of chromosome duplications and deletions regarding gene expression?

Abnormal gene dosage (imbalances in gene products).

What is an inversion?

A chromosomal rearrangement where a segment of DNA is reversed in orientation

What is a paracentric inversion?

An inversion that DOES NOT include the centromere

What is pericentric?

An inversion that includes the centromere within the inverted region

When can inversions affect phenotype?

If breakpoints disrupt a gene or its regulatory regions

How can inversions affect meiosis? What can result from this?

They can cause improper crossing over which causes deletions or duplications of genetic material and produces abnormal chromosomes

What is the "position effect" in chromosome translocations?

Genes translocated to new locations may come under the control of different regulatory sequences or other genes that affect their expression

What is reciprocal translocation?

Segments from two different chromosomes have been exchanged

What is nonreciprocal translocation?

A segment of one chromosome is transferred to a different, nonhomologous chromosome without any segment being exchanged back

What occurs during a Robertsonian translocation?

The long arms of two acrocentric chromosomes fuse, and the short arms are typically lost.

What is nullisomy?

Loss of both members of a homologous pair of a chromosome; 2n - 2

What is monosomy?

Loss of a single chromosome; 2n - 1

What is trisomy?

Gain of a single chromosome; 2n + 1

What is tetrasomy?

Gain of two homologous chromosomes; 2n + 2

What is the primary biological cause of aneuploidy?

Nondisjunction in meiosis I, meiosis II, and meiosis II

What is nondisjunction?

The failure of homologous chromosomes or sister chromatids to separate correctly which produces daughter cells with abnormal numbers of chromosomes

During meiosis I, II, and mitosis in nondisjunction, what occurs?

Meiosis I: homologous chromosomes fail to separate during anaphase I

Meiosis II: sister chromatids fail to separate during anaphase II

Mitosis: sister chromatids fail to separate during anaphase

What is the common name for Trisomy 21?

Down syndrome.

What is chromosome duplication?

Duplication of a chromosome segment

What is chromosome deleiton?

Deletion of a chromosome segment

What is polyploidy?

Addition of entire chromosome sets

Which factor is significantly correlated with an increased incidence of primary Down syndrome?

Maternal age.

How does an autopolyploid differ from an allopolyploid?

Autopolyploidy involves chromosome sets from the same species, while allopolyploidy involves sets from two or more species.

In bacteria, what is the role of Cas1 and Cas2 complex during the immune response?

They are involved in the acquisition of new spacer DNA from viral infections.

What is the term for a chromosome rearrangement where a portion of a chromosome is transferred to a nonhomologous chromosome without exchange?

Nonreciprocal translocation.

What is the specific result of an unequal crossing over event between misaligned chromosomes?

One chromosome with a duplication and one chromosome with a deletion.

Why are duplications often harmful to development?

They alter the relative amounts (dosage) of gene products interacting in developmental processes.

Which type of chromosome mutation is generally considered "balanced" because there is no net gain or loss of DNA?

Inversions.

Concept: Protospacer.

Definition: The segment of DNA in an invading phage that is cleaved and then inserted into the bacterial CRISPR locus as a new spacer.

A chromosome that has a centromere near one end, resulting in one very short arm and one long arm, is called _____.

acrocentric.

What is the result of deleting the centromere from a chromosome?

The entire chromosome may be lost during cell division because it cannot segregate.

True or False: Deletions frequently accompany translocations.

True.

In the CRISPR-Cas9 system, what does the 'cr' in crRNA stand for?

CRISPR-derived.

What is the specific enzymatic function of the $BCR-ABL1$ fusion protein?

Constitutively active tyrosine kinase.

How many autosomes are typically found in a human somatic cell?

22 pairs (or 44 total).

What classification is given to a chromosome with the centromere located exactly in the middle?

Metacentric.

What classification is given to a chromosome where the centromere is located at the very end?

Telocentric.

How does the CRISPR locus promoter relate to crRNA biogenesis?

Transcription of the CRISPR locus into pre-crRNA starts at the promoter within the leader sequence.

What is the primary risk of using NHEJ for gene repair in genome editing?

It is error-prone and can cause frameshift mutations due to indels.

In bacterial innate immunity, what is the consequence of "induced suicide" in infected cells?

It prevents the spread of the phage infection to the rest of the bacterial colony.