ag genetics exam 2 study guide

What is the central dogma?

DNA → RNA → protein.

What is transcription?

The process of making RNA from a DNA template.

What are the five main steps of transcription?

1. RNA polymerase binds the promoter. 2. DNA unwinds. 3. RNA polymerase reads the template strand and builds RNA. 4. Transcription stops at a termination signal. 5. RNA is released and DNA rewinds.

In what direction is RNA synthesized?

5′ → 3′.

In what direction does RNA polymerase read the DNA template?

3′ → 5′.

What is the DNA template strand?

The strand RNA polymerase reads to make complementary RNA.

What is the DNA coding strand?

The strand that matches the mRNA sequence, except DNA has T and RNA has U.

How do you write mRNA from a DNA template?

Write the complementary bases antiparallel to the template, using A–U, T–A, C–G, and G–C.

If the DNA template is 3′-TAC GGA CTT-5′, what is the mRNA?

5′-AUG CCU GAA-3′

If the DNA coding strand is 5′-ATG CCT GAA-3′, what is the mRNA?

5′-AUG CCU GAA-3′.

What does RNA polymerase I transcribe?

Most rRNA.

What does RNA polymerase II transcribe?

mRNA and some regulatory RNAs, including many snRNAs and miRNA precursors.

What does RNA polymerase III transcribe?

tRNA, 5S rRNA, and some small RNAs

What do plant RNA polymerases IV and V do?

They help produce small RNAs and establish RNA-directed DNA methylation and gene silencing.

What is a promoter?

A DNA region where transcription machinery assembles to start transcription.

What is the TATA box?

A promoter DNA sequence that helps transcription factors position the transcription machinery in many eukaryotic genes.

What are enhancers?

DNA sequences that increase transcription, often by binding activator proteins.

What are silencers?

DNA sequences that decrease transcription by binding repressor proteins.

What are transcription factors?

Proteins that bind DNA or interact with transcription machinery to activate or repress transcription.

What does RNA polymerase do at the start of transcription?

It is recruited to the promoter, opens the DNA locally, and begins RNA synthesis.

What are the main parts of mature eukaryotic mRNA?

5′ cap, 5′ untranslated region (UTR), coding region, 3′ UTR, and poly(A) tail.

What are the three main pre-mRNA processing steps?

Adding a 5′ cap, removing introns by splicing, and adding a poly(A) tail.

What is the function of the 5′ cap?

Protects mRNA, helps ribosomes recognize it, and supports export from the nucleus.

What is RNA splicing?

Removing introns and joining exons together.

What are introns?

Sequences removed from pre-mRNA during splicing.

What are exons?

Sequences retained in mature RNA after splicing; they often contain coding information.

What is the function of the poly(A) tail?

Improves mRNA stability and helps with nuclear export and translation.

What is the role of mRNA?

Carries genetic instructions from DNA to ribosomes.

What is the role of tRNA?

Brings amino acids to the ribosome and matches its anticodon to an mRNA codon.

What is the role of rRNA?

Forms the core of the ribosome and helps catalyze peptide-bond formation.

What is the role of snRNA?

Helps splice introns from pre-mRNA as part of the spliceosome.

What are miRNAs and siRNAs?

Small RNAs that help silence genes by targeting complementary RNA for degradation or blocking translation; some also guide chromatin silencing.

What is translation?

The process of using mRNA instructions to build a protein.

What is a codon?

A sequence of three mRNA nucleotides that specifies an amino acid or stop signal.

What does it mean that the genetic code is triplet?

Three nucleotides make up each codon.

What does it mean that the genetic code is non-overlapping?

Each nucleotide belongs to only one codon in a given reading frame.

What does it mean that the genetic code is degenerate?

More than one codon can code for the same amino acid.

What does it mean that the genetic code is nearly universal?

Most organisms use the same codons for the same amino acids, with a few exceptions.

What is the start codon?

AUG; it codes for methionine and usually starts translation.

What are the three stop codons?

UAA, UAG, and UGA.

What is wobble?

Flexible base pairing at the third codon position that allows one tRNA to recognize multiple codons.

What is a frameshift mutation?

An insertion or deletion of nucleotides not in multiples of three that shifts the reading frame.

Why are frameshift mutations usually severe?

They change downstream codons and often create an early stop codon, producing a shortened or nonfunctional protein.

Will inserting three nucleotides usually cause a frameshift?

No. It adds one amino acid but generally preserves the reading frame.

What is the role of tRNA in translation?

It carries a specific amino acid to the ribosome.

What is an anticodon?

A three-nucleotide sequence on tRNA that pairs with a complementary mRNA codon.

What happens at the ribosome A site?

An incoming aminoacyl-tRNA enters and matches the codon.

What happens at the ribosome P site?

The tRNA holding the growing polypeptide chain is positioned here.

What happens at the ribosome E site?

The empty tRNA exits the ribosome.

What are the three stages of translation?

Initiation, elongation, and termination.

What happens during translation initiation?

The ribosome assembles on the mRNA and recognizes the start codon with the initiator tRNA.

What happens during elongation?

tRNAs bring amino acids, peptide bonds form, and the ribosome moves along the mRNA.

What happens during termination?

A stop codon is recognized by a release factor, and the finished polypeptide is released.

What is Bt cotton?

Genetically engineered cotton that produces an insecticidal protein from the bacterium Bacillus thuringiensis (Bt).

How does Bt cotton kill susceptible insect pests?

The Bt protein becomes active in the insect gut, binds to susceptible gut cells, disrupts the gut lining, and can kill the insect.

How did codon optimization help Bt cotton?

The Bt gene's DNA sequence was adjusted to use codons preferred by cotton cells, improving expression without changing the intended protein sequence.

Why is promoter choice important in Bt cotton?

A suitable promoter helps the plant express enough Bt protein in the tissues where protection is needed.

What is a refuge in Bt cotton management?

An area planted with non-Bt cotton that supports susceptible insects.

How do refuges slow Bt resistance?

They allow susceptible insects to survive and mate with rare resistant insects, reducing the chance that resistance becomes common.

What is pathogenicity?

The ability of a pathogen to cause disease.

What is virulence?

The degree or severity of disease caused by a pathogen.

What are the three parts of the disease triangle?

A susceptible host, a pathogen capable of causing disease, and a favorable environment.

Why is the disease triangle important?

Disease develops when a susceptible host, a capable pathogen, and suitable environmental conditions come together.

What is PTI?

Pattern-triggered immunity; plant surface receptors detect common pathogen-associated molecules and activate defenses.

What is ETI?

Effector-triggered immunity; plant resistance proteins recognize specific pathogen effectors or their effects and activate stronger defenses.

What is the hypersensitive response (HR)?

A localized, often rapid death of plant cells around an infection site that can restrict pathogen spread.

How do PTI and ETI differ?

PTI detects common pathogen patterns, while ETI detects particular pathogen effectors or their effects.

What is Flor's gene-for-gene model?

Resistance occurs when a plant resistance (R) gene recognizes a corresponding pathogen avirulence effector gene.

What happens when a plant R protein recognizes a pathogen effector?

It can activate defense responses that restrict infection.

Why can one change in a pathogen effector defeat an R gene?

A mutation may alter or remove the effector so the plant's R protein no longer recognizes it, allowing infection.

What is a plant susceptibility (S) gene?

A host gene that a pathogen uses or exploits to establish infection.

How do TAL effectors help some bacterial pathogens infect plants?

They enter plant cells and activate specific host genes that benefit the pathogen.

What are SWEET genes in rice?

Genes encoding sugar transporters that certain bacterial blight pathogens can activate to increase sugar availability.

How can changing a SWEET gene promoter increase disease resistance?

Changing the promoter's effector-binding site can prevent the pathogen from activating the gene while preserving its normal function when possible.

What is Ug99?

A group of highly virulent wheat stem rust strains that overcame resistance in many wheat varieties and threatened wheat production.

Why was Ug99 a major concern?

It could infect wheat varieties that previously had effective resistance genes, creating a risk of large crop losses.

What is gene pyramiding?

Combining multiple resistance genes in one crop variety.

Why is gene pyramiding more durable than relying on one R gene?

A pathogen must overcome several resistance mechanisms rather than a single one.

What is quantitative resistance?

Resistance controlled by multiple genes, often reducing disease severity rather than completely preventing infection.

Why can quantitative resistance be durable?

It usually involves multiple small effects and can be harder for a pathogen to overcome with one mutation.

What do adhesion genes do?

Help pathogens attach to host cells; for example, E. coli adhesins can help bacteria attach to the intestinal lining of livestock

What do invasion genes do?

Help pathogens enter host cells or tissues; for example, Salmonella uses invasion factors to enter intestinal cells.

What do immune-evasion genes do?

Help pathogens avoid or resist host defenses; for example, Mycoplasma can vary surface proteins to evade immune recognition.

What do toxin genes do?

Produce substances that damage host cells or disrupt normal function; for example, Shiga toxin-producing E. coli can cause serious disease in cattle and people.

What are plasmids?

Small DNA molecules separate from the bacterial chromosome that can carry genes for antimicrobial resistance or virulence.

What are transposons?

Mobile DNA segments that can move between DNA locations and carry resistance or virulence genes.

How can bacteriophages spread virulence genes?

They are viruses that infect bacteria and can transfer bacterial genes between cells through transduction.

What is horizontal gene transfer?

The movement of genetic material between organisms other than through parent-to-offspring inheritance.

What is co-selection?

When selection for one trait also favors another linked trait, such as an antibiotic resistance gene carried on the same plasmid as a metal-resistance gene.

How can mobile genetic elements spread antimicrobial resistance?

They move resistance genes among bacteria, potentially spreading them through animal populations and environments.

What is antigenic variation?

Changes in pathogen surface antigens that help the pathogen escape immune recognition.

What is antigenic drift?

Gradual antigen changes caused by mutations accumulating over time.

What is antigenic shift?

A major, abrupt antigen change, often due to reassortment of genome segments in viruses such as influenza A.

Why can antigenic drift cause vaccine escape?

Mutations can change vaccine-targeted antigens enough that antibodies recognize the pathogen less effectively.

Why can antigenic shift be especially important?

It can create a substantially different viral antigen combination to which a population may have little existing immunity.

What does DIVA stand for?

Differentiating Infected from Vaccinated Animals.

How does a DIVA vaccine work?

It is designed so vaccinated animals have a distinguishable antibody or test profile from naturally infected animals.

What is PRRS?

Porcine reproductive and respiratory syndrome, a viral disease of pigs.

What is CD163's role in PRRS infection?

CD163 is a pig cell-surface protein that PRRS virus uses during infection.

How can CD163 gene editing help pigs resist PRRS?

Editing the relevant CD163 region can prevent effective viral entry while aiming to preserve the protein's other important functions.