ag genetics exam 2

What is the central dogma of molecular biology?

DNA—RNA—Protein

Who coined the term central dogma?

Francis Crick

What is transcription?

copying information from a DNA template into a single-stranded RNA molecule

What is translation?

using the mRNA base sequence to build a polypeptide (amino acid chain)

what are the main functions of proteins?

provide structure, act as enzymes and hormones, transport substances, and regulate genes

what is gene expression?

whether, when, and how strongly a gene is transcribed and used to produce a functional product

what are regulatory elements?

DNA sequences that control whether and how strongly a gene is expressed

what enzyme carries out transcription?

RNA polymerase

what must happen to DNA before it can be transcribed?

the double helix must unwind to expose the template strand

what is a promoter?

a DNA region where transcription machinery assembles to begin transcription

what are the five basic steps of transcription?

1.RNA polymerase binds the promoter. 2. DNA unwinds. 3. complementary RNA nucleotides are added. 4. RNA is synthesized 5’ to 3’. transcription stops and RNA is released

what are the DNA to RNA base-pairing rules?

DNA A to RNA U; DNA T to RNA A; DNA G to RNA C; DNA C to RNA G

Why does RNA use uracil instead of thymine?

uracil replaces thymine

in which direction is the DNA template read?

3 to 5

what are three differences between RNA polymerase and DNA polymerase?

RNA polymerase does not require a primer, is less accurate than DNA replication, and synthesizes RNA 5’ to 3’

What is the template strand?

the DNA strand read by RNA polymerase to make complementary RNA

What is the coding (non-template) strand?

the DNA strand with the same 5’ to 3’ sequence as the RNA, except DNA has T where RNA has U

Does every gene use the same DNA strand as its template?

No. Different genes can use different strands, including neighboring genes transcribed in opposite directions

when do transcription and translation occur compared with DNA replication?

transcription and translation occur throughout the cell’s life as needed; DNA replication occurs during S phase

How many RNA polymerases do prokaryotes have?

one main RNA polymerase transcribes all genes

how many major nuclear RNA polymerases do eukaryotes have?

three: Pol 1, Pol 2, and Pol 3

What does RNA polymerase I transcribe?

all major rRNAs except 55 rRNA

What does RNA polymerase II transcribe?

protein-coding genes (mRNA), most snRNAs, and microRNAs

what does RNA polymerase III transcribe?

tRNA, 55 rRNA, and other small RNAs

What are polymerases IV and V?

plant specific polymerases involved in RNA-directed DNA methylation and gene silencing

What is the agricultural importance of Pol I?

It produces rRNA needed for ribosomes and is closely linked to growth.

What is the agricultural importance of Pol II?

It transcribes protein-coding genes affecting traits such as yield, quality, and stress tolerance.

What is the agricultural importance of Pol III?

It produces RNAs needed for the translation machinery.

What is the function of plant Pol IV and Pol V?

They help silence genes and transposable elements through RNA-directed DNA methylation

What is OsDREB1A?

A rice gene involved in drought responses; increased expression is associated with greater drought tolerance.

What is a transcription factor?

A protein that binds DNA regulatory sequences and helps control transcription.

Why does RNA polymerase II need transcription factors?

They help recognize the promoter and recruit Pol II to initiate transcription

What are the three steps of transcription initiation?

1. Transcription factors bind the promoter. 2. Pol II is recruited. 3. DNA unwinds and transcription begins at the transcription start site

What is the transcription start site (TSS)?

The DNA position where RNA synthesis begins.

What is the TATA box?

A promoter element with the consensus sequence TATAAA, usually about 25–30 base pairs upstream of the TSS; it helps position Pol II.

What is the CAAT box?

A promoter element that binds transcription factors and helps regulate transcription.

What are GC-rich promoter regions?

DNA regions rich in guanine and cytosine that can bind transcription factors and regulate transcription.

What is an enhancer?

A regulatory DNA sequence that increases transcription, sometimes from far away.

What is a silencer?

A regulatory DNA sequence that decreases or represses transcription.

Where can enhancers and silencers be located?

Upstream, downstream, or within a gene.

What does up-regulated mean?

A gene is expressed more than usual.

What does down-regulated mean?

A gene is expressed less than usual.

What is a cis-regulatory element?

A DNA sequence that regulates a gene on the same DNA molecule.

What are the main functions of cis-regulatory elements?

They influence when transcription begins, its rate, and the tissues or conditions in which a gene is expressed.

What are core promoter elements?

Elements, such as the TATA box, that help establish basic transcription initiation.

What are response elements?

Regulatory DNA sequences that activate or repress genes in response to particular conditions, such as drought.

How can a promoter mutation change a trait without changing the protein sequence?

It can alter gene expression, changing when or how much protein is produced.

What is GmNAC12?

A soybean transcription factor gene associated with drought tolerance; overexpression has improved drought tolerance in soybean lines.

How can cis-regulatory elements explain differences between crop varieties?

Varieties may produce the same protein but differ in when, where, or how strongly the gene is expressed.

What are the three genomes found in plants?

Nuclear, plastid (including chloroplast), and mitochondrial genomes.

How does plant transcription differ from animal transcription?

Plants have plastids and plant-specific Pol IV and Pol V, and they have complex transcriptional responses to environmental stress.

Why is plant transcription highly responsive to environmental conditions?

Plants cannot move away from stress, so they adjust gene expression in response to light, drought, temperature, pathogens, and insects.

What is HY5?

A plant light-responsive transcription factor.

What is RNA-directed DNA methylation (RdDM)?

A mechanism that uses small RNAs to direct DNA methylation and silence genes without changing the DNA sequence.

What are plastids?

Organelles, including chloroplasts, descended from bacteria that have their own DNA and transcription machinery.

What is PEP?

Plastid-encoded RNA polymerase, similar to bacterial RNA polymerase, that mainly transcribes photosynthesis-related genes.

What is NEP?

Nucleus-encoded RNA polymerase imported into plastids that mainly transcribes housekeeping genes.

What type of RNA polymerase do plant mitochondria use?

A single-subunit RNA polymerase similar to NEP.

Why must the nuclear, plastid, and mitochondrial genomes be coordinated?

Many organelle proteins are encoded by nuclear genes and imported into organelles, so their functions must work together.

What can happen when chloroplast function is disrupted?

Plants may become pale, lose chlorophyll, and have reduced photosynthesis

What is mRNA?

Messenger RNA that carries genetic information from DNA to ribosomes.

What is a codon?

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

What are the five parts of mature eukaryotic mRNA, from 5′ to 3′?

5′ cap → 5′ UTR (leader) → coding sequence → 3′ UTR (trailer) → poly(A) tail.

What is the function of the 5′ cap?

Protects mRNA from degradation, helps ribosome binding, and supports nuclear export.

What is the 5′ untranslated region (5′ UTR)?

The region before the coding sequence that is not translated but helps regulate ribosome positioning and translation efficiency.

What is the coding sequence of mRNA?

The region between the start and stop codons that specifies the amino acid sequence.

What is the 3′ untranslated region (3′ UTR)?

The region after the stop codon that contains regulatory sites affecting mRNA stability and translation.

What is the poly(A) tail?

A chain of adenine nucleotides at the 3′ end of eukaryotic mRNA that supports stability, export, and translation.

What is a primary transcript (pre-mRNA)?

The initial RNA product of eukaryotic transcription before processing.

What are the three major steps of eukaryotic mRNA processing?

5′ capping, RNA splicing, and 3′ polyadenylation.

What is the 5′ cap chemically?

A modified guanine nucleotide called 7-methylguanosine.

How is the 5′ cap attached to RNA?

By an unusual 5′–5′ linkage.

When is the 5′ cap added?

When the growing RNA is about 20–30 nucleotides long.

What are exons?

Sequences retained in mature RNA after splicing; they often encode protein but can also include untranslated regions

What are introns?

Sequences transcribed into pre-mRNA but removed during RNA splicing

What is RNA splicing?

Removing introns and joining exons together.

What is a spliceosome?

A complex of snRNPs and other components that removes introns from pre-mRNA.

What are snRNPs?

Small nuclear ribonucleoproteins made of snRNA and proteins that participate in RNA splicing.

What are the three key splicing signals?

The 5′ splice site, branch point containing adenine (A), and 3′ splice site.

What are the usual intron boundary sequences?

The intron begins with GU and ends with AG; a branch-point adenine is located near the 3′ splice site.

What is a lariat during RNA splicing?

A loop-shaped intron intermediate formed when the intron's 5′ end bonds to the branch-point adenine.

What is 3′ polyadenylation?

Adding a chain of adenines to the 3′ end of RNA after it is cut downstream of a polyadenylation signal.

What is the common polyadenylation signal?

AAUAAA.

Is the poly(A) tail copied directly from DNA?

No. Poly(A) polymerase adds it to the RNA after transcription.

What happens when the poly(A) tail gradually shortens?

The mRNA becomes more likely to be degraded.

What is alternative splicing?

Processing the same pre-mRNA in different ways to produce different mature RNAs and potentially different proteins.

How can alternative splicing affect agriculture?

It can affect crop stress tolerance, flowering, nutrient metabolism, livestock muscle growth, and disease resistance.

How do transcription and translation differ between prokaryotes and eukaryotes?

In prokaryotes, they can occur simultaneously because there is no nucleus. In eukaryotes, transcription and RNA processing occur in the nucleus before mRNA is exported for translation in the cytoplasm

How can scientists check whether an inserted crop gene is expressed?

They can measure its mRNA, which shows whether the gene is being transcribed.

What are the major classes of RNA and their functions?

mRNA carries coding information; tRNA delivers amino acids; rRNA forms and catalyzes ribosomes; snRNA helps splice RNA; miRNA and siRNA silence genes; eRNA helps regulate transcription.

What is mRNA's function?

Carry genetic instructions from DNA to the ribosome.

What is tRNA's function?

Deliver specific amino acids to the ribosome and match them to mRNA codons using an anticodon.

What is rRNA's function?

Forms the structural and catalytic core of ribosomes and catalyzes peptide bond formation.

What is snRNA's function?

Participates in spliceosomes and eukaryotic pre-mRNA processing.

What are miRNA and siRNA?

Small RNAs that silence genes by promoting mRNA degradation or blocking translation; plant siRNAs can also direct DNA methylation.

What is enhancer RNA (eRNA)?

RNA transcribed from enhancer regions that can help activate target genes.

What is a structural gene (protein-coding gene)?

A gene whose mRNA is translated into a polypeptide.

Are tRNA and rRNA translated into proteins?

No. Their RNA molecules are the functional products of their genes.

What is a polypeptide?

A chain of amino acids connected by peptide bonds.

What determines a protein's shape and function?

Its amino acid sequence and the way the chain folds.