Biology Exam 4

What is the purpose of DNA replication?

To make an exact copy of DNA so each new cell has the same genetic material.

Where does DNA replication occur in eukaryotic cells?

In the nucleus.

What enzyme builds the new DNA strand?

DNA polymerase.

What is transcription?

The process of making mRNA from DNA.

Where does transcription occur?

In the nucleus.

What enzyme carries out transcription?

RNA polymerase.

What is the difference between RNA and DNA base?

RNA has uracil (U) instead of thymine (T).

What happens to the mRNA before it leaves the nucleus?

It’s processed- spliced (introns removed), get a 5’ cap and a poly-A tail.

What is translation?

the process of making a protein using the information in mRNA

Where does translation occur?

At the ribosome in the cytoplasm.

What is the role of mRNA in translation?

It carries the genetic code (codons) that determine the amnio acid sequence.

What does tRNA do during translation?

tRNA brings amino acids to the ribosome and matches it anticodon to the mRNA codon.

What is the final product of translation?

A polypeptide chain that folds into a functional protein.

What question did Beadle and Tatum want to answer?

Whether one gene controls one enzyme (or one protein).

What organism did they use in their experiment?

The bread mold Neurospora crassa.

What did they do in the experiment?

They exposed the mold to X-rays to cause mutations, then grow the mutants on minimal media with or without a specific nutrients.

What did they discover?

Some mutants could not grow unless a certain nutrient was added- each mutation affected a single enzyme in a biochemical pathway.

What conclusion did they draw?

“One gene, one enzyme” (later updated to “One gene, one polypeptide”)

What is hemoglobin?

A protein in red blood cells that carried oxygen.

How is hemoglobin an example of gene regulation?

Different forms of hemoglobin genes are turned on or off during development.

What’s an example of hemoglobin gene regulation?

Fetal hemoglobin (HbF) has a higher oxygen affinity and is expressed in the fetus; after birth, adult hemoglobin (HbA) replaces it.

Why is this important?

It shows how gene expression changes over time to meet the body's needs.

What is RNA made of?

Nucleotides with a ribose sugar, a phosphate group, and one of four nitrogen bases: A, U, C, G.

How is RNA different from DNA?

RNA is single-stranded (DNA is double-stranded).

RNA has uracil (U) instead of thymine (T).

RNA uses ribose (DNA uses deoxyribose)

What are the types of RNA?

mRNA – messenger RNA (carries code from DNA)

tRNA – transfer RNA (brings amino acids)

rRNA – ribosomal RNA (makes up ribosome

What is a codon?

A group of 3 RNA bases that codes for one amino acid.

What is the start codon?

AUG, which also codes for methionine.

How does the genetic code work?

The sequence of codons in mRNAis read by ribosomes to build proteins.

What does it mean that genetic code is universal and redundant?

Universal: All life uses the same code.

Redundant: Some amino acids are coded by more than one codon.

If given a DNA template strand, how do you write the mRNA sequence?

Use the complementary base pairing: A,U T,A C,G G,C

If given a coding (non-template) DNA strand, how do you write the mRNA?

Copy it exactly but change T → U (since RNA has uracil, not thymine).

What happens in initiation?

RNA polymerase binds to the promoter region of DNA 9with hep from transcription factors).

What is the promoter?

A DNA sequence that signals where transcription should start (e.g., TATA box in eukaryotes).

What happens in elongation?

RNA polymerase reads the template strand and builds the mRNA strand adding nucleotides 5’ → 3’.

What happens in termination?

RNA polymerase stops when it reaches a termination sequence, and the mRNA is released.

What are the 3 main steps in mRNA processing?

1. 5’ Cap- A modified G added to the 5’ end (helps with ribosome binding and stability)

2. Poly- A Tail- A string of adenines added to the 3’ end (protects mRNA from degradation)

3. Splicing- Introns (non-coding regions) are removed, exons (coding regions) are joined.

What is the final product called?

Mature mRNA - ready to leave the nucleus and be translated in the cytoplasm.

What is splicing?

It’s the process of removing introns (non-coding regions) from pre-mRNA and joining exons (coding regions) together.

What does the spliceosome do?

It’s a complex made of proteins and small RNAs that cuts out introns and joins exons during RNA processing.

What is alternative splicing?

The process where different combinations of exons are joined to make different mRNAs from the same gene.

Why is alternative splicing important?

It allows one gene to code for multiple proteins, increasing protein diversity.

What is tRNA?

Transfer RNA—a molecule that brings amino acids to the ribosome during translation.

What are the key parts of a tRNA?

Anticodon: A 3-base sequence that pairs with the mRNA codon.

Amino acid: Attached to the other end of the tRNA.

How does translation happen?

Ribosome reads mRNA codons (in groups of 3 bases).

Each tRNA with the matching anticodon brings the correct amino acid.

Ribosome links amino acids into a chain (polypeptide).

Where does translation happen?

In the cytoplasm, at the ribosome.

What does mRNA do?

Messenger RNA carries the genetic code from DNA to the ribosome for protein synthesis.

What does tRNA do?

Transfer RNA brings specific amino acids to the ribosome and matches them to the codons on mRNA using its anticodon.

What does rRNA do?

Ribosomal RNA is a structural and catalytic part of the ribosome—it helps assemble amino acids into proteins.

What happens in initiation?

The small ribosomal subunit binds to the mRNA at the start codon (AUG), and the first tRNA carrying methionine binds. Then, the large ribosomal subunit joins.

What happens in elongation?

The ribosome moves along the mRNA:

Each new tRNA brings an amino acid.

The ribosome forms peptide bonds between amino acids.

The chain grows one amino acid at a time.

What happens in termination?

A stop codon (UAA, UAG, UGA) is reached.

No tRNA matches it, so a release factor binds, and the polypeptide chain is released.

What is a mutation?

A change in the DNA sequence that can affect the protein made.

Silent

Codon changes, but same amino acid is made. No effect protein effect

Missense

Codon changes to code for a different amino acid. One amino acid change

Nonsense

Codon changes to a stop codon. Protein is shortened (often nonfunctional)

What happens after translation to make a function; protein?

The polypeptide must fold, modify, and sometimes combine with other chains.

What helps a protein fold correctly?

Chaperone proteins assist in proper folding

What are common post-translational modifications?

Cleavage (cutting parts off)

Addition of groups (e.g., phosphate, sugar, lipid)

Disulfide bonds (stabilize structure)

Why are these steps important?

They are critical for the protein’s function, shape, and location in the cell.

What is an operon?

A cluster of genes controlled by one promoter and regulated together.

Where are operons found?

In prokaryotes (like bacteria).

What are the main parts of an operon?

Promoter – where RNA polymerase binds

Operator – on/off switch

Genes – the protein-coding sequences

Regulatory gene – makes the repressor protein

How do eukaryotic cells regulate genes at the DNA level?

DNA methylation – Adds methyl groups (CH₃) to DNA, turns genes off.

Histone modification – Changes how tightly DNA is wrapped.

Acetylation loosens DNA → activates genes.

Deacetylation tightens DNA → silences genes.

Chromatin remodeling – Changes access to DNA by shifting nucleosomes.

Why is this important?

It allows cell type–specific expression, developmental control, and response to the environment.

G-Protein Coupled Receptors (GPCRs), How is the signal turned off?

The G-protein hydrolyzes GTP → GDP (inactive).

The receptor may be phosphorylated and internalized.

Receptor Tyrosine Kinases (RTKs), How is the signal turned off?

Dephosphorylation of tyrosine residues by phosphatases.

Receptor may be degraded or endocytosed.

Ligand-Gated Ion Channels, How is the signal turned off?

Ligand detaches, channel closes, and ion flow stops.

Ion pumps restore original ion gradient.

What is RAS normally?

A G-protein that helps relay signals from RTKs to trigger cell division.

What happens when RAS is mutated?

It becomes stuck "on", continuously sending signals even without growth factors → uncontrolled cell growth (can lead to cancer).

What is p53’s normal role?

A transcription factor that:

Stops the cell cycle if DNA is damaged,

Can trigger DNA repair or apoptosis.

What happens when p53 is lost or mutated?

Damaged cells can keep dividing → mutations build up → cancer risk increases.

How do GPCRs work?

Ligand binds GPCR → receptor changes shape.

GPCR activates G-protein (GDP → GTP).

G-protein activates effector enzyme (e.g. adenylyl cyclase).

This produces a second messenger like cAMP.

How do RTKs work?

Ligand binds → two RTKs dimerize.

They auto-phosphorylate (add P to each other’s tyrosines).

Phosphorylated RTKs act as docking sites for relay proteins.

Signal is passed on through a cascade (often involving RAS).

Ligand-Gated Ion Channels, How do these work?

Ligand binds channel → channel opens.

Ions (e.g. Na⁺, Ca²⁺) rush in or out.

Change in ion concentration triggers cell response (e.g. muscle contraction).

What is phosphorylation?

Adding a phosphate group (PO₄³⁻) to a protein—usually activates it.

What enzyme does phosphorylation?

Kinase adds the phosphate.

What is dephosphorylation?

Removing the phosphate—usually deactivates the protein.

What enzyme removes the phosphate?

Phosphatase.

How is cAMP made?

Adenylyl cyclase converts ATP → cAMP.

What does cAMP do?

Activates protein kinase A (PKA) → triggers phosphorylation cascades.

Where is Ca²⁺ usually stored?

In the ER or mitochondria

How is it released?

Via second messengers like IP₃, opening calcium channels

What does Ca²⁺ do?

Activates proteins (like calmodulin) → changes cell activity (e.g. muscle contraction, secretion).

How is one signal amplified into a big response?

Each step in a cascade can activate many targets:

1 ligand → 1 receptor → 10 G-proteins

→ 100 cAMP → 1,000 kinases → 10,000 responses!

Why is amplification important?

It allows a small signal to produce a big cellular effect, quickly and efficiently.