AP Bio Unit 6 Studyguide

DNA Replication:

1. Initiation

• DNA replication begins at specific sites called origins of replication

• The enzyme helicase unwinds and separates the double-stranded DNA by breaking hydrogen bonds between complementary bases, forming a replication fork

• Single-strand binding proteins (SSBs) bind to the separated stranded to prevent them from reannealing

• Topoisomerase prevents supercooling and tension ahead of the replication fork by making temporary cuts in the DNA strand

2. Elongation

• Primate synthesizes a short RNA primer, which serves as a starting point for DNA synthesis

• DNA polymerase III (in prokaryotes) or DNA polymerase δ/ε (in eukaryotes) adds nucleotides to the growing strand in the 5’ to 3’ direction, using the original strand as a template

• Since DNA polymerase can only add nucleotides in one direction, replication occurs differently on the two strands:

-Leading Strand: Synthesized continuously in the 5’ to 3’ direction toward the replication fork

-Lagging Strand: Synthesized discontinuously in short segments called Okazaki fragments, each requiring a new RNA primer

• DNA polymerase I (in prokaryotes) or RNase H (in eukaryotes removes the RNA primers and replaces them with DNA

3. Termination

• DNA ligase joins Okazaki fragments on the lagging strand by sealing the gaps between the fragments, forming a continuous strand

• In eukaryotic cells, replication ends when the telomeres (ends of linear chromosomes) are reached. Since DNA polymerase can note fully replicate the ends, telomerase extends the telomeres to prevent genetic loss

4. Final Outcome

• 2 identical DNA molecules, each consisting of one original (parent) strand and one newly synthesized (daughter) strand, ensuring genetic consistency in cell division

Mutations:

1. Based on Location in the Body

- Somatic Mutations:  

  - Occur in body (somatic) cells and cannot be passed on to offspring.  

  - Only affect the individual in which they occur.  

  - Example: Mutations leading to cancer in skin cells due to UV exposure.  

- Germline Mutations:  

  - Occur in gametes (sperm or egg cells) and can be passed on to offspring.  

  - These mutations affect every cell in the organism that inherits them.  

  - Example: Cystic fibrosis and sickle cell anemia are caused by inherited germline mutations.  

2. Based on Scale

- Gene Mutations:  

  - Affect a single gene by altering the nucleotide sequence.  

  - Examples: Point mutations, deletions, duplications.  

- Chromosomal Mutations:  

  - Affect large sections of chromosomes or entire chromosomes.  

  - Can result in structural changes or an abnormal number of chromosomes (e.g., Down syndrome).  

  - Examples: Inversions, translocations, duplications.  

3. Based on DNA Sequence Changes

- Point Mutations: (Affect a single nucleotide)  

  - Silent Mutation: A nucleotide change occurs but does not change the amino acid due to the redundancy in the genetic code. (No functional change).  

    - Example: Changing GAA (Glutamate) to GAG (also Glutamate).  

  - Missense Mutation: A single nucleotide change does alter the amino acid sequence, possibly affecting protein function.  

    - Example: Sickle cell anemia (GAG → GTG, causing Glutamate → Valine).  

  - Nonsense Mutation: A single nucleotide change creates a premature stop codon, leading to a truncated, nonfunctional protein.  

    - Example: Duchenne muscular dystrophy.  

- Frameshift Mutations (Shift the reading frame)  

  - Deletion: A nucleotide (or multiple) is removed, altering the reading frame and changing all downstream amino acids.  

    - Example: Cystic fibrosis (3-base deletion in the CFTR gene).  

  - Duplication: A segment of DNA is copied multiple times, leading to excessive protein production or altered function.  

    - Example: Charcot-Marie-Tooth disease.  

4. Based on Chromosome Structure Changes

- Inversions: A segment of a chromosome flips and reattaches in reverse order.  

  - May or may not affect gene function depending on location.  

  - Example: Hemophilia A (caused by an inversion in the factor VIII gene).  

- Translocations: A segment from one chromosome moves to another, non-homologous chromosome.  

  - Can disrupt genes and cause diseases.  

  - Example: Chronic myeloid leukemia (CML) is caused by the Philadelphia chromosome, a translocation between chromosomes 9 and 22.  

5. Based on Cause 

- Spontaneous Mutations:  

  - Occur naturally due to errors in DNA replication or repair.  

  - Example: DNA polymerase making a mistake during replication.  

- Induced Mutations:  

  - Caused by external factors, such as radiation, chemicals, or viruses.  

  - Example: UV radiation causing thymine dimers, leading to skin cancer.  

RNA Functions:

1. Messenger RNA (mRNA)- The Blueprint for Proteins

Purpose: mRNA carries genetic information from DNA to the ribosome where it serves as a template for protein synthesis

Function:

• Synthesized in the nucleus (eukaryotes) or cytoplasm (prokaryotes) during transcription

• Contains codons (sets of 3 nucleotides) that specify amino acids

• Travels to ribosomes, where it is translated into a protein

• In eukaryotes, it undergoes modifications such as 5’ capping, polyadenylation (poly A tail), and splicing before leaving the nucleus

Ex.) The hemoglobin mRNA carries instructions for making hemoglobin protein in red blood cells

2. Transfer RNA (tRNA)- The Amino Acid Transporter

Purpose: tRNA delivers the correct amino acids to the ribosome during protein synthesis

Function:

• Each tRNA molecule has an anticodon that is complementary to an mRNA codon

• Binds to a specific amino acid and brings it to the ribosome

• Helps assemble amino acids into a growing polypeptide chain during translocation

• Facilitates peptide bond formation between amino acids

Ex.) A tRNA with the anticodon UAC pairs with the mRNA codon AUG (start codon) and delivers the amino acid methionine

3. Small Nuclear RNA (snRNA)- The RNA Editor 

Purpose: snRNA is involved in RNA processing, specifically splicing, where introns (non-coding regions) are removed from pre-mRNA

Function;

• Forms part of the spliceosome, a molecular complex that removes introns and joins exons together in pre-mRNA splicing

• Ensures proper mRNA maturation before translation

• Helps regulate gene expression by modifying mRNA transcripts

Ex.) U1, U2, U4, U5, and U5 snRNAs are key components of the spliceosome that process mRNA before it exits the nucleus

Steps of Transcription:

1. Initiation- Starting Transcription

• RNA polymerase binds to the promoter region of the DNA

• In prokaryotes, the sigma factor helps RNA polymerase recognize the promoter. In eukaryotes, transcription factors assist RNA polymerase in binding

• The DNA double helix unwinds at the transcription start site, forming a transcription bubble

• RNA polymerase begins to synthesize RNA by adding complementary ribonucleotides (A,U,C,G)

2. Elongation- Synthesizing the RNA Strand

• RNA polymerase moves along the template strand (3’-> 5’), synthesizing RNA in the 5’ -> 3’ direction

• RNA polymerase unwinds the DNA ahead and reanneals it behind as transcription proceeds

• The growing RNA strand is complementary to the DNA template strand (except uracil (U) replaces thymine (T) in RNA)

3. Termination- Ending Transcription

In prokaryotes:

• Rho-independent termination: A GC-rich hairpin loop forms in the RNA, causing RNA polymerase to detach

• Rho-dependent termination: The Rho protein binds to the RNA and pulls it away from RNA polymerase

In eukaryotes:

• RNA polymerase transcribes a polyadenylation signal (AAUAAA).

• Special proteins cut the RNA transcript, and a poly-A tail is added to stabilize the mRNA

Steps of Translation:

1. Initiation:

• The small ribosomal subunit binds to mRNA

• It finds the start codon (AUG)

• The first tRNA carrying methionine (Met) attaches at the P site

• The large ribosomal subunit joins to form the complete ribosome

2. Elongation:

• A new tRNA enters the A site with the next amino acid

• A peptide bond forms between amino acids in the P site and A site

• The ribosome shifts:

-tRNA in the A site moves to the P site

-Empty tRNA exits via the E site

• The chain grows as the ribosome reads the mRNA

3. Termination:

• The ribosome reaches a stop codon (UAA, UAG, UGA)

• A release factor binds, and the protein is released

• Ribosome parts detach

Sites:

• A site= Accepts new tRNA

• P site= Holds growing protein

• E site= tRNA exits

What happens to the polypeptide chain after it is finished being translated? Signal sequences? Post-translational modifications?

1. Folding:

• The polypeptide folds into its specific 3D shape

• Chaperone proteins may help it fold correctly

2. Signal Sequences:

• Some proteins have a signal sequence at the beginning

• This targets the protein to specific locations, like the endoplasmic reticulum (ER), mitochondria, or outside the cell

• If the signal directs it to the ER, the ribosome binds to the ER and finishes translation there

3. Post-Translational Modifications (PTMs):

• Cleavage: Parts of the protein may be cut off (like removing the signal sequence)

• Phosphorylation: Adding phosphate groups to regulate activity

• Glycosylation: Adding sugars, often for proteins that are secreted or on the cell surface

• Lipidation: Adding lipids to anchor proteins to membranes

• Ubiquitination: Tagging for degradation

4. Transport:

• Once modified, proteins are shipped to where they’re needed (nucleus, membrane, secretion)

Lac Operon (Inducible Operon- Turns ON when lactose is present):

Goal- To break down lactose only when it’s available (and glucose is low).

How It Works:

• No lactose → the repressor binds to the operator → RNA polymerase is blocked → no transcription.

• Lactose present → lactose binds to the repressor, making it let go of the operator → RNA polymerase binds at the promoter and transcribes the genes → enzymes to digest lactose are made.

• Low glucose → CAP (catabolite activator protein) binds to the CAP site, helping RNA polymerase attach and speed up transcription.

Diagram Elements:

• Promoter: where RNA polymerase binds to start transcription.

• Operator: where the repressor binds to block transcription.

• Repressor: protein that blocks transcription by binding to the operator.

• CAP site: where CAP binds to increase transcription when glucose is low.

• RNA polymerase: enzyme that transcribes the genes into mRNA.

Trp Operon (Repressible Operon- Turns Off when tryptophan is present)

Goal- To make tryptophan when the cell doesn’t have enough.

How It Works:

• No tryptophan → repressor is inactive → RNA polymerase binds the promoter → genes are transcribed → enzymes to make tryptophan are produced.

• Tryptophan present → tryptophan binds to the repressor and activates it → active repressor binds to the operator→ RNA polymerase is blocked → no transcription.

Diagram Elements:

• Promoter: where RNA polymerase binds.

• Operator: where the repressor (with tryptophan bound) can block RNA polymerase.

• Repressor: blocks transcription when activated by tryptophan.

• (No CAP site involved in trp operon).

Inducible gene= switched ON when needed

Constitutive gene= always ON, always needed

Inducible operon= normally OFF, turned ON by inducer (like lac operon)

Repressible operon= normally ON, turned OFF by corepressor (like trp operon)

How are eukaryotic genes regulated?

1. Chromatin Structure (Epigenetic Regulation)

• DNA is wrapped around histone proteins, forming chromatin.

• Tightly packed chromatin (heterochromatin) is inaccessible and genes are OFF.

• Loosely packed chromatin (euchromatin) allows access and genes can be ON.

✅ Histone modification (e.g., acetylation loosens DNA → turns genes ON).
✅ DNA methylation (adds methyl groups to DNA → turns genes OFF).

2. Transcriptional Control

• Transcription factors (TFs) bind to promoters and enhancers to help RNA polymerase start transcription.

• Activators boost transcription.

• Repressors block transcription.

✅ Enhancers (can be far away but loop DNA to affect transcription).
✅ Silencers prevent transcription when bound by repressors.

3. RNA Processing (Post-Transcriptional Regulation)

• mRNA is spliced (introns removed, exons joined).
  ✅ Alternative splicing creates different proteins from one gene.

• 5' cap and poly-A tail added for stability and export.

4. mRNA Stability and Transport

• How long mRNA lasts affects how much protein is made.

• Some mRNAs are quickly degraded; others are stable for a long time.

5. Translation Control

• MicroRNAs (miRNAs) or small interfering RNAs (siRNAs) can block translation or lead to mRNA degradation.

• Repressor proteins can prevent ribosome binding to mRNA.

6. Post-Translational Modifications

• After the protein is made, it can be modified to activate or deactivate it:
  ✅ Phosphorylation, glycosylation, cleavage, etc.
  ✅ Some proteins are sent to specific locations or degraded when not needed.

Summary of Eukaryotic Gene Regulation Levels:

1. Chromatin remodeling (epigenetic)

2. Transcription initiation (transcription factors)

3. RNA processing (splicing, caps/tails)

4. mRNA stability and transport

5. Translation control

6. Post-translational modifications

What is epigenetics? How do histones affect transcription? How does methylation affect transcription? How is translation regulated?

Epigenetics: (gene expression changes without altering DNA)

-The study of heritable changes in gene expression that do not change the DNA sequence itself

-It controls which genes are turned on or off in different cells

-These changes are influenced by things like environment, diet, stress

Histones: (control access to DNA by winding/unwinding it)

-Histones are proteins that DNA wraps around to form chromatin

-How tightly DNA is wrapped determines gene activity:

Loosely wrapped (euchromatin)= transcription ON

Tightly wrapped (heterochromatin)= transcription OFF

Histone modifications:

-Acetylation (adding acetyl groups)= loosens DNA -> promotes transcription

-Deacetylation (removing acetyl groups)= tightens DNA -> represses transcription

Methylation: (silences genes by adding methyl groups to DNA)

-DNA methylation adds methyl groups (CH3) to cytosine bases (usually at CpG sites)

-more methylation -> turns genes OFF

-methyl groups block transcription factors or attract proteins that compact the chromatin

Translation: (controls how and when proteins are made from mRNA)

-Regulation controls when, where, and how much protein is made from mRNA

-MicroRNAs and siRNAs can bind mRNA and block translation or cause degradation

-Repressor proteins can block the ribosome from binding to mRNA

-mRNA stability: some mRNAs are quickly degraded, reducing protein production, while others are more stable and translated more often

-Upstream regulatory sequences in mRNA can control how efficiently ribosomes bind and start translation