AP Biology Unit 7: Gene Expression & Regulation

Gene

A physical and functional unit of heredity, a sequence of DNA that codes for a protein

The Central Dogma

Genetic information flows from DNA → RNA → Protein through transcription and translation.

Nucleus

Holds the cell’s genetic information in DNA. mRNA leaves the nucleus through its nuclear pores.

Nucleolus

Builds ribosome subunits from rRNA & proteins which then exit through nuclear pores and into the cytoplasm and combine to form functional ribosomes.

Ribosomes

There are two types of ribosome (free & bound) and they make proteins.

Free Ribosomes

Are suspended in the cytosol and synthesizes proteins that function within the cytosol.

Bound Ribosomes

Are attached to the endoplasmic reticulum and synthesizes proteins for export to membranes.

RNA

Made up of RNA nucleotides. The sequence of the RNA bases and the structure of the RNA molecule determines its function.

mRNA (messenger RNA)

Carries information from DNA to the ribosome.

tRNA (transfer RNA)

Carries amino acids to the ribosome.

rRNA (ribosomal RNA)

Building blocks of ribosomes

microRNA

Small RNA molecules that bind to other RNA molecules to degrade them.

Transcription Overview

Then nucleotide in the DNA is used to make a complementary sequence in mRNA using RNA nucleotides through Initiation → Elongation → Termination.

RNA Polymerase

Uses a single template strand of DNA to make mRNA using free RNA nucleotides after it unwinds the helix. Works in the 5’ to 3’ direction.

Coding Strand

The side of DNA that is not used in synthesizing the mRNA.

Template Strand

The DNA strand that is used to transcribe the mRNA.

Promoter

In prokaryotes, the RNA polymerase directly binds to this. It is located on the template strand and provides a starting point for reading the beginning of a gene. It also ensures that the DNA is read 3’ → 5’ and mRNA is built 5’ → 3’. Also contains the TATA box.

DNA is read from:

3’ → 5’

mRNA is built from:

5’ → 3’

Transcription Factors

In eukaryotes, they bind directly to the TATA box of the promoter region first, allowing the RNA polymerase to bind on top. They are a suite of proteins that can turn on or off transcription.

TATA Box

A recognition site for transcription factors, located on the promoter region

Termination Sequence

Once the RNA polymerase reaches this, it detaches and various proteins help free the newly transcribed mRNA.

5’ Cap

It’s (a modified guanine nucleotide) is added to the first nucleotide during transcription. It protects the transcript from breaking down and helps the ribosome attach to the mRNA and start reading it.

Poly-A Tail

It is make up of many repeating adenine nucleotides and helps making the transcript more stable while also helping it get exported to the cytosol.

Introns

Stays in the nucleus, and does not code for proteins. Splicesomes “cut” this out.

Exons

Exits in the nucleus to go to the ribosomes and do code for proteins.

Alternative Splicing

Different mRNA versions result from combining different exons.

Spliceosome (snRNPs)

An enzyme complex made up of protein and small RNAs. It does the cutting and gluing back together of the pre-mRNA to make it mature.

Translation Overview

The mRNA sequence is organized in codons, which are decoded by pairing with complementary anticodons on tRNA molecules to assemble amino acids into a polypeptide chain, forming a protein.

Initiation → Elongation → Termination

Translation - Initiation

1. Small ribosomal subunit binds to mRNA at the start codon (AUG)

2. An initiator tRNA is added

3. The large ribosomal subunit attaches

Translation - Elongation

1. Ribosome moves down the mRNA in the 5’ → 3’ direction

2. For each codon, a tRNA with a corresponding anticodon brings an amino acid to the ribosome

3. Amino acids are added to the preceding one by a peptide bond using peptidly transferase through dehydration synthesis

4. Goes through the APE sites until the ribosome reaches a stop codon in the mRNA

A Site (Aminoacyl-tRNA site)

Holds tRNA carrying next amino acid to be added to the chain

P Site (Peptidyl-tRNA site)

Location at which the amino acid is transferred from its trNA to the growing polypeptide chain.

E Site (Exit site)

Empty tRNA leaves the ribosome

Start Codon

AUG

Stop Codons

UGA, UAA, UAG

Translation - Termination

When the ribosome reaches the stop codon, a protein called the release factor, causes the polypeptide chain to separate from the ribosome.

Post Translation

The polypeptide chain folds into a specific, 3D shape based on the amino acid sequence, forming its secondary, tertiary, or quaternary structure. Special helper proteins called chaperoning help this process.

Cells use “targeting signals” to route proteins to the right place.

Post Translation - Proteins going OUTSIDE of the cell (or an organelle)

Made on bound ribosomes on the rough ER.

1. They are sent to the rough ER where they are folded (and sometimes modified).

2. Then, they are sent to the golgi and undergo further modification. Vesicles transport these proteins.

Post Translation - Proteins STAYING inside the cell (cytoplasm or organelles)

Made on free ribosomes in the cytoplasm.

1. They are folded into their functional shape in the cytoplasm

2. Remain in the cytoplasm or are sent to organelles using specific targeting signals

*Do NOT go through the rough ER or golgi

Protein Synthesis - Prokaryotes

Transcription occurs in the cytoplasm, no mRNA editing, & transcription + translation occur simultaneously.

Protein Synthesis - Eukaryotes

Transcription occurs in the nucleus, mRNA is edited prior to translation, translation occurs after transcription is completed.

Mutations

A change in the DNA sequence that may be caused by factors such as mutagens, errors in DNA replication, or errors in mitosis or meiosis.

Mutagens

External factors such as radiation and reactive chemcials.

Point Mutations

A base is changed, but the number of bases stays the same. There are three types of point mutations: silent, missense, and nonsense.

Silent Point Mutations

Still codes for the same amino acid.

Missense

Codes for a different amino acid, which changes its property, and ultimately, the protein’s shape and function.

Nonsense

Codes for a stop codon early, so the remainder of the codons will not be read.

Frameshift Mutations

The number of bases changes due to the addition or removal of one or more nucleotides in the DNA sequence. This causes the reading frame to shift, thereby changing all the codons after the mutation.

Operon

A group of genes of related function, used to regulate gene expression by controlling related genes at the same time. The transcribed mRNA contains the sequence for all the genes in the operon.

Lac Operon

Controls genes needed to break down lactose. It is inducible, meaning it is turned on when lactose is present.

Ara Operon

Regulates genes needed to metabolize arabinose sugar. It can be both activated and repressed depending on environmental conditions.

Regulatory Gene

Produces transcription factors (proteins) that regulates if the gene is transcribed or not.

Operator

On/off switch where regulatory proteins bind.

Promoter

Where RNA polymerase attaches.

Negative Control

Repressor blocks transcription and RNA polymerase (transcription OFF) → gene is off unless repressor is removed.

→ Inducible Operons & Repressible Operons

Positive Control

Activator helps RNA polymerase bind (transcription ON)→ gene is on or transcribed more.

→ Activators

Inducible Operon

Off → On

Negative Control

Produces enzymes only when nutrients are available. They avoid making proteins that have nothing to do and are usually used in catabolic pathways.

Repressible Operon

On → Off

Negative Control

When the end product is present, transcription is repressed (turned off) to allocate resources to other uses. Usually functions in anabolic pathways.

Activators

Positive Control

Activators are proteins that bind near the promoter. They increase transcription by helping RNA polymerase bind to the enhancer (near the promoter)

Chromatin

The packaged form of DNA inside the nucleus

Chromatin Structure

Made up of coiled and folded nucleosomes.

Nucleosomes

Strucutures formed by DNA wrapping around proteins called histones.

Heterochromatin

Tightly packed chromatin, making genes less likely to be expressed.

This is because DNA is less accessible, and the transcription machinery cannot easily bind to it. The methyl groups are present, and transcription cannot occur.

Euchromatin

Loosely packed chromatin, making genes more likely to be expressed.

This is because DNA is more accessible, and the transcription factors + RNA polymerase can bind. The acetyl groups are present, and transcription can occur.

DNA Methylation

Genes OFF

Methyl groups (-CH₃) can attach to DNA bases, preventing transcription by blocking transcription factor binding and recruiting silencing proteins.

Histone Acetylation

Genes ON

Acetyl groups (-COCH₃) are added to histone, preventing them from binding to the DNA as tightly, making room for proteins to bind for transcription.

Enhancer

A sequence of DNA nucleotides that is the binding site for an activator

Repressors

Transcription factors that bind to the silencer. This prevents RNA polymerase from binding to the DNA, decreasing or completely stopping the rate of transcription.

Silencer

A sequence of DNA nucleotides that is the bonding site for the repressor.

Small Interfering RNAs (siRNA)

Short segments of RNA about 21-28 bases that bind to mRNA to create sections of double-stranded mRNA. This tags mRNA for degradation and turns off the gene so no protein can be produced.

Controlling how long mRNA lasts regulates how much of a protein is made.

Blocking Translation Initiation

Occurs when a ribosome does not form or mRNA cannot attach (translation cannot occur). Regulatory proteins can attach to the 5’ end of mRNA to prevent attachment of ribosomal subunits and initiator tRNA.

Ubiquitin

A molecule that triggers proteasomes to break down the protein if it is not needed.

*Not common

Gene Regulation in Prokaryotes

Regulates a cluster of genes (operon) and regulation only occurs in the cytoplasm and only at the transcriptional level. There are no histones and introns.

Gene Regulation in Eukaryotes

Regulates individual genes and regulation can occur in the nucleus and cytoplasm and at many levels. DNA is wrapped around histons and introns are involved in alternative splicing.

Restriction Enzymes

Cuts DNA into segments at specific sequences.

Can be used to cut a specific gene out of a DNA strand and simultaneously cut a plasmid vector, allowing DNA ligase to join them together, forming recombinant DNA.

Polymerase Chain Reaction (PCR)

The process of making many DNA copies for analysis by amplifying specific DNA sequences

Steps: Denaturation → Annealing → Extension

Gel Electrophoresis

When electricity is used to separate DNA fragments of different sizes to be used in DNA fingerprinting, diagnosing genetic diseases, etc.

DNA is negatively charged, so it moves towards the positive end of the electrophoresis chamber.

DNA Sequencing

When fluorescent markers are added to PCR, and the fragments are then separated by size. The order of colors from the markers are recorded, each color representing a different base.

This is used in disease/medical diagnosis, newborn screenings, paternity testing, etc

Virus Replication

Viruses cannot replicate on their own, instead they hijack their host’s cellular machinery to make more DNA & RNA.

Prophage

A viral DNA joined with the host cell DNA.

Lytic Cycle

When new viruses are produced.

Retrovirus

A virus that uses RNA as their genetic material, so they use RNA to make DNA with the help of the enzyme reverse transcriptase. Then the DNA becomes integrated with the host genome to be used to make more viruses.

Can be used as vectors in gene therapy to deliver functional genes into a patient’s DNA.

Gene Therapy

The technique of using genetic material as a drug to treat or prevent disease by replacing, silencing, or correcting faulty genes.

Can be used to treat conditions such as cystic fibrosis, sickle cell anemia, etc.