Unit 6- AP Bio

Flow of information (Central Dogma):

• DNA → RNA → Protein

Genetic Code:

• 1 codon = 3 Consecutive bases = amino acid

• 64 Codons

• 20 amino acids

- 2 or more codons code for the same amino acid

AUG:

• 1st amino acid in every protein

Transcription:

• Copies a portion of DNA (gene)

• Makes pre-mRNA (hnRNA) in eukaryotes and mRNA in prokaryotes

Three steps of Transcription:

1. Binding & Initiation

2. Elongation

3. Terination

Binding & Initiation (1st step of Transcription):

• RNA polymerase binds to the DNA at the promoter region with help of transcription factors

Elongation (2nd step of Transcription):

• RNA polymerase adds complementary nucleotides in 5’ to 3’ direction (60 per second).

Termination (3rd step of Transcription):

• Termination signal is reached and transcription stops

Ends receive a cap and tail:

• Protects mRNA from enzymes

• Help ribosome attachment

• May help RNA leave nucleus

Pre - mRNA →

• mRNA

RNA Splicing:

• Introns (non-coding segments) are removed

• Exons (coding segments) are joined together

• Requires a spliceosome

→ = proteins and several snRNPs = snurps

Introns:

• Non-coding segment

Exons:

• Coding Segments

Translation:

• Occurs at ribosome

• Reads mRNA

• Puts amino acids in proper order to form protein

(translation) tRNA (transfer RNA):

• Carries amino acids to ribosome

(translation) Amino acids are:

• Joined to tRNA by enzyme in cytoplasm

• (amino acid activation)

3 steps of Translation:

1. Chain Initiation

2. Chain Elongation

3. Chain Termination

Chain Initiation (1st step of Translation):

• Ribosome sunbunits

• Initiator tRNA

• mRNA bind together

Chain Elongation (2nd step of Translation):

• Amino acids are added one by one as mRNA is read → tRNA brings amino acid into the a-site (codon recognition)

• Peptide bonds form

• mRNA + tRNA shift over to p-site

a-site:

• Codon recognition

Chain Termination (3rd step of Translation):

• Stop codon is read (UGA, UAA, UAG)

• Release factor binds to the stop codon

• Polypeptide is released and may be modified → goes to the Golgi Complex for processing

• tRNA, mRNA, and ribosome subunits are released → mRNA can be used again

Mutation:

• Changes in the DNA (or RNA sequences of RNA viruses)

What causes mutations?

• Errors in DNA replication

• Mutagens

- Radiation (x-rays, gamma rays, UV rays)

- Chemicals (carcinogenic, cigarette smoke)

Silent Mutation:

• No effect

• Codon still codes for the same amino acid

Missense Mutation:

• Altered Protein

• Codon codes for a different amino acid

• Polypeptide chain is still produced

Nonsense Mutation:

• No protein

• Codon is changed to a stop codon

Types of Mutations:

• DNA Point Mutations

• Chromosomal Alteration

Substitution (DNA Point Mutation):

• 1 base replaces the other

• May change the codon and amino acid

Insertion or Deletion (DNA Point Mutation):

• Bases are added or deleted which change the reading of codon = frameshift mutation

2. Chromosomal Alterations:

• Change the chromosome structure

• Effect depends on what gene(s) is/are changed

Prokaryotic Genome:

• Bacterial Chromosome (genophore)

• Plasmid

Bacterial Chromosome (genophore):

• Single

• Circular

- Contains 4300 genes

- Only exons

• Tightly packed into nucleoid region

Plasmid:

• Small circular piece of DNA

• Often contain genes for antibiotic resistance

• 2 - 50 extra genes

Sources of Variation and Recombination:

1. Mutations

2. Transformation

3. Conjugation

4. Transduction

5. Transposons

1. Mutations:

• Spontaneous changes to DNA

2. Transformation: Prokaryotic

• DNA from environment is picked up and incorporated into bacterial chromosome or plasmid

3. Conjugation (Bacterial Mating):

• Direct transfer of genes by exchanging a plasmid

• This is how bacteria pass antibiotic resistance

4. Transduction:

• Gene transfer from 1 bacterium to another by bacteriophages (viruses)

5. Transposons

• “Jumping Genes”

• Pieces of DNA that move from 1 location to another

• Found in both prokaryotes and eukaryotes

Prokaryotic Gene Control:

• Repressible Operon

• Inducible Operon

Operons:

• Cluster of genes that can be turned on or off by the process or absence of certain compounds

Repressible Operons:

• Normally turned on, but can be turned off (repressed)

• Common in anabolic pathways

Inducible Operons:

• Normally turned off, turned on when a particular protein is needed

• Common in catabolic pathways

TRP Operon (TRP = Tryptophan):

• Contains genes needed to produce TRP

• Repressible

• Operon turned on = Repressor Protein is inactive

• Operon turned off = Active Repressor binds to operator + blocks RNA polymerase. No transcription or translation will occur. No TRP is produced because it is not needed.

LAC Operon (LAC = Lactose):

• Contains genes to produce proteins to break down lactose

• Inducible

• LAC Operon off = If Lactose is absent the Lac operon is off. Repressor protein binds to operator blocking RNA Polymerase

• LAC Operon on = Allolactose (Inducer) isomer of Lactose

- Allolactose binds to repressor and inactivates it allowing RNA Polymerase to transcribe genes

Eukaryotic Genome: DNA in Nucleus:

• Complex, Linear

• 20,000 - 25,000 human genes

• Contains large amounts of DNA + Protein

• To fit in nucleus, must be packaged

→ 1 Human chromosome average length = 5 - 6 cm

Levels Of DNA Packacking:

1. DNA is wrapped around histone proteins = nucleosomes

2. 30nm Chromatin Fiber

3. Looped Domains

4. Mitotic Chromosome

Step One of DNA Packaging : 1. DNA is wrapped around histone proteins :

• Proteins have a + charge and DNA has a - charge

Step two of DNA Packaging: 2. 30nm Chromatin Fiber:

• Tightly wound coil with 6 nucleosomes/turn

Step three of DNA Packaging: 3. Looped Domains:

• Fibers fold & attach to a scaffold of proteins

Step four of DNA Packaging: 4. Mitotic Chromosome:

• Looped domains coil & fold

Non-nuclear or Extra-nuclear Inheritance:

• DNA can also be found in the mitochondria or chloroplasts

• Mitochondrial DNA is usually inherited through the mother

- 37 mitochondrial genes

- Mitochondrial gene mutations can cause problems with mitochondria function and can lead to mitochondrial diseases

Point of Gene Control in Eukaryotes:

• The control of genes can occur at any step in process of protein synthesis

• All cells in an organism contain the same DNA but specific genes are expressed based on the cell type

A. Pre- Transcription Control:

1. DNA Packaging

2. Histone Acetylation: generally activates genes

3. DNA Methylation: generally inactivates genes

1. DNA Packaging (Pre-Transcription Control)

• What level of packing will determine if DNA (chromatin) is available for transcription or not

2. Histone Acetylation: generally activates genes (Pre- Transcription Control) Eukaryotic

• Attachment of acetyl groups (-COCH₃) to histone proteins

-Changes shape of proteins

-DNA is held less tightly (chromatin is loosened)

• Allows DNA to unwind

• Transcription is easier (increases transcription in that area)

3. DNA Methylation: generally inactivates genes (Pre - Transcription Control)

• Methyl group (-CH₃) attaches to cytosine

-Blocks transcription factors

-Transcription decreases

Epigenetic inheritance:

• Modifications on chromatin can be passed on to offspring

- Unlike DNA mutations, these changes to chromatin can be reversed

• De-methylation of DNA

• Explains differences between identical twins
  

B. Transcription Control

1. Transcription Factors

2. Enhancer sites and Activator Proteins

1. Transcription Factors (Transcription Control)

• Bind near promoter

• Attract &/or help RNA polymerase bind

2. Enhancer sites and Activator Proteins (Transcription Control)

• Enhancer sites (regulatory switches) bind activator proteins which bind to DNA to interact with promoter

• Initiates transcription (increases rate of transcription)

C. Post - Transcription Control: RNA Processing

1. 5’ Cap

2. 3’ Cap

3. Alternative Splicing

1. 5’ Cap (Post- Transcription Control)

• Allows mRNA to last longer

• Guides mRNA to ribosome

• GTP

2. 3’ Tail (Post - Transcription Control)

• Allows mRNA to leave nucleus

• Poly-A tail

3. Alternative Splicing (Post- Transcription Control)

• Splicing of mRNA exons together in different combinations to produce different proteins

-12345 Spliced to → 1235 or → 1245

D. Translation Control (RNA → Protein)

1. mRNA Degradation

2. Translation

3. siRNA = small interfering RNAs

1. mRNA degradation (Translation Control)

• How long mRNA lasts is influenced by 3’ end (untranslated region)

• miRNAs (microRNAs) degrade mRNA

2. Translation (Translation Control)

• Initiation of translation can be blocked by regulatory proteins or miRNAs

• Prevents mRNA from binding to ribosome

3. siRNAs = small interfering RNAs

• RNA interference

-Blocks gene expression

• Similar to miRNA but form from different RNA precursors

E. Post -Translation Control (Eukaryotic)

1. Protein Processing

2. Protein Degradation

1. Protein Processing (Post-Translation Control)

• Addition of chemical groups or removal of part of protein are involved in control

2. Protein Degradation (Post-Translation Control)

• Death tag (ubiquitin) can be attached to proteins so they can be destroyed by proteasomes