Unit 4: DNA Replication, Transcription, Translation, and Protein synthesis.

Laura Mozingo BIO 135 At JCCC

Hershey and Chase

DNA is the genetic material.

Chargaff's Rule

DNA has equal amounts of A=T and G=C.

Chemical Structure of DNA

(-) including a nitrogenous base, pentose sugar, and phosphate group.

DNA REPLCIATION

Semiconservative Model of Replication

Type of DNA replication where double helix has parent and daughter strands.

Leading Strand Replication

Nucleotides continuously added in 5' to 3' direction

TOWARDS replication fork.

Lagging Strand Replication

Nucleotides discontinuously added in Okazaki fragments in 5' to 3' direction

AWAY from replication fork.

DNA Polymerase I

Removes RNA nucleotides of primer and replaces them with DNA.

DNA Polymerase III

Adds nucleotides to RNA primer or DNA strand

Builds new DNA strands.

Uses parental DNA as a template

Helicase

Unzips DNA at replication forks

Ligase ‘gluer’

Glues bonds between Okazaki fragments to form one continuous DNA strand.

Nuclease

Cuts damaged DNA.

Primase

Makes RNA primer by adding RNA nucleotides.

RNA Primer

Short nucleotide chain

Starting point for DNA synthesis.

Single Strand Binding Protein

Binds DNA strands during replication

Stabilizes and keeps separated.

Telomerase

Adds DNA to telomeres in eukaryotic germ cells, healing their length after replication.

Topoisomerase

Breaks and rejoins DNA strands after trauma.

Telomere

Nucleotide sequences at the end of chromosomes

Act as buffer zones and delay shortening of genes

Histone

Protein molecules that pack DNA into chromatin in interphase.

Origins of Replication

Sites where DNA replication occurs

Prokaryotic Origin of Rep.

ONE circular chromosome

Eukaryotic Origin of Rep.

INFINITE number of linear chromosomes

Replication Fork

Y-shaped region

Parental strands unwind, and new strands are created.

Antiparallel Elongation

Two new strands must run ANTIPARALLEL to parent strands.

Okazaki fragment

Short strands of DNA that make up lagging strand.

DNA proofreading and repair

DNA polymerases check each nucleotide against its template as it's added. If incorrect, it's removed and corrected.

Mismatch repair

Enzymes fix DNA mistakes by removing and replacing incorrectly paired nucleotides.

Nucleotide excision repair

A repair system where damaged DNA is removed and replaced, using undamaged strand as template.

NUCLASE, DNA POLYMERASE, LIGASE

Damage can pass into replication accidentally.

Telomere function

Acts as a buffer zone, delays gene shortening/loss

Telomerase function

Adds DNA to telomeres, helping restore length.

Histones

Proteins that pack DNA in Interphase chromatin.

Eukaryotic DNA

• Nucelus

• Long

• Linear

• Many proteins (histones)

• No correlation with gene #

Prokaryotic DNA

• No Nucleus, uses cytoplasm

• Short

• Circular

• Fewer proteins

• Correlation with gene #

How is DNA packaged in the cell? How does this change throughout the cell cycle?

Prophase: Condensin II (Large Loops), Condensin I (Small Loops)

Metaphase: chromosomesare fully condensed, MOST dense

Euchromatin

• Less condensed chromatin

• Available for transcription (gene expression)

Heterochromatin

• Very compacted chromatin that stays condensed during Interphase

• Not used for gene expression

Central Dogma of Molecular biology

DNA —> RNA —> Protein

Prokaryotic Transcription/Translation

Cytoplasm

Eukaryotic Transcription/Translation

• Nucleus

• Cytoplasm

Transcription

a cell makes an RNA copy of a piece of DNA

Codon

3 nucleotides in mRNA that code for a specific amino acid or signal the end of protein synthesis. (Stop Signals)

Template strand

DNA Strand used as a guide to transcribe complementary RNA strand during transcription.

Coding Strand

• Not used as template for transcription

• Has same nucelutide sequence as transcribed RNA strand, but has T (Thymine) instead of U (Uracil)

TATA box

• Found in Eukaryotic promoters

• Transcription initiation complex

Transcription Factors

Proteins that bind to DNA, helping RNA polymerase attach to the template strand to initiate transcription.

Describe Eukaryotic pre-mRNA processing.

- Both exons and introns are transcribed into RNA.

• Introns: interrupted, removed via splicing.

• Exons: expressed.

• 5' cap is added.

• Poly-A tail is added.

• Location: Nucleus.

Alternative RNA splicing

• Different mRNA versions can be produced from the original transcript

• Depends on the exon included/excluded pattern.

Results of alternative RNA splicing

More than one kind of protein

Translation

• Happens in ribosomes in the cytoplasm

• The ribosome reads the mRNA codons

• tRNA has an anticodon that matches the mRNA codon.

• tRNA (transfer RNA) brings specific amino acids to the ribosome.

• They form a polypeptide chain, which becomes a protein

Wobble

• Third base of codon.

• Can pair with more than one base in tRNA anticodon

What happens to the polypeptide when released from ribosome?

• Modifications can happen

• Adding sugars, lipids, phosphates

• Join or cut polypeptides

• Remove amino acids

Signal proteins

• Amino acid tags on a polypeptide

• Tell cell where it should go

Nonsense mutation

• Premature stop codon

• Short protein

• Often non-functional

Mutation

• Change in nucleotides in DNA

• Affects all new genes

Silent Mutation

• Same amino acid

• ‘Silent’

Missense Mutation

Different amino acid.

• Can be a slight or drastic effect on protein.

Nonsense Mutation

Introduces a premature stop codon

• Short and often non-functional protein.

What is the difference between substitution, insertion, and deletion? What results in each case?

Substitution: One nucleotide is replaced by another. Can result in silent, missense, or nonsense mutations.

Insertion: Addition of one or more nucleotides. Can cause frameshift mutations, altering the entire protein sequence after the insertion point.

Deletion: Removal of one or more nucleotides. Similar to insertions, can cause frameshift mutations.