The Watson-Crick Model

The foundational three-dimensional structure of DNA

Ribonucleic Acid

A polymer consisting of several nucleotides, uses ribose(sugar), uracil(pyrimidine),and does not form helix(is single stranded), use primarily to synthesize proteins

mRNA(messenger RNA)

The first type of RNA molecule, Codes for a specific amino acid sequence (protein structure), nucleotides are “read” in groups of three called codons

tRNA(transfer RNA)

The second type of RNA molecule, transports amino acid to ribosome  Each binds to a specific amino acid  tRNA + amino acid = aminoacyl-tRNA  Contains an anticodon

rRNA(ribosomal RNA)

The third type of RNA molecule, Forms the ribosomes (site of protein synthesis)  Consists of a large subunit and a small subunit

Central Dogma of Molecular Biology

The sequential flow of information  “DNA makes RNA, and RNA makes Protein”  Proteins are the physical expression of a gene Involves three steps: Replication, Transcription, and Translation

Replication

The first step of Central Dogma Uses DNA to synthesize more DNA Each strand acts as a template for new copies  Starts one of many origin of replication points  Replication is bidirectional, constructed 5′ to 3′  Performed by a replisome (complex array of proteins)

The process of DNA replication

1. DNA is unwound at the origin of replication 2. Helicase opens DNA forming two replication forks 3. SSB proteins attach to prevent rewinding of DNA 4. Topoisomerase binds to DNA ahead of replication fork 5. Primase adds RNA nucleotides to form a primer 6. DNA Polymerase III adds DNA nucleotides starting at the primer 7. Elongation of both leading and lagging strands continues 8. DNA Polymerase I removes RNA Primers and replaces them with DNA nucleotides 9. DNA Ligase fills the gaps between DNA fragments by forming the needed phosphodiester bonds, making sure the new DNA molecule is complete

First step of DNA replication

DNA is unwound at the origin of replication

Second step of DNA replication

Helicase opens DNA forming 2 replication forks

Third step of DNA replication

SSB proteins attach to prevent rewinding of DNA

Fourth step of DNA replication

Topoisomerase binds to DNA ahead of replication fork

Fifth step of DNA replication

Primase adds RNA nucleotides to form a primer

Sixth step of DNA replication

DNA Polymerase III adds DNA nucleotides starting at the primer

Seventh step of DNA replication

Elongation of both leading and lagging strands continues

Eighth step of DNA replication

DNA Polymerase I removes RNA Primers and replaces them with DNA nucleotides

Ninth (and last) step of DNA replication

DNA Ligase fills the gaps between DNA fragments by forming the needed phosphodiester bonds, making sure the new DNA molecule is complete

Protein Synthesis

The process of turning DNA into protein Involves 2 steps: Transcription and Translation

Transcription

The first step in protein synthesis and gene expression

Deoxyribonucleic acid (DNA)

A polymer consisting of millions of nucleotides  Purine bases: Adenine and Guanine  Pyrimidine bases: Cytosine and Thymine  Nucleotides bonded 5′—3′  This forms a sugar—phosphate “backbone”  Forms a double helix  Hydrogen bonds hold strands together  Base pairing rule: A—T and C—G  Strands are complementary and antiparallelu

Transcription

The first step of protein synthesis and gene expression. Gene DNA is 'read' to make RNA -Occurs in the Nucleus DNA is used as a template for RNA synthesis - Non-coding(anti sense) strand is the template strand - Coding(sense) strand is the non-template strand

Translation

The second step of protein synthesis. mRNA is 'read' to make a protein -Occurs in the Cytoplasm, often on the Rough ER

Genetic Code

When genes(DNA) code for proteins(amino acids) It is universal to all life.

How many nucleotides are in DNA and RNA?

4 each

What are proteins composed of?

They are composed of amino acids.

How many nucleotides form a codon?

3

How many possible codons coding for 20 amino acids?

64

Transcription unit

-Coding sequence(gene) -Regulatory sequences -Promoters sequence(TATA box) - Transcription start site(TSS) - Terminator sequence(AATAAA)

Promoters

Occur upstream of the coding sequence Vary between 100-1000 bp long Recognition of the promoter involves the TATA box

Initiation step

Transcription factors(TF) bind to the promoter sequence RNA polymerase binds to the Transcription factors RNA polymerase forms a Transcription bubble

Transcription step

RNA polymerase reads DNA 3'-5': adding nucleotides to growing RNA molecule 5'-3'

Termination step

Transcription stops when Terminator sequence is encountered

Post Transcription processing of mRNA(not in order)

5' cap added (5 prime guanine cap) Poly-A tail added to 3' end -30-200 adenines Introns removed Exons spliced together

Translation step(RNA-> protein)

Occurs after post transcription Step 1. Initiation (1 start codon- AUG) -Small subunit added to mRNA -Initiation codon(AUG) codes for methionine -Large subunit attaches to tRNA at P-binding site Step 2. Elongation -tRNA binds to A-binding site - Peptide bond forms between amino acids - Ribosome shifts 3'-ward, exposing A-binding site -1st tRNA exits Step 3. Termination (3 stop codons- UAA, UAG, UGA) -Release factor enters A-binding site at stop codon - Polypeptide and Ribosome subunits released

First step in Translation

Initiation (1 start codon- AUG) -Small subunit added to mRNA -Initiation codon(AUG) codes for methionine -Large subunit attaches to tRNA at P-binding site

Second step in Translation

Elongation -tRNA binds to A-binding site - Peptide bond forms between amino acids - Ribosome shifts 3'-ward, exposing A-binding site -1st tRNA exits

Third step in Translation

Termination (3 stop codons- UAA, UAG, UGA) -Release factor enters A-binding site at stop codon - Polypeptide and Ribosome subunits released

Mutations

Altering the sequence of bases in the DNA

Gene Expression

Genes can be turned 'on' and 'off' as needed Chromatin modification - Histane acetylation - DNA methylation - Epigenetic inheritance (environmental change in genes) RNA interference -Noncoding RNA- involved with heterochromatin - MicroRNA- binds to mRNA and prohibits translation

DNA repeat sequences

Tandem repeats -Satellite DNA -Minisatellites Trinucleotide repeats Interspersed repeats New gene formation

Satellite DNA

Long arrays of tandem repeated, non-coding DNA 'Found mostly in centromeres, telomeres, and heterochromatin

Minisatellites

Repeat units 10-60 bp long

Microsatellites

Repeat units <10 bp long -simple sequence repeats(SSRs) and short-tandem repeats(STRs) -used in DNA finger printing(compares length of repeat region

Trinucleotide repeats(triplet repeats)-3 bp repeats

-Trinucleotide repeat disorders(triplet number increases)

Interspersed repeats

-Transposons -Retrotransposons(very common in plant genomes)

New gene formation

-Interspersed DNA elements can isolate alleles -This allows for the (potential) development of new genes