I. Central Dogma "Central Dogma": Term coined by Francis Crick to explain how information flows in cells.

II. DNA Replication A. Steps DNA helicase (enzyme) attaches to DNA molecule. Single Strand Binding Proteins ("SSBP's"): Keep the strand open Helicase moves along DNA breaking hydrogen bonds- “unzips” DNA into two strands. Each strand now has unpaired nitrogen bases.

Primase: Puts down a small RNA primer which is necessary for DNA polymerase to bind to at the origin. Free floating nucleotides in the nucleus form hydrogen bonds with unpaired nitrogen bases. DNA Polymerase bonds together nucleotides Topoisomerase: Rotates the DNA to decrease torque (which would shred the helix) Ligase (enzyme) repairs DNA a) Final result = 2 exact copies of DNA * Each copy = 1 “old” strand and 1 “new” strand

B. Replication occurs at many sites along DNA

If unzipped old segment = C-C-A-T-G-A-G-T What will the new segment be?

C. Leading and Lagging Strand 1. Nucleotides are added to the 3' end of the DNA strand a. DNA replication can only occur in the 5' to 3' direction 2. DNA is "anti-parallel": Both strands have opposite 5' to 3' orientations (one is "upside-down" compared to the other) 3. Leading strand made continuously 4. The other strand ("lagging strand") made in smaller, discontinuous fragments a) "Okazaki fragments"

D. Telomeres 1. Each round of replication shortens the 5' end of the lagging strand (by about 100-200 bp) 2. If this continued indefinitely, chromosomes would get shorter and shorter after each replication. a. Information would start to be lost

3. Telomeres at end of eukaryotic chromosomes a. short, repeating DNA sequence 4. TELOMERASE - enzyme responsible for replicating the ends of eukaryotic chromosomes a. add more telomere sequence during replication

III. RNA (Ribonucleic Acid) and Transcription Structure of RNA DNA RNA # of strands 2 Strands 1 Strand Type of Sugar Deoxyribose sugar Ribose Sugar Nucleotide Base pairs A-T C-G A-Uracil

Nucleic Acids

*All made in the nucleus and travel to the ribosomes 3 types of RNA *All made in the nucleus and travel to the ribosomes Messenger RNA (mRNA) Single straight strand Transmits DNA information Serves as template (pattern) for making proteins

Transfer RNA (tRNA) Single folded strand Complimentary bases pair up Also involved in protein synthesis

Ribosomal RNA (rRNA) Globular form Part of ribosome structure

Protein enzyme called RNA polymerase binds to DNA. Transcription – process of making RNA from DNA Protein enzyme called RNA polymerase binds to DNA. RNA polymerase separates portion of DNA into two separate strands. Free floating nucleotides in nucleus match their nitrogen bases with bases of “unzipped” DNA. DNA base code = C-G-A-T-A Complimentary RNA = G-C-U-A-U

RNA polymerase forms bonds (hydrogen) between nitrogen bases. Polymerase connects nucleotides by bonding sugars to phosphates Enzyme releases new RNA strand when it reaches “stop sign” on DNA.

GENE

Transcription happens in the nucleus. An RNA copy of a gene is made. Then the mRNA that has been made moves out of the nucleus into the cytoplasm Once in the cytoplasm, the mRNA is used to make a protein Cytoplasm of cell Nucleus DNA mRNA

D. Processing mRNA

A modified nucleotide is added to the 5' end of the transcript. A tail of several hundred adenine residues is put on the 3' end of the transcript. These modifications function in nuclear export and maintenance of the mRNA

4. Exons and Introns Eukaryotic genes contain large stretches of non-coding DNA ("introns") interspersed between coding DNA ("exons") To produce a functional protein, the introns must be removed the exons must be spliced together by a spliceosome

5. Why Introns? Not really answered. Evolutionary baggage? Selfish genes? We do know that having multiple exons in a gene allows eukaryotes to make multiple functional proteins from one gene ("alternative splicing")

IV. TRANSLATION - Protein Synthesis Many amino acids linked by peptide bonds 100’s to 1000’s of AA’s per protein 20 different AA’s Sequence of AA’s determine structure and function of each protein

Codon – a group of 3 sequential bases of an mRNA 64 different codons mRNA u c u u a g c u a g c g -How many codons? Each codon codes for: 1 of the 20 amino acids Start or stop codons

1. 3 base sequence at the bottom of tRNA C. Anticodon 1. 3 base sequence at the bottom of tRNA a) Matches the codon on mRNA strand

The code was cracked largely by Marshall Nirenberg Put synthetic RNA into "cell free" E. coli extract and analyzed the polypeptides that were made. Nobel Prize: 1968

D. Translation – putting amino acids (AA’s) together to build protein from info in mRNA mRNA and tRNA transcribed from DNA in nucleus. This RNA exits the nucleus through pores. mRNA travels to ribosomes.

Free floating AA’s are brought to ribosomes by tRNA. Protein always starts with methionine (aug) AA A second AA on tRNA enters ribosome. Codon and anticodon pair up and peptide bonds form between AA’s.

7. When a stop codon (UAG, UAA, or UGA) is encountered, a release factor binds to the A-site. 8. The polypeptide chain is released. 9. The ribosome disassembles.

The Process of Translation Figure 8.9

E. Translation in prokaryotes Since prokaryotes do not have a nucleus, transcription and translation can be coupled. Polyribosomes: simultaneous translation of a transcript (even while transcript is still being made.

V. Mutations Types 1. Point mutations: One DNA base is replaced by another DNA base. 2. Frame-shift mutations: DNA bases are inserted or deleted 3. Each type of mutation can have different effects, depending on the situation.

B. Point Mutations Silent - substitution changes a codon to another codon for the same amino acid. Missense - substitution changes a codon to a codon for a different amino acid Nonsense- substitution changes a codon to a stop codon

C. Frameshift Shift the codons Insertions – additions of a nucleotide Deletion – loss of a nucleotide Duplication – repeating sequences of codons

Review questions What does DNA polymerase do? What does Helicase do? What does ligase do? Match the bases below. 5’ – A T C G T A – 3’ List 3 differences between RNA/DNA. What are the 3 types of RNA? Where does RNA go after it is made?

What does RNA attach to when it leaves the nucleus What does RNA attach to when it leaves the nucleus? Amino Acids are the building block of ________. What type of RNA brings an amino acid? When does translation stop? Where is the codon located? Anticodon? What is a codon?