Chapter 12 and 13 DNA RNA and Protein

Chapter 12 and 13 DNA, RNA and Protein Synthesis Power. Point Lectures for Biology: Concepts and Connections, Fifth Edition – Campbell, Reece, Taylor, and Simon Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Discovery of the Role of DNA A. 1928 - Frederick Griffith discovers transformation in bacteria : * discovered that “something” was able to transform harmless (non – virulent) bacteria into harmful (virulent) Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Discovery of the Role of DNA (cont’d) B. 1944 -Oswald Avery and colleagues show that DNA can transform bacteria C. 1952 - Alfred Hershey and Martha Chase use bacteriophage to confirm that DNA is the genetic material Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Hershey-Chase Experiment: Infected cells make more virus by injecting their DNA animation 1 Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Discovery of the Role of DNA (cont’d) D. 1953 - James Watson and Francis Crick propose a structural model for the DNA molecule Based On: 1. X-Ray crystallography images prepared by Maurice Wilkins and Rosalind Franklin 2. Chargraff’s Rule: # of Adenines = # of Thymines # Guanines = # of Cytosines Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

DNA and RNA are Polymers of Nucleotides • Both are nucleic acids made of long chains of nucleotide monomers • A nucleotide (building block of a nucleic acid) has 3 parts: 1. A phosphate (PO 4 -) group that is negatively charged 2. A 5 -Carbon sugar (deoxyribose in DNA or ribose in RNA) 3. A nitrogencontaining base Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

DNA (deoxyribonucleic acid) bases: Thymine (T) Cytosine (C) Adenine (A) Guanine (G) pyrimidines Pyrimidines: single ring bases Purines: double ring bases Complimentary binding pattern: • Adenine + Thymine (share 2 hydrogen bonds) • Cytosine + Guanine (share 3 hydrogen bonds) Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings purines

RNA: ribonucleic acid Similar to DNA except: • Sugar in RNA = ribose • Base “uracil” instead of thymine • Single stranded Figure 10. 2 C, D Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

The Structure of DNA • Two polynucleotide strands wrapped around each other in a double helix • A sugar-phosphate backbone • Steps made of hydrogen-bound bases (A=T, C = G) Twist Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

DNA REPLICATION: Starts with the separation of DNA strands • Enzymes use each strand as a template to assemble new nucleotides into complementary strands…“semi-conservative” (Meselson & Stahl 1958) • Portions to be replicated must untwist first Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

DNA replication begins at specific sites on double helix 1. DNA segments unwind 2. 2. Helicase splits H bonds between bases, unzip DNA replication forks 3. 3. Binding proteins keep unzipped DNA apart (Single Stranded Binding Proteins) 4. 4. Primase makes a short RNA primer because DNA polymerase can only extend a nucleotide chain, not start one. 5. 5. DNA polymerase adds new nucleotides to the 3’ end of daughter strand that are complimentary to the parent strand 6. 6. RNase H cuts out original primers 7. 7. DNA polymerase fills in gap of removed primers 8. 8. DNA ligase glues S/P backbone where needed Animation/tutorial 9. Two identical double helices • Topoisomerase: prevents further coiling at replication fork Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

A Structural Problem with DNA Replication • Each strand of the double helix is oriented in the opposite direction (“anti-parallel”) • “prime” #’s refer to carbons in the sugar • At one end, the 3’ carbon has an (OH) and at the opposite, a 5’ carbon has the PO 4 - • Why does this matter? DNA polymerase can only add nucleotides to the 3’ end. A daughter strand can only grow from 5’ 3’ • Therefore, only one daughter strand is made continuously (leading strand) • The other strand (lagging strand) is made in a series of short pieces (Okazaki fragments), later connected by DNA ligase Animation/tutorial Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings animation

When DNA can repair mistakes and when it can’t DNA Repair enzymes work like a spell checker • Cut out wrong sequences • Undamaged strand is template • Only 2 or 3 stable changes per year : some severe, others are not • Mutations Inheritable changes occur in gametogenesis • • Now the “wrong” sequences are copied – Ex: cystic fibrosis (CF): a deletion of 3 nucleotides in a certain gene – Ex: sickle cell anemia: one nucleotide substitution in the hemoglobin gene Mutagen: a mutation causing substance (can break DNA) – Ex: X-Rays, radioactivity, nicotine Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Protein Synthesis: the transfer of information from: DNA RNA Proteins “gene expression”: A gene is a linear sequence of many nucleotides. 3 Types: 1. Structural genes: have info to make proteins 2. Regulatory genes: are on/off switches for genes 3. Genes that code for t. RNA, r. RNA, histones DNA • double stranded • A T C G • deoxyribose sugar vs. • • RNA single stranded A U C G ribose sugar 3 types of RNA: • messenger, transfer, ribosomal m. RNA (messenger): copies DNA’s message in nucleus brings it to cytoplasm t. RNA (transfer): carries amino acids to m. RNA so protein can be made r. RNA (ribosomal): major part of the ribosome. Helps link amino acids from t. RNA’s together assemble protein Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Protein Synthesis is Two Steps: 1. Transcription: The DNA of the gene is transcribed into m. RNA 2. Translation: decoding the m. RNA and assembling the protein Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Transcription: Eukaryote • DNA sequence (message for protein) is transcribed by m. RNA • Only one strand (non-coding strand) is needed as a template • Steps: 1. 2. 3. 4. 5. 6. RNA polymerase splits H bonds in DNA section RNA polymerase travels along non-coding strand of DNA. RNA nucleotides join in a complimentary pattern (A=U, C=G) A termination signal is reached, transcription is over m. RNA strip detaches from DNA, DNA helix closes up m. RNA is processed: Introns are cut out, Exons are glued together, cap and tail are added. Mature m. RNA leaves nucleus through pores cytoplasm for next step Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Translation: the synthesis of proteins using m. RNA, t. RNA and ribosomes • The Genetic Code: the language in which instructions for proteins are written in the base sequences • Each triplet of m. RNA bases is a “codon” because it will “code” for 1 amino acid – Ex: AUG GUC CCU AAU CCU Met – Val – Pro – Asn – Pro – Original coding strand of DNA (the actual gene): ATG GTC CCT AAT CCT • Only difference: U is substituted for T – Use the Genetic Code chart to “decode” m. RNA message Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

The Genetic Code is the Rosetta Stone of Life – –Nearly all organisms use exactly the same genetic code – More than one codon for most amino acids = degenerate nature…a change (mutation) in gene does not always mean a different amino acid. – what does CAU code for? ACU? UAU? GCC? – how many codons for Leu? – what is special about AUG and it’s amino acid, Methionine? – what is special about UAA, UAG, and UGA? Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

An exercise in translating the genetic code: Step 1: fill in corresponding DNA bases to dark blue strand (non-coding) Step 2: Transcribe the dark blue strand into m. RNA (pink) A T G A A Coding strand (gene) Step 3: Translate the codons into correct amino acids (use chart) Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings G T T transcription translation A G

An exercise in translating the genetic code: answers Step 1: fill in corresponding DNA bases to dark blue strand (non-coding) Step 2: Transcribe the dark blue strand into m. RNA (pink) Step 3: Translate the codons into correct amino acids (use chart) Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

How Does Translation Happen? Need: t. RNAs and ribosomes (r. RNA) t. RNA: single stranded RNA, folded up – 2 parts: anticodon and aa attachment site Ribosome: 2 protein subunits and ribosomal RNA • allows aa’s to attach by making peptide • • bonds travels along m. RNA strip, t. RNA’s join and bring correct amino acids 3 sites on ribosome: • A site – where new t. RNA’s and amino acids join • P site – where protein is growing • E site – where empty t. RNA’s exit ribosome Translocation: as ribosome moves, t. RNA’s move from A site to P site. “A” site is now open for new t. RNA with attached amino acid to join animation Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Put It All Together: Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

Mutations can change the message of genes Mutations: • changes in DNA base sequence • caused by errors in DNA replication, recombination, or by mutagens • substituting, inserting, or deleting nucleotides also alters a gene “point mutation”…may or may not alter amino acid sequence “frame-shift mutation”…most devastating to protein structure Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings

MUTANTS – • Mutant Animals! Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings