Ch. 12 DNA and RNA What kind of DNA do clones have? Xeroxyribonucleic Acid What kind of DNA do joggers have? Reeboxyribonucleic Acid

Chapter 12 Outline 12-1: DNA Griffith and Transformation Avery and DNA The Hershey-Chase Experiment The Components and Structure of DNA 12-2: Chromosomes and DNA Replication DNA and Chromosomes DNA replication

Chapter 12 Outline 12-3 RNA and Protein Synthesis The structure of RNA Types of RNA Transcription RNA Editing The Genetic Code Translation The Roles of RNA and DNA Genes and Proteins

Chapter 12 Outline 12-4: Mutations Kinds of Mutations Significance of Mutations 12-5: Gene Regulation Gene Regulation: An Example Eukaryotic Gene Regulation Development and Differentiation

Griffith and Transformation The discovery of how the molecular structure of a gene began in Frederick Griffith was trying to figure out how bacteria make people sick. Griffith’s Experiments: Griffith injected mice with one of two strains of bacteria (one harmless and one that caused pneumonia). The harmful bacteria caused the mice to die. Next, Griffith heated some of the disease-causing bacteria and injected it, but the mice lived. This confirmed that the bacteria did not produce a poison. What happened?

Griffith’s Experiment (con’t) Finally, Griffith injected some of the heated disease-causing bacteria with some of the harmless bacteria into the mice, and, to his amazement, many of them died. Griffith named this process transformation because the bad bacteria had transferred their disease causing abilities to the harmless bacteria.

Griffith’s Experiment Disease-causing bacteria (smooth colonies) Harmless bacteria (rough colonies) Heat-killed, disease- causing bacteria (smooth colonies) Control (no growth) Heat-killed, disease-causing bacteria (smooth colonies) Harmless bacteria (rough colonies) Dies of pneumoniaLives Live, disease-causing bacteria (smooth colonies) Dies of pneumonia

Avery and DNA In 1944, Griffith’s work was repeated by Oswald Avery and added enzymes to digest molecules. The digested macromolecules then couldn’t be the molecule passing on information in their experiments. Avery and other scientists discovered that the nucleic acid DNA stores and transmits the genetic information from one generation to another.

The Hershey-Chase Exp. Alfred Hershey and Martha Chase worked together in 1952 to study DNA in viruses. They studied one particular type of virus called a Bacteriophage. Bacteriophage: Virus that infects Bacteria Their research supported the fact that genetic material was DNA

The Hershey-Chase Exp. Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium

Hershey-Chase Exp. Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium

The Hershey-Chase Exp. Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium

The Components and Structure of DNA Scientists knew that DNA has 3 functions: 1. Genes had to carry info from one generation to the next. 2. Genes put information to work by determining the inheritable characteristics of an organism. 3. Genes have to be easily copied because genes are replicated every time a cell divides DNA is made up of monomers called nucleotides. Components of a nucleotide: 5-carbon sugar (deoxyribose) Phosphate Group Nitrogenous Base

The Components and Structure of DNA Four types of nitrogenous bases: Guanine Adenine Cytosine Thymine Purines: Double-Ring structure Adenine and Guanine Pyrimidines: Single Ring Cytosine and Thymine Backbone of DNA: Sugar-Phosphate

The Bases PurinesPyrimidines AdenineGuanine CytosineThymine Phosphate group Deoxyribose

Chargaff’s Rules After finding out that DNA was a series of nucleotides, with the nitrogen bases in random and different orders, scientists still worked to figure out the complete structure of DNA. Erwin Chargaff discovered that the percentage of A’s and T’s was equal and C’s and G’s was equal. A=T and C=G became known as Chargaff’s rules

X-ray Evidence Around this same time (late 1940’s – early 1950’s), Rosalind Franklin discovered that DNA was a double helix. She used a process called X-ray Diffraction She shot X-rays at the DNA and recorded where the X-rays reflected. Her picture did not reveal the exact structure, but it did paint the picture.

The Double Helix In addition to Franklin and Chagraff’s work, two scientists named Watson and Crick were determined to discover the structure of DNA. Once given Franklin’s results, they discovered the actual structure of DNA and made a model of it. This model is a double helix, in which the nitrogenous bases are connected in the middle by hydrogen bonds.

The Double Helix Bonding Pattern: A and T are joined by two hydrogen bonds and C and G are joined by 3 hydrogen bonds. They always bond in this pattern, which explain’s Chargaff’s rules. This is called base pairing.

Structure of DNA Hydrogen bonds Nucleotide Sugar-phosphate backbone Key Adenine (A) Thymine (T) Cytosine (C) Guanine (G)

DNA and Chromosomes Prokaryotes: DNA molecules out in cytoplasm, most bacteria have circular DNA, called a plasmid. Eukaryotes: much more complicated because there is about 1000x as much DNA as a prokaryote. DNA not found out in cytoplasm, it’s in the nucleus in the form of chromosomes The Number of chromosomes varies between organisms

DNA and Chromosomes Chromosome Structure Chromatin: long, stringy DNA in the cell DNA is wrapped around proteins called histones DNA cell division, the chromatin condenses to form tightly packed structure called a chromosome.

Prokaryote DNA Structure Chromosome E. coli bacterium Bases on the chromosome

Chromosome structure Chromosome Supercoils Coils Nucleosome Histones DNA double helix

DNA replication Watson and Crick’s model of DNA became a quick success because it revealed the mechanism by which DNA can copy itself. Each strand of DNA can be used to make another strand. Because of this we say that DNA is “complementary”. Replication: The process of duplicating DNA

DNA replication How DNA replicates: DNA separates into two strands Two new strands are produced using the base pairing rules What separates the DNA? An enzyme called helicase separates the DNA (by breaking apart the hydrogen bonds) What builds the new strands of DNA? An enzyme called DNA polymerase

DNA replication DNA replication occurs at hundreds of places at once until the entire strand is copied. Replication fork: The site where replication begins in each section of DNA

RNA and Protein Synthesis Genes: Coded DNA instructions that control the production of proteins within a cell In order to make a protein, DNA is copied into RNA (ribonucleic acid). RNA then carries the code to make a protein.

The Structure of RNA Monomer: Nucleotides Differences between RNA and DNA: 1. Single Stranded 2. Ribose Sugar 3. Uracil instead of Thymine Types of RNA: Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

Concept Map fromtoto make up Section 12-3 also calledwhich functions toalso called which functions to can be RNA Messenger RNA Ribosomal RNA Transfer RNA mRNACarry instructions rRNA Combine with proteins tRNA Bring amino acids to ribosome DNARibosomeRibosomes

Structure of RNA All three types of RNA are involved with making proteins mRNA – carries the DNA copy of genes tRNA – carries amino acids that link together to make a protein rRNA – makes up ribosomes (the site of protein synthesis)

Transcription Transcription is the process of making an mRNA copy of DNA. Why make a copy of DNA to make proteins? Because DNA never leaves the nucleus, it’s protected there! mRNA goes out into the cytoplasm where proteins are made. An enzyme called RNA polymerase (very similar to DNA polymerase) is required for transcription to happen. RNA polymerase binds to DNA and separates the strands. It also reads one strand of DNA (the template) and assembles nucleotides to make a corresponding strand of RNA.

Transcription How does RNA polymerase “know” where to start and stop? Promoters: specific base sequences on DNA that signal RNA polymerase to start transcribing. A similar process occurs to signal stopping.

RNA editing DNA is extremely long and contains a lot of sequences that don’t code for any amino acids. Only small sections of DNA actually code for proteins. Introns – Non-coding sections of DNA Exons – DNA segments that code for proteins When mRNA is made from DNA, both introns and exons are copied

RNA Editing Introns are cut out of mRNA and the remaining exons are “spliced” together so the mRNA can read it to make a protein So what is the purpose of introns? Scientists continue to research that question. The believe it might be leftover DNA from Evolution (they call it “junk DNA”)

Genetic Code Proteins are made by joining amino acids into long chains called polypeptides. The properties of proteins are determined by the order in which different amino acids are joined together. So how do the order of nitrogen bases in DNA and RNA code for the order of amino acids in a protein? The “language” of mRNA instructions is called genetic code.

The Genetic Code Four bases in the code: A, U, C, G How do these four letters code for 20 different Amino acids? The Genetic Code is read three letters at a time. For example, “GUC” Codes for the amino acid, serine. The three letter “word” in the genetic code is called a codon. Codon: three consecutive nucleotides that specify a single amino acid.

The Genetic Code Example: mRNA – UCGCACGGU Codon – UCG-CAC-GGU Amino Acids – Serine-histadine-glycine There are 64 possible codons in the genetic code. Therefore, one amino acid can be specified by more than one codon Ex. Lysine (AAG or AAA)

The Genetic Code Three of these codons signal “stop” and don’t code for an amino acid. One signal “start” (AUG) or the amino acid, methionine.

Genetic “Decoder”

Translation The sequence of nucleotide bases in an mRNA molecule serves as instructions for the order in which amino acids line up to make the primary structure of a protein. Translation: the decoding of an mRNA message into a protein Location: this all takes place on a ribosome

Translation To understand the process of translation, we must first learn the structure of tRNA. tRNA’s carry amino acids Each tRNA can only carry one amino acid At the bottom of every tRNA molecule is an anticodon Anticodon: a three-nucleotide sequence that is complimentary to an mRNA codon

Translation The process: mRNA attaches to a ribosome in the cytoplasm The codons are read by the tRNA If the tRNA anticodon matches up with the codon, then tRNA delivers its amino acid. The Amino acid is transferred to the growing polypeptide chain The empty tRNA molecule (without any Amino acid) then leaves The Ribosome then shifts down so that another codon can be read The Process repeats until a stop codon is reached.

Translation

Mutations Sometimes there are mistakes in copying DNA. Mutations: Changes in the genetic material Kinds of Mutations Gene Mutations Changes in a single gene Chromosome Mutations Changes in whole chromosomes

Gene Mutations Point mutations – a change in one or a few nucleotides Substitution Insertion Deletion Insertion and deletion mutations can be more dangerous than a simple change in one amino acid (sub). The code is still read in groups of three. Inserting an extra nitrogen base will throw off the entire “reading” of the code.

Gene Mutations Frameshift Mutations – shift the reading frame of the genetic message These can lead to a completely different protein Substitution Insertion Deletion

Chromosome Mutations This involves a change in an entire chromosome, not just one or a few bases. Four types: Deletion Duplication Inversion Translocation

Chromosomal Mutations Deletion Duplication Inversion Translocation

Significance of Mutations Many mutations are neutral and have no effect on the expression of genes (making of proteins!). Some have very harmful effects (defective proteins). Others are beneficial. Ex. Polyploidy – the condition of having an extra set of chromosomes (good for plants) Mutations are a source of genetic variation, and variation can be beneficial

Gene Regulation How does an organism “know” when to turn a gene on (and make a protein) or off? An example of gene regulation: In E. coli, there is a cluster of 3 genes that are turned on or off together. This cluster is called the lac operon (operon: cluster of genes that work together) because it is turned on to help bacteria use lactose as food.

Gene Regulation The lac genes are turned off by the repressors and turned on by the presence of lactose. On one side of the 3 genes there are two important regulatory regions: Promoter and operator Promoter (P) – RNA Polymerase binds and transcription begins Operator (O) – Contains repressor protein (blocks transcription). Transcription can only happen when the lac repressor protein is removed. It is removed when lactose binds to it.

Eukaryotic Gene Regulation The lac operon represents a simple version of gene regulation. It is often much more complicated in eukaryotic cells. Before many eukaryotic genes, there is a sequence of nucleotides “TATATATA” or “TATAAA”. This marks where genes will begin so the RNA polymerase knows where to bind. It is so common in eukaryotic cells that it has a name  the “TATA box”