THE STRUCTURE OF THE GENETIC MATERIAL 1

DNA is a Double-Stranded Helix In 1953, James D. Watson and Francis Crick deduced the structure of DNA, using X-ray crystallography data of DNA from the work of Rosalind Franklin and Maurice Wilkins and Chargaff’s observation that in DNA the amount of adenine was equal to the amount of thymine and the amount of guanine was equal to that of cytosine. 2

DNA is a Double-Stranded Helix Watson and Crick reported that DNA consisted of two polynucleotide strands wrapped into a double helix. The sugar-phosphate backbone is on the outside. The nitrogenous bases are perpendicular to the backbone in the interior. Specific pairs of bases give the helix a uniform shape. A pairs with T, with two hydrogen bonds G pairs with C, with three hydrogen bonds 3

DNA and RNA are Polymers of Nucleotides DNA and RNA are nucleic acids composed of long chains of nucleotides A nucleotide contains a nitrogenous base, five-carbon sugar, and phosphate group Nucleotides are joined to one another by a sugar-phosphate backbone. © 2012 Pearson Educaton, Inc. 4

Each DNA nucleotide has a different nitrogenous base: Adenine (A), Cytosine (C), Guanine (G) or Thymine (T) Nitrogenous base (A, G, C, or T) Thymine (T) Phosphate group Figure 10.2A_3 The structure of a DNA polynucleotide (part 3) Sugar (deoxyribose) DNA nucleotide 5

Nitrogenous Bases of DNA Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Pyrimidines Purines Figure 10.2B The nitrogenous bases of DNA 6

Each RNA nucleotide also has a different nitrogenous base: Adenine (A), Cytosine (C), Guanine (G) or Uracil (U) Nitrogenous base (A, C, G, or U) Figure 10.2C An RNA nucleotide Sugar (ribose) 7

The DNA Molecule is Antiparallel The polynucleotide strands of DNA run in opposite directions or, are antiparallel DNA has 5’ (prime) and 3’ (prime) ends The sugar on the 3’ end is attached to a hydroxyl group The sugar on the 5’end is attached to a phosphate group

Partial chemical structure Phosphate group on 5’ end Hydrogen bonds Hydroxyl group on 3’ end G C T A A T Figure 10.3D_2 Three representations of DNA (part 2) C G Partial chemical structure 9

DNA Replication Depends on Specific Base Pairing Rules DNA replication follows a Semiconservative Model The two DNA strands separate and serve as templates for new DNA Enzymes read parental strands, linking nucleotides according to base pairing rules; this forms complementary strands This follows the Semiconservative Model of replication because half of the parental molecule is kept (conserved) in each new DNA helix DNA replication ensures that all somatic cells in a multicellular organism carry the same genetic information 10

Daughter DNA molecules A T G C A T Parental DNA molecule A T T A C G C G T Daughter strand A C G C G C G Parental strand T C G A Figure 10.4B The untwisting and replication of DNA C G A T T A A T C G G C A T T A T A A T G C Daughter DNA molecules 11

DNA Replication Proceeds in Two Directions at Many Sites Simultaneously DNA replication begins at the origins of replication where, DNA unwinds producing a replication bubble Replication proceeds in both directions from the origin Replication ends when products (new DNA) from the bubbles merge 12

Two daughter DNA molecules Parental DNA molecule Origin of replication Parental strand Daughter strand “Bubble” Figure 10.5A Multiple bubbles in replicating DNA Two daughter DNA molecules 13

Daughter Strand Synthesis in DNA Replication Both daughter strands are synthesized 5’ to 3’; new nucleotides are only added to the 3’ end of a growing strand The daughter strand that is synthesized toward the replication fork in one continuous piece is the leading strand The daughter strand synthesized away from the replication fork in (Okazaki) fragments is the lagging strand Lagging strand synthesis is due to the antiparallel nature of DNA 14

Leading Strand Lagging Strand 3 DNA polymerase molecule 5 Parental DNA 5 3 Replication fork Lagging Strand 3 5 https://www.youtube.com/watch?v=TEQMeP9GG6M 5 3 DNA ligase Overall direction of replication 15

DNA Replication Requires a Host of Enzymes Important Enzymes are involved in DNA replication Helicase-breaks H-bonds, unwinding (separating) the DNA double helix DNA polymerase reads template strand and adds nucleotides to a growing chain, proofreads and corrects improper base pairings DNA ligase joins Okazaki fragments into a continuous DNA strand *DNA polymerases and DNA ligase also repair damaged DNA* 16

THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN 17

Connections between genes and proteins: The DNA Genotype is Expressed as Proteins, Which Provide the Molecular Basis for Phenotypic Traits Connections between genes and proteins: In the 1940’s Beadle and Tatum hypothesized that one gene codes for one enzyme by doing studying inherited metabolic diseases Their hypothesis is still accepted but with important changes: The hypothesis includes all proteins and that one gene codes for one polypeptide 18

The DNA Genotype is Expressed as Proteins, Which Provide the Molecular Basis for Phenotypic Traits DNA specifies traits by determining the sequence of amino acids in a protein; proteins give us our phenotype so genotype determines phenotype The molecular chain of command is from DNA to RNA to protein Transcription is the synthesis of RNA using DNA as a template. Translation is the synthesis of proteins using RNA as a template. 19

DNA Transcription RNA NUCLEUS CYTOPLASM Translation Protein Figure 10.6A_s3 The flow of genetic information in a eukaryotic cell (step 3) Protein 20

Genetic Information in DNA is written in mRNA as Codons The genetic instructions for the amino acid sequence of a polypeptide is written in DNA as three base sequences called triplets During transcription triplets in DNA are copied into complementary three base sequences in mRNA called codons Each codon determines the amino acid to be added to a growing polypeptide chain 64 codons are possible A A A C C G G C A A A A Transcription U U U G G C C G U U U U Translation amino acid 1 Polypeptide amino acid 2 amino acid 3 amino acid 4 21

Second base First base Third base Figure 10.8A Dictionary of the genetic code (RNA codons) 22

Transcription RNA polymerase oversees transcription by RNA polymerase oversees transcription by Unwinding DNA, reading DNA bases, and joining appropriate RNA nucleotides together RNA polymerase synthesizes (all) RNA molecules Transcription occurs in Three Phases: Initiation - RNA pol. binds the promoter Elongation - mRNA strand grows longer Termination –RNA pol. reaches the terminator sequence and detaches from mRNA and the gene 23

RNA polymerase Terminator DNA DNA of gene Promoter DNA 1 Initiation Figure 10.9B_1 The transcription of a gene (part 1) 24

2 Elongation Area shown in Figure 10.9A Growing RNA Figure 10.9B_2 The transcription of a gene (part 2) Growing RNA 25

Growing RNA 3 Termination Completed RNA RNA polymerase Figure 10.9B_3 The transcription of a gene (part 3) Completed RNA RNA polymerase 26

Eukaryotic mRNA Messenger RNA (mRNA) Messenger RNA (mRNA) The RNA formed from transcription, carrying information to build a protein is called mRNA mRNA carries the message from DNA (nucleus) to ribosomes (cytoplasm) In prokaryotes transcription and translation occur at the same place and time In eukaryotes, mRNA exits nucleus via nuclear pores Eukaryotic mRNA has introns or interrupting sequences that separate exons or coding regions 27

Eukaryotic RNA is Processed Before Leaving the Nucleus mRNA processing : Occurs in nucleus of eukaryotic cells Involves the addition of extra nucleotides to the ends of mRNA. A 5’ guanine cap and 3’ poly A tail helps to: facilitate export of mRNA from nucleus protect mRNA from attack by cellular enzymes help ribosomes bind mRNA RNA splicing removes introns and joins exons to produce a continuous coding sequence. 28

Transcription Addition of cap and tail Cap Exon Intron Exon Intron Exon DNA Transcription Addition of cap and tail Cap RNA transcript with cap and tail Introns removed Tail Exons spliced together mRNA Coding sequence Figure 10.10 The production of eukaryotic mRNA NUCLEUS CYTOPLASM 29

The Genetic Code Dictates How Codons are Translated into Amino Acids Translation involves switching from nucleotide “language” to amino acid “language” tRNA’s act as interpreters Transfer RNA (tRNA) molecules read codons in mRNA to help synthesize a polypeptide chain Each tRNA has a three base sequence or anticodon it uses to read an mRNA codon Amino acid attachment site Anticodon 30

T A C T T C A A A A T C A T G A A G T T T T A G A U G A A G U U U U A Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Transcription RNA A U G A A G U U U U A G Figure 10.8B_s3 Deciphering the genetic information in DNA (step 3) Start codon Stop codon Translation Polypeptide Met Lys Phe 31

The Genetic Code Dictates How Codons are Translated into Amino Acids Characteristics of the Genetic Code Three RNA nucleotides (one codon) specify one amino acid AUG = the start codon signals the ribosome to start translating; AUG also codes for methionine There are 3 “stop” codons that signal the ribosome to stop translating The Genetic Code is: Redundant, there is more than one codon for the same amino acid Unambiguous, any codon for an amino acid does not code for any other amino acid Nearly universal, the genetic code is shared by organisms from the simplest bacteria to the most complex plants and animals 32

Ribosomes Build Polypeptides With the Help of tRNA’s Translation occurs on the surface of a Ribosome. Ribosomes have binding sites for mRNA and tRNA to coordinate protein synthesis Ribosomes have small and large subunits composed of ribosomal RNA (rRNA) and proteins The next amino acid to be added to the polypeptide Growing polypeptide tRNA Codons mRNA 33

Translation Translation occurs in Three Phases Initiation Translation Translation occurs in Three Phases Initiation An mRNA molecule binds to a small ribosomal subunit and the first tRNA binds to mRNA at the start codon The first tRNA has the anticodon UAC The large ribosomal subunit joins the small subunit, forming a functional ribosome The first tRNA occupies the P site, which will hold the growing polypeptide chain The A site is available to receive the next tRNA 34

Large ribosomal subunit Met Met Initiator tRNA Large ribosomal subunit mRNA P site A site U A C U A C A U G A U G Start codon Figure 10.13B The initiation of translation Small ribosomal subunit 1 2 35

Translation Elongation involves the addition of amino acids to the polypeptide chain. Each cycle of elongation has three steps. Codon recognition: The anticodon of an incoming tRNA molecule, (w/ its amino acid), pairs with the mRNA codon in the A site of the ribosome. Peptide bond formation: The new amino acid is joined to the chain held by tRNA in A site. Translocation: the P site tRNA now lacking an amino acid leaves ribosome; the ribosome moves tRNA (holding the polypeptide) from the A site to the P site. 36

Polypeptide Amino acid Anticodon mRNA Codons Codon recognition P site A site Anticodon mRNA Codons 1 Codon recognition mRNA movement Stop codon Figure 10.14_s4 Polypeptide elongation (step 4) 2 Peptide bond formation New peptide bond 3 Translocation 37

Translation Termination The Ribosome reaches a stop codon Translation Termination The Ribosome reaches a stop codon The completed polypeptide is freed from the last tRNA The ribosome splits into separate subunits 38

Mutations Can Change the Meaning of Genes A mutation is any change in the nucleotide sequence of DNA. Mutations can be caused by spontaneous errors that occur during DNA replication or crossing over mutagens, like high-energy radiation (X-rays), UV light and chemicals, viruses 39

Mutations Can Change the Meaning of Genes Mutations within a gene can be divided into two general categories. Base substitutions involve the replacement of one nucleotide and its base pairing partner. Base substitutions may Produce a silent mutation there is no effect on the polypeptide because the right amino acid is still added Produce a missense mutation where the mutation causes the wrong amino acid to be added to the polypeptide Produce a nonsense mutation where the mutation produces a stop codon in the mRNA instead of an amino acid. 40

Mutations Can Change the Meaning of Genes Mutations can result in deletions or insertions that may Cause frame shift mutations that alter the reading frame (triplet grouping) of the mRNA; all nucleotides after the insertion or deletion will be regrouped into different codons This leads to significant changes in amino acid sequence downstream of the mutation, and produces a nonfunctional polypeptide 43