The Structure and Function of DNA

Chapter 10Winter Quarter 2015

The H1N1 Virus• In 2009, a cluster of unusual flu cases broke out around Mexico City• In June 2009, the World Health Organization (WHO)

• declared H1N1 a pandemic (global epidemic) and• unveiled a massive effort to contain it.

• Scientists soon determined that H1N1 was a hybrid flu strain, made when• a known flu virus mixed with• an Asian swine flu virus.

• The hybrid H1N1 flu strain had a combination of genes that infected young, healthy people instead of the elderly or people who were already sick

• Many countries produced a coordinated response, and the WHO declared the pandemic over in August 2010

• Each year in the United States, over 20,000 people die from influenza infection

• From 1918 to 1919, the deadliest pandemic killed about 40 million people worldwide in just 18 months

DNA

• Macromolecule • built of nucleotides: dAMP, dCMP. dGMP, dTMP• Sugar-phosphate backbone• Bases project to the side• Duplex: two opposite strands with the bases hydrogen bonding

together• A:T, C:G

• Sugar = deoxyribose

DNA RNA

Sugar Deoxyribose Ribose

Bases A, C, G and T A, C, G and U

Locations Nucleus, Mitochondria, Chloroplasts

Nucleus, Mitochondria, Chloroplasts, Cytoplasm

Primary StructureFig 10.1 p 174

Sequence of nucleotides joined by sugar-phosphate bonds

Sequence of nucleotides joined by sugar-phosphate bonds

Secondary Structure

Helix Various Figure 10.2, p 175

Quaternary Structure

Double stranded Single or double stranded

DNA Replication

• complete copy of the DNA must pass from one generation to the next• all the body cells in multicellular organisms carry the same genetic information• DNA replicates by a template mechanism Fig 10.6, p 177

• begins at specific sites on a double helix (called origins of replication) and• proceeds in both directions

• DNA polymerases• enzymes• make the covalent bonds between the nucleotides of a new DNA strand• involved in repairing damaged DNA

Information in DNA Molecules

• DNA provides instructions to• a cell and an organism as a whole• Describes the proteins (enzymes, structural proteins) and the ways they are

used• A parts list and instruction manual rolled into one

• Beadle and Tatum: one gene : one enzyme• Genotype: genetic makeup, the sequence of nucleotide bases in DNA• Phenotype: the organism’s physical traits, which arise from the

actions of a wide variety of proteins• Figure 10.8, p 178

Overview of Gene Expression

DNA specifies the synthesis of proteins in two stages:• transcription, the transfer of genetic information from DNA into an RNA

molecule • translation, the transfer of information from RNA into a protein

• DNA has coding and non-coding sequences. • Coding sequences are transcribed and translated• Non-coding sequences regulate these and other processes

Genetic Code

• Codon: a three nucleotide sequence = one amino acid• 64 possible codons 43; • 61 codons define 22 amino acids; multiple codons/aa • start and stop codons

• Nearly universal across organisms• Crucial for genetic engineering• Multiple codons per amino acid – codon usage bias

Transcription - 1

• makes RNA from a DNA template,• process resembles the synthesis of a DNA strand during DNA

replication• substitutes uracil (U) for thymine (T)• Initiation

• Begins at promoters, located at the beginning (5’-end) of a gene• RNA polymerase attaches• First amino acid = methionine

Transcription 2

• Elongation• RNA Chain grows longer• Nucleotides are joined to the chain one-by-one• RNA strand peels away from the DNA template

• Termination• Occurs when polymerase reaches a stop codon• Polymerase detaches from DNA strand

• Figure 10.13, page 181

RNA Processing• Transcript: direct RNA copy of the DNA

• Introns: (noncoding regions of the RNA)• Exons: directly correspond to eventual protein sequence• Exons are expressed

• Transcript processing occurs in the nucleus• Splicing: removal of introns; • Addition of a “cap” at the 5’-end or the tail (the 3’-end)• Product is messenger RNA or mRNA• Allows 21000 genes to produce thousands more polypeptides

• Other forms of RNA transcript• Ribosomal (rRNA) and transfer RNA (tRNA) are used for protein synthesis• snRNAs and similar sequences regulate cell function

Translation

• conversion from the nucleic acid language to the protein language• Machinery:

• mRNA• ATP• enzymes• ribosomes• transfer RNA (tRNA)

Transfer RNA

• acts as a molecular interpreter,• carries amino acids, and• matches amino acids with codons in mRNA using anticodons, a

special triplet of bases that is complementary to a codon triplet on mRNA

Ribosomes

• organelles that• coordinate the functions of mRNA and tRNA • made of two subunits.

• each subunit is made up of• proteins and • a considerable amount of ribosomal RNA (rRNA).

• fully assembled ribosome • holds tRNA and mRNA for use in translation• Has two sites, A and P, each holds a tRNA Figure 10.18, p 184

Translation Process - 1• Initiation

• brings together mRNA, the first amino acid with its attached tRNA, and two subunits of the ribosome.• mRNA molecule has a cap and tail that help the mRNA bind to the ribosome• Initiation occurs in two steps• An mRNA molecule binds to a small ribosomal subunit, then a special initiator tRNA binds to the start

codon, where translation is to begin on the mRNA.• A large ribosomal subunit binds to the small one, creating a functional ribosome.

• Elongation• Step 1: Codon recognition. The anticodon of an incoming tRNA pairs with the mRNA codon at the A

site of the ribosome.• Step 2: Peptide bond formation.

• The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site.• The ribosome catalyzes the bond formation between the two amino acids.

• Step 3: Translocation.• The P site tRNA leaves the ribosome.• The tRNA carrying the polypeptide moves from the A to the P site.

Translation Process 2

• Termination• Elongation continues until a stop codon reaches the ribosome’s A site,• the completed polypeptide is freed, and• the ribosome splits back into its subunits.

Mutations• Mutation is any change in the nucleotide sequence of DNA

• can change the amino acids in a protein

• Mutations can involve• large regions of a chromosome or• just a single nucleotide pair, as occurs in sick-cell disease.

• Two general categories:• nucleotide substitutions (the replacement of one base by another) • nucleotide deletions or insertions (the loss or addition of a nucleotide).

• Mutations within a gene can alter its function• Insertions and deletions can change the reading frame of the genetic message • Substitions alter the amino acid composition of the eventual protein

• Mutations in regulatory regions can alter proteins and cell processes• May be silent, mild or even disastrous

Mutagens

Mutations may result from• errors in DNA replication or recombination • physical or chemical agents called mutagens, which damage DNA

• X-rays, UV light, various chemicals, especially chelators

Mutations• are often harmful but• are useful in nature and the laboratory as a source of genetic

diversity, which makes evolution by natural selection possible.

Viruses

• Non-cellular infectious agents; cannot reproduce on their own• Protein + nucleic acid (DNA or RNA)• Bacterial cells infected with bacteriophages

• Lysis: reproduction and bursting of the bacterial cell• Lysogeny: phage genome is (copied into duplex DNA) and inserted into the

bacterial genome

• Plant viruses• Most contain RNA as their genetic material• Stunt plant growth or diminish crop yields• Plants that can resist viral infection can be bred in the lab

Viruses 2

• Animal viruses• Common disease agents (pathogens)• DNA or RNA; single or multiple segments• May contain outer phospholipid membranes (enveloped viruses)

• HIV: human immunodeficiency virus• Causes AIDS (acquired immunodeficiency syndrome• a retrovirus, an RNA virus that reproduces by means of a DNA molecule• uses reverse transcriptase to catalyze reverse transcription, synthesis of DNA on an RNA

template• infects and eventually kills several kinds of white blood cells that are important in the

body’s immune system• there is no cure for AIDS but disease progression can be slowed by two categories of

medicine that interfere with the reproduction of the virus

Viroids and Prions

• Two classes of pathogens are smaller than viruses• Viroids are small, circular RNA molecules that infect plants• Prions are misfolded proteins that somehow convert normal proteins

to the misfolded prion version, leading to disease• responsible for neurodegenerative diseases including • mad cow disease, scrapie in sheep and goats, chronic wasting disease in deer

and elk, and • Creutzfeldt-Jakob disease in humans.

Guided Discussion Questions - 1

• What is the composition of DNA? Of RNA?• What is the polarity of DNA or RNA strands?• Compare and contrast the two macromolecules.• How does complementary base pairing make DNA replication

possible? Hint: remember the template mechanism• Which enzymes join nucleotides together?• When are new DNA strands needed?• What is transcription?• What is translation?

Guided Discussion Questions - 2

• Consider the following DNA sequence5’ –A-T-T-C-G-C-G-T-A-A-T-G-T-C-A-C-G-A-C-A-T-3’

• What is the sequence of the complementary DNA strand?• What is the structure of an RNA transcript of this DNA sequence?• How many amino acids are encoded by that sequence?• Which amino acids does that sequence define? Figure 10.11, p 180• What is the size of an average enzyme protein?

• How many amino acids does it contain?• How many codons would be in its transcript?• How many base pairs would there be in its gene?• Why are these numbers not strictly calculated?

Guided Discussion Questions - 3• Compare and contrast transcript and messenger RNA• Give several examples of non-coding DNA sequences.• How does RNA polymerase know where to begin transcription?• What is an anticodon? A stop codon? A start codon?• Describe the structure of a ribosome.• What are the critical parts of a transfer RNA?• Name two ways that viruses propagate their genes?• Why is herpes virus infection permanent?• Why is HIV called a retrovirus?• Why are prions unusual?