1. The Structure and Function of DNA
Chapter 10
Winter Quarter 2015

2. 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

3. 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

4. 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 Structure
Fig 10.1 p 174
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

5. 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

6. 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

7. 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

8. 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

9. 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

10. Transcription 2 Elongation Termination Figure 10.13, page 181
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

11. 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 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

12. Translation
conversion from the nucleic acid language to the protein language
Machinery:
mRNA
ATP
enzymes
ribosomes
transfer RNA (tRNA)

13. 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

14. Ribosomes organelles that each subunit is made up of
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

15. Translation Process - 1 Initiation Elongation
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.

16. 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.

17. 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

18. 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.

19. 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

20. Viruses 2 Animal viruses HIV: human immunodeficiency virus
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

21. 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.

22. 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?

23. Guided Discussion Questions - 2
Consider the following DNA sequence
5’ –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?

24. 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?