DNA Chapter 2 – read principal points TimelineTimeline for genetics

Deoxyribonucleic acid Functional Properties 1. Replication – DNA is copied prior to cell division why?

2. Storage of information DNA inherited from parent to offspring from cell to cell Gene expression – Genes encode proteins 3. Mutation – DNA changes to allow variation and adaptation, the basis of evolution

A six-legged green frog. (Reproduced by permission of JLM Visuals Neutral, harmful, adaptive?

DNA History 1869 Meischer extracted nuclein from pus 1900s – chromosomes discovered The genetic material must have the 3 functional properties microscopy.bio.cmich.edu

Griffith finds “transforming factor” 1928 London Streptococcus pneumoniae bacterium pneumonia in mice, deadly to humans sputum with bacteria

Smooth strain (IIIS) virulent polysaccharide capsule capsule allows bacteria to evade immune system Fluorescent stain of capsule

 isolate live IIIS from mouse

S pneumococcus kills mouse in 24 hours. But 100 million IIR strain bacterial cells is harmless SRSR (Research photographs of Dr. Harriet Ephrussi-Taylor, courtesy of The Rockefeller University.) Appearance when grown on an agar plate

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Rough strain IIR is avirulent IIR lacks capsule -> isolate live IIR

The experiment: Heat kill IIIS strain  mouse ?

Heat killed IIIS strain + live strain IIR  mouse ? Which strain is isolated?

Griffith’s experiment and conclusion A “transforming factor” in killed S strain transformed live R strain into S DNA or protein?

1944 Avery, McCarty, Macleod 1. Heat kill IIIS 2. Remove lipids and sugars – how? FYI iGenetics: DNA as Genetic Material: Avery’s Transformation Experiment

3. Divide into 3 and treat with: protease RNase DNase  next, add live R cells to each

1952 Hershey and Chase Used T2 bacteriophage + E. coli A phage is a virus that infects bacteria

How phage work 1. phage adsorbs onto bacterial surface 2. Genetic material injected 3. Cell makes progeny phage IS the genetic material DNA, or protein?

Experiment 1. Label phage protein with 35 S  infect E. coli  strip phage off cell surface New phage are not radioactive

2. Label phage DNA with 32 P -> infect E.coli -> blend -> New phage contain 32 P

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Hershey and Chase conclusion DNA is responsible for function and reproduction of phage virus = the genetic material

Structure of DNA = nucleotide polymers NUCLEOTIDES 1. Nitrogenous base Purines = guanine and adenine G A Purines attached to 1 carbon of sugar at 9 nitrogen, covalent bond, pyrimidines attached to 1 carbon at 1 nitrogen How big IS a nucleotide? UTAH cell scale

Pyrimidines Thymine T Cytosine C RNA contains uracil U

2. Deoxyribose sugar RNA (ribose) 2’ OH makes RNA less stable than DNA Sugar + base = nucleoside

3. Phosphate (PO 4 ) Nucleotide = base + sugar + phosphate Phosphate covalently (phosphodietster bond) attached to 5’C of sugar Phosphodiester bond - Covalent bond between phosphate of one nucleotide and 3’ sugar carbon of another 9 N (purine) or 6N (pyrimidine) covalently bonded to 1C of sugar

DNA is a polymer of nucleotides polarity 5’carbon to 3’hydroxyl

DNA (double helix) Watson and Crick 1953 X-ray diffraction data Rosalind Franklin, Maurice Wilkins

DNA properties include:

Complementary base pairing 1. Hydrogen bonds between complementary bases How many bonds in a G-C pair? A-T? Which is stronger?

Complementary base pairs Which are the G-C pairs?

2. antiparallel stands 5’  3’ and 3’  5’

3. Sugar phosphate backbones

4. Base composition DNA 50% purine 50% pyrimidine A = TG = C A/T = 1C/G = 1 A +T does not equal C+G A + G = C + T Chargaff (1950)

5. DNA can denature and renature Melt hydrogen bonds (chemical or heat)

And 5. Right handed helix 6. Complete turn of the helix is 0.34 nm, 10 bases per turn 7. Major and minor grooves

Major and minor grooves

Forms of DNA B DNA right helix 10 bp/ turn A DNA right helix 10.9 bp/ turn Z DNA left helix 12 bp/turn (role?) Cellular DNA closest to B DNA 10.4 bp/turn

Replication of DNA by Complementary Base Pairing HHMI interactive DNA replicationHHMI interactive DNA replication advanced

Organization of DNA in chromosomes Genome Full amount of genetic material in a single cell

Influenza ssRNAHIV ssRNA Bacteriophage ds DNA Viral chromosome Single or double stranded DNA or RNA Circular or linear Herpes ds DNA Parvovirus ssDNA

Genetic material in prokaryotes 1 (usually) chromosome Circular (most) chromosome Supercoiled DNA located in nucleoid region Neisseria gonorrhoeae

E. coli = 4.6 million bp, circular chromosome 1500 um genome stuffed into a 1 um cell via supercoiling E. Coli cellsE. coli DNA map of chromosome

Some bacteria contain extra-chromosomal DNA called a plasmid

Eukaryotic Chromosomes C value - Amount of DNA varies among species

The structure of chromatin DNA + proteins Highly conserved

Histones and non-histones Histone proteins basic net + charge interacts with – charged DNA Package DNA Highly conserved Non-histone proteins vary among species

What do histones do? 1. pack DNA into chromatin Condense DNA 10,000X (2 meters  nanometers) 1. Modifications to histone proteins affect gene expression

5 histone proteins Histone type #amino acidscontent_________________ H %lysine, 2%arginine H2A % lysine, 9% arginine H2B % lysine, 6% arginine H %lysine, 15% arginine H % lysine, 4% arginine Note: all are lysine/arginine rich, they contain other amino acids, but at small percentages. Basic, + charge

Gel electrophoresis

epigenetics Modification of histone proteins changes gene expression. Chemical tags can be inherited and are stable in cell division

Pbs: A Tale of Two Mice Pbs: A Tale of Two Mice Epigenetics with deGrassi w/3411/02.html w/3411/02.html Agouti Mice Epigenetics and gene silencing Mouse and twin studies Diet and the epigenome Methyl group tags

Chromosome packaging 1. Nucleosomes 1 nucleosome “beads on a string” The 10 um chromatin fiber 2(H2A).2(H2B) 2(H3).2(H4) octomer

Dual role of nucleosomes stable to shelter DNA and compact it labile to allow DNA information to be used

2. The 30 nm chromatin fiber Histone H1 a ttaches linker DNA to nucleosomes

The 30 nm chromatin fiber (11nm string-> 30 nm helical fiber) See Science article

3. Further packaging into loops and scaffolds……

Summary of DNA packaging 30nm chromatin fiber Nucleosomes DNA helix

Metaphase chromosome is 10,000 X condensed compared to double helix Condensed scaffold The scaffold with loops

Euchromatin and Heterochromatin

1. Heterochromatin Condensed Transcriptionally inactive Ex. centromeres

Heterochromatin stains darkly

Heterchromatin example Barr body (facultative, extent of inactivity varies) Inactivated X chromosome in females

2. Euchromatin Lighter staining regions of DNA that contain genes Transcriptionally active

Unique Sequences and Repetitive DNA

What genes are on a chromosome? Chromosome 11 flyover Terms: Transposon Pseudogene Olfactory Polymorphism

1. Unique Sequence DNA (1 to a few copies) a. Genes Encode proteins ~60% of DNA Only 2% of DNA is coding (H. sapiens) Estimated 20,000 genes in humans

b. Gene families  encodes embryonic beta globin  encode fetal beta globin  is a pseudogene (not functional)  encodes normal beta globin  encodes normal adult beta globin Example: Beta globin (encode subunits of hemoglobin)

2. Repetitive DNA Repeated 10 – 1000sX in the genome a. Dispersed repeated DNA LINES = long interspersed elements 1000 – 7000 bp Ex. humans have 500,000 copies of L1 = 15 % of genome. some are transposons = copy and move

SINES 100 – 400 bp Ex. Alu repeats repeated 1 million times = 10% of genome

b. Tandem repeats 1 – 10 bp long tandemly repeated Centromeres, telomeres, rRNA genes Ex. telomere sequence repeated 2000X 5'...TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG..3' 3'...AATCCC AATCCC AATCCC AATCCC AATCCC AATCCC..5'

Ex. rRNA genes