dna the nuclear genome consists of dna in the nucleus of eukaryotic cells – this is what we...

DNA

The Nuclear genome consists of DNA in the nucleus of eukaryotic cells – this is what we typically think of as our Genome:

A Genome is the unique set of chromosomes (or DNA) in one cell of an organism.

• Humans have 2 sets of chromosomes (one from each parent: we are diploid.) • Our genome consists of 3 x109 base pairs• ~25,000 genes (no one knows exactly yet).

Chloroplast Mitochondrion

Nucleus

Plant Cell Animal Cell

Chloroplasts (photosynthesis machinery in plants, algae) have their own DNA (called the Plastid genome)

• 7.5-25 x 103 base pairs • 100-1000 copies depending on whether the cell is actively dividing (more when dividing). • ~100 genes

Mitochondria have their own DNA (called the Mitochondrial genome)

• ~1.7 x 104 base pairs• several copies • ~40 genes

Nucleic Acids

•DNA

•RNA

DNA

•Deoxyribonucleic acid

•double helix

•“intelligent molecule”

•made of nucleotides

One human cell Has ~1 meter of DNA

DNA is partitioned into 46 separate linear molecules (chromosomes, 23 fromeach parent)

All of it is crammed into the cell's nucleus(a few micrometers)

Robert H. Austin, James P. Brody,Edward C. Cox, Thomas Dukeand Wayne Volkmuth FEBRUARY 1997 PHYSICS TODAY

image from the National Human Genome Research Institute

(NHGRI) Genetic Illustrations.

CELL

Nucleus

2 nm

11 nm

300 nm

30 nm

700 nm

1400 nm

DNA

Chromatin

ChromosomeRicharddawkins.net

Nucleotide

•Sugar (deoxyribose)

•Phosphate

•Nitrogenous Base

•adenine (A)

•thymine (T)

•cytosine (C)

•guanine (G)

•DNA is double-stranded

•adenine is always across from thymine

•cytosine is always across from guanine

•bases are held across from each other by weak hydrogen bonds

A T

C G

This OH group is replaced by H (hydrogen atom) inDeoxy-ribose

The Sugar in the “backbone” is

RNA: riboseDNA: deoxyribose

5’

3’

3’

5’

DNA is anti-parallel:

One strand is 5’to 3’

The strand across from itis 3’ to 5’

How do We Know the Structure of DNA?

Watson & Crick 1953

Diffraction PatternsReciprocal Space

http://www.matter.org.uk/diffraction/geometry/3D_reciprocal_lattices.htm

X-ray crystallography revisited

Click here for a groovy interactive experience

(Grab and drag one of the white dots)

DNA X-ray diffraction pattern

X-ray crystallography revisited

34 Angstroms

X-ray crystallography revisited

3.4 Angstroms

X-ray crystallography revisited

X-ray crystallography revisited

X-ray crystallography revisited

X-ray crystallography revisited

X-ray Diffraction pattern → Molecular Structure 1953 Discovery → Nobel Prize

Why x-rays?

Wavelength of diffracted light should match size of object for optimal resolution

A DNA molecule

• not a rigid, static structure (as x-ray diffraction pictures might suggest)

• under constant thermal fluctuations local twisting, stretching, bending, and unwinding of the double-strands.

http://www.uic.edu/classes/phys/phys461/phys450/ANJUM04/X-ray crystallography revisited

The most common DNA structure in solution is B-DNA.

DNA has several helical conformations A-DNA, Z-DNA, S-DNA

Under conditions of• applied force • low hydration ...  

A

B

Z

A-DNAShort and broad Low hydrationRight handed helix25.5A diameter2.3A rise/base pair~11 bases/ turn

B-DNALong and thin Most common in solutionRight-handed helix27.3 A diameter3.4 A rise/base pair~ 10 bases/turn

Z-DNA Longer and thinner Left-handed helix18.4 A diameter3.8 A rise/base pair~12 bases/ turn

DNA Replication

•2 strands of DNA “unzip” - separate

•primers are placed on each strand

•DNA polymerase (an enzyme) builds new strands of DNA, using the original strands as templates

RNA

•Ribonucleic acid

•single stranded

•also made of nucleotides

RNA nucleotides

•Sugar (ribose)

•Phosphate

•nitrogenous base

•adenine

•cytosine

•guanine

•uracil

Types of RNA

•mRNA: messenger RNA, carries the DNA code out of the nucleus to the ribosome

•tRNA: transfer RNA, carries amino acids to the ribosome

•rRNA: ribosomal RNA, part of the ribosome

Transcription (making RNA)•DNA unzips

•one strand of DNA acts as a template

•RNA polymerase reads the DNA bases

•RNA nucleotides are placed across from the complimentary DNA bases

•RNA separates from DNA

•DNA zips back up

•The “code” of DNA is the order of the bases

•The code is universal among organisms

•DNA from one organism can be read in the cells of another organism