DNA & Chromosomes

Chapter 5

(Please do read every single page)

Learn…

• Nucleotides

• Nucleosides

• DNA

• RNA

Facts

• The DNA in each human cell is enormous

• End to end - all 24 chromosomes would stretch 1.8 metres

• Cell diameter is = WHO CARES!!!• Nucleus diameter is = few um• How is it squeezed in and also

controlled?

DNA

• Deoxyribonucleic acid• It is a Macromolecule• Made of Subunits - nucleotides• IT HAS DIRECTIONALITY

– dictated by the free end groups– always written 5’ to 3’ direction for each

single strand

Three-dimensional structure

Figure 9.7

• DNA and RNA can be VERY VERY VERY large macromolecules with several levels of complexity

– 1. Nucleotides form the repeating units– 2. Nucleotides are linked to form a single strand – 3. Two strands can interact to form a double strand -

for DNA this is called the double helix– 4. The double helix is nursed and managed by P’s

• which bend and twist the DNA - eventually resulting in 3-D structures in the form of chromosomes

NUCLEIC ACID STRUCTURE

• The nucleotide is the repeating structural unit of DNA and RNA

• HOW IS IT CONSTRUCTED?

• Many varieties• Each has three components

– A phosphate group– A pentose sugar– A nitrogenous base

Nucleotides

Figure 9.8

Figure 9.9 The structure of nucleotides found in (a) DNA and (b) RNA

A, G, C or T

• The red atoms below are found within individual nucleotides– However, they are removed when nucleotides join together to make

strands of DNA or RNA

A, G, C or U

• Base + sugar nucleoside – Example

• Adenine + ribose = Adenosine• Adenine + deoxyribose = Deoxyadenosine

• Base + sugar + phosphate(s) nucleotide– Example

• Adenosine monophosphate (AMP)• Adenosine diphosphate (ADP)• Adenosine triphosphate (ATP)

• Next…

SIMPLE PLAN OF A SINGLE STRANDED NUCLEOTIDE CHAINSIMPLE PLAN OF A SINGLE STRANDED NUCLEOTIDE CHAIN

Figure 9.11

LEARN WHICH ATOMS CONNECTS THE SUBUNITS TO EACH OTHER…

Just LOOK here to determine if this is RNA or DNA

Figure 9.10

Base always attached here

Phosphates are attached there

Other important nucleotides within cells

ATPADPAMP

• Individual nucleotides are covalently linked together by phosphodiester bonds– A phosphate connects the 5’ carbon of one nucleotide to

the 3’ carbon of another

• Therefore the strand has directionality– 5’ to 3’

• The phosphates and sugar molecules form the backbone of the nucleic acid strand– The bases project from the backbone

5’ to 3’ how?

DNA

• Deoxyribonucleic acid

• Macromolecule

• Subunits - nucleotides

• 5’ to 3’ direction for each single strand

• Two strands run in opposite directions

The two strands are not equally spaced because of bond angles

P’s and the those enzymes that manage DNA interact with the DNA mainly via the major groove.

The two strands are not equally spaced because of bond angles

P’s and the those enzymes that manage DNA interact with the DNA mainly via the major groove.

Minor groove Major groove

Definitions -

• Genome - The complete set of INFORMATION in an organism’s DNA– That is the haploid complement for all organisms

• Chromosome - A single molecule of DNA– Circular or linear

• Gene - a section of the DNA coding for the production of a single protein*

• Karyotype - figure or picture showing the full set of chromosomes from a cell during cell division when they are condensed and visible...

*simplification of the current data

Human Karyotype

Human DNA facts• Genome = 3.2 billion base pairs of DNA across 24

different distinct chromosomes (22 automomes + X + Y)

• Take about 9.5 years to read out loud (without stopping) the three billion pairs of bases in one person's genome sequence

• Biologist simply say 23 pairs of chromosomes• For diploid cells = 6.4 billion base pairs per somatic

cell• Each ? is a single enormous DNA double-helix -

chromosome

Genome sizes

• Humans do not have the most chromosomes - Plants tend to have these

• Humans do not have the largest gemone size - Fish tend to have these

• An ant species has just 1 chromosome• No real association between genome size

and evolutionary complexity - human near the middle some where

Chromosomes Structure

• During the cell cycle the structure of chromosomes changes visibly

• Interphase state = very fine threads• Metaphase state = distinct defined

chromosomes• Ends of chromosomes are known as

telomeres• Middles, where the spindles attach, as

centromeres

Nucleolus

• Within the nucleus are one or more nucleoli.

• The nucleolus is the coming together of genes from different chromosomes that are involved in making ribosomes.

• An average, healthy cell can produce up to 10 000 ribosomes per minute.

Nucleolus

DNA management

• 10,000 fold difference in size between DNA helix stretched out and the size of a metaphase chromosome - How?

• Answer = Proteins associated with DNA– Histone Proteins (H1, H2a, H2b, H3, and

H4)– DNA plus these proteins is called

Chromatin

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Nucleosome• Complex consisting of

– 200 bp of DNA– 8 histone proteins in core– H1 histone stabilizing

– Core = 146 bp DNA and two each of H2a, H2b, H3 and H4

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• Overall structure of connected nucleosomes resembles “beads on a string”

– This structure shortens the DNA length about seven-fold

Figure 10.14

Vary in length between 20 to 100 bp, depending on species and cell type

Diameter of the nucleosome

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Figure 10.14

Play a role in the organization and compaction

of the chromosome

Higher Order Folding

• DNA -double-stranded helix is 2 nm thick

• Nucleosome - 11 nm thick• 30nm chromatin fibre - 30 nm thick• Chromatin loops - 300 nm thick• Condensed chromatin - 700 nm thick• Chromosome (mitotic) - 1400 nm thick

– DNA is wrapped or looped using a protein matrix

10-63Figure 10.21

10-64Figure 10.21

Compaction level in euchromatin

Compaction level in heterochromatin

During interphase most chromosomal

regions are euchromatic

Heterochromatin

• Regions close to telomere and centromere are classes as heterochromatin based on observations

• These are not very active for transcription

• DNA thought to be tightly packed here• Few proteins can enter region - it it too

tight for them to get to the DNA

Chromatin Remodeling Complexes

• Large Protein complexes which selectively act at the nucleosome level to unwind DNA to allow proteins access

• IMPORTANT control mechanism in the cell.

• Transcription occurs when needed.