GENES, GENOME AND DNA

The base materials for inheritance.

HUMAN GENOMEGenome refers to the total genetic material within a cell. In

humans there are 30000 genes.Most is in the nucleus.Some is in mitochondria. (Believed to be engulfed organisms

in the distant evolutionary past of eukaryotic cells)

DNA

Is the main component of chromosomes.

It bears the genetic material of organisms.

DNA’s structure is similar to a twisted ladder with 4 nucleic bases Adenosine, Thymine, Cytosine and Guanine.

The study of DNA and its manipulation is known as Genetics.

The four nucleic acids always join together in a particular way, in complementary base pairs.

Adenosine with Thymine (A=T)

Cytosine with Guanine (C=G)

Each pair is called the base pair.

The 2 strands are called complementary strands.

There are 2.9 billion combinations of A-T, G-C

STRUCTURE OF NUCLEOTIDES

The chemical structure of nucleotides :

Symbolic form

Phosphate: Links neighboring sugars

Sugar: One of two types possible: ribose in RNA and deoxyribose in DNA

Base: Four types are possible in DNA: adenine, guanine, cytosine and thymine. RNA has the same except uracil replaces thymine.

Purine – double ringed structure. (A & G)

Single ringed structure called pyrimidine. ( T & C)

The complementary strands of DNA are referred to as antiparallel because one runs 5’ to 3’, while the other runs 3’ to 5’ ( ‘ read as prime).

5’ end has an unlinked phosphate group3’ end has an unlinked ribose sugarIn eukaryotes the DNA is coiled around small proteins

called histones.The DNA wrapped around the histone proteins is called

a nucleosome. In fact there is about twice as much protein as DNA in chromosomes.

This packaging protects it from enzymatic degradation and is an efficient form of packaging.

When cells prepare to divide the nucleosomes fold in a regular manner to produce supercoils that become visible under the light microscope.

GENES

A gene is a unit of heredity made up of a unique sequence of DNA. Together with proteins, it is organised into chromosomes.• The whole set of genes in an organism is a genome.

GENES

Are the basic units of heredity. They are made up of a unique sequence of DNA.

The complete set of genes make up the genome.Genes are located on chromosomes.A gene is a section of DNA with a specific sequence of

nitrogenous bases. This sequence is the code that directs the manufacture of a protein.

Some genes code for tRNA or rRNA.The position of the gene on a chromosome is called the

locus (pl. loci)Genes are named for the function they control or there

observable effect in an organism. Eg. RH gene controls Rhesus blood type.

Genes are linked if they are carried on the same chromosome. Eg. Sex-linked diseases.

GENES – HOW DO THEY CONTROL THINGS?

Remember, Genes are inherited

from parents through egg and sperm cell

Genes are made of DNAGenes differ from each

other in their length and in the order of their DNA base pair.

GENE’S JOB

Genes job is to control the production of proteins which serve critical roles in cellular structure and function and in development.

One gene-one protein hypothesis has now been modified to one gene- one polypeptide

GENES IN ACTIONGenes act by

specifying the production of polypeptides which form proteins.

Proteins perform a myriad of essential functions in the cell.

Eg: Enzymes,

transport, carrying oxygen, antibodies

CHROMOSOMES

All living cells & viruses contain genetic information in chromosomes.

Therefore they are made of DNA & found in the nucleus.

They are supercoils of DNA.

They are the most compact form of data storage known.

Each gene has its own position on the chromosome. (locus)

NUMBERS OF CHROMOSOMES

Chromosome numbers vary considerably among organisms.

The numbers may differ markedly even between closely related species:

Organisms Chromosome No.

human 46

chimpanzee 48

gorilla 48

cattle 60

cat 38

goldfish 94

Drosophila 8

honey bee 32 or 16

Hydra 32

cabbage 18

beans 22

orange 18, 27 or 36

garden pea 14

HOW MANY CHROMOSOMES?

All nucleated cells of an organism contain a fixed number of chromosomes.

Somatic cells (body cells, except gametes) contain a fixed number of chromosomes per species.

humans 46, koala 16, fern 1260, The ploidy level of a cell refers to the

number of chromosome sets it carries.Diploid (2n) means 2 sets of chromosomes

(somatic cells – body cells)Haploid (n) means 1 set of chromosomes

(gametes – sex cells)

Nucleus

Structure of the nucleus

Eukaryotes have genetic information stored in chromosomes in the nucleus of each cell:

GENES IN EUKARYOTE CELLS

Nucleus contains inherited information: The total collection of genes located on chromosomes in the nucleus has the complete instructions for constructing a total organism.

Cytoplasm: The nucleus controls cell metabolism; the many chemical reactions that keep the cell alive and performing its designated role.

Nuclear pores are involved in the active transport of substances into and out of the nucleus

Nucleolus is involved in the construction of ribosomes

Nuclear membraneencloses the nucleus in eukaryotic cells

Chromosomes are made up of DNA and protein and store the information for controlling the cell

GENES OUTSIDE THE NUCLEUSIN EUKARYOTE CELLS

Eukaryotes have two types of organelles with their own DNA:

mitochondriachloroplasts

The DNA of these organelles is replicated when the organelles are reproduced (independently of the DNA in the nucleus).

Mitochondrion

Ribosome

MitochondrialDNA

Chloroplast

Chloroplast DNA

GENES IN PROKARYOTE CELLS

Bacteria have no membrane-bound organelles.Cellular reactions occur on the inner surface of the cell membrane or in the cytoplasm.Bacterial DNA is found in:

One, large circular chromosome.Several small chromosomal structures called plasmids.

Flagellum

Cell wall

Single, circularchromosome

Cytoplasm(no nucleus)

Cell membrane

Ribosomes

Plasmids

PLASMID DNA

Bacteria have small accessory chromosomes called plasmids.Plasmids replicate independently of the main chromosome.Some conjugativeplasmids can beexchanged with otherbacteria in a processcalled conjugation.Via conjugation, plasmidscan transfer antibiotic resistance to other bacteria.

Recipientbacterium

Plasmid of the conjugative type

Plasmid of thenon-conjugative type

A plasmid about to pass one strand of the DNA into the sex pilus

Sex pilus conducts the plasmid to the recipient bacterium

Donorbacterium

2005-2006

THE BIG QUESTIONS…How are genes turned on & off in

eukaryotes?How do cells with the same genes

differentiate to perform completely different, specialized functions?

WHY TURN GENES ON & OFF?

Specializationeach cell of a multicellular eukaryote expresses only

a small fraction of its genesDevelopment

different genes needed at different points in life cycle of an organism afterwards need to be turned off permanently

Responding to organism’s needshomeostasiscells of multicellular organisms must continually turn

certain genes on & off in response to signals from their external & internal environment

MOLECULAR BIOLOGY

the central DOGMA of Molecular Biology can be summarised in the form:

HOW DO WE MAKE PROTEINS?

• In order to make proteins we first must have a set of instructions.

• That is the DNA or more particularly the genes and their nucleotide bases.

• It can be considered our blue print.

TRANSCRIPTION

We don’t want to lose our good copy of instructions so the first step is to make a copy of DNA which we can use outside the nucleus.

This process is called transcription and the copy is called messenger RNA

DNA never leaves the nucleus, but proteins are synthesized in the cytoplasm, so a copy of each gene is made to carry the “message” from the nucleus to the cytoplasm. This copy is mRNA, and the process of copying is called transcription.

TRANSCRIPTION

As the RNA polymerase moves along the RNA is formed.

RNA has slight differences to DNA it is single stranded and instead of thymine it has uracil. The nucleotides pair exactly the same.

Here is how it works:DNA is separated by

RNA polymerase which is an enzyme.

This makes a copy of DNA and then attaches nucleotides from within the cell according to base pair rules.

RNA polymerase enzyme

Template strand of DNA contains the information for the construction of a functional mRNA product (e.g. a protein)

TRANSCRIPTION

A mRNA strand is formed using the DNA molecule as the template.

Free nucleotides with bases complementary to the DNA are joined together by the enzyme RNA polymerase.

DNA

Coding strand

The two strands of DNA coil up into a double helix

Free nucleotidesused to constructthe mRNA strand

Single-armedchromosome as found in non-dividing cell

Direction of

synthesis

Formation of a single strand of mRNA that is complementary to the template strand (therefore the same “message” as the coding strand)

5’ is the 5 prime end which has a free phosphate group.

3’ is the 3 prime end which has a free hydroxyl group

This is why it is known as an anti parallel double stand.

Replication starts at the 5 prime end.

THE NEXT STEP

Once we have a copy of DNA in the form of mRNA we can then send the instructions outside the nucleus where we can begin to make protein.

This is called Translation

•The mRNA copy is made with the help of RNA polymerase. This enzyme joins up the mRNA nucleotides to make a mRNA strand.•This mRNA strand is a complementary copy of the DNA (gene)•The mRNA molecule leaves the nucleus via a nuclear pore into the cytoplasm

MOVEMENT OF MRNA

In eukaryot ic cel ls, the two main steps in protein synthesis occur in separate compartments: transcript ion in the nucleus and translat ion in the cytoplasm.

mRNA moves out ofthe nucleus, to thecytoplasm, through pores inthe nuclear membrane.

In prokaryot ic cel ls, there is no nucleus, and the chromosome is in direct contact with the cytoplasm, and protein synthesis can begin even whi le the DNA is being transcribed.

Cytoplasm

Nuclear pore throughwhich the mRNA passesinto the cytoplasm

Nucleus

mRNA

Ribosomes

TRANSLATION

In the process of translation the sequence of bases in the mRNA is read and the amino acids are assembled in a corresponding order to form a polypeptide.

As the ribosome moves along the mRNA then another amino acid is joined with a peptide bond.

As the amino acid is joined the tRNA moves off.

mRNA is read by the ribosome which attaches amino acids via transfer RNA

The sequence is the genetic code.

GENETIC CODE

The gene code works in triplets.

Every three letters represent a amino acids. For example UAA means STOP.

The Three letter code is called a CODON

Gene code

TRANSLATION. MRNA USED TO MAKE POLYPEPTIDE CHAIN

(PROTEIN)

1.

•First the mRNA attaches itself to a ribosome (to the small subunit).•Six bases of the mRNA are exposed.•A complementary tRNA molecule with its attached amino acid (methionine) base pairs via its anticodon UAC with the AUG on the mRNA in the first position P.•Another tRNA base pairs with the other three mRNA bases in the ribosome at position A.•An enzyme initiates the formation of a peptide bond between the amino acids.•The first tRNA (without its amino acid) leaves the ribosome.

TRANSLATION 2

The ribosome moves along the mRNA to the next codon (three bases).The second tRNA molecule moves into position P.Another tRNA molecule pairs with the mRNA in position A bringing its amino acid.A growing polypeptide is formed in this way until a stop codon is reached.

END OF TRANSLATION

A stop codon on the mRNA is reached and this signals the ribosome to leave the mRNA. A newly synthesised protein is now complete!

GENE REGULATION

Virtually every cell in your body contains a complete set of genes

But they are not all turned on in every tissueEach cell in your body expresses only a small

subset of genes at any timeDuring development different cells express

different sets of genes in a precisely regulated fashion

While the expression of some genes is continuous, the expression of others is regulated in cells.

Although all somatic cells in an organism carry identical gene sets, only a proportion of those genes are switched on in a given cell type or stage of development.

GENE REGULATION

In eukaryotic organisms like ourselves there are several methods of regulating protein production

Most regulatory sequences are found upstream from the promoter

Genes are controlled by regulatory elements in the promoter region that act like on/off switches or dimmer switches

GENE REGULATION

Specific transcription factors bind to these regulatory elements and regulate transcription

Regulatory elements may be tissue specific and will activate their gene only in one kind of tissue

Sometimes the expression of a gene requires the function of two or more different regulatory elements

Introns and Exons

TranscriptionBoth exons and introns are transcribed to produce a long primary RNA transcript

Primary RNA transcript The primary RNA transcript is edited

messenger RNA

Exons are spliced

together

Introns are

removed

Introns

DNA Intron Intron Intron Intron IntronDouble stranded molecule of genomic DNAExon Exon Exon Exon Exon Exon

Translation

Protein

Messenger RNA is an edited copy of the DNA molecule (now excluding introns) that codes for a single functional RNA product, e.g. protein.

Most eukaryotic genes contain segments of protein-coding sequences (exons) interrupted by non-protein-coding sequences (introns).

Introns in the DNA are long sequences of codons that have no protein-coding function.

Introns may be remnants of now unused ancient genes.

Introns might also facilitate recombination between exons of different genes; a process that may accelerate evolution.

INTRONS AND EXONSAfter the initial transcript is produced the introns are spliced out to form the completed message ready for translation

Introns can be very large and numerous, so some genes are much bigger than the final processed mRNA

1. A ribosome attaches to the mRNA at an initiation codon (AUG). The ribosome encloses two codons.

2. met-tRNA diffuses to the ribosome and attaches to the mRNA initiation codon by complementary base pairing.

3. The next amino acid-tRNA attaches to the adjacent mRNA codon (leu in this case).

4. The bond between the amino acid and the tRNA is cut and a peptide bond is formed between the two amino acids.

5. The ribosome moves along one codon so that a new amino acid-tRNA can attach. The free tRNA molecule leaves to collect another amino acid. The cycle repeats from step 3.

6. The polypeptide chain elongates one amino acid at a time, and peels away from the ribosome, folding up into a protein as it goes. This continues for hundreds of amino acids until a stop codon is reached, when the ribosome falls apart, releasing the finished protein.

2005-2006

1

23

5 4

6