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DNA, Genes and Genomics. Prokaryotic DNA. The prokaryotes usually have only one chromosome, and it bears little morphological resemblance to eukaryotic chromosomes. Consists of single, circular DNA molecule located in the nucleoid region of cell. Referred to as being “naked”

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prokaryotic dna
Prokaryotic DNA
  • The prokaryotes usually have only one chromosome, and it bears little morphological resemblance to eukaryotic chromosomes.
  • Consists of single, circular DNA molecule located in the nucleoid region of cell. Referred to as being “naked”
  • Bacterial cells may also contain multiple plasmids - small circular fragment of DNA separate from the main chromosome.
eukaryotic dna structure
Eukaryotic DNA Structure
  • DNA consists of two molecules that are arranged into a ladder-like structure called a Double Helix.
  • A molecule of DNA is made up of millions of tiny subunits called Nucleotides.
  • Each nucleotide consists of:
    • Phosphate group
    • Ribose sugar
    • Nitrogenous base
nucleotides
Nucleotides

Phosphate

Nitrogenous

Base

Ribose

Sugar

nucleotides1
Nucleotides
  • The phosphate and sugar form the backbone of the DNA molecule, whereas the bases form the “rungs”.
  • There are four types of nitrogenous bases.
nucleotides2
Nucleotides

A

T

C

Adenine

Thymine

G

Guanine

Cytosine

nucleotides3
Nucleotides
  • Each base will only bond with one other specific base.
  • Adenine (A)
  • Thymine (T)
  • Cytosine (C)
  • Guanine (G)

Form a base pair.

Form a base pair.

dna structure
DNA Structure

A

A

T

A

T

A

T

T

Because of this complementary base pairing, the order of the bases in one strand determines the order of the bases in the other strand.

C

C

C

G

G

G

dna replication
DNA Replication
  • unfolding and unwinding of the DNA double helix at hundreds of points, known as replication origins, along the chromosome.
  • The enzyme helicase separates the two DNA strands, separating them like opening a zipper, with the point of opening being termed the replication fork.
  • Where the DNA strands are separated, a short length of RNA binds to each DNA strand under the control of the enzyme, DNA primase. This RNA acts as a primer (see figure 11.26a page 405).
dna replication1
DNA Replication
  • A DNA polymerase enzyme can then proceed to build new DNA strands using each of the old strands as a template (see figure 11.26b).
  • Replication of DNA can occur only in the 5´ to 3´ direction. This is no problem with the so-called leading strand because its new complementary strand can be built continuously in the 5´ to 3´ direction. The other strand, known as the lagging strand, can be built only backwards and in short discontinuous pieces (Okasaki fragments - see figure 11.26b).
  • When finished, the RNA primers are removed, the gaps are filled by another DNA polymerase and the pieces are joined by the enzyme, DNA ligase.
dna replication2
DNA Replication

Watch DNAi clip

mitochondrial dna
Mitochondrial DNA
  • Mitochondria contain mtDNA,a double strandedcircular molecule comprising:
    • 16 568 base pairs and code for 37 genes:
    • 13 genes code for proteins that are involved in cellular respiration
    • 2 genes code for ribosomal RNA (rRNA)
    • 22 genes code for transfer RNAs (tRNAs).
slide13

An individuals characteristics are determined by their DNA.

The DNA determines which proteins are made.

The most important proteins are enzymes.

The sequence of bases in the DNA determines the sequence

of amino acids in the protein.

This is known as the GENETIC CODE.

PROTEIN SYNTHESIS

slide14

TRIPLET CODE

3 bases in the DNA code for one amino acid in the protein. Each triplet is known as a CODON.

UNIVERSAL

Found in all organisms.

DEGENERATE

More than one codon for each amino acid.

NON-OVERLAPPING

START AND STOP CODONS

THE GENETIC CODE

slide16

PROTEIN SYNTHESIS

TRANSCRIPTION

AMINO ACID ACTIVATION

TRANSLATION

slide19

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide20

A

U

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide21

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide22

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide23

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide24

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide25

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide26

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide27

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide28

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide29

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide30

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide31

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide32

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide33

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide34

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide35

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide36

U

A

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide37

A

U

C

C

C

A

A

A

A

A

U

U

U

U

U

U

G

HELICASE unwinds and unzips the relevant part of the DNA helix.

RNA POLYMERASE attaches to the DNA.

As RNA POLYMERASE moves along the sense strand, ribonucleotides are assembled in a precise order due to complementary base pairing (A <-> T/U ; G <-> C).

One DNA strand acts as the template (SENSE STRAND), the other is redundant (ANTISENSE STRAND).

G

G

G

G

T A C G G C T A A C A T A C A A T C

slide38

U

A

C

C

A

A

A

U

U

U

U

U

U

G

Fully formed mRNA peels off the DNA and leaves the nucleus via a nuclear pore.

The DNA rewinds.

G

G

G

G

slide39

U

A

C

C

A

A

A

U

U

U

U

U

U

G

Fully formed mRNA peels off the DNA and leaves the nucleus via a nuclear pore.

The DNA rewinds.

G

G

G

G

slide40

U

A

C

C

A

A

A

U

U

U

U

U

U

G

G

G

G

G

slide41

U

A

C

C

A

A

A

U

U

U

U

U

U

G

G

G

G

G

slide43

C

U

A

ACTIVATION OCCURS WHEN

THE tRNA COMBINES WITH A SPECIFIC AMINO ACID

THE ANTICODON DETERMINES WHICH SPECIFIC AMINO ACID IS ATTACHED

slide45

C

U

A

A ribosome binds to the mRNA near the START CODON.

C

G

G

U

U

C

A

A

A

A U G C C G A U U G U A U G U U A G

A

A

C

slide46

C

U

A

tRNA with the complementary ANTICODON (UAC) binds to the start codon (AUG) held in place by the large subunit of the ribosome. It brings with it the amino acid methione.

U

U

C

A

A

A

A U G C C G A U U G U A U G U U A G

A

A

C

C

G

G

slide47

C

U

A

The ribosome now slides along the mRNA to “read” the next codon.

U

U

C

A

A

A

A U G C C G A U U G U A U G U U A G

A

A

C

C

G

G

slide48

C

U

A

A second tRNA now bind to this codon, bringing a second amino acid with it.

U

U

C

A

A

A

A U G C C G A U U G U A U G U U A G

A

A

C

C

G

G

slide49

C

U

A

A peptide bond is formed between the two amino acids.

U

U

C

A

A

A

A U G C C G A U U G U A U G U U A G

A

A

C

C

G

G

slide50

The tRNA which carried the first amino acid is released but leaves its amino acid behind as a DIPEPTIDE.

U

U

C

A

A

A

C

A U G C C G A U U G U A U G U U A G

A

U

A

A

C

C

G

G

slide51

The ribosome now slides along the mRNA to “read” the next codon.

U

U

C

A

A

A

C

A U G C C G A U U G U A U G U U A G

A

U

A

A

C

C

G

G

slide52

One by one each codon is read as the ribosome moves along the mRNA.

U

U

C

A

A

A

C

A U G C C G A U U G U A U G U U A G

A

U

A

A

C

C

G

G

slide53

Each time the growing polypeptide is linked to the amino acid on the incoming tRNA.

U

U

C

A

A

A

C

A U G C C G A U U G U A U G U U A G

A

U

A

A

C

C

G

G

slide54

U

C

A

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

U

G

A

A

C

U

slide55

U

C

A

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

U

G

A

A

C

U

slide56

U

C

A

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

U

G

A

A

C

U

slide57

U

C

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

A

U

U

G

A

A

C

slide58

U

C

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

A

U

U

G

A

A

C

slide59

U

C

A

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

A

U

U

G

A

A

C

slide60

A

C

C

A U G C C G A U U G U A U G U U A G

G

A

A

U

U

G

A

A

C

U

A

C

slide61

The polypeptide is complete when the ribosome reaches the STOP codon.

A

C

C

A U G C C G A U U G U A U G U U A G

A

G

A

U

U

G

A

A

C

U

A

C

STOP !

slide62

U

A

C

A

A

C

The polypeptide is released.

A

C

C

A U G C C G A U U G U A U G U U A G

A

A

G

U

U

G

slide63

U

A

C

A

A

C

The polypeptide is released.

A

C

C

A U G C C G A U U G U A U G U U A G

A

A

G

U

U

G

slide64

The polypeptide may combine with other polypeptides and will become variously coiled/folded to produce a protein.

slide65

U

A

A

C

A

C

The tRNAs are recycled.

A

C

C

G

A

A

U

U

G

slide66

The mRNA may be used again in this form, or it may be broken down into nucleotides which can be reassembled to produce a different polypeptide.

A U G C C G A U U G U A U G U U A G

slide68

Ribosomes work in groups so that many slide along a mRNA molecule simultaneously.

These groups are called POLYRIBOSOMES.

Each ribosome takes about 1 minute to travel along a mRNA molecule.

slide69

What sort of chemical is helicase?

Why is DNA double stranded if one strand is redundant?

Where in the cell are the ribosomes?

What is the start codon?

Give the three alternative stop codons.

Give the primary structure (sequence of amino acids) of the polypeptide made in this animation.

What is the difference between a polypeptide and a protein?

What is the advantage of ribosomes operating as polyribosomes?

What are the similarities and differences between DNA replication and protein synthesis?

QUIZ

slide70

Helicase is an enzyme and therefore also a protein.

DNA is double stranded to permit replication.

Ribosomes are located in the cytoplasm.

The start codon is AUG.

The three stop codons are UGA, UAG and UAA.

Give the primary structure of the polypeptide is methionine, proline, isoleucine, valine, cysteine.

Polypeptides have less than 100 amino acids, protein have more. A protein may consist of several polypeptides.

Polysomes increase efficiency, they enable one mRNA molecule to produce many polypetides simultaneously.

HINT - Think about the enzymes and nucleotides used, the end product and the location of the process.

ANSWERS

really good website
Really good website
  • http://www.le.ac.uk/ge/genie/vgec/he/index.html
what is a genome
What is a genome?
  • All of the genetic material (the base pairs) found in one complete set of an organism’s chromosomes.
  • The study of genomes is called genomics.
does genome size matter
Does genome size matter?

Why would a single celled animal like the amoeba need a genome that is about 200 times larger than the human genome?

Ans: They carry a lot of junk DNA!

what is a gene
What is a gene?
  • Segment of DNA that codes for formation of a protein
    • Structural genes express structural and/or functional proteins.
    • Regulatory genes are short nucleotide sequences that express proteins that control the activity of structural genes by feedback mechanisms.
number of genes
Number of genes

Should we be offended that a mustard plant has as many genes as a human?

an overview of gene structure
An Overview of Gene Structure

Coding Region

DNA sequence that will be transcribed

from the template strand.

5’

3’

5’

STOP

Regulatory region

START

3’

Promoter region

Terminator region

gene expression
Gene Expression
  • The expression of genetic information is one of the fundamental activities of all cells.
  • Instructions stored in DNA are transcribed and translated into various RNA molecules.
introns and exons
Introns and Exons
  • The coding region in eukaryotes contain:
    • introns - non-coding regions of DNA
    • exons - coding regions of DNA
  • Prokaryotes do not have introns – why?
    • They don’t carry “junk DNA” due to short replication cycles
rna processing in eukaryotic cells
RNA Processing in Eukaryotic Cells

DNA Template Strand

Pre-mRNA transcript of DNA template strand

Introns are spliced out by spliceosomes leaving only the sequences that will be expressed. This is an example of RNA processing. The introns usually are degraded. The result is a mature mRNA strand that will leave the nucleus to be translated.

INTRON

INTRON

EXON

EXON

EXON

Spliceosome

Spliceosome

EXON

EXON

EXON

genome to proteome
Genome to proteome
  • The human genome has about 25,000 genes but our proteome (the total number of different proteins) is much larger (~100,000)
    • How can this occur?
  • Many genes can produce more than one protein because the mRNA transcript contains different combinations of exons. This process is called alternative splicing.
alternative splicing
Alternative splicing

INTRONS

Pre-mRNA transcript

Possible mRNAs using different combinations of exons

Result: when each mRNA is translated, a different protein is produced.

EXON 1

EXON 2

EXON 3

EXON 4

EXON 1

EXON 4

PROTEIN 1

EXON 2

EXON 3

EXON 2

EXON 1

EXON 4

PROTEIN 2

EXON 2

EXON 3

EXON 4

PROTEIN 3

gene regulation
Gene Regulation
  • Each cell contains an entire organism’s genome.
  • All cells of an organism have the same genome, but can have different phenotypes.
  • For example, cells in your eye have the gene for producing fingernail protein (keratin) but this gene is not expressed.
  • How do genes get switched on or switched off?
why regulate gene expression
Why regulate gene expression?
  • Cells conserve energy and materials by blocking unneeded gene expression.
  • If a substrate is absent in the environment why produce the enzyme for that substrate!
  • Repressor molecules keep the cell from wasting energy by not transcribing mRNA or making enzyme molecules that have no use.
  • The cell can control its metabolism – resources are used only when there is a metabolic need and can be redirected to other metabolic pathways.
gene regulation in prokaryotes
Gene regulation in prokaryotes
  • Bacteria have groups of genes that are controlled together and are turned on/off as required.
  • E.g. the lac operon is a set of genes in bacteria used for lactose metabolism.
  • Bacteria produce the enzymes to break down lactose to glucose and galactose only when lactose is present.
  • http://www.sumanasinc.com/webcontent/animations/content/lacoperon.html
  • http://pages.csam.montclair.edu/~smalley/LacOperon.mov
lac operon an example of gene regulation in e coli
Lac Operon – an example of gene regulation in E. Coli
  • The bacterium Escherichia coli is capable of producing the enzyme b-galactosidase which splits lactose to produce glucose and galactose.
  • This enzyme is only produced when the bacteria encounters lactose. When lactose is not present, a protein binds to the promoter region of the b-galactosidase gene and prevents transcription (RNA polymerase cannot access the promoter). This protein is referred to as a repressor protein.
  • When lactose is present in the growth medium of the bacteria, it enters the cell and binds to the repressor protein causing it to be removed from the DNA and allowing transcription to occur.
  • The gene is ‘on’ or ‘off’ depending on the nutrients available to the cell.
gene regulation in eukaryotes
Gene regulation in Eukaryotes
  • Still being investigated
  • Proteins involved (like prokaryotes) – but more complicated
    • Enhancers: act as binding sites for activator proteins and increase number of DNA polymerase molecules transcribing genes
    • Chemical modification: eg presence or absence of histone proteins
other factors in gene regulation
Other factors in gene regulation
  • It is important to realize that the environment of a cell can also influence the expression of genes. This includes factors such as:
    • Light
    • Temperature
    • Ions
    • Hormones