Download Chapter 6: Genetic Control: DNA and RNA

Chapter 6:
Genetic Control:
DNA and RNA
Genetic control of protein
structure and function
Structure of DNA
and RNA
Nucleotides
DNA replication
Polynucleotides
DNA, RNA
Protein
Synthesis
....the features of the “genetic molecule”
• Ability to carry instruction (a blueprint)
for the construction and behavior of
cells
• and the way they grow together to form
a complete living organism
....the features of the “genetic molecule”
• Ability to be copied (perfectly) over and
over again
• Whenever the cells divide it can pass on
an exact copy of each “genetic molecule”
to the nuclei of each daughter cells
The discovery of the DNA
(a) describe the structure of RNA and DNA and
explain the importance of base pairing and the
different hydrogen bonding between bases
Structure of DNA and RNA
• DNA stands for
deoxyribonucleic acid
• RNA stands for
ribonucleic acid
• Both DNA and RNA
are macromolecules
like protein and
polysaccharide.
• They are polymers
• DNA and RNA are made of smaller molecules
known as nucleotides.
• DNA and RNA are therefore polynucleotides.
• Refered simply as nucleic acid.
• Nucleotides have three parts to them:
(i) a phosphate group, which is negatively
charged.
• Nucleotides have three parts to them:
(ii) a pentose sugar, which has 5 carbon atoms in
it. In RNA the sugar is ribose. In DNA the sugar
is deoxyribose.
Nucleic Acids
Phosphate
Phosphate
Sugar
Sugar
The joined sugar is either ribose (RNA) or deoxyribose
(DNA), and the only difference is that deoxyribose has
one fewer oxygen atoms in its molecule
Pentose sugar
• 5-carbon pentose sugar.
• Nucleotides have 2 kinds of pentose; units
of RNA contains “ribose” sugar and DNA
contains “deoxyribose” sugar
• The base of a nucleotide is covalently
joined to C1 of the pentose through
glycosidic bond (N-1 of pyrimidine ; N-9 of
purine)
•The phosphate of a nucleotide is covalently
joined to C5 (-OH) of the pentose through
phosphoester bond.
Nitrogenous base
• Large, double ring molecule found in both
DNA and RNA.
•Adenine (A) and Guanine (G)
•N-9 of the ring will form covalent bond
(glycosidic bond) with C1 of the pentose in a
nucleotide.
• Small, single ring molecule found in both DNA
and RNA.
•Cytosine (C), Thymine (T) [DNA] and Uracil (U)
[RNA]
•N-1 of the ring will form covalent bond
(glycosidic bond) with C1 of the pentose in a
nucleotide.
Nucleic Acids a.k.a Nucleotide
Pyrimidine base
Phosphate
Purine base
Phosphate
Sugar
Sugar
There are two types of bases - purine and pyrimidine you only really need to know that adenine and guanine
are the purine bases and that purine bases are larger.
Nitrogenous Base
Purine
Adenine
Pyrimidine
Thymine (DNA)
Guanine
Cytosine
Uracil (RNA)
Polynucleotide
• To form both DNA
and RNA, many of
these nucleotides
are linked together
in a polynucleotide
chain.
• The structure of this
poly nucleotide
chain is seen in this
picture
As you can see, it is
formed by alternating
sugars and phosphates,
and the nitrogen bases
project sideways.
Polynucleotide
• Nucleotides are
connected to each
other via the
phosphate on one
nucleotide (C5) and the
sugar (C3)on the next
nucleotide
• A Polynucleotide
• Sugar-phosphate bonds
(backbone of DNA)
• A-T(U) and G-C
Reading frame of DNA
Phosphate grp
covalently attached
to C5 of the pentose
sugar, hence -5’ end
term is used.
Phosphodiester
bond
Hydroxyl grp
covalently attached
to C3 of the pentose
sugar, hence -3’ end
term is used.
• In a leading strand (template) of a long
polynucleotide chain (DNA), the reading frame is
always from “ 5’ – 3’ ”. What does this means???
• As you start reading the nucleotides of a leading
strand, you will realize a FREE phosphate grp is
always attached to C5 of the pentose sugar. This
group is called as the 5’ end of the chain
• As you reach the end of the chain, you will see
the final nucleotide has a FREE hydroxyl grp
attached to the C3 of the pentose sugar. This
group is called as the 3’ end of the chain.
• Therefore we always read the leading strand of
any given DNA as 5’ – 3’. It’s complementary
strand is the reverse, we read as 3’ – 5’, because
we start off a complementary nucleotide with a
FREE –OH at C3 of the sugar.
• DNA molecules
are simply two of
these strands next
to each other,
running in
opposite
directions held
together by
hydrogen bonds.
• The bases do not take
part in the
polymerisation
• Adenine always pairs with thymine, cytosine
always pairs with guanine (A-T, C-G, and in
RNA, it is A-U, since thymine does not
appear).
Base pairing of Nucleotides
In 1940s, Erwin Chargaff calculated
a “rough
equivalent” between adenine and
thymine molecules and between
cytosine and guanine molecules
Chargaff’s DNA Database Composition in
Various Species (%)
Species
A
T
G
C
Homo sapiens (Human)
Drosophila melanogaster (fruit fly)
Zea mays (Corn)
Neurospora crassa (fungus)
Escherichia coli (bacteria)
31.0
27.3
25.6
23.0
24.6
31.5
27.6
25.3
23.3
24.3
19.1
22.5
24.5
27.1
25.5
18.4
22.5
24.6
26.6
25.6
Base pairing – Conclusion of Chargaff’s
experiment
Polynucleotides
DNA molecules
forms a 3D double
helix
shape, bonded by
hydrogen,
whereas RNA
remains as single
strands of
polynucleotide.
The Rule:
• Adenine always base pairs with Thymine (or
Uracil if RNA)
• Cytosine always base pairs with Guanine.
• This is because there is exactly enough room
for one purine and one pyramide/pyrimidine
base between the two polynucleotide strands
of DNA.
Types of RNA
There are three major classes of RNA. Each
class of RNA has its own unique size, shape
and function in protein synthesis
• Ribosomal RNA (rRNA) – alone with ribosomal
proteins, makes up the ribosomes, where proteins
are synthesised.
• Messenger RNA (mRNA) – takes a message from DNA
in the nucleus to the ribosomes in the cytoplasm
• Transfer RNA (tRNA) – transfers amino acid to the
ribosomes
RNA vs DNA
RNA is a nucleic acid like DNA, but with 4
differences:
• RNA has the sugar ribose instead of deoxyribose
• RNA has the base uracil instead of thymine
• RNA is usually single stranded
• RNA is usually shorter than DNA
(b) explain how DNA replicates semi
conservatively during interphase;
Nature of the Genetic Material
• Property 1 - it must contain, in a stable form,
information encoding the organism’s
structure, function, development and
reproduction
• Property 2 - it must replicate accurately so
progeny cells have the same genetic makeup
• Property 3 - it must be capable of some
variation (mutation) to permit evolution
Dianne Chabira
• The discoverers of DNA,
Watson and Crick suggested
that the two polynucleotide
strands of DNA could spilt
apart, and
• new nucleotides (the correct,
complimentary ones) could line
up along each strand, making a
new DNA molecule.
• This process is known as semiconservative replication, since
half of the original molecule is
conserved in each of the new
molecules.
`
DNA Replication
dispersive
model
dispersive
model
• Semi-conservative: Each new molecule would contain one old
strand and one new strand.
dispersive
model
• Conservative model: One completely new double helix
would be made from the old one
dispersive
model
• Dispersive model: Each new molecule would be old bits and
new bits scattered randomly through the molecules
Experimental proof
• Nitrogen is a major constituent of DNA, and
there are two different isotopes - 14N and
15N.
• 14N is by far the most abundant isotope of
nitrogen, but DNA with the heavier 15N
isotope also works.
The conditions of DNA replication
1.
2.
3.
4.
5.
6.
7.
8.
Replication fork
Helicase
Continuous synthesis
DNA polymerase III
Discontinuous synthesis
RNA primer
DNA polymerase I
DNA ligase
(c) state that a gene is a sequence of nucleotides
as part of a DNA molecule, which codes for a
polypeptide and state that a mutation is a
change in the sequence that may result in an
altered polypeptide;
DNA, RNA and Protein Synthesis
How can a single type of molecule
like DNA
control all the activities of a cell?
What are proteins made of?
Strings of amino acids
The triplet code
• The sequence of bases or nucleotides in a
DNA molecule is a code for the sequence of
amino acids in a polypeptide.
• A sequence of amino acids is coded for by the
sequences of nucleotides in a DNA molecule three bases form a triplet code or the codon
on the mRNA strand.
The Codon???
• A triplet of bases that codes for a specific
amino acid is called a codon.
• Hence, the complementary set of triplet bases
for the codon is knows as the anticodon.
• Each triplet code
(codon) codes for
one amino acid
• E.g.:
T-T-T, thyminethymine-thymine
stand for the amino
acid lysine and it is
always read in the
same direction.
• Short piece
of DNA
carries the
instruction
to the cell.
• Deciphering
the codes
of life!!
The nature of genetic codons
• Triplets
• Non-overlapping
• degenerate
Genes and Genomes
• A gene is a part of a DNA molecule that codes
for just one polypeptide, and in humans alone
there is an estimated 140,000 genes.
•
•
•
•
One DNA molecule contains many genes.
One gene = one polypeptide
One codon = one amino acid
In human it is estimated that there are about 30
000 genes.
• Total DNA of a human cell is 3 x 109 base pair long
• Only 3% of this DNA actually code for protein.
• The rest are known as junk DNA.
• The total set of genes in a cell is called the
genome.
• The genome is the total information in one
cell.
• All cells in the same individual contain the
same information, the genome represents the
genetic code of that organism.
Human Genome Project
• A global project to
sequence the complete
human genome which
launched in 1990.
• The human genome
contain about 3 billion
bases
• To Identify every human
gene and find out how at
least some of them affect
human health.
mRNA
RNA in protein
synthesis
rRNA ribosome
tRNA
(d) describe the way in which the nucleotide
sequence codes for the amino acid sequence in
a polypeptide with reference to the nucleotide
sequence for HbA (normal) and HbS (sickle cell)
alleles of the gene for the β-haemoglobin
polypeptide;
Sickle Cell Anemia
• If even one amino
acid in the sequence
is changed, that can
potentially change
the protein’s ability to
function.
• Sickle cell anemia is a
blood disorder that
affects hemoglobin
Sickle Cell Anemia
• It is caused by a change in
only one nucleotide in the
DNA sequence that causes
just one amino acid in one
of the hemoglobin
polypeptide molecules to
be different.
• Because of this, the whole
red blood cell ends up
being deformed and unable
to carry oxygen properly.
One amino acid change
•
•
•
•
Clumping of cells in bloodstream
Spleen concentrates sickle cells
Rapid destruction of sickle cells
Anemia, causing weakness,fatigue,
impaired development, heart
chamber dilation
• Spleen enlargement
• Heart failure, paralysis, pneumonia,
rheumatism, gut pain, kidney failure
(e) describe how the information on DNA is used
during transcription and translation to construct
polypeptides, including the role of messenger
RNA (mRNA), transfer RNA (tRNA) and the
ribosomes;
Protein Synthesis
• There is a direct relationship between the
base sequence of DNA and the sequence of
amino acids that makes up a protein
DNA mRNA tRNA protein
triplet
codon
anticodon
Amino acid
CCA
GGU
CCA
Glycine
AAA
UUU
AAA
phenylalanine
GTG
CAC
GUG
histidine
Transcription
• Transcribe means to
copy – using DNA as a
template,
complementary RNA
nucleotides are joined
to make mRNA
Transcription
• RNA polymerase
unwinds a short
section of the DNA
double helix near
the start of the gene.
• This unwound
section is known as
the transcription
bubble.
Transcription
• The RNA polymerase,
and therefore the
transcription bubble,
travels along the
coding strand in the 5'
to 3' direction, and
along the noncoding
strand in the opposite,
3' to 5', direction,
Transcription
• as well as polymerizing a
newly synthesized strand
in 5' to 3' or downstream
direction. The DNA
double helix is rewound
by RNA polymerase at
the rear of the
transcription bubble.
• Like how a zipper works,
only it unzips it and rezips
it without going back and
forth.
Transcription
• Where the helix is unwound, the
coding strand consists of
unpaired bases, whilst the
template strand consists of an
RNA:DNA composite, followed
by a number of unpaired bases
at the rear.
• This hybrid consists of the mostrecently-added nucleotides of
the RNA transcript,
complementary base-paired to
the template strand
Transcription
• mRNA can now leave
the nucleus.
• Each triplet code of
bases from DNA is now
represented by three
bases on mRNA called
a codon.
Stages of Translation
Structure of tRNA
An aminoacyl-tRNA synthetase joins a
specific amino acid to a tRNA
Anatomy of a ribosome
Initiation of translation
Sequence in mRNA
is complementary
to a sequence in
the tRNA anticodon
in the small
ribosomal subunit
Translation elongation
Termination of translation