MKBS221
• Study Material
– Prescott 10th Ed
– Brock Biology of
Microorganisms 15th Ed–
Madigan et al.
– Practical Guide
1
MKBS221
• Components
– Microbial & eukaryotic Genetics Chap 13,
14, 15, 16
– Virology Chap 27
– Immunology Chap 33 and 34
2
MKBS221
• Evaluation (Participation mark)
– Class tests (x2) and Assignments (x2)
= 25% (1:1)
– Semester test (1 opportunity)
= 25%
– eFundi Practical tests (4) and reports
(x4) and exam (x1) = 50% (1:1)
3
MKBS221
• Preparation for contact sessions
– READ the chapter BEFORE the contact
session
– EFUNDI tests at the start of EACH WEEK
– ASK questions
– ASSIGNMENTS: Do ALL the questions in the
study guide and textbook
– Other assignments
– All definitions in the textbook is important
4
Warning against plagiarism
• Assignments, Practical reports are individual
tasks and NOT group activities
• Internet theft is NOT ALLOWED
5
Study Unit 1.1
Chapter
DNA, RNA and Genetic
Information
OUTCOMES
• On completion of this study unit you
should be able to:
• formulate important concepts that
form the basis of genetics;
• explain the flow of genetic information –
Central Dogma;
• describe the chemical composition of the
different nucleic acids;
• discuss the double-helix structure of
DNA;
• describe the organisation of DNA in a
cell.
• discuss protein structure. 7
Terminology and
Concepts
• What is DNA? DNA is the storage molecule
for all living processes in organisms for the
duration of life of the organism – metabolism
and reproduction
– Definition
– Deoxyribonucleic acid is a polymer of
deoxy-ribonucleotides linked together by
phosphodiester bonds.
8
Three Major Macromolecules
• Deoxyribonucleic acid (DNA)
– storage molecule for genetic instructions to carry out
metabolism and reproduction
• Ribonucleic acid (RNA)
– expresses the information in DNA
• proteins and enzymes
– build cellular structures and do cellular work
• Genome
– All DNA present in a cell or virus
• Bacteria, Archaea generally one set (haploid – 1N)
• Includes plasmids
• Eukaryotes two sets (diploid – 2N)
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Central Dogma
Replication
DNA polymerase
Both strands DNA
Transcription
RNA polymerase
Gene expression
Only template strand (gene)
mRNA, tRNA, rRNA
RNA
Translation
Ribosome
mRNA decoded
Protein Synthesis of polypeptide
tRNA and rRNA involved
10
Figure 12.4 Flow of genetic information
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The Flow of Genetic
Information
• Central dogma:
– the pathway from DNA to RNA to protein is
gene expression
– it is conserved in all cellular forms of life
• from one generation to the next :
– DNA stores genetic information
– information is duplicated by replication and is
passed on to next generation
12
Central Dogma: Gene
Expression
• DNA divided into genes
– transcription yields a ribonucleic acid (RNA)
copy of specific genes
– translation uses information in messenger
RNA (mRNA) to synthesize a polypeptide
• also involves activities of transfer RNA
(tRNA) and ribosomal RNA (rRNA)
13
Story of DNA
• Mid 1865: Gregor Mendel's studies with
peas. Suggested that the traits that he
observed are determined by discrete factors
(genes). The origin and nature of the
material was unknown.
• 1860-1870: Johann Friedrich Miescher
• Isolated a substance from cell nuclei and
called it "nuclein".
• 1909:Wilhelm Johannsen: Coins the term
“Gene” (1909)
• 1928: Frederick Griffith: The transforming
principle
• 1929:Phoebus Levene: Discovers that DNA
is made up of nucleotides, phosphates,
sugars and 4 bases 14
Griffith 1928 - Streptococcus pneumoniae
Injected into
mice:
•Virulent isolate –
death
•Avirulent isolate –
live
•Boil virulent
isolate – live
•Avirulent + boiled
virulent
isolate – death
Conclusion:
A macromolecule is
responsible 15
DNA AS THE GENETIC MATERIAL
16
Transformation experiment of Frederick Griffith, 1928
Avery, McCleod & McCarty 1944
Aim: Is DNA, RNA or protein responsible for
transformation?
Experiment:
Used enzymes to destroy macromolecules selectively.
Result:
Only when DNA is destroyed did transformation not
occur.
Conclusion: DNA is the basis of heredity
17
Demonstrating that DNA is the transforming principle Avery,
18
MacLeod, and McCarty, 1944
1950
https://www.khanacademy.org/science/high-school-biology/hs-molecular-genetics/hs-
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discovery-and-structure-of-dna/a/discovery-of-the-structure-of-dna
Importance of Chargaff’s rule (1950)
1) (A+G= T+C)
2) (A=T, & G=C)
3) AT/GC = 1
This rule can be applied
almost universally in all
organisms.
He also observed that
DNA extracted from
higher plants and
animals had a higher
(A:T) whereas DNA
extracted from
microorganisms had a
higher( G:C) 20
1. It suggested that the total amount of purine bases
equaled the total amount of pyrimidine.
2. This structure suggests a way in which the DNA
molecule can be replicated since each base can
specify its complementary base by hydrogen bonding.
3. Each strand serves as a template for the synthesis of a
complementary strand.
4. It also suggests that the sequence of nucleotide pairs
in DNA dictates the sequence of amino acids in a
protein encoded by a gene (Genetic code)
• In other words, a genetic code contains information in
DNA as a sequence of nucleotide pairs can be
translated into different languages of amino acid
sequences in protein. 21
• 1952 – Alfred Hershey and Martha Chase
provide convincing evidence that DNA is
genetic material.
• Waring blender experiment using T2
bacteriophage and bacteria
• Radioactive labels
32P for DNA and
35S for protein
22
23
-Hershey and Chase Waring blender experiment 1952
24
25
Research of James Watson and
Francis Crick on DNA structure
In 1951 James Watson traveled from
the United States to work with Francis
Crick at Cambridge University
Watson and Crick used the “Model
Building” approach
They physically built models out of
wire, sheet metal, nuts and bolts to
come up with the structure of DNA
Why did they build models?
“Sometimes the fingers can grasp what
the mind cannot” (Biology the Science of
Life) 26
• Francis Crick continued to work
in genetics and then moved
into brain research, becoming
a professor at the Salk Institute
for Biological Studies in
California. He died on 28 July
2004.
• From 1988 to 1992, James
Watson directed the Human
Genome Project at the
American National Institutes of
Health. He was instrumental in
obtaining funding for the
project and in encouraging
cooperation between
governments and leading
scientists.
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28
29
DNA sequencing is the process
of determining the nucleic acid
sequence – the order of
nucleotides in DNA. It includes
any method or technology that
is used to determine the order
of the four bases: adenine,
guanine, cytosine, and thymine
30
Human genome
3 billion bp = 3.2 Gbp
7 countries, > 20 centres
$2.7 billion
1990-2003
HiSeq X
1.8 Tb/run or 600 Gb/day
$1000
31
DNA and RNA structure
• DNA and RNA are nucleic acids – polymers of
nucleotides
• Consist of
– Nitrogenous bases
– Sugar
– Phosphate
• Sugar-phosphate backbone
– Phosphodiester bonds: Covalent bonds
between 3’-OH of sugar and 5’-phosphate
attached to an adjacent sugar 32
Carbon-5
5
4 1
3 2
OH at
Carbon-3
33
Methyl group
Uracil
Carbonyl group
Amine group
34
Sugar
Sugar
The two strands are held together by hydrogen bonds
3 hydrogen bonds are between Guanine and cytosine 35
Sugar
Sugar
The two strands are held together by hydrogen bonds
2 hydrogen bonds are between Adenine and thymine 36
Nitrogenous bases
37
Figure 13.4
(b) Examples of nucleosides-adenosine and 2'-deoxyadenosine-and
the nucleotide 2'-deoxyadenosine monophosphate. The carbons of
nucleoside and nucleotide sugars are indicated by numbers with
primes to distinguish them from the carbons in the bases. 38
Figure 13.4
(a) A diagram showing the relationships of various nucleic acid components.
Combination of a purine or pyrimidine base with ribose or deoxyribose
gives a nucleoside (a ribonucleoside or deoxyribonucleoside).
(b) A nucleotide contains a nucleoside and one or more phosphates.
(c) Nucleic acids result when nucleotides are connected together 39 in
polynucleotide chains
Differences
DNA / DNA RNA / RNA
Nucleotides Adenine, guanine, Adenine, guanine,
cytosine, thymine cytosine, uracil
Sugar Deoxyribose ribose
Strands Double strand helix Single or double
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41
How do you make DNA from nucleotides?
Briefly, the energy for the formation of the
phosphodiester bond comes from the dNTP,
which has to be added. dNTP is a nucleotide
which has two additional phosphates attached
to its 5' end. In order to join the 3'OH group
with the phosphate of the next nucleotide, one
oxygen has to be removed from this phosphate
group.
3’ This oxygen is also attached to two extra
phosphates, which are also attached to a Mg+
+. Mg++ pulls up the electrons of the oxygen,
which weakens this bond and the so called
nucleophilic attack of the oxygen from the 3'OH
succeeds, thus forming the phosphodiester
bond.
5’ If you try to join the dNTP's 3'OH group to the 5'
phosphate of the next nucleotide, there won't
be enough energy to weaken the bond between
the oxygen connected to the 5' phosphorous 42
(the other two phosphates of the dNTP are on
Polynucleotide chain
5'
3'
• Free phosphate group at 5'-C of sugar
• Free hydroxyl-group at 3'-C
• New nucleotides added at 3' end of sugar
• Chain elongation 43
Exercise
• Complementary DNA strand of:
• 5’-AGGTTCAATG-3’
• 3’-TCCAAGTTAC-5’
• 3’-GACTTACGAT-5’
44
Importance of hydrogen bonds
• Hydrogen bonds form strong associations
• These bonds stabilize helix structure
• Re-annealing after heat denaturation
• GC bonds stronger than TA
• GC composition – indication of melting
temperature – If large numbers of GC occur
then high melting temperature
• Allows for 2 dimensional structures of single
strand molecules to form e.g. stem-loop
45
DNA structure
• Double
stranded
• Anti-parallel –
sugars
orientated in
opposite
directions
• Free 5'
phosphate
• Free 3' OH
• Chemical
polarity 46
Complementary
bases:
A and T
C and G
Complementary
strands:
2 strands that can
bind
according to AT
and GC
sequences
47
• The base pairing is called
complementary because
there are specific geometry
requirements in the
formation of hydrogen
bonds between the
heterocyclic amines.
• Heterocyclic amine base
pairing is an application of
the hydrogen bonding
principle.
• In the structures for the
complementary base pairs
given in the graphic on the
left, notice that the thymine
- adenine pair interacts
through two hydrogen
bonds represented as (T=A)
and that the cytosine-
guanine pair interacts
48
through three hydrogen
Why is complimentary base pairing vital to the structure
of DNA?
1)It allows enzymes such as RNA polymerase to attach the correct
base to the new strand, and therefore conserve the genetic code
of the organism (keep it the same)
2)A::T and G=C is essential. The importance to the DNA structure
is that it prevents loss of genes and malformation of encoded
products (protein and mRThe base pairing is called
complementary because there are specific geometry
requirements in the formation of hydrogen bonds between the
heterocyclic amines.
3)Heterocyclic amine base pairing is an application of the
hydrogen bonding principle.
4)In the structures for the complementary base pairs notice that
the thymine - adenine pair interacts through two hydrogen bonds
49
represented as (T=A) and that the cytosine-guanine pair interacts
DNA structure
• Each bp 36° rotation
• Vertical length of one turn = 34
Å
34 Å = 34.0 x 10 -10 m = 3.4 nm
10.5 bp per helix turn
• Helix is turned right-handed –
anti-clockwise
• Major groove and minor
groove/
(b) A simplified model that
highlights the antiparallel
arrangement and the major and
minor grooves.
(c) A space-filling model of the
B form of DNA.
Note that the sugar-phosphate
backbone spirals around the
outside of the helix and the 50
base pairs are embedded
Chemically
• DNA consists of two • It is the sequence of
long polymers of simple these four bases along
units called nucleotide, the backbone that
• The backbones made of encodes information.
sugars and phosphate • This information is read
groups joined by ester using the genetic code,
bonds. which specifies the
• These two strands run sequence of the amino
in opposite directions acids within proteins.
to each other and are • The code is read by
therefore anti-parallel. copying stretches of
• Attached to each sugar DNA into the related
is one of four types of nucleic acid RNA, in a
molecules called bases. process called
transcription.
51
A-DNA B-DNA Z-DNA
right-handed. its bases seem to
still right-handed,
One turn spans 3.4 nm, zigzag.
but Z DNA is left-handed.
comprising 10 base
every 2.3 nm makes One turn spans 4.6 nm,
pairs in solid state and
a turn and helically coiled in comprising 12 base
there are 11 base chromatin but 10.5 in pairs.
pairs per turn. solution. The DNA molecule with
alternating G-C
52
sequences in alcohol or
Main points of the DNA model
by Watson & Crick:
1) Two polynucleotide chains coiled around a central axis, forming a
right-handed double helix.
2) Two chains are antiparallel
3) The bases of both strand are lying inside of the structure and
stacking flat on one another, 3.4Å (0.34 nm) apart.
4) The two strands are held together by hydrogen bonds. Between
Thymine and Adenine are two hydrogen bonds while three
hydrogen bonds exist between Guanine and Cytosine
5) Adenine always pairs with Thymine and Guanine always pairs with
Cytosine
6) The ratio of A:T = 1 and the ratio of G:C=1
7) One complete turn of the helix is 34 Å long and contains 10.5
bases.
8) The distance between one base and the one below is 3.4 Å
9) The two strands of DNA coil around each other in an α helical
structure fashion and with an angular tilt produces two types of
grooves called major grooves and minor grooves along the axis.
10) The double helix measures 20 Å in diameter 53
RNA Structure
• polymer of nucleotides
– contains the bases adenine, guanine, cytosine,
and uracil
– sugar is ribose
– phosphodiester bonds
• most RNA molecules are single stranded;
• Can form hair-pin structures
54
55
1. List the conclusions Griffith & Avery, Hershey
& Chase drawn from their experiments.
2. Summarize the relationship between genes &
DNA.
3. Describe the overall structure of the DNA
molecule.
4. What are the 4 kinds of bases in DNA?
56
Protein Structure
• polymers of amino acids
linked by peptide bonds
– amino acids have central
carbon (the α carbon)
• carboxyl group (C-
terminal)
• amino group (N-terminal)
• side chain
– amino acids can be polar,
non-polar, or charged
depending on side chain
– 20 different amino acids
• Peptide bonds form between
• carboxyl group and amino group
• of next amino acid
57
58
Figure 12.7
59
Protein structure
A tetrapeptide chain is shown. One of the peptide bonds linking
the four amino acids together is highlighted by a black arrow.
At one end of the peptide is an amino group (amino or N
terminal); at the other end is a carboxyl group (carboxyl or C
terminal).
60
Learning activities
• Define the following terms: polymer, monomer, nucleotide,
nucleoside, double helix base pair, complementary base
pairing, nucleic acid, DNA
• What experiments led to our knowledge of DNA as the genetic
material of the cell
• Diagrammatically illustrate the structure of a nucleotide
• Explain the importance of Chargaff's rule in the discovery of
the DNA structure
• What are the chemical components that make up DNA
• Illustrate how nucleotides are attached together to form a
polynucleotide
• What are the functions of DNA?
• What are the important features of the double helix structure?
• What is meant by ‘complementary base pairing’ and why is it
important in the DNA structure?
• Who were the scientists that discovered the double helical
structure of DNA and what were their findings?
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