Molecular genetics

(BCHEM 365)

Lecturer: Dr Ir. Peter Twumasi

(twumasipeter@gmail.com)

Assistants Dr. Lord Jephthah Joojo Gowans

(Ljj.gowans@gmail.com )
Mr. Bright Amoah
(amoahbright21@gmail.com)
 Goals….
1. Acquire fundamental understanding of molecular genetics which
is necessary for molecular biology and all aspects of
biotechnology.

2. Gain experience in interpretation of biometric data and genetic

backgrounds of diseases.

3. Enhance general scientific reasoning, understanding of methods,

& rigor of experimental approaches.

4. Enhance your ability to “teach yourself” what you need & stay
current.
 Requirements
1. Attendance rewards you 2% of the final mark. Only students having attended
all lectures but two or less would enjoy this privilege.

2. Assignments and class presentations would be conducted periodically.

3. A 10-minute quiz will be conducted weekly. Questions would mainly come

from discussion in the previous lecture .

4. Mid-Semester examination (equivalent to 15% of the final mark) would

consist of MCQs and short-answer questions.

5. The End of Semester Examination, made up of MCQs, short-answer questions

and essay questions.
 Caution

1. Ensure that your mobile phones are switched off or muted before
entering the lecture room.

2. Quizzes/tests will be conducted either in the first or last 10 min of each

lecture.

3. Lateness will deprive you of participation in the weekly quizzes as they

would be organized within the first 30 minutes of the lecture.
 Structure and process
1. Lecture format with in-depth discussion.

2. A 10-minute break within Wednesday’s lecture.

3. Thursday’s lecture would be mainly for solving problems.

Students are advised to send their problems to course instructors
via email not later than 8 hours before the Tutorial Class.
4. Advance preparation towards lectures is strongly advised.
 Lecture materials

• Soft copies lecture slides would be made available prior to every

lecture.

• You MUST supplement the lecture notes with the following

recommended books .

1. Molecular Biology of the Cell by Alberts, Johnson, Lewis, Raff,

Roberts, and Walter.

2. An Introduction to Genetic Analysis, 7Ed, by Griffiths and others.

• Chapters 8-12 (Food Sci & Tech: Add Chapters 13-20).
3. Molecular Cell Biology, 4 ed., by Lodish and others
• Chapters 4, 9 (Food Sci & Tech: Add Chapter 7).

4. Genetic Analysis of Genes and Genomes, 5Ed, by Daniel

Hartl and Elizabeth Jones.

5. Principles of Biochemistry by Lehninger

5. Read authentic materials from the internet as well.

 Course content
1. Structures, properties and role of DNA and
RNA.
2. Biosyntheses of DNA (or replication) and RNA
(transcription) processes.
3. Protein biosynthesis (or translation).
4. Deciphering the Genetic Code
 Course content (cont’d)
5. Mutations
6. Regulation of protein synthesis
7. Control of gene expression
8. Some important techniques and
applications of genetic engineering.
Central dogma of molecular biology

transcription

DNA RNA PROTEIN (phenotype)

replication
translation

… to understand the (1) flow of genetic information,

(2) development of phenotype, and (3) control of
gene expression.
What are nucleic acids?
1. Nucleic acids are essential biomolecules present in all living
entities where they serve as carriers of genetic information.

2. NAs contain information necessary for ordering amino acids in

in proteins.

Two forms of nucleic acid molecules

1. Deoxyribonucleic acid (DNA) - Storehouse or cellular library
containing all information necessary for building cells and
tissues of an organism.
2. Ribonucleic acid (RNA) – mostly serve as copied information
from DNA during transcription. S
The three distinct structures/roles of RNA in
protein synthesis

1. Messenger RNA (mRNA) carries instruction from DNA

2. Transfer RNA (tRNA) interprets info within mRNA
with and carries right a/a to ribosome complex for
protein synthesis
3. Ribosomal RNA (rRNA) is the most abundant form of
RNA which maintain the translational enzyme complex
(ribosome) during protein synthesis
 Where in the cell are Nucleic
acids located?
1.In higher organisms, nuclei contain genomic DNA.

2.In prokaryotes, the nucleic acids are boundless in the cytoplasm.

3.Mitochondria and chloroplast contain extra or maternal genetic

material - thus in many cases an offspring receives, in addition to
nuclear genetic information, maternal cytoplasmic genes.
 Composition of nucleic acids
• DNA and RNA are made up of nucleotide building units
A nucleotide consist of

Base (A,C,G,T/U) + (deoxy)ribose + phosphate

• Consists of four basic subunits, defined by the base

Adenine (A), Cytosine (C), Guanine (G), Thymidine (T) or
Uraacil U (in case of RNA).

• Linked by covalent phosphodiester bonds between 5’ C of one

(deoxy)ribose and 3’ C of another (deoxy)ribose
- Nucleoside = Base (A,C,G,T/U) + deoxyribose
- Nucleotide = Base (A,C,G,T/U) + deoxyribose + phosphate
Nucleotide structure
The 5 naturally occurring nucleotides
Examples of three nitrogenous bases found
in DNA, depicted with ATP rather than the
single phosphate group of the DNA
molecule

Purines: A, G
Pyrimidines: C, T, U [RNA]
Different forms of nucleic molecle representation
(1) Stick representation (2) Simplified representation

AGT ATC
3’ 5’ AGTATC 3’
P OH
5’

Nucleotide polymerization (condensation reaction)

(base )b
(base )a O
+ HO-P-O-(sugar)
(sugar)-OH
O- Phosphodiester bond

(base )a O (base )b + H2O

(sugar)-O-P-O-(sugar)
O-
 Complementary Base Pairing
E. Chargaff’s Rule

A=T and G=C moles, NOT equal amounts of purine and

pyrimidine as had been postulated earlier

• A + T: 2 hydrogen bonds
• G + C: 3 hydrogen bonds

• Two strands intertwined into a double helix

• Sugar-phosphate backbone on the exterior
• Four different bases inside X-ray diffraction photo
• Form base pairs (specific and stable) by R. Franklin
• Complementary strands
• Antiparallel strands (3’>5’ and 5’>3’ based on ribose carbons)
The helices of nucleic acid = spiral staircase?
 Major Groove Minor Groove

James Watson (left) and Francis Ball and stick model of DNA showing
Crick published the structure of individual atoms
DNA in Nature in 1953,
basically launching the field of
Biophysics

Ribbon model of DNA

showing base pairing of
complementary, anti-parallel
strands
Molecular View of the DNA Helix
 Problem 1
1. If the thymidine makes up to 13% of the bases in a specific
DNA molecule, what percentage of the bases is cytosine?

2. The percentage base composition of the Coliphage Ø174 is

25% A, 33%T, 24%G and 18%C.
a. Does this composition make sense in regard to Chargaff’s
rule?
b. What is the genetic material in the virus?
c. Is the genetic material single stranded or double stranded?
d. How might such a phage replicate its genetic material?
-Although G.T and C.T pairs are normally not found in DNA double-
helical regions, G.U base pairs are common in single stranded RNA
(ssRNA).

- the two strands in DNA are complimentary in that all their

nucleotides form base pairs with one another.
- Two polynucleotide strands can form either
- right-handed helix or left handed helix
- stacked bases are regularly spaced 0.34nm apart along the helix axis
- helix makes complete turn every 3.4nm, thus 10 bp per each turn.

- 2nm diameter of DNA double helixh

 Chromosomes, Genes, Chromatin Fibers
• Chromosomes are composed of a linear strand of DNA with
an array of associated structural and functional proteins
– Bacterial chromosomes are circular
• Nuclear diameter is about 6 microns, yet it contains 2
meters of DNA distributed
• Humans are diploid, meaning that their chromosomes come
in pairs
– 22 autosomes (paired, for a total of 44)
– 2 sex chomosomes (XX, females or XY, males)
• No systematic correlation between genome size and
organism complexity
– Roughly, the more genes, the more complex the organism
– HIV has 5 genes, humans have ~35,000
– Splice variants per gene may be the true indicator of complexity
 The Human Genome
1. Rough draft sequence with 3X coverage was announced in 2001
2. Human genome has 3.2 x 109 nucleotides
3. Codes for proteins, as well as regulatory and catalytic RNAs
4. Only 3% contains genes, several % codes for RNAs
a. Evolutionary relics and raw material
b. Structural and perhaps regulatory functions
5. Most of the genome – transposable, mobile, small elements,
repetitive sequences
6. Gene size is large, 27,000 bp on average
1. NB: 430 amino acids = 1,300 bp in exons
2. Cis acting sequences and regulatory regions spread over tens of thousands of
bp
7. Disorganized/cluttered
Detection of nucleic acids in the
laboratory
1. Spectropphotometric measurements:
Polynucleotides absorb maximally at 260nm (UV region)
– absorption caused by thes bases (purines and
pyrimidines).

2. Staining and microscopy:

Nucleic acids can be made visible by staining with dyes
such as DAPI (4, 6-diamidino-2-phenylindole), ethedium
bromide and propedium iodide and observed under UV.
3. Restriction digestion with nucleases:
DNA and RNA can be selectively digested by their
corresponding nuclease enzymes. Deoxyribonuclease (DNase)
digests DNA while and Ribonuclease (RNase) digest RNA.
(Read about restriction enzymes – endo- and exo-nuclease).

4. Denaturation and absorbance

measurements:
Heat and alkaline denaturation of DNA results in hyperchromic
shift in the absorbance measurements at 260 nm which is
depicted by a sigmoidal curve..
 Organismal Genetic material
composition
Viral Genetic Material
1. Viral DNA is simplest of all DNAs, e.g. the lambda
phage viruses that use E. coli as host have linear dsDNA,
17.2 microns in length

2. Viruses have either DNA or RNA as their genetic material

3. Viral DNA or RNA can be circular or linear.

4. Some have single stranded or double stranded DNA or

RNA. In the host organisms, ssDNA is converted into
dsDNA before replication or transcription. e.g. ØX174 is
ssDNA which has been studied extensively (Read further).
5. For single stranded RNA viruses, it can be Plus (+) strand
(sense strand, i.e. sequence is equivalent to one translated into
protein) or minus (-) or antisense.

6. Nucleotide bases in viral DNAs are usually modified, e.g.

hydroxymethyl cystosine replaces cytosine in some viruses.

Bacterial Genetic Material

1. Most microorganisms are used for DNA replication because of
the high growth or replication rate, i.e., shorter generation time
(Gt).

2. Bacteria stores its genetic information as DNA and translates into

proteins via RNA.

3. Bacterial DNA is circular.

4. E. coli chromosome is a circular dsDNA with MW of 2.8E9,
length of 1.36mm and 2nm tin thickness, about 4 Mbp.

Escherichia coli has been thoroughly been studied through

autoradiographic and x-ray chrystallographic techniques.

Genetic material for higher organisms (yeast,

plants and animals)
1. Genetic information is stored is stored as DNA packaged by
specialized proteins (histones) into many chromosomes.

2. Each chromosome therefore has a large DNA molecule.

3. In mammalian cell, chromosomes in a single cell is calculated to
be about 2 m long and contain nearly 5.5Gbp (giga base pairs).
4. A condensed chromatin fibre measures up to 20 mm in
diameter, made up of NA (mainly DNA) and proteins (mainly
histones) – well packed (see movie).