Molecular Genetics

• A branch of genetics that study genetics at a molecular level

o Genes, heredity, and variation at a molecular level
o Structure and function of informational macromolecules
• Classical/Mendelian Genetics:-
o Is the branch of genetics/biology that studies:-
 Genetics at a phenotypic level
 Based solely on visible results of reproductive act/crossbreeding
 The oldest discipline in the field of genetics
Structure of Chromosome
• Chromosome(s) is/are:
o DNA packaging cellular structure
o Made from:- (Xsome = DNA + Histones)
 DNA (single huge molecule), and
 Histones (globular and basic proteins)
o Made from DNA tightly wound around on histones
o Long strand of DNA on which a large NO of gene is stored
• Xsome can be found in 3 form/shapes:
o Chromatin fibre (loosely organized form)
o Chromatid (after DNA duplication/replication)
o Chromosome (condensed and compacted form)
• When a cell is not dividing, Xsomes:
o Become very long and thin = Chromatin
o Duplicates to form chromaids
o The loose state makes the chromatin:
 Become very long and thin
 Individuals can’t be distinguished
 All genes can be active
 Can’t be moved around in a cell
• As a cell prepares to divide, chromatin:
o Becomes condensed/compacted to form Xsome
o The compact state makes the Xsomes:
 Become much shorter and fatter
 Individuals can be distinguished
 The genes become inactive
 Can easily be moved around in a cell
• Genes:-
o Small/short sections of DNA within the Xsome

Class work/Home work (1)

• Q1. Describe the similarities and d/cs b/n chromatin, chromatid and chromosome?
• Q2. How does a DNA molecule wraps/wound around on histones proteins? (10 marks for
full account)

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 – The mechanism of action behind DNA wound around histone octamer.
– What makes DNA a (-)vely charged molecule?
– What makes histone protein a (+)vely charged molecule?

Structure of DNA
• DNA (Deoxyribo-Nucleic Acid):-
o Molecule that stores genetic information (Genetic material)
o One of the two types of nucleic acids (DNA and RNA)
o A double stranded helix (except some viral DNA)
o The strands are anti-parallel (upside down)
 Run in opposite direction
 One run 5’→3’ and the other 3’→5’
• Nucleotides:-
o Building block/monomers of nucleic acids (DNA and RNA)
• All nucleotides are made of:-
o A phosphate group (PO43-)
o A pentose (5 “C”) sugar
o A nitrogenous base
 A, C, G, and T in DNA
 A, C, G, and U in RNA
• There are 4/5 types of nucleotides:-
o Adenine (A) containing nucleotides
o Guanine (G) containing nucleotides
o Cytosine (C) containing nucleotides
o Thymine (T)/Uracil (U) containing nucleotides
• DNA is a huge molecule made from two anti-parallel strands
• The nucleotides in a single strand linked by:
o A phosphodiester bond
o Form sugar-phosphate backbone
• The nucleotides in one strand paired with the other by:
o The base-pairing rule
o “A” pair with “T” (with double H-bonds, A=T)
o “C” pair with “G” (with triple H-bonds, C≡G)
• DNA is very stable molecule at normal TO. B/c:
o The sheer number of H-bonds hold the two strands in position
o The bonds b/n nucleotides are much stronger than the H-bonds
• The stability of DNA molecule is important. B/c:
o It ensures the genetic codes not to become corrupted
The D/c B/n Prokaryotic and Eukaryotic DNA
• The DNA in prokaryotic cells (genophore) are:
o Resides/found in cell region = Nucleoid
o Much smaller
o Usually single DNA

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 o Circular, not linear
o Not associated with histone to form Xsomes

Class work/Home work (2)

• Q1. If a DNA segment has 210 “T” and 120 “C” bases in one strand, what would be the
total number of pentose sugar in the molecule?
• Q2. If the ratio (A+G)/(T+C) in one strand of DNA is 0.7, what is the same ratio in
complementary strand?
• Q3. What is the number of H-bonds in a double-helix of DNA structure of 100 base pairs
with 20 Adenines and 10 Thymines in one of the two strands?
• Q4. A double-stranded DNA molecule contains 20% Adenine. What is the number of
Cytosine bases in the DNA molecule 1cm long?
• Q5. Describe the role of nucleotides other than their role in nucleic acids?

DNA Replication/Synthesis
• DNA replication is:
o The process by which a DNA makes an exact copy of itself
o The basis of:
 All methods of reproduction/growth
 Passing genetic information from one to the next generation
• Before a cell can divide:
o It must replicate/duplicate its entire DNA
o Occurs during S-phase of cell cycle (Interphase)
• Watson and Crick in 1953:
o Discovered the structure of DNA
o Proposed semi-conservative DNA replication
Semi-conservative DNA Replication
• This means that:
o Half of the parental DNA is conserved in each new DNA
o Both/each new DNA formed:
 Contains one strand from the original DNA
 Identical to each other and to the original DNA
Stages of Semi-conservative DNA Replication
• DNA helicase:- the enzyme that:
o Move along DNA and separate the strands
o Break hydrogen bonds and unwind part of the DNA helix
• DNA polymerase:- the enzyme that:
o Follow the helicase along each single stranded region
o Create polynucleotide chains by assembling nucleotides
o The original strand acts as a template for new strand synthesis
• The DNA polymerase assembles free DNA nucleotides:
o Creating a new strand alongside each template strands
o Synthesize DNA in the 5’→3’ direction
o The new and template strands are complementary

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  B/c of base-pairing rule (A = T, C ≡ G)
• The process of unwinding followed by new strand synthesis
o This progresses along the whole DNA molecule
• The result is two DNA molecules that:-
o Are identical to each other and to the original molecule
o Contains one original and one newly synthesized strands

Class work/Home work (3)

• By going through different reference materials and the internet, answer the following
questions.
– Q1. Explain the d/c b/n Leading strand and Lagging strand.
– Q2. Describe the role of the following enzymes and proteins in DNA replication.
• Replisome =
• DNA polymerase I, II, III, IV and V =
• DNA gyrase =
• DNA helicase =
• Primase =
• Primosome =
• DNA ligase =
• Single strand binding proteins =
• Topoisomerases =

Cloning
• The process of creating/producing:
o Genetically identical copy of a biological matter
o May includes:- genes, cells, tissues or entire organism
• Cloning is divided into:
o Natural cloning:- Occurs naturally mostly as asexual reproduction
o Artificial cloning:- There are 3 d/t types
 Gene cloning, Organism cloning and Therapeutic cloning
Gene Cloning
• Process of making multiple copies of a gene
• Two main types/methods
o In vivo cloning
 The gene is introduced into a cell and is copied as the cell divides
 Involves the use of Restriction endonuclease (enzyme), Ligases, Vectors and
Host cells
o In vitro cloning
 The DNA/gene is copied many times over using PCR
 Does not take place in living cells
 Mimics the natural semi-conservative DNA replication
• Both methods have advantages and disadvantages
o In Vitro cloning using PCR is:
 Quicker and cheaper (save time and cost)

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  Produce billion copies within a few hours
o In Vivo cloning using living cell is:
 Used to produce gene products (E.g., Insulin)
 Also produce/copy the gene many times
Organism Cloning
• A.K.A Reproductive cloning
• The deliberate production of genetically identical organisms
• It is artificially induced asexual reproduction
• Organism cloning divided into: Plant cloning and Animal cloning
Plant Cloning
• Carried out through two methods
o Vegetative/Asexual propagation
o Tissue culture/Micropropagation
• Plant/Stem cuttings:
o Cut off a region of a stem near a bud
o Remove some of the leaves (reduce water loss)
o Dip the cut end in some hormone rooting powder
o Plant the cutting in compost
o Becomes independent plant within a few weeks
 Genetically identical to parental plant
• Micropropagation:
o A method of propagating a large number of plants from single plant
o Take small section of the growing shoot/root (explants)
o Sub-divide it into small groups
o Place these in test tube containing Special medium with hormone that induce root growth
o Transfer to another medium containing Hormones to induce shoot growth
o Then transfer small plantlets to compost
o Now, most of the world’s banana are produced by micropropagation
Animal Cloning
• The first animal ever cloned was:-
o An African toad (Xenopus laevis)
o Performed by Gurdan (1962)
• The first mammal/higher life form to be cloned was:-
o Dolly the sheep (still the most famous)
o Performed by Wilmut and coworkers (1997)
• Dolly was produced by:-
o Somatic cell nuclear transfer (SCNT)
o Transferring a diploid nucleus to an enucleated egg cell
o The egg cell stimulated to divide by a small electric current
o When dev’t reached a Blastocyst stage the embryo implanted into a surrogate mother
o Seven months later/gestation period, Dolly born

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Class work/Home work (4)
• Q1. List in detail other advantages and disadvantages of:
– In-Vivo gene cloning method, and
– In-Vitro gene cloning method
• Q2. How does a PCR machine work? What are the stages and processes involved?
• Q3. If it is made possible and allowed, how can you go about human cloning? Explain the
stages in detail.

Genetic Engineering (GE)

• Is the process in which the genome of an organism is altered;-
o Usually by having an extra gene from a d/t organism
o It’s called Genetically Modified/Transgenic Organism (GMO)
o Introduce desirable traits into organisms
o Has been practiced since 1980
• Bacteria were the 1st to be modified in lab
o B/c of their simple genetics
o To produce useful products/specific products
 E.g., Transgenic bacteria producing human insulin
• Gene that control production of insulin was:
o Extracted from human pancreas cells,
o Transferred to the bacteria,
o GM bacterium were cultured on massive scale in a fermenter,
o Then the insulin harvested, purified, and distributed for use
• GM bacteria produce a range of products, including:-
o Enzymes for food industry
o Thermostable enzymes for washing powders
o Human insulin
o Human growth hormone
o Vaccines (E.g., for Hepatitis B)
o Bovine somatotrophin (Growth hormone)
• Plants also been genetically modified (GM) so that they
o Are disease resistant
o Have an improved yield
o Produce a specific product E.g., Golden rice
• Fewer animals have been genetically modified so that they:
o Are disease resistant
o Have an improved yield E.g., GM Salmon and Tilapia fish
o Produce specific products (sometimes called Pharming) E.g., Mammals producing human
proteins in their milk
• Most GMs have been carried out with the aim of:
o Improving yield (crop plants and stock animals)
o Producing a useful/specific products (like insulin)
• But some have been carried out with the aim of:
o Prevention and control of env’tal pollution

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 o Producing organisms for ornamental/pit market E.g., Glofish (Zebra fish)

Class work/Home work (5)

• Q1. Why only few animals have been genetically modified compared with bacteria (MOs)
and plants?
• Q2. List and explain some other (at least six) potential benefits/advantages of genetic
engineering.
• Q3. Compare and contrast, with examples, genetic engineering and the traditional
selective breeding.

Gene Technology in Forensic Science

• Forensic Science (Forensics):
o The science of crime identification/investigation
• Fingerprints:
o Have been used to place a suspect at crime scene
o Are unique to individuals (except identical twins)
o Do not change throughout life
o Provide strong evidence
• Genetic Fingerprints:
o A forensic technique used to solve crimes
o By comparing the DNA profile of d/t people
o Used as a DNA based evidence (DNA evidence)
• The DNA in Xsome is composed of:-
o Coding regions
o Non-coding regions
• Coding DNA:
o Small fraction of the DNA molecule (2%)
o Protein coding regions (Genes)
• Non-coding/Junk DNA:-
o Much of the DNA in the body cells (98%)
o DNA which does not codes for proteins
o Found b/n genes (b/n coding DNA/sequences)
o Contains repeating base sequences = Mini-satellites
 Form the basis of a genetic fingerprint
• DNA fingerprinting analysis used for:
o Personal identification
o Determination of paternity
o Identify genetic disease using markers
o Criminal investigations and forensic science
• DNA can be analyzed from various samples, including:
o Blood (WBCs), skin, semen, saliva, urine, hair, buccal (check cells), tissues, or bones
o Any type of cell with nucleus
• If samples contain not sufficient DNA:
o The amount amplified using PCR (exponentially)

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 o PCR allows to amplify a specific DNA sequence
Main Stages of DNA Fingerprinting
• DNA is isolated from the cells
• Cutting the DNA into fragments using restriction enzymes (One or more)
o Fragments treated with alkali/weak acid
• Fragments are separated by Gel-electrophoresis
o Allow separation of DNA fragments by size/molecular mass
o Smaller fragments move more quickly and further than larger
o Forms invisible patterns/bands of separated DNA fragments
• The Gel-separated pattern of DNA fragments are then:
o Transferred to a white nitrocellulose paper
o The paper now carries an exact replica of the DNA on the Gel
o This is called “Southern blotting”
• Apply/Add radioactive gene probe to the membrane
o Probe is a fragment of DNA of variable length
o Made of single stranded DNA (called c-DNA)
o Used to detect target DNA with complementary sequence
• Visualize the assay using autoradiography
• The chance of two people having the same genetic fingerprinting:
o Is about 1 in 1,000,000 (unless identical twins)
o Provide strong evidence to solve a crime

Class work/Home work (6)

• Q1. Explain the similarities and d/cs b/n Gene technology and Genetic Engineering
(rDNA technology)?
• Q2. In Southern blotting;-
– Explain the materials and steps involved
– What is the importance of the nylon membrane?
– Describe the use of gene probes

Protein Synthesis
An Overview of Protein Synthesis in Cell
• DNA molecule contains the code for protein synthesis
o It is a huge molecule and remain in the nucleus all the time
o The code has to be carried (by mRNA) to the ribosome for protein synthesis
o Ribosome is site for protein synthesis. It assemble amino acids in the correct sequence to
form proteins.
• During protein synthesis:-
o The DNA code is rewritten in mRNA (This is called transcription)
o mRNA travels from nucleus to the Ribosome (through nuclear pores in nuclear envelope)
o tRNA (transfer RNA) carried free amino acids (aas) from cytoplasm to ribosome
o The Ribosome reads the mRNA codes and assemble the amino acids carried by tRNA
into a protein. (This is called Translation)

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 Genetic Code/DNA Code
• Genetic code is sequence of bases held in a DNA molecule/gene
• It codes for protein (dictate the sequence of amino acids)
• Each amino acids (aas) coded by a triplet bases (sequence of three bases)
• Only one of the DNA strands carries codes for protein:-
o It is called coding/sense strand or mRNA-like strand
• The other DNA strand is Non-coding/antisense strand/template strand
o It is used as a template/copied during mRNA synthesis)
• With 4 d/t bases to work with (A, C, G, T):
o There are 64 possible triplet codes (43 = 64)
o But only 20 aas are used to make all the d/t proteins
o What is the purpose of the other 44 codes?
• Most aas (amino acids) have more than 1 triplet code
o E.g. Arginine, Leucine, and Serine = each coded by 6 triplets
o Arginine (6 triplet) = AGG, AGA, CGG, CGA, CGC, CGT
o Leucine (6 triplet) = TTA, TTG, CTT, CTC, CTA, CTG
o Serine (6 triplet) = TCT, TCC, TCA, TCG, AGC, AGT
• Only Methionine and Tryptophan have 1 triplet
o Methionine = ATG; Tryptophan = TGG
• Not all triplet (64) codes for aa (amino acid).
o Three triplets are stop codes (TAA, TAG, and TGA)
o They signify the end of coding sequence
• Of all the 64 possible triplet codes:-
o Sixty-one (61) of them are called the sense triplet codes
 Codons that specify/codes (aa amino acid)
o Three (3) of them are called the nonsense triplet codes
 Codons that do not specify/code aa (amino acid)
 Stop codes = signify the end of coding sequence (Signal chain termination)

Class work/Home work (7)

• Q1. What is the significance of having 64 codons in the genetic code? What is the value,
if any, in the redundancy in the code?
• Q2. In a hypothetical strand of DNA the base sequence is: 3'-AAGTTTGGTTACTTC-5'
a) What is the mRNA sequence transcribed from this DNA?
b) What is the amino acid sequence translated from this mRNA?
c) State three ways in which RNA differs from DNA.
d) Name three types of RNA and give the function of each type.
e) Show how the sequence of bases in DNA determines the amino acid sequence in
the protein.

Characteristics of Genetic/DNA Code

• Genetic/DNA code is a Triplet code
o A.K.A a code word/codon (in mRNA)
o A sequence of 3 bases code one aa (amino acid)

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 o The 61 codons for the 20 aas (amino acids)
o There are more than one code for the same aa (Since each codons code for only one aa)
• Genetic/DNA code is a Degenerative code
o Several code words have the same meaning
o D/t codons specify the same aa (amino acid)
o There is more than one triplet code for many of the aas (amino acids)
 Except Methionine and Tryptophan. = coded by 1 triplet
 Arginine, Leucine, and Serine = each coded by 6 triplets
 The other 15 aas (amino acids) = coded by 2, 3, or 4 triplet
o All aas except Methionine and Tryptophan are coded by several codons (Some codons
are synonyms)
• Genetic/DNA code is a Non-overlapping code
o Each triplet is distinct from all other triplets
o It is sequentially read in group of three (5’→3’ direction)
o The end base of one triplet can’t be a beginning of another
o E.g. It the coding strand of a DNA sequence 5’-AUGUCUCCA-3’
 5’-AUG-3’ codes for Methionine
 5’-UCU-3’ codes for Serine
 5’-CCA-3’ codes for Proline
• Genetic/DNA code is a Universal code
o Each triplets code the same aa in all organism
o E.g. TAT code for tyrosine in all living organism (animals, plant, mos…) [With few
exceptions in mitochondria]
• Genetic/DNA code is a Comma-less code
o There is no punctuation b/n each triplet code/codon
o Each codon is immediately adjacent to the next (without any spacer nucleotides in b/n)
• Genetic/DNA code is a Non-ambiguous code
o It is non-ambiguous under normal conditions
o Each triplet/codon specifies the same aa all the time
• The coding Dictionary:
o A coding dictionary that show which code specifies which aa
• Start code (Chain initiation codon):
o It signal chain initiation
o ATG (AUG in mRNA) is the beginning of all protein-coding regions
o It is initiation signal for synthesis of polypeptide chain
o It signal for translation to begin
o Also encodes the amino acid Methionine (Met.)
• Stop code (Chain termination codon):
o It signal chain termination
o It tells the cellular machinery (ribosome) to stop protein synthesis
o There are three stop-codes/codons (AKA Nonsense codes/codons)
 TAA/UAA = Ochre
 TAG/UAG = Amber
 TGA/UGA = Opal/Umber

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 o Do not code for any of the aas and (hence termed as Nonsense codons)

Class work/Home work (8)

• Q1. Describe the genetic code and its important characteristics.
• Q2. Explain the significance of an AUG codon.
• Q3. Why is the genetic code read three bases at a time?
• Q4. ‘The genetic code is universal.’ Explain this statement.
• Q5. What might happen if codons encoded more than one amino acid?
Class work/Home work (9)
• Q1. Use the diagram (Page 143) to answer Questions 1–6.
1. What are the words along the outside of the circle?
2. What can you find by reading this diagram from the inside out?
3. For which amino acid is AAA a codon?
4. What is the codon for tryptophan?
5. For which amino acid is GGA a codon?
6. What are the codons for alanine?

Transcription in Eukaryotic Cell

• Transcription:
o Synthesis of mRNA from (one gene of) a DNA molecule
o Converts genetic information from a DNA code into an mRNA code
• mRNA (messenger RNA):- a nucleic acid that;
o Transmits/Carry the genetic code from DNA to ribosome
o Similar to DNA in that, it’s built from nucleotides (both are nucleic acids = made from
nucleotides)
o Differ from DNA in that, mRNA is:
 Much smaller molecule (often one gene long)
 Single stranded
 Thymine replaced by Uracil
 The sugar in the nucleotides is ribose (not deoxyribose)
• The triplet bases in mRNA that code for aa are called Codons
• The codons of mRNA are identical to the triplets of sense/coding strand of DNA
o Except Uracil (U) replaced Thymine (T)
• During transcription,
o mRNA is synthesized/transcribed from Antisense/Template strand of DNA. Why?
o B/c, only the sense strand carries the gene that codes for a protein, and
o Transcribing the sense strand would produce a complementary sequence of bases similar
to the antisense strand which would not code for anything.
Stages of Transcription in Eukaryotic cell
• In Eukaryotic cells, transcription occur in the following steps:
1. The Enzyme RNA polymerase (AKA DNA-dependent RNA polymerase):
 Binds with DNA next to the gene to be transcribed
 It bind at a specific sequence of nucleotides called Promoter (TATA box)
2. Transcription factors activate the enzyme

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 3. The enzyme begins to ‘unwind’ a section of DNA
 It move along the antisense strand to synthesize mRNA, and
 It use the antisense strand as a template for mRNA synthesis
4. The polymerase assembles free RNA nucleotides into a chain
 It synthesise RNA in the 5’ → 3’ direction
 The base sequence is complementary to the antisense strand, and
 The mRNA, therefore, carries the same triplet code as the sense strand
 Except Uracil (U) replaces Thymine (T)
5. This process continues until it reaches the terminator (stop codon)
 Stop codon signal the end of transcription
6. Finally, the completed mRNA molecule leaves the DNA
 It contains the code for the protein that was held in the DNA, and
 The DNA strands rejoin and re-coil

Class work/Home work (10)

• Q1. What is the enzyme that transcribes DNA into RNA?
– How does this enzyme know where to start and stop?
– Which direction does this process take place in?
• Q2. Diagram a protein coding gene and label it correctly.
– Explain what a promoter is and what it does.
– Explain what a coding sequence is and what it does.
– Explain what a terminator is and what it does.
• Q3. List the similarities and d/cs b/n DNA & RNA molecule
– Explain how a DNA and an RNA nucleotide are different.
– Give the purine and pyrimidine bases for RNA.
• Q4. What does the complement strand of RNA look like if the DNA strand were the
following: ATGC

Translation
• Translation:
o Is the synthesis of protein (polypeptide) from the mRNA code
o It requires energy from hydrolysis of GTP (Guanosine Triphosphate) [GTP → GDP + Pi
(energy)]
o Depends on the interaction b/n mRNA and tRNA in a ribosome
• Transfer RNA (tRNA):
o Carry/transport amino acid (aa) to the ribosome
o All have the same basic stricture (‘Cloverleaf’ configuration)
o At one end of tRNA there is a triplet base called Anticodon (Anticodon is complementary
to one of the mRNA codons)
o The other end of tRNA has an aa attachment site (This site is specified by the mRNA
codon)
• Ribosome:
o An organelle of a cell where protein synthesis takes place (Site for protein synthesis)
o It is made from:
 Ribosomal RNA (rRNA), and

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  Proteins (a larger and a smaller subunits)
o It has three tRNA-binding/occupying sites. These are: A (Aminoacyl) site, P (Peptidyl)
site, and E (Exit) site
Stages of Translation
• In Eukaryotic cells, translation occur in the following steps:
1. The first two codons of the mRNA enter the ribosome
2. tRNA molecules (with aas attached) that have complementary anticodons to the first two
codons of the mRNA binds to those codons
3. A peptide bond forms b/n the aas carried by the two tRNA molecules and the dipeptide is
transferred to tRNA in the ‘A’ site
4. Ribosome moves along the mRNA by one codon
 This bring the 3rd codon into the ribosome (‘A’ site)
 At the same time the ‘free’ tRNA exits the ribosome (‘E’ site), and
 The tRNA with dipeptide moves into the ‘P’
5. A tRNA with a complementary anticodon bind with the 3rd codon bringing its aa next to
the 2nd amino acid (aa)
6. A Peptide bond forms b/n the 2nd and 3rd amino acids (aas)
7. The Ribosome moves along the mRNA by one codon
 This Bring the 4th mRNA codon into the ribosome (‘A’ site), and
 The whole process is repeated until a ‘stop’ codon is in position and translation
ceases
• The process translation requires energy, and this energy:
o Does not come from hydrolysis of ATP as is usual in a cell
o It comes from hydrolysis of GTP (Guanosine Triphosphate)
 GTP is a similar molecule with ATP
 It is hydrolyzed to GDP and Pi (inorganic phosphase)
 The hydrolysis of GTP release small amount of energy
D/c B/n Prokaryotes and Eukaryotes in Protein Synthesis
• The process is essentially similar in both cells, in that:
o DNA is transcribed to mRNA (Transcription), and
o mRNA is translated to Polypeptide (Translation)
• There are some differences and these differences are based on the fact that:
o Prokaryotic cell don’t have nucleus
o Prokaryotic mRNA doesn’t need post- transcriptional processing/modification
• In Prokaryotic cells:
o Transcription and translation are coupled (occur together)
o Both transcription and translation occur in the cytoplasm
o No post-transcriptional processing of mRNA
o mRNA doesn’t need post-transcriptional processing/modification
• In Eukaryotic cell:
o Transcription and translation are separated (occur separately)
o Transcription occur in nucleus; Translation occur in cytoplasm
o There is post-transcriptional processing of mRNA

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  mRNA is modified before leaving the nucleus

Class work/Home work (11)

• Q1. The sense strand of a DNA molecule is: C C C A C G T C T
– The mRNA sequence from this DNA is :____________________
– The amino acids (use chart on page 144) sequence: ____________
• Q2. Given the DNA sequence below, list the conversion to mRNA, tRNA and the
corresponding amino acids.
– DNA : TAC GAG AAC CCT AGC ACT
– mRNA (codon) : _____
– tRNA (anti-codon) : _____
– Amino Acid : _____
• Q3. Given the DNA sequence below, list the conversion to mRNA, tRNA and the
corresponding amino acids.
– DNA : TAC GTA ATG GCA AAC ACT
– mRNA (codon) : _____
– tRNA (anti-codon) : _____
– Amino Acid : _____
Class work/Home work (12)
• Q1. Explain what happens at the 5’ end of a pre- RNA molecule.
• Q2. Explain what happens at the 3’ end of a pre- RNA molecule.
• Q3. What is the 5’cap used for?
• Q4. What is the 3’ cap used for?
• Q5. Explain what an intron and an exon are.
• Q6. Explain what happens in RNA processing.
• Q7. Give another name for pre-RNA splicing.
• Q8. Give the three steps in this process.

Some of the Proteins our Body Synthesize

• Our body synthesize a vast array of d/t proteins that broadly categorized into five groups
Type of Example Function of Examples
Proteins
Structure Collagen Building fibres of cartilage
Keratin Building nails and feathers
Enzyme ATP synthesis (ATPase) Producing ATP from ADP and Pi (ADP + Pi →ATP)
DNA helicase Unwinding the double helix of DNA
Peptide Insulin Control of plasma glucose concentration
hormone Adrenaline (epinephrine) Fight of flight response
Antigen Antigen on RBCs (A or B) Determine blood group
CD4 Allow binding of HIV to T-cells (T-lymphocytes)
Antibodies Anti-a Antibodies Cause clotting of RBCs with A antigen
HIV Antibodies Destroys some HIV antigens
Table 3.2 Some of the proteins our body synthesizes
• To continually synthesize these proteins, our body:
o Requires a constant supply of aas (amino acids)

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 o Obtain the aas from the protein in the foods we eat (Average adult protein requirement ≈
50 g/day)
o The proteins are hydrolyzed to aas in the gut, and these aas are:
 Absorbed into blood plasma by active transport, and then
 Carried/transported to the cells (used for protein synthesis)
• Only 20 aas are used to make all the d/t proteins
o Some aas can be made in our bodies by a process called Transamination
 The amino group of an aa is removed and transferred to a keto acid, and
 The keto acid becomes a d/t aa; and the aa becomes a keto acid
o The other aas can only be obtained from foods
 These are 8 aas and they are called Essential aas
 Some source of proteins includes:
 Animal protein sources
 E.g. Meat, fish, poultry, egg, and milk
 Provide good balance of all essential aas
 Non-animal protein sources. E.g.:
 Some cereals (wheat, rice, maize),
 Nuts and pulses, and
 Quinoa, buckwheat, hempseed and amaranth
 Contain lower amount than the rest

Class work/Home work (13)

• Q1. List/Give examples of the best animal and non-animal sources of proteins.

Control of Gene Expression

• Gene expression is:-
o The synthesis of protein (product) from a gene
o Switching on gene (Gene activation)
• All the cells don’t synthesize all our proteins. B/c:-
o All genes aren’t active all the time.
o E.g., Sex-limited genes/traits [Only expressed in one sex (lactation gene)], or
o Genes that control the colour of iris are present in all our body cells, but not expressed in
all our cells. Hence, all cells aren’t this colour, just the iris.
o Somehow, we can control which genes are active and where
Switching On/Activating Genes
• Genes are switched on/activated by Transcription factors:- these are proteins that;
o Binds to the promoter regions (a regulatory sequence) near/next to a gene
o Allow RNA polymerase to transcribe the gene
Stages to Switch On/Activate Genes
• The main stages to activate genes includes:
1. Transcription factors bind to a promoter sequence of DNA near the gene to be activated
2. RNA polymerase binds to the DNA-transcription factor complex
3. The RNA polymerase is ‘activated’ and move away from the complex along the gene

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 4. The RNA polymerase transcribe the antisense strand of the DNA as it moves along (The
gene is now being expressed)
• Some cancers are caused by hormones acting as transcription factors
o E.g. Oestrogen (a steroid hormone) activates genes that cause cell division in breast and
uterus lining.
o Many breast cancers are Oestrogen-receptor positive and it cause increase in cancer cell
division as in normal breast tissue
Switching Off/Silencing Genes
• Genes are switched off (silenced) by a number of factors/substance
o One group of these factors is called siRNA
• Short Interfering RNA (siRNA):
o Are unusual RNA molecules. B/c, they are:
 Very short (21-23 nucleotide long)
 Double stranded (made of two strands)
o Interfere with genes by degrading the mRNA once transcribed from the gene
 This is called post-transcriptional interference
• If mRNA is prevented from translation, then:
o The protein for which the gene codes can’t be built/synthesized, and
o Hence, the gene has effectively silenced
Stages to Switch Off/Silencing Genes
• The main stages to switch off genes includes:
1. Double-stranded RNA (dsRNA) is produced in the nucleus from a range of genes
2. It is then split into very small length by an enzyme “Dicer” (siRNA is produced)
3. The antisense strand of siRNA then binds with RISC (a complex of molecules)
4. The siRNA binds with mRNA & allow RISC to degrade the mRNA into small fragments

Class work/Home work (14)

• Q1. What is the central dogma of molecular biology?
• Q2. Explain what it means for transcription and translation to be coupled.
– In what organisms are these processes coupled?
– Explain why these processes are coupled.
– Where do these processes occur in eukaryotic organisms?
• Q3. What is a pre-mRNA molecule?
– What happens to this pre-mRNA molecule?
– What then happens to the mature mRNA molecule?
• Q4. Are all genes transcribed into RNA? Explain
• Q5. Give the name and function of the following: mRNA, tRNA, rRNA, snRNA, siRNA
Class work/Home work (15)
• Q1. siRNA hold a great deal of promise to treat AIDS and some cancers. Account on how
siRNA can silence genes associated with cancer and prevent HIV replication?

Mutations
• Mutation(s) is/are:- (change [Δ] in the genetic material)
o Any change in the genetic material (random/spontaneous change)

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 o An alteration/change in genome/genetic information of organisms
o A random change in the genetic material (in a DNA)
• The change can be on/involve:
o The whole Xsomes (Xsomal/Large-scale mutation)
o Parts of the Xsomes (Xsomal/Large-scale mutation)
o A single base (Point mutation)
• Mutations are:
o Rare, random, spontaneous and inevitable events
o Errors/mistakes or accidents which results during DNA replication (usually), or from
env’tal factors (mutagens)
Point Mutation
• Point Mutation:
o A.K.A Gene mutation or Single base modification
o The simplest kind of genetic mutation (a small scale mutation)
o It is a change in one/few base pair in a gene (cause a single/few nucleotide base change)
o A single base (base pair) is altered in the DNA sequence of a gene (It is change within a
gene)
o It is caused either due to mistakes during DNA replication (usually), or Env’tal factors
(like UV light, smoking…)
• Types of point mutations are:
o Substitution (Transition and Transversion)
o Frameshift (Addition and Deletion)
• These point mutations:
o Occur quite randomly during DNA replication, and
o Each involves a change to just one base
o However, they can result a dramatic change to the gene
o This is b/c, the protein that the gene codes for may become a d/t and non-functional
protein (it may lose its function b/c of change in the aas), or may not be produced/made at
all
Substitution
• In substitution mutations:
o One base pair is replaced by another (a d/t base)
o It replace one base (pair) with another
o It affect/alter just only one triplet (three bases that codes for one aa)
 No other triplet is affected
 It also affect the respective aa
• It is the least harmful type of point mutations
• It is divided into two subtypes
o Transitions (switch b/n the same “version”)
 It is substitution b/n the same “version”
 Purine replaced by Purine or Pyrimidine replaced by Pyrimidine
 Purine with another Purine (Purine to Purine substitution):
 E.g. “A” to “G” or “G” to “A”

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  Pyrimidine with another Pyrimidine (Pyrimidine to Pyrimidine):
 E.g. “C” to “T” or “T” to “C”
o Transversion (switch to a d/t “version”)
 It is substitution b/n d/t “version” (Purine to Pyrimidine or Pyrimidine to Purine)
 Purine replaced by Pyrimidine or vice versa
 There are more possibilities for transversion than transition
 E.g. “A” has:
 One way of transition = “A” to “G”
 Two way of transversion = “A” to “T” or “C”
• There are 3 possible outcomes/consequence of a substitution
o Missense mutation = codes for a d/t aa
o Silent mutation = codes for the same aa
o Nonsense mutation = codes for a stop codon instead of aa (results a truncate protein)
• Missense mutation (In missense mutation):
o The new/mutated triplet codes for a d/t aa,
o Thus, a d/t protein will be synthesized, and
o The protein may or may not be significantly d/t from the original
o B/c, one d/t aa in a protein does not always make a functional change
 Conservative mutation (has little effect on the protein/still functional protein)
 Non-conservative mutation (has great effect on the protein/nonfunctional protein)
 E.g. Sickle-cell anaemia
• Sickle-cell anaemia:
o An inherited and recessive blood disorder (genetic disease)
o Occurs when RBCs develop abnormally (b/c of abnormal haemoglobin)
o Caused by a missense mutation in β–haemoglobin gene
 The gene that codes one of the 4 polypeptides of the haemoglobin molecule
o This mutation/change on the β–globin gene:
 Convert a GAG triplet code/codon into GUG, and
 Thus, it convert the aa Glutamic acid into valine
o If a person inherits two copies of the mutated gene, then:
 All the RBCs will contain abnormal haemoglobin
 This cause RBCs to collapse into sickle-shape (under conditions of low O2 conc.)
 These cell often fracture, stick together and block capillaries
• Silent mutation (In silent mutation):
o The new/mutated triplet still codes for the same aa, (b/c, DNA code is a degenerate code)
o Thus, the same protein will be synthesized,
o Effectively, it would be the same gene
• Nonsense mutation (In nonsense mutation):
o The new/mutated triplet become a ‘stop’ triplet/codon,
 Stop triplet/codon does not codes for aa,
 Transcription and translation ceases when it reaches the stop code, and
 A short or non-functional mRNA results
o Thus, no protein or short, non-functional protein synthesized

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 Addition and Deletion Mutations
• Addition and Deletion Mutations:
o A.K.A Framshift Mutation
o In Addition/Insertion mutation an extra base is added (during DNA replication)
o In Deletion mutation a base (pair) is missed out/omitted (during DNA replication)
o Both cause a shift in the reading frame (Affect/alter all the triplet after the point of
mutation)
o The most harmful types of point mutation (result more disastrous effect on the protein)
• In Frameshift (Addition and Deletion) mutation:
o The whole sequence/triplet altered after the point of mutation (B/c there is one fewer or
one extra base)
o A totally d/t mRNA is produced (if one is produced at all)
o Thus, a non-functional protein or no protein produced at all
 Extensive missense = produce a d/t and non-functional protein
 Immediate nonsense = no protein produced at all
• If a whole triplet is inserted or missed out, then:
o Either one extra or one fewer codon result in the mRNA,
o Thus, one extra or one fewer aa in the polypeptide chain, and
o A relatively functional protein produced (Depending on the location of aa in the protein)
o This is not a frameshift mutation (It do not result a shift in the reading frame)

Class work/Home work (16)

• Q1. There are several types of gene mutations.
– List two main types of gene mutations.
– What do they have in common?
– How are they different?
• Q2. A geneticist found that a particular mutation had no effect on a protein coded by a
gene. What do you think is the most likely type of mutation in this gene? And why?
• Q3. Name one amino acid that has more than one codon. Name an amino acid that has
only one codon.

Causes of Point Mutations

• Mutations are:
o Errors/mistakes/accidents that usually occurs when DNA is replicating (DNA replication)
o Spontaneous, random and rare event. B/c, most mutations are detected and repaired in a
cell, and unlikely to affect coding genes (5% of the DNA) [95% of DNA is non-coding or
junk DNA].
• Factors that increase rate of mutation includes:
o Carcinogenic/Mutagenic chemicals (detected by Ames test) E.g. Tobacco smoke
o High-energy electromagnetic radiation E.g. UV (sun), X-rays
• Mutations are categorized into two, based on their causes (Spontaneous and Induced Mutations)
• Spontaneous Mutations:
o A.K.A Natural mutations/Background mutations

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 o Caused as a result of natural process/agents in cells (E.g. Arise from errors/mistakes
during DNA replication)
o Account for the “background rate” of mutations (very low) [It is One in fifty million base
pairs, 120 in each new cell]
o It is the ultimate/major source of natural genetic variation (Fuels for evolutionary change)
• Induced Mutation:
o Caused by an outside/external/env’tal agents (mutagens)
o Occurs due to purposeful exposure to mutagens (by man)
o Frequency of mutation is very high (very faster)
o Caused by mutagens (env’tal agents that increase rate of mutation):-
 Physical agents (High-energy radiation):-
 X-rays, UV-rays, α-, β-, and γ- rays
 Chemical agents (specific chemicals):-
 Alkylating agents:- Ethyl methane sulfonate (EMS), Methyl methane
sulfonate (MMS), Acridine mustard gas
 Base analogs:- Aminopurine, Bromouracil
 Transposon insertion
Consequence of Gene Mutations
• Mutations can be categorized into two (Based on where they occur):
o Somatic mutations
o Germ-line/Germinal Mutation
• Somatic mutations:-
o A.K.A Autosomal Mutation
o Occurs in non-reproductive body (somatic) cells
o Only affect new cells created from the mutated cell
o May cause (possible consequences):-
 No harm at all (harmless),
 Damage the cell,
 Kill the cell, or
 Make the cell cancerous (Might kill the person/organism)
o It can’t/won’t:- Affect other person (non transmittable/contagious/communicable) or
passed onto the offspring/future generation. E.g.
• Germ-line/Germinal Mutation:
o Occurs in gametes/sex cells and germ-line (gamete producing) cells
o Can be passed onto offspring/future generation:-
 Future generation will carry the mutation in all their cells
 In both somatic and germ-line/gamete cells.
 E.g. Sickle cell anemia, Cystic fibrosis, Color blindness, Albinism
• Mutations in d/t genes will produce d/t effects:
o But two types of genes are really important.
o i.e., Proto-oncogenes and Tumour suppressor genes (Gatekeeper genes)
• These genes play important roles in:-
o Regulating cell division/growth/proliferation
o Preventing formation of tumour

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 o Work like the accelerator and brake of cell division
• Controlled cell division/growth is maintained by:
o Regulation of proto-oncogenes (accelerate growth)
o Regulation of tumor-suppressor genes (slow cell growth)
o Mutations that produce oncogenes accelerate growth, and uncontrolled cell growth occurs
o Mutations that affect tumor suppressors prevent the normal inhibition of growth, and
uncontrolled cell growth occurs
• Proto-oncogenes (growth promoting):
o Are genes that regulate/help normal cell growth/division
o Code for proteins that normally regulate/enhance cell division or inhibit normal cell death
o Have a role in the regulation of normal cell growth (Increase/turn on the rate of cell
division)
o When mutate, it becomes active oncogenes (Cancer-causing forms/genes). Actively
promote proliferation. Stimulate uncontrolled cell division (Without normally stimulated
by external growth factors). It’s called gain-of-function mutation
• Tumour suppressor genes (growth inhibitory):
o Recognize and suppress uncontrolled cell division
o Prevents/suppress tumour formation by regulating cell division
o Encode proteins that normally inhibit formation of tumour
o Inhibit cell proliferation (Act as a “brake” for the cell cycle. Put the brakes on cell
proliferation)
o If these genes mutate, it becomes inactive (loss-of-function mutation). Uncontrolled cell
division occurs and form tumour. It’s called loss-of-function mutation
• Tumour:-
o A mass of cells created with uncontrolled cell replication
o Cause of the disease cancer

Class work/Home work (17)

• Q1. Mutations in d/t genes will produce d/t effects. But two types of genes are really
important (Gatekeeper genes).
– List these two genes.
– What do they have in common?
– How are they different?
• Q2. Discuss how mutations in proto-oncogenes and tumour suppressor genes can lead to
uncontrolled cell growth and division. Include in your answer an example of a proto-
oncogene and a tumour suppressor gene.
• Q3. Cancer-causing viruses often carry mutant alleles of proto-oncogenes. No cancer-
causing virus has been found to carry a mutant allele of a tumour suppressor gene. Why
might this be?

Benefits of Mutations for Organisms

• Mutation is very important (must be studied), b/c:
o Can cause genetic diseases/harmful effect/ (so, must be studied)
o Needed for natural selection and evolution to take place

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• Mutations are:
o The raw material of evolution (Fuels evolutionary change)
o The only process that creates new genes/genetic material (The major/ultimate source of
genetic variation/diversity)
• But, crossing over, segregation, random/independent assortment and random fertilization:
o They reshuffle the existing genetic material (genes)
o They rearrange/reorganize existing alleles within a population,
o Introduce new combinations of genes every generation,
o Gives offspring a combinations which differ from parents,
o They are caused through sexual reproduction
• Genetic variation:
o The genetic d/cs that exist within a population (The d/cs in DNA segments/genes b/n
individual)
o It is advantageous to a population, b/c it maintain the survival of the population. It
enables some individuals to adapt to the env’t.
o An important force in evolution, b/c it allows natural selection to increase/decrease
(Frequency of alleles already exist in the population)
o Caused/happen within a species by two ways: Mutations and Reshuffling of genetic
material (genes)
• Mutation may give advantage/benefit to an organism
o If a mutated allele gives an advantage, then:
 Frequency of the allele increases in successive generations,
 The NOs of organism with the mutated allele will also increase
 This is b/c of natural selection (acts by selecting against deleterious alleles).
o Examples of beneficial mutations includes:
 Antibiotics resistance in bacteria, Bacteria that metabolize nylon,
 Sickle cell resistance to malaria, Lactose tolerance,
 Resistance to Atherosclerosis, Immunity to HIV
• Mutations in the DNA of bacteria can give them:
o Resistance to a specific antibiotic (such as Penicillin or Ampicillin)
o They only give advantage if the particular antibiotic is being used
 Resistance to Streptomycin is no advantage if Penicillin is being used
 Resistance to Penicillin confers advantage if Penicillin is being widely used
o E.g. Penicillin Resistant Staphylococcus aureus (PRSA):
 The first Penicillin-resistant bacterium found in USA (in 1947)
 It was detected just four years after the drug was widely used (mass-produced)
 Today over half S.aureus infections are caused by PR-types
• Bacteria can also ‘swap’/exchange antibiotic resistance genes (with each other)
o Most of the resistance/mutant genes are found in Plasmid
o This is short/small ‘extra’ circular pieces of DNA (separate from the main bacterial
DNA)
• Bacteria can transfer these plasmids to another bacterium by:
o Conjugation:- (by conjugation tube/sex pili) Passes through a special ‘conjugation’ tube
from one bacterium to another

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 o Transduction:- (by bacteriophages) A virus carries the plasmid from one to another
o Transformation:- (by absorbing) The plasmid is absorbed from a dead bacterium/env’t
• Antibiotic resistance:
o The evolution of bacterial strains that are not affected by antibiotics
o It is caused by the overuse/misuse of antibiotics
Chromosomal Mutations
• Chromosomal Mutation:
o Is any change in the arrangement/structure of Xsomes
o Mostly occurs during meiosis at crossing over (Prophase I)
o Much bigger event and harmful than point mutation
 It is a large scale mutation
 It usually result in cell death, and
 May also affect the whole organism (E.g., Foetus abortion)
• Types of Xsomal mutations includes: (several d/t types)
o Inversion:
 Occurs when an area of DNA on a Xsome reverse its orientation
 E.g. Just one inversion on Xsome 16 (Can cause Leukemia)
 An inversion resulting too few or too many copies of a gene (Can cause an
embryo to Miscarry, Fail to grow, or Born with substantial medical problems)
o Deletion:
 Occurs when an area of DNA on a Xsome is deleted
 Results a decrease in the number of genes in the Xsome
 E.g. Prader-Willi syndrome:- results from a malfunction of the Hypothalamus:
 It is a small endocrine organ at the base of the brain,
 It plays a crucial role in many bodily functions, including Hunger and
satiety regulation, Temperature and pain regulation, Fluid balance,
Puberty, Emotion and fertility
o Insertions:
 Occurs when an area of DNA on a Xsome is added
 Results an increase in the number of genes in the Xsome
 Caused when unequal crossover happens during meiosis
 The Xsome may become abnormally long or short, and thus, stop functioning
 E.g.
o Duplications:
 Occurs when an area of DNA/gene on a Xsome duplicated
 Usually harmless (as the Xsome has all the gene)
 But duplication of whole Xsome is more serious
 E.g. Trisomy 16 (having 3 copies of Xsome 16):- results to babies born with
range of medical problems: Poor foetal growth, Muscular and skeletal anomalies,
Congenital heart defects, and Underdeveloped lungs
o Chromosome non-disjunction:
 Occurs when homologous Xsome don’t separate successfully to opposite poles
during meiosis

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  The result is one of the gametes lacking a Xsome, and the other having an extra
Xsome
 E.g. Down’s syndrome:- results if this happen with Xsome 21. The person will
have 47 Xsomes in every cells. It is characterized by Mental retardation, Heart
defects and Stunted growth
o Translocations:
 Occurs when a piece of one Xsome is transferred to another non-homologous
Xsome
 E.g. Chronic myelogenous leukemia
• Chromosome 16:- One of the 23 pairs of Xsomes in humans. It spans about 90 million base pairs,
and accounts for nearly 3% of the DNA in cells.
• Chromosome 21:- One of the 23 pairs of Xsomes in humans. The smallest of the Xsomes

Class work/Home work (18)

• Q1. Define these terms and explain their importance for evolution:
– Natural selection =
– Genetic variation =
– Genetic drift =
– Gene flow =
– Reshuffling of genetic material =
• Q2. Write an essay using your own words (not more than 150 words) about:
– Mutation and what causes it,
– Positive benefits of mutation, and
– Damaging aspects of mutation

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