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Module 1 Biology of Microbial and Animal Cells

Gene structure
Genes are specific sequence of DNA (deoxyribonucleic acid);
DNA is composed of nucleotides (nitrogenous base, deoxyribose
sugar, and a phosphate group)
- Four types of nitrogenous bases are: thymine (only in DNA),
adenine, cytosine, and guanine (former two are pyrimidines
and latter two are purines)
- Nucleotides are linked together by hydrogen bonds in a linear sequence
DNA usually exist in double-stranded form linked together by hydrogen bonds
between the bases (A-T and C-G); each strand is complementary to each other;
pairing basis for replication
- DNA information is coded via the sequence of the nitrogenous bases
DNA gene chromatin chromosome

Gene replication
DNA double strand is unwound by enzyme known as helicase; DNA polymerase adds
complementary bases to the two template strands and synthesize two new strand of
DNA. Replication is semi-conservative because one strand is from the parent DNA
double helix.

Gene function
Each gene is composed of a particular length of DNA with a particular function; most
produce polypeptides which can fold up to become a particular protein (e.g enzyme
which are essential for metabolism or non-enzymatic proteins such as haemoglobin
which is a protein with four polypeptide chains, 2 alpha and 2 beta chains)
- Polypeptides are polymers of amino acids joined
together via amide bonds; there are 20 different amino
acids
DNA within the nucleus of the cell is transcribed into
mRNA and is transported to the cytoplasm of the cell to be
translated by ribosomes to form polypeptides
RNA (ribonucleic acid) is single stranded, contains uracil
instead of thymine and ribose instead of deoxyribose
pentose sugar
Transcription: DNA is unwound by helicase;
RNA polymerase recognizes key sequence on
the DNA strand and binds to the DNA; RNA
polymerase adds complementary bases to the
unwound DNA strand and forms the primary
transcript; primary transcript undergoes
RNA splicing to cut out the introns (none
coding sequence; not translated into proteins)
and link the exons (coding sequence); the
RNA transcript is further processed as a 5
cap (methylated guanine base cap; important
for stabilizing mature mRNA to undergo translation) and a poly-A tail is added (latter
protects the mRNA molecule from enzymatic degradation in the cytoplasm and aids in
transcription termination, export of the mRNA from the nucleus, and translation)
Translation: process in which a mRNA strand is manipulated to form a polypeptide
chain. Ribosome binds to the mRNA and recognizes the start AUG (methionine)
codon. Each tRNA molecule attaches to an amino acid and contains a codon
complementary to the mRNA strand. Ribosomes stops at a stop codon and the
methionine is broken off the polypeptide chain, releasing the coding
strand.
- Ribosome: contains a small (binding and reading mRNA) and
big subunit (synthesizes polypeptide chain); associated with the
endoplasmic reticulum
- Genetic code: a sequence of three nitrogenous bases code for a
single amino acid; since there are four different types of
nitrogenous bases, there are 64 (43) different combinations to
code for 20 types of amino acid redundancy (prevents errors)
- tRNA: contains an anticodon region which is complementary to
the mRNA sequence; each tRNA is attached to a
specific amino acid; the tRNA binds to the
ribosome during the translation process and allows
the amino acid to bind to each other via amide
bonds.
tRNA contains 4 ends. Left and right loops
bind to the ribosome, the end that is not a
loop binds to the amino acid. The anticodon
binds to the mRNA.
One gene equals to one polypeptide; the gene may
encode a RNA, be regulatory genes or structural genes
(form structural tissues such as connective tissue);
flanking regions (GC and CAAT box) of the gene allow
the RNA polymerase to bind
Gene regulation via cytosine methylation: mammalian genes are rich in 5-CG-3
sequences which are located mostly upstream of coding sequences. The cytosine in the CpG
island is often methylated and this prevents transcription (i.e gene turned off). When both
strand are methylated, DNA replication will cause this methylation to be passed on to his
offspring epigenetic phenomenon (inherited change in DNA, but not in change in the
sequence)
Errors in the DNA will form a non-functional polypeptide (protein) which will lead to
human diseases
- Alkaptonuria : lack of homogentisic acid oxidase to break down homogentisic acid;
accumulation of this acid forms black urine; a recessive trait, found in families which
cousins interbreed
- Phenylketonuria: lack of phenylalanine hydroxylase and phenylalanine accumulates
which causes mental retardation; however if the consumption of phenylalanine is limited
the baby can lead a normal life (this is because at birth the mothers metabolism can help
the baby break down phenylalanine, but increases rapidly after birth and can cause mental
retardation if not treated via diet)
If PKU are treated, the incidence of PKU will increase because the defective
genes will remain in the gene pool relaxed selection
PKU can also affect intelligence, hair colour and head size-length and breadth
demonstrates that genes can have multiple effects (i.e pleiotropy); the effect of
the gene also varies as the phenotype also varies (i.e genes have variable
expressions)
Since PKU can be treated by diet, the effect of a gene can also be affected by
environment (genotype and the environment interacts)
As there are many enzymes within a metabolic pathway, if there are mutations in
any of the genes which encode for these enzymes, it would produce the same
consequence several genes can have the same effect on the phenotype (genetic
heterogeneity)
- Albinism: lack of tyrosinase to produce melanin (issues with sunburn, skin cancer and
eye pigmentation)
- Scurvy: lack of consumption of vitamin C (humans cannot synthesize it because we lack
the genes for it)
- Inborn errors of drug metabolism (e.g lack the enzyme to metabolize muscle relaxant,
suxamethonium; which leads to easy overdose)
Causes of mutation may due to DNA replication error in the S-phase of mitosis
- Spontaneous mutation in the DNA sequence which leads to mis-pairing of bases
- mutagens which increases the chance of mutation:
UV radiation thymine dimers which prevents
transcription/replication and cell death; usually
dimers are excised, but if not xenoderma
pigmentosum
Ionizing radiation (X-ray, power generation,
consumer products, nuclear explosions); more exposure, higher chance of
mutation
food preservatives
caffeine
saccharine
Rate of mutation is difficult to measure; 1 mutation/109 bases per gamete; everyone has at
least 1-5 lethal mutations if it was homozygous

Cognitive biases
Confirmation bias (like to agree with group)
In group bias (suspicious of new ideas/outsiders)
Post-purchase rationalization (rationalize mistakes)
Gamblers fallacy (what has happened will happen again)
Neglecting probability (biased by perception)
Observational selection bias (looking for patterns that is not there)
Status-quo bias (dislike for change)
Negativity bias (pay attention to bad)
Bandwagon effect (want to conform)
Projection bias (we think other people will act like us)
Current moment bias (prefer present than the future unknown)
Anchoring effect (dont see the big picture)