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Cell theory:
1. Cells are the smallest unit of life
2. All cells arise from pre-existing cells by dividing into 2
3. All known living things are made of one or more cells.
Nucleus:
Diagnostic features:
● Enclosed by a nuclear envelope
- Nuclear envelope is a double membrane. The 2 membranes are separated by a
narrow space, known as perinuclear space.
- Outer membrane is continuous with the endoplasmic reticulum
- Nucleoplasm, a semi-fluid matrix, that fills the nucleus
- Perforated with nuclear pores that regulates entry and exit of substances into and
out of the nucleus
● Contains chromatin, coils of negatively charged DNA wrapped around positively charged
histone proteins
- Heterochromatin: electron dense, and appears as coarse granules under the electron
micrograph because it is more tightly packed
- Euchromatin: a less compact form of chromatin and is often under active
transcription
● Contains nucleolus, a prominent, dense, spherical structure in a non-dividing nucleus
- Contains large loops of DNA from a number of chromosomes. Loops contains genes
coding for a specific type of RNA known as ribosomal RNA
Functions:
Nucleus:
1. Stores hereditary material (DNA)
2. Controls gene expression. Site of transcription
Nucleolus:
1. Site of rRNA synthesis
2. Assembly of proteins and rRNA, where proteins imported from the cytoplasm are
assembled with rRNA to form small and large ribosomal subunits.
Nuclear pores:
1. Regulates exchange of substances between the nucleus and cytoplasm, thus effectively
controlling processes on either side of the nuclear membrane.
Diagnostic features:
1. Comprises continuous network of sheets of membrane
2. Outer surface is studded with ribosomes
Function:
1. Site of synthesis of proteins destined for secretion of incorporation into membranes
2. Facilitation of folding of polypeptide chain
Diagnostic features:
1. Comprises network of membranous tubules
2. Lacks ribosomes
Function:
1. Synthesis of lipids, including phospholipids, oils and steroids
2. Detoxification of drugs and poisons
Golgi Apparatus:
Diagnostic feature:
1. Consists of stack of flattened membrane-bound sacs called cisternae
2. Comprises a system of associated vesicles, Golgi vesicles
Functions:
1. Further modifies products of the ER, sorts and packages them into vesicles to be transported
into other parts of the cell, or to be released out of the cell
2. Synthesis of secretory polysaccharides
3. Synthesis of lysosomes
Polypeptides are synthesised at the ribosomes on the RER. These polypeptides enter the lumen of
RER and fold into proteins. The proteins are then modified and packaged into transport vesicles
which pinched off from RER. Transport vesicles then fuse with the cis face of the Golgi Apparatus
and release the proteins into the cisternae of the Golgi Apparatus. The proteins are further
modified, sorted and packaged into secretory vesicles at the Golgi Apparatus. The secretory vesicles
containing the modified protein are pinched off from the trans of Golgi apparatus. They then move
to fuse with the cell surface membrane. Secretory vesicles fuse with the cell surface membrane and
protein is released out of the cell via exocytosis.
Lysosomes:
Diagnostic features:
1. Spherical sac bound by a single membrane
2. Uniformly granular electron-dense appearance in electron micrographs
3. Constraints hydrolytic enzymes that digest macromolecules
Functions:
1. Digestion of material taken in from the environment by endocytosis
2. Autophagy: degradation of unwanted structures within the cell
3. Autolysis: self-destruction of a cell
Mitochondria:
Diagnostic features:
1. Wall comprises 2 membranes separated by an extremely narrow fluid-filled space called the
intermembrane space
- Outer membrane is smooth
- Inner membrane is highly convoluted with numerous infoldings called cristae
2. Interior of mitochondria is an organic, semifluid matrix (mitochondrial matrix) with 70s
ribosome, circular DNA and various enzymes
3. The mitochondrial space is separated into 2 compartments: mitochondrial matrix and
intermembrane space
Function:
1. Main site of ATP production during aerobic respiration
Chloroplast:
Diagnostic features:
1. Enclosed by a double membrane known as chloroplast envelope, with a very narrow
intermembrane space separating the two membranes
- Inner membrane encloses a semi-fluid material known as stroma
- Stroma contains enzymes, circular DNA, 70s ribosomes, starch grains, sugars and
lipid granules
2. In the stroma is another membranous system in the form of flattened, interconnected
disc-like sacs called thylakoids
- The thylakoids are arranged in stacks called grana
- Stacks of grana are linked by intergranal lamellae
- Photosynthetic pigments and enzyme systems involved in photosynthesis are
embedded in the thylakoid membranes
3. The membranes of the chloroplast divide the chloroplast space into three compartments:
the intermembrane space, stroma and thylakoid space
Function:
1. Site of photosynthesis
Ribosomes:
Diagnostic features:
1. Complexes of ribosomal RNA and protein
2. 80s eukaryotic ribosomal consists of small (40s) and large (60s) subunits
3. Four different locations in the cell
- Suspended as free ribosomes in cytosol
- Bound ribosomes attached to rough ER
- Mitochondrial matrix
- Chloroplast stroma
Function:
1. Site of polypeptide synthesis
2. Key role in translation of mRNA base sequence into specific amino acid sequence of a
polypeptide chain
Centrioles:
Diagnostic features:
Function:
1. Key role in nuclear division in animal cells by acting as microtubules organising centres
Diagnostic features:
1. A rigid layer surrounding the cell, composed of insoluble cellulose fibres embedded in a
matrix of other polysaccharides and proteins
2. Middle lamella allows for adjacent cells walls to adhere to each other
3. Cell walls perforated with channels known as plasmodesmata
Functions:
1. Provides mechanical support to plant cells and maintain their shape
2. Allows development of turgor when water enters the plant cells by osmosis
3. Prevents excessive uptake of water
CELLULAR TRANSPORT:
The fluid mosaic model of biological membrane comprises phospholipids and proteins that are
constantly moving freely within the layer in a lateral motion, making it fluid. Proteins are
interspersed and randomly embedded in a phospholipid bilayer giving it a mosaic appearance.
Generally, the longer the fatty acid hydrocarbon chains, the higher the melting point of the
membrane. (membrane fluidity decreases) This is because a longer chain length increases the
surface area of contact, thus increasing the tendency of the hydrocarbon tails interacting with one
another via hydrophobic interactions.
Unsaturated fatty acid chains with cis carbon-carbon double bonds have kinks. These kinks hinder
the hydrocarbon chains from packing closely together, thus increasing membrane fluidity.
Saturated fatty acid chains are long and straight hydrocarbon chains. This facilitates close packing,
thus decreasing membrane fluidity.
Cholesterol:
● At higher temperatures, cholesterol limits fluidity. This is because cholesterol partly
immobilises adjacent phospholipid molecules, thus restraining their mobility. This
contributes to membrane stability at higher temperatures.
● At low temperatures, cholesterol interferes with the close packing of the phospholipids,
therefore enhancing membrane fluidity.
Endocytosis: Macromolecules
Movement of large quantities of
macromolecules into the cell, via invagination
of the membrane, enclosing the
macromolecules, pinching off as a vesicle and
membrane reforms with the additional
investment of energy
Exocytosis: Macromolecules
Movement of large quantities of
macromolecules out of the cell. The vesicle
containing macromolecules move to the cell
surface membrane, membrane of the vesicle
fuses with a small portion of the cell surface
membrane, enabling macromolecules to be
released out of the cell via exocytosis, and
membrane reforms with the additional
investment of energy.
Phagocytosis:
1. A small portion of the cell surface membrane invaginates to enclose the solid particle
2. The particle is packaged within a membrane-enclosed sac that is large enough to be called a
vacuole
3. Phagocytic vacuole pinches off from the cell surface membrane
4. Cell surface membrane reforms
Receptor-mediated endocytosis:
1. When the specific substance, known as ligands, binds to the specific receptor sites of
receptor proteins, they trigger the invagination of the cell surface membrane
2. This results in the formation of coated vesicles that contain specific ligand molecules
3. After the ligands are taken up by the cells, the receptors are brought back to the cell surface
membrane by the same vesicles
CARBOHYDRATES:
a-glucose b-glucose
6 carbon sugar
Condensation:
During condensation reaction, the hydroxyl group of carbon 1 of one glucose molecule and the
hydroxyl group of another glucose molecule’s carbon 4 react to form a glycosidic bond with the
elimination of one water molecule, catalysed by enzymes.
Elimination:
During hydrolysis, bonds between glucose monomers are broken by the addition of water; with a
hydrogen atom from the water molecule attaching to carbon 4 of one glucose monomer, and the
hydroxyl group from the water molecule attaching to carbon 1 of another glucose monomer.
Cellulose:
1. Large molecule composed of several thousands of glucose monomers → insoluble in water
and stores energy
2. Alternate glucose monomers are inverted. Glucose residues are linked by b-1,4 glycosidic
bonds → the bonds result in long, straight chains
3. Hydroxyl groups project outwards from cellulose chain in all directions → allows
microfibrils to be arranged in large bundle to form macrofibrils → resulting in high tensile
strength
LIPIDS:
Condensation:
3 fatty acid molecules combine with 1 glycerol molecule. Each hydroxyl group in the glycerol
molecule reacts with the carboxyl group of a fatty acid. An ester bond is formed between the
glycerol and fatty acid, with the removal of a molecule of water - condensation reaction. Since
glycerol has 3 hydroxyl groups, 3 fatty acids attach themselves to the glycerol molecule and hence, 3
molecules of water are removed. Reaction is catalysed by enzymes.
Hydrolysis:
3 ester bonds are broken by 3 hydrolysis reactions with the addition of 3 water molecules. The H
atom of each water molecule attaches to glycerol and the OH group of each water molecule attaches
to a fatty acid. This reaction is catalysed by enzymes.
Triglycerides:
Triglyceride molecules are large and uncharged Can be stored in large amounts without having
- Insoluble in water any effect on the water potential of the cells
Large amounts of hydrogen atoms in their Storage of energy: they store more energy per
hydrocarbon chains which can be oxidised unit mass than any other respiratory substrates
during cellular respiration
Phospholipid:
The phosphate group of the phospholipid The hydrophobic region of the bilayer forms a
forms the hydrophilic “head” of the molecule barrier between the aqueous interior and
whilst the hydrocarbon chains of the fatty acid exterior of the cell, whilst the hydrophilic
moieties form the hydrophobic “tails” of the regions of the bilayer make possible the
molecule. existence of a hydrophobic boundary.
PROTEINS:
Condensation:
The carboxyl group of one amino acid and the amino group of another amino acid reacts to form a
peptide bond in a condensation reaction, with the elimination of a water molecule. The reaction is
catalysed by enzymes
Hydrolysis:
1 peptide bond is broken by 1 hydrolysis reaction with the addition of one water molecule. The H
atom of the water molecule attaches to one amino acid, while the hydroxyl group of the water
molecule attaches to another amino acid. The reaction is catalysed by enzymes.
B-pleated sheet:
Maintained by hydrogen bonds
between adjacent regions of a
polypeptide chain that lie parallel to
each other, either running in the
same or opposite direction
Haemoglobin:
The haemoglobin molecule is compact and Many haemoglobin molecules can be packed
globular in shape into a red blood cell for transport of oxygen
Haemoglobin is an allosteric protein that Maximises the amount of oxygen loaded and
exhibits cooperative binding of oxygen released at the lungs
The polypeptide chain of the subunit folds in Haemoglobin is soluble in red blood cells
such a way that the hydrophobic amino acids
are buried on the interior while the hydrophilic
amino acid residues are on the exterior
Globin contains a deep hydrophobic cleft, ie. Provides a hydrophobic environment for the
haem-binding site binding of haem
Haem group contains a porphyrin ring and a Fe2+ can combine reversibly with oxygen, thus
Fe2+ ion enhancing the release of oxygen into
metabolically active tissues
Tropocollagen:
Every third amino acid of each polypeptide Allows the three polypeptide chains to lie close
chain is a glycine together to form a tight coil
Each polypeptide chain contains many proline The bulky and inflexible proline and
and hydroxyproline residues hydroxyproline residues contribute to the
rigidity of the molecule
Within the tropocollagen molecule, extensive Results in high tensile strength for its structural
cross linking of hydrogen bonds between the role
NH group of glycine and CO group of
hydroxylysine holds the three polypeptide
chains together to form the triple helix.
ENZYMES:
Substrate alignment:
The enzyme molecule holds the different substrate molecules in an arrangement that forces close
together in the correct orientation. The proximity of the substrates within the enzyme-substrate
complex greatly increases the probability of a reaction occurring.
Substrate concentration:
At low substrate concentrations:
As substrate concentration increases, the frequency of successful collisions between enzymes and
substrates would increase. More enzyme-substrate complexes are formed per unit time and rate of
reaction increases. Hence the rate of reaction is limited by enzyme concentration.
Temperature:
As temperature increases, the average kinetic energy of enzyme and substrate molecules increases.
There is an increase in frequency of successful collisions between enzyme and substrate molecules,
more enzyme-substrate complexes are formed per unit time and rate of reaction increases.
Above the optimum temperature, the atoms which make up the enzyme molecule vibrate so
vigorously that the hydrogen bonds and hydrophobic interactions between the R groups of the
amino acid residues begin to break. The enzyme is said to be denatured and the shape of its active
site is no longer complementary to that of the substrate.
pH:
At optimum pH, the intramolecular bonds maintaining the 3D confirmation of the enzyme
molecule are still intact. Majority of enzymes have the shape of the active site most ideal for binding
with substrate. Frequency of successful collisions between enzymes and substrate molecules is the
highest. Hence, the number of enzyme-substrate complexes formed per unit time is the highest and
rate of reaction is the fastest.
Above optimum pH, change in concentration of H+ in the environment alters the charges in the
acidic and basic R groups of the amino acid residues. This disrupts ionic bonds and hydrogen bonds
between R groups of amino acid residues. The shape of the active site is no longer complementary
to that of the substrate. Enzymes are denatured. Hence, less/no enzyme-substrate complexes are
formed per unit time and the rate of reaction decreases.
Competitive inhibition:
Non-competitive inhibition:
● No structural similarity to the substrate. It binds at a region other than the active site
● Renders a proportion of enzyme molecules out of action by decreasing the number of
enzyme-substrate complexes formed per unit time
● Not reach maximum value as that in the absence of inhibitors
● Cannot be overcome by increasing substrate concentration
DNA REPLICATION:
Each nucleotide is composed of a nitrogenous base, pentose sugar and phosphate group.
Pentose:
- A five carbon sugar that occurs as a ring form
- Ribose in RNA and deoxyribose in DNA
Nitrogenous base:
- Heterocyclic ring of carbon and nitrogen atoms
- Purines: double ring (adenine, guanine)
- Pyrimidine: single ring (cytosine and thymine)
Semi-conservative DNA replication: this involves the separation of parental DNA strands, whereby
each strand acts as a template for the synthesis of a new daughter strand. The daughter molecule
therefore comprises one parental strand and one new daughter strand.
DNA Replication:
1. Helicases catalyses the breakage of hydrogen bonds, thus separating the two parental DNA
strands
2. Single-stranded binding proteins bind tightly to the single-stranded regions of DNA to help
maintain the stability of the replication fork
3. Topoisomerase creates a transient break by nicking a strand of DNA. This helps to unwind
the double helix ahead of the replication fork for initiation of replication
1. A portion of each parental DNA strand serves as a template for making the RNA primer
with complementary base sequence.
2. An enzyme called primase catalyses the synthesis of RNA primer in the 5’ to 3’ direction
3. DNA polymerase (III) can now elongate the strand by adding the next dNTP to the free 3’
hydroxyl group of the primer.
4. DNA polymerase (I) will later replace RNA nucleotides of the primers with DNA
nucleotides
1. The separated parental DNA strands form the template along which deoxyribonucleoside
triphosphate (dNTP) align themselves by complementary base pairing
2. DNA polymerase (III) catalyses the formation of a phosphoester bond between the 3’
hydroxyl group of the last nucleotide in the growing strand and the 5’ phosphate group of
the incoming dNTP
3. DNA polymerases (III) thus catalyses the polymerisation of the new DNA strand in the 5’ to
3’ direction
4. Each growing new DNA strand is antiparallel to its parental template strand
5. The leading strand is synthesised continuously as a single polymer along the template strand
6. The lagging strand is synthesis discontinuously as a series of short fragments called Okazaki
fragments along the template strand
7. DNA ligase catalyses the formation of a phosphoester bond between the 3’ end of each new
Okazaki fragment and the 5’ end of the growing strand to form a continuous strand
8. Each daughter DNA molecule now consists of a parental strand and a newly synthesised
strand
This shortening of DNA strands after every replication limits the number of times a cell can divide
before apoptosis is triggered.
Telomeres found at the ends of DNA molecules are used to buffer the loss of important genetic
information as a result of this end replication loss.
TRANSCRIPTION:
1. RNA polymerase recognises and attaches to the promoter of the gene on DNA
2. RNA polymerase breaks the hydrogen bonds between complementary base-pairs of the
DNA double helix
3. The DNA double helix unwinds and the two DNA strands separates
4. One of the DNA strands acts as a template for the formation of mRNA
1. Free ribonucleoside triphosphates are aligned along the DNA template strand
2. According the complementary base-pairing rule
3. RNA polymerase catalyses the linkage of ribonucleotides via phosphoester bond
4. RNA polymerase catalyses elongation of the RNA in the 5’ to 3’ direction by adding
ribonucleotides to the free 3’OH end of the growing RNA molecule
5. The separated DNA strands rewind into the double helix behind the RNA polymerase
1. Transcription proceeds until after the RNA polymerase transcribes a termination sequence
in the DNA
2. RNA polymerase detaches from the DNA molecule. mRNA is released
Post-transcriptional modifications:
The 5’ end is immediately capped off with a modified form of guanine nucleotide. This 5’ cap has at
least 2 important functions:
a. Helps protect the mRNA from degradation by hydrolytic enzymes
b. After the mRNA reaches the cytoplasm, the 5’ cap functions as part of an “attach here” sign
for ribosome
At the 3’ end, an enzyme makes a poly(A) tail consisting of some 50 to 250 adenine nucleotides
a. Serves to inhibit degradation and probably helps ribosomes attach to it
b. Facilitate export of mRNA from the nucleus
Spliceosome cuts out the introns from the pre-mRNA and joins all the exons together into a
continuous coding strand via splicing.
Genetic code:
T: genetic code occurs in triplet of bases
U: genetic code is universal ie. the same codons apply for the same amino acids
N: genetic code is non-overlapping: the mRNA sequence is read continuously without skipping any
nucleotides
D: genetic code is degenerate, >1 codon may code for the same amino acid
Start codon: AUG
Stop codon: UGA, UAA, UAG
Structure-function of tRNA
Anticodon at one end Specifies the identity of the amino acid at the 3’
end
Specific sequence of bases in amino acid Allows complementary base pairing with
corresponding codon mRNA
tRNA adopts a compact L shape Anticodon lies at one end and the point of
attachment of the amino acid lies on the end
end: to reduce steric hindrance during
translation
Ribosome:
1. Small subunit has a binding site for mRNA
2. Large subunit has 3 binding sites for tRNA
a. peptidyl-tRNA site holds the tRNA carrying the polypeptide chain
b. aminoacyl-tRNA site holds the tRNA carrying the next amino acid to be added to
the polypeptide chain
c. Exit site allows the discharged tRNA to leave the ribosome
TRANSLATION:
1. An amino acid is attached to each tRNA molecule at its 3’ CCA end forming
aminoacyl-tRNA complex
2. tRNA molecules bind to their specific amino acid as determined by their anticodon
3. This reaction is catalysed by the enzyme aminoacyl-tRNA synthetase
1. Anticodon of incoming tRNA molecule carrying its amino acid pairs with the mRNA codon
in the aminoacyl-tRNA site of the ribosome
2. Peptidyl transferase catalyses the peptide bond formation between the amino acid carried by
the tRNA in the A site with the amino acid bound to tRNA in peptidyl-tRNA site
3. The ribosome translocates the tRNA in the A site, with its attached polypeptide, to the P
site, taking the mRNA with it
4. The mRNA is moved through the ribosome from the 5’ to 3’ direction on the mRNA
5. Elongation cycle is repeated until the ribosome reaches a stop codon
EUKARYOTES:
Coding sequences:
Exons
Non-coding sequences:
1. Introns
2. 5’ and 3’ untranslated regions (UTR)
3. Promoters
4. Enhancers and silencers
5. Replication origin and termination
6. Promoters and telomeres
Function:
The centromere binds several proteins with high affinity. This complex, called the kinetochore,
provides the anchor for the spindle fibres. The centromere is thus an essential structure for
chromosome segregation during cell division.
Telomere:
Structure:
Telomeric sequences are repetitive DNA sequences. They are typically short, repeated T-G rich
sequences.
Function:
1. To prevent fusion of the ends of the chromosomes
2. To prevent exonucleases from degrading the ends of the DNA molecules
3. To prevent the loss of genetic information by acting as a disposable buffer
4. To facilitate replication of the ends of the linear DNA
5. To prevent cell cycle arrest
Several thousand different genes Few hundred and several thousand different
Interspersed throughout the chromosome genes
Interspersed throughout the chromosome
Short repetitive sequences but may but - Contains a centromere that forms a
interspersed recognition site for kinetochore
- Telomeres contain specialised
sequences
- Repetitive sequences are commonly
found near centromeric and telomeric
regions but may be interspersed
CONTROL:
Histone acetylation:
● In acetylation, acetyl groups are attached to lysines in histone tails. The enzyme catalysing
the transfer is histone acetyltransferase.
● When lysines are acetylated, their positive charges are neutralised. As such histone tails no
longer interact with the neighbouring nucleosomes.
● Electrostatic interaction between neighbouring nucleosomes promotes folding of chromatin
into a more compact structure.
● Histone acetylation does not only promote transcription initiation by remodelling the
chromatin structure, the enzyme HAT also binds to and aids in the recruitment of the
transcription machinery
Histone deacetylation:
● Histone deacetylases >> remove acetyl groups from lysines in histone tails >> form a
condensed structure >> no transcription
Histone Methylation:
● The addition of methyl groups to histone tails promotes condensation of chromatin >> no
transcription
DNA methylation:
● Cytosine residues can be methylated to produce 5-methylcytosine. These methylated
cytosine residues are located in GC-rich sequences, which are often near or in the promoter
region of a gene
● Comparison of the same genes in different tissues shows that genes are usually more heavily
methylated in the cells in which they are not expressed.
● Moreover, proteins that bind to methylated DNA can recruit deacetylation enzymes. DNA
methylation and histone deacetylation work together to repress transcription
Transcription occurs:
1. Histone acetylation
2. Histone demethylation
3. DNA demethylation
Transcription suppressed:
1. Histone deacetylation
2. Histone methylation
3. DNA methylation
Core promoter contains the transcription start site and TATA box:
1. TATA box is an A-T rich consensus sequence found upstream of transcription start site
2. TATA box serves as the binding site of general transcription factors to facilitate binding of
RNA polymerase II to the promoter, for transcription to occur
3. Core promoter determines the basal level of expression
Post-transcriptional modifications:
1. 5’ capping: A modified guanosine triphosphate residue is added to the 5’ nucleotide of the
pre-mRNA to create a “capped” RNA
2. 3’ polyadenylation: The 3’ end of the pre-mRNA is cleaved and 50-250 adenine nucleotides
are added to the new 3’ end to create the poly(A)taill
Functions:
A. Facilitate export of mRNA from the nucleus
B. Protect the mRNA from degradation by hydrolytic enzymes
C. Help ribosomes attach to the 5’ end of mRNA once the mRNA reaches the nucleus
RNA Splicing:
➔ Non-coding sequences are known as introns and coding sequences are known as exons.
➔ The introns are cut out and the exons are joined together to form a continuous coding
sequence via mRNA splicing.
Significance of splicing:
The biological advantage lies in alternative splicing whereby a pre-mRNA can be spliced in more
than one way. Hence, alternative splicing produces two or more polypeptides with differences in
their amino acid sequences, leading to possible variation in their functions.
Factors affecting mRNA stability:
Length of poly(A)tail:
1. Longer poly(A)tail >> more stable, longer time to shorten the poly(A)tail by cellular
exonucleases >> increase stability of mRNA, translation occurs repeatedly
2. Shorter poly(A)tail >> less stable, less time to shorten the poly(A) tail >>less translation, less
proteins synthesised
Destabilising sequences:
mRNAs contain sequences that act as destabilising elements >> most commonly found within the 3’
untranslated region >> consensus rich AUUUA is recognised by cellular proteins that bind to the
ARE >> influencing whether mRNA is rapidly degraded
Biochemical modifications:
1. Cleavage of initial insulin polypeptide forms the active hormones
2. Chemical modifications such as phosphorylation and glycosylation
3. Cell-surface proteins and secretory proteins must be transported to target destinations
inside and outside the cells to function
4. Regulation may occur at any of the steps involved in modifying or transporting a protein
Denaturation:
1. An excess or primer is mixed with DNA fragment to be amplified
2. The thermal cycler heats the mixture of primer and DNA fragment to 94 degrees celsius
3. At this temperature, hydrogen bonds holding the double-stranded DNA fragment break and
double-stranded DNA dissociates into single strands
Annealing of primers:
1. The solution is allowed to cool to 65 degrees celsius
2. As it cools, the single strands of DNA tend to reassociate into double strands
3. Because of the large excess of both the forward and reverse primers, primers base pair with
complementary sequences in the single-stranded DNA
Primer extension:
1. The thermal cycler then raises the temperature to 72 degrees celsius, the temperature at
which the Taq polymerase functions best
2. Using the primer, the heat stable polymerase copies the rest of the fragment as if it were
replicating DNA
3. The primer is then lengthened into a complementary copy of the entire single-stranded
fragment
4. Because both DNA strands are replicated, there are now two copies of the original fragment
Gel electrophoresis:
1. The gel acts as molecular sieve to separate nucleic acids or proteins on the basis of size,
electrical charge and other physical properties
2. A gel material consisting of agarose is poured as a thin slab on a glass
3. After the gel has solidified, the researcher loads samples containing a mixture of
macromolecules of different sizes in wells formed at one end of the gel
4. The gel is bathed in an aqueous solution and electrodes are attached to both ends and an
electrical current is applied
5. The DNA molecules, which are negatively charged due to their phosphate groups, migrate
towards the positive electrode
6. The distance a DNA molecule travels is inversely proportional to its length. Larger
molecules travel more slowly through the pores in the gel, thus the smallest DNA fragments
travel the longest distance
7. The gel slows down the large molecules more than the smaller molecules because the large
molecules have more difficulty in moving through the pores in the gel
8. When the current is turned off, the DNA molecules in each sample are arrayed in bands
along a “lane” according to their size. The shortest molecules having travelled the furthest,
are in bands at the bottom of the gel.
9. These bands of separated molecules can be visualised with stains
10. The actual size of the DNA fragments is determined by comparison to migration distances
of known marker fragments
1. The restriction fragments from each sample are then separated by electrophoresis
2. Each sample forms a characteristic pattern of bands
1. These fragments will then be transferred by capillary action from the gel to a sheet of
nitrocellulose membrane
2. Capillary action pulls an alkaline solution upward through the gel and through a sheet of
nitrocellulose membrane laid on top of it, transferring the DNA to the membrane and
denaturing it
3. The single strands of DNA stick to the membrane, positioned in bands exactly as on the gel
DNA MUTATIONS:
DNA Mutations:
1. Point mutations: involves chemical changes in 1 base-pair of DNA
● Base-pair substitution: replacement of 1 base-pair
● Base-pair addition: insertion of 1 base-pair
● Base-pair deletion: removal of 1 base-pair
2. Chromosomal aberration
● Numerical aberration: changes in number of chromosomes
● Structural aberration: changes to structure of chromosomes
● Base-pair substitution:
○ Silent mutations: no effect on the amino acid sequence
○ Missense mutations: little effect on/ major change to final protein
○ Nonsense mutations: production of a stop codon
Silent mutation:
● No effect on the amino acid sequence >> degenerate nature of genetic code >> mutation is
not observed
1. Base-pair substitution
2. Change in DNA sequence
3. Change in corresponding mRNA codon but still codes for the same amino acid
4. No change in amino acid sequence of polypeptide chain
5. No change to properties of R group
6. No change to structure, properties and function of protein
7. Polypeptide chain folds to produce the same 3D conformation
Missense mutation:
● Two different outcomes: little effect on final protein or major change to the final protein
Nonsense mutation:
● Produces a stop codon >> premature termination of translation >> truncated polypeptide
1. Base-pair substitution
2. Change in DNA sequence
3. Change in corresponding mRNA codon, resulting in STOP codon
4. Premature termination of translation
5. Truncated polypeptide
6. Non-functional or no protein
Frameshift mutation:
● If base-pair addition and substitution does not occur in multitudes of 3 >> frameshift
mutation >> missense and nonsense mutation
Missense mutation:
1. Base-pair deletion
2. Change in DNA sequence
3. Shift in reading frame
4. Change in sequence of mRNA codons
5. Significant change in amino acid sequence of polypeptide chain
6. Change in structure, property and function of protein
Nonsense mutation:
1. Base-pair addition
2. Change in DNA sequence
3. Shift in reading frame
4. Results in STOP codon on mRNA
5. Premature termination of translation
6. Truncated polypeptide chain
7. Non-functional or no protein
Chromosomal aberration:
a. Deletion: loss of gene >> shorter chromosome formed
b. Duplication: addition of genes >> section of chromosome replicates
c. Inversion: a chromosome breaks at 2 locations and the middle portions inverts 180o before
rejoining
d. Translocation: a section of chromosome breaks off and becomes attached to another
chromosome
Mitosis:
Prophase:
Behaviour of chromosomes:
- Chromatin fibres become more tightly coiled, condensing into discrete chromosomes
- Each duplicated chromosome now appears as 2 identical sister chromatids, joined together
at the centromere
Nucleus:
- Nucleoli disappears as their DNA passes to certain chromosomes
- During late prophase, the nuclear envelope breaks down into small vesicles which disperse
Spindle fibres:
- Outside the nucleus, duplicated pair of centrioles move towards opposite poles of the cell
- Short microtubules may be seen radiating from the centrioles
- Microtubules extending from each centrosome then invade the nuclear area. Chromosomes
attach to kinetochore microtubules via their kinetochores, and thus undergo active
movement.
Metaphase:
Behaviour of chromosomes:
- Chromosomes are aligned at the metaphase plate of the spindle
- Kinetochore microtubules attach sister chromatids to opposite poles of the spindle
Nucleus:
- Nucleus absent
Spindle fibre:
- Centrosomes are now at opposite poles of the cell
Anaphase:
Behaviour of chromosomes:
- The centromere of each chromosome separates into 2, causing sister chromatids of each
chromosome to separate
- Each chromatid becomes a daughter chromosome
Nucleus:
- Nucleus absent
Spindle fibres:
- Kinetochore microtubules shorten, pulling the daughter chromosomes to opposite poles
centromeres first
- Interpolar microtubules lengthen, causing spindle fibres to move apart and the cell to
elongate
Telophase:
Behaviour of chromosomes:
- The two sets of daughter chromosomes arrive at the opposite poles of the spindle
- Chromosomes decondense into chromatins
Nucleus:
- A new nuclear envelope reassembles around the chromosomes at each pole and the nucleoli
reappear
Spindle fibres:
- Microtubules dis-assemble
Meiosis:
Significance:
1. Genetic stability
2. Growth and development of zygote
3. Cell replacement: supplies new cells required to replace damaged or worn-out cells
4. Regeneration
5. Asexual reproduction
Meiosis I:
Prophase I:
Behaviour of chromosome:
- Chromatin becomes more tightly coiled, condensing into discrete chromosomes
- Homologous chromosomes pair up to form a bivalent via synapsis
- The bivalents shorten and thicken further, partly by coiling
- The homologous chromosomes appear to repel each other and partially separate
- A process known as crossing over occurs between non-sister chromatids of homologous
chromosomes >> new combinations of alleles
- The bivalents assume particular shapes
Nucleus:
- The nucleoli disappear and nuclear envelope disintegrates
Spindle fibres:
- Outside the nucleus, the mitotic spindle assembles between the two centrosomes, which
moves towards opposite poles of the cell
Metaphase I:
Behaviour of chromosome:
- Homologous pairs of chromosomes are aligned on the metaphase plate of the spindle, with
one chromosome in each bivalent facing each pole
- Independent assortment of homologous chromosomes occurs >> orientation of each
bivalent along the metaphase plate is random and independent
Nucleus:
- Nucleolus and nuclear envelope absent
Spindle fibres:
- Centromeres of chromosomes are attached to kinetochore microtubules via kinetochore
proteins
Anaphase I:
Behaviour of chromosomes:
- Homologous chromosomes move towards opposite poles of the spindle
- This separates the chromosomes into 2 haploid sets
Nucleus:
- Nucleolus and nuclear envelope absent
Spindle fibres:
- Kinetochore microtubules shorten, pulling homologous chromosomes, centromeres leading
towards opposite poles of the spindle
- Interpolar microtubules lengthen, causing spindle fibres to move apart and the cell to
elongate
Telophase I:
Behaviour of chromosomes:
- Homologous chromosomes reach opposite poles of the cell, thus marking the end of meiosis
I
- Chromosomes decondense to form chromatin
Nucleus:
- Nucleolus reappears and nuclear envelope reforms
Spindle fibres:
- Spindle fibres disassemble
Meiosis II:
Prophase II:
Behaviour of chromosomes:
- Chromatin becomes more tightly coiled, condensing into discrete chromosomes
Nucleus:
- Nucleoli disappear and nuclear envelope disintegrates
Spindle fibre:
- Centrosomes move to opposite poles of the cells
- New microtubules appear and become attached to kinetochore region of the chromosomes
- The new spindle microtubules are orientated at right angles to the original spindle
microtubules of meiosis I
Metaphase II:
Behaviour of chromosomes:
- Chromosomes, each with its two sister chromatids, are aligned individually along the
metaphase plate
Nucleus:
- Nucleolus and nuclear envelope absent
Spindle fibres:
- Kinetochore microtubules attach each of the two sister chromatids of a chromosome to
opposite poles of the spindle
Anaphase II:
Behaviour of chromosomes:
- Centrosomes separate, sister chromatids separate at the centromeric region. Each sister
chromatid is now known was a daughter chromosome
Nucleus:
- Nucleolus and nuclear envelope absent
Spindle fibres:
- Kinetochore microtubules shorten, pulling the daughter chromosomes to opposite poles,
centromeres leading
- Interpolar microtubules lengthen, causing spindle fibres to move apart and the cell to
elongate
Telophase II:
Behaviour of chromosomes:
- Daughter of chromosomes reach opposite poles of the cell
- Chromosomes decondense to chromatin
Nucleus:
- Nuclear envelope reform around each nucleus and nucleoli reappears, completing the
formation of four daughter nuclei
Spindle fibres:
- Spindle fibres disassemble
Proto-oncogenes: codes for proteins that stimulate normal cell-division
>> Gain-in-function mutation
Oncogenes: excess protein [hyperactive protein degradation resistant protein]
Tumor suppressor gene: codes for proteins that inhibit normal cell-division
>> Loss-in-function mutation