BHCS1002 Summary Notes
Robert Hooke discovered the cell in 1665
First living cell seen by Antony van Leeuwenheok in 1674
Classic cell theory – all cells arise from pre-existing cells and are the unit of structure, physiology
and organisation in living organisms
Modern cell theory – same as classic with addition of energy flow understanding (metabolism
and biochemistry) that occur within cells
• Cells contain DNA which passed on during cell division
• Same chemical composition when of similar species
• Unicellular
• Multicellular
• Activity of organism depends on total activity of independent cells
Prokaryote
• Oldest, original cell
• Cell membrane, cytoplasm, ribosomes (70S from 50S + 30S subunits), nucleoid
• E.g. bacteria and archae
Eukaryote
• More complex – more organelles
Cell structure
3 main components; cell membrane, nucleus and cytoplasm (which contains cytosol where
organelles are suspended)
Cell membrane;
• Function
o Physical isolation – separates extracellular fluid (ECF) from intracellular fluid
(ICF)
o Regulation of exchange – controls entry and exit
o Cell communication – contains proteins which recognise and respond to
environmental signals
o Structural support
• Composition
o Cholesterol – lipid bilayer
o Phospholipids, sphingolipids – lipid bilayer, glycolipids
o Carbohydrate - glycolipids
o Proteins – glycoproteins
• Membrane lipids are amphipathic - contain hydrophobic and hydrophilic parts
• Membrane proteins can be associated with the lipid polar heads (peripheral proteins) or
the hydrophobic core matrix (integral proteins)
• Proteins and lipids are static but in constant movement
o Rotational – lipids speed 1x1010 s-1, proteins speed 1x104 s-1
o Lateral – lipid and protein speed is 1x108-1x1010 s-1
o Transverse (flip) – rarely happens as difficult to overcome energy barrier
presented by moving through hydrophobic core
• Asymmetric
o Different proportion of lipids in each layer of bilayer
o Every single protein in membrane occurs with exact same orientation
o Integral proteins are anchored to one or both sides of the membrane immediately
after synthesis and insertion into bilayer
o Carbohydrates always project out of membrane
1
,BHCS1002 Summary Notes
• Fluid-Mosaic model
o By Singer-Nicholson in 1972
o Thought to be one integral protein - now known lots of transmembrane protein
presenting, barely leaving any part of bilayer unperturbed
• Membrane proteins
o Purely in membrane
o Purely in ECF or ICF
o Interact reversibly with membrane
o React weakly through electrostatic and polar forces
o React strongly through hydrophobic forces
▪ Some don’t alter membrane lipids
▪ Some don’t lead to covalent modification (e.g. phospholipases)
• Lamellar phases
o Lamellar – 2 lipid layers whose non-polar moieties are in contact and away from
water
o Lamellar-alpha – bilayer is at high temperature so becomes disrupted, liquid
form, diffusion easier
o Lamellar-beta – normal bilayer, gel form, diffusion normal
• Shape and curvature
o Original model was flat – membrane now understood to be curved
o Curvature requires presence of specific proteins (e.g. dynamin, clathrin)
o Dynamically modulated by changes in lipid composition, protein binding and
insertion
o Several enzymes have their activity regulated by curvature of membrane
• Lateral heterogeneity
o Singer-Nicholson model was homogenous except for protein insertions
o In reality, heterogeneity is described by domains
▪ Protein-protein interactions
▪ Protein-lipid interactions
▪ Protein crowding
▪ Lipid packing parameters
▪ Lateral segregation of lipids
▪ Restrictions to protein movement
• Membrane (lipid) rafts
o Small heterogenous, highly dynamic, sterol- and sphingolipid-enriched domains
that compartmentalise cellular processes – e.g. clathrin-coated pits used in
endocytosis
Cytoplasm;
4 compartments
• Cytosol - semi gelatinous fluid containing dissolved nutrients, ions and waste products
where everything is suspended
• Inclusions – particles of insoluble materials
• Cytoskeleton
• Maintains cell shape, hols organelles in places, assist vacuole formation, internal and cell
motility
• Microtubules
o Hollow rods that support and shape the cell
o Act as ‘routes’ which organelles move along
• Microfilaments
o Composed of actin
o Thin, solid rods which are active in muscle contraction
• Intermediate fibres
o Abundant in many cells
2
,BHCS1002 Summary Notes
o Hold microtubules and filaments in place
• Organelles – membrane bound compartments that play specific roles in function of the cell
o Mitochondrion
▪ Originated from aerobic bacteria due to DNA and ribosome presence
▪ Spherical and elliptical in shape, double walled (space between membranes
called intermembrane space – role in ATP production)
▪ Mitochondrial matrix contains enzymes, ribosomes and DNA
▪ Mitochondrial DNA (mtDNA)
• 16kb, 37 genes coding for proteins used in ATP synthesis
• Replicates independently from cell’s DNA
o Golgi apparatus/complex
▪ Series of hollow, curved sacs called cisternae stacked on top of one another
surrounded by vesicles
▪ Receives proteins from RER – modifies and packages them into vesicles
o Endoplasmic reticulum (ER)
▪ Attached to nucleus
▪ Synthesis, storage and transport of biomolecules
▪ Rough ER
• Main site of protein synthesis
• Proteins assemble into ribosomes attached to surface, then inserted
into ER lumen to undergo chemical modification
▪ Smooth ER
• No ribosomes
• Synthesis of fatty acids, steroids and lipids
• Detoxifies drugs in liver and kidney
• Specialised smooth ER in muscle stores Ca2+ - sarcoplasmic
reticulum
o Ribosomes
▪ Float in cytoplasm or attached to RER
▪ 80S ribosomes made of small (40S) and large (60S) subunits – S is
Svedberg unit relating to sedimentation rate
▪ Functions
• Translation – assemble amino acids into a specific protein based on
mRNA
o Cytoplasmic vesicles
▪ Secretory vesicles – proteins to be released from cell
▪ Storage vesicles – never leave cytoplasm
• Lysosomes
o Formed from breaking off of Golgi and merging with endosome
o Digestive system of cell – contain hydrolytic enzymes that
breakdowns down bacteria or old organelles
o Enzymes require low pH so lysosomes take up H+
• Peroxisomes
o Smaller than lysosomes
o Derived from ER
o Degrade long chain fatty acids and potentially toxic foreign
molecules
o Contain oxidase enzymes that produce H2O2 which is
converted to H2O and O2
o Peroxisomal disorders disrupt processing of lipids and neural
function by altering structure of nerve cell membranes
o Nucleus
▪ Nuclear envelop
3
, BHCS1002 Summary Notes
• Trialmellar appearance
• Nuclear lamina – intermediate filaments equivalents
▪ Nuclear pores
• Allow transport of RNA, ribosomes and proteins
▪ Nucleolus
• Synthesis of DNA, RNA and ribosomes
• No membrane
• Size correlates to activity of cell
▪ Chromatin
• In non-dividing cells, nucleus appears to be full of randomly scattered
granular material of chromatin
• Composed of DNA and associated proteins.
Genetic variation – important consequence of sexual reproduction, contributing to evolution
Darwin’s theory of evolution by natural selection involves three participants; principle of
variation, heredity and selection
Measuring genetic variation
• Within populations
o Polymorphism
▪ ‘Occurrence together in the same habitat at the same time of two or more
distinct forms of a species such that the rarest of them cannot be maintained
by recurrent mutation’
▪ Considered polymorphic if frequency of rare allele >1%
o Heterozygosity
▪ Average frequency of heterozygous individuals per locus
▪ Considers number of alleles at each locus
▪ Useful for differentiating populations when number of alleles per locus is low
o Nucleotide diversity
▪ Heterozygous or gene diversity average over all the nucleotide sites in a
gene/DNA stretch
▪ Usually, two nucleotides in any 2 copies of a gene from same species is the
same
▪ Values are typically very small
▪ Used to make comparisons between populations
o Segregating sites – number of variable or polymorphic nucleotide sites in a set of
homologous DNA sequences
o Haplotype number – number of haplotypes at a locus
• Between populations
o Genetic identity, I
∑𝑋1𝑌1
▪ Nei’s measure 𝐼 = √(∑𝑋12 ∑𝑌1^2)
o Genetic distance, D – measure related to genetic identity = -loge(I)
o Genetic diversity analysis – amount of genetic differentiation between populations
▪ FST = (HT – HS) / HT
▪ FST – Fixation index
• =0-0.5 => little genetic differentiation
• =0.05-0.15 => moderate
• =0.15-0.25 => great
• =0.25-1.0 => very great
▪ HT – total heterozygosity, HS – avg sample heterozygosity
Population genetics – study of genetic variation within a population
4
Robert Hooke discovered the cell in 1665
First living cell seen by Antony van Leeuwenheok in 1674
Classic cell theory – all cells arise from pre-existing cells and are the unit of structure, physiology
and organisation in living organisms
Modern cell theory – same as classic with addition of energy flow understanding (metabolism
and biochemistry) that occur within cells
• Cells contain DNA which passed on during cell division
• Same chemical composition when of similar species
• Unicellular
• Multicellular
• Activity of organism depends on total activity of independent cells
Prokaryote
• Oldest, original cell
• Cell membrane, cytoplasm, ribosomes (70S from 50S + 30S subunits), nucleoid
• E.g. bacteria and archae
Eukaryote
• More complex – more organelles
Cell structure
3 main components; cell membrane, nucleus and cytoplasm (which contains cytosol where
organelles are suspended)
Cell membrane;
• Function
o Physical isolation – separates extracellular fluid (ECF) from intracellular fluid
(ICF)
o Regulation of exchange – controls entry and exit
o Cell communication – contains proteins which recognise and respond to
environmental signals
o Structural support
• Composition
o Cholesterol – lipid bilayer
o Phospholipids, sphingolipids – lipid bilayer, glycolipids
o Carbohydrate - glycolipids
o Proteins – glycoproteins
• Membrane lipids are amphipathic - contain hydrophobic and hydrophilic parts
• Membrane proteins can be associated with the lipid polar heads (peripheral proteins) or
the hydrophobic core matrix (integral proteins)
• Proteins and lipids are static but in constant movement
o Rotational – lipids speed 1x1010 s-1, proteins speed 1x104 s-1
o Lateral – lipid and protein speed is 1x108-1x1010 s-1
o Transverse (flip) – rarely happens as difficult to overcome energy barrier
presented by moving through hydrophobic core
• Asymmetric
o Different proportion of lipids in each layer of bilayer
o Every single protein in membrane occurs with exact same orientation
o Integral proteins are anchored to one or both sides of the membrane immediately
after synthesis and insertion into bilayer
o Carbohydrates always project out of membrane
1
,BHCS1002 Summary Notes
• Fluid-Mosaic model
o By Singer-Nicholson in 1972
o Thought to be one integral protein - now known lots of transmembrane protein
presenting, barely leaving any part of bilayer unperturbed
• Membrane proteins
o Purely in membrane
o Purely in ECF or ICF
o Interact reversibly with membrane
o React weakly through electrostatic and polar forces
o React strongly through hydrophobic forces
▪ Some don’t alter membrane lipids
▪ Some don’t lead to covalent modification (e.g. phospholipases)
• Lamellar phases
o Lamellar – 2 lipid layers whose non-polar moieties are in contact and away from
water
o Lamellar-alpha – bilayer is at high temperature so becomes disrupted, liquid
form, diffusion easier
o Lamellar-beta – normal bilayer, gel form, diffusion normal
• Shape and curvature
o Original model was flat – membrane now understood to be curved
o Curvature requires presence of specific proteins (e.g. dynamin, clathrin)
o Dynamically modulated by changes in lipid composition, protein binding and
insertion
o Several enzymes have their activity regulated by curvature of membrane
• Lateral heterogeneity
o Singer-Nicholson model was homogenous except for protein insertions
o In reality, heterogeneity is described by domains
▪ Protein-protein interactions
▪ Protein-lipid interactions
▪ Protein crowding
▪ Lipid packing parameters
▪ Lateral segregation of lipids
▪ Restrictions to protein movement
• Membrane (lipid) rafts
o Small heterogenous, highly dynamic, sterol- and sphingolipid-enriched domains
that compartmentalise cellular processes – e.g. clathrin-coated pits used in
endocytosis
Cytoplasm;
4 compartments
• Cytosol - semi gelatinous fluid containing dissolved nutrients, ions and waste products
where everything is suspended
• Inclusions – particles of insoluble materials
• Cytoskeleton
• Maintains cell shape, hols organelles in places, assist vacuole formation, internal and cell
motility
• Microtubules
o Hollow rods that support and shape the cell
o Act as ‘routes’ which organelles move along
• Microfilaments
o Composed of actin
o Thin, solid rods which are active in muscle contraction
• Intermediate fibres
o Abundant in many cells
2
,BHCS1002 Summary Notes
o Hold microtubules and filaments in place
• Organelles – membrane bound compartments that play specific roles in function of the cell
o Mitochondrion
▪ Originated from aerobic bacteria due to DNA and ribosome presence
▪ Spherical and elliptical in shape, double walled (space between membranes
called intermembrane space – role in ATP production)
▪ Mitochondrial matrix contains enzymes, ribosomes and DNA
▪ Mitochondrial DNA (mtDNA)
• 16kb, 37 genes coding for proteins used in ATP synthesis
• Replicates independently from cell’s DNA
o Golgi apparatus/complex
▪ Series of hollow, curved sacs called cisternae stacked on top of one another
surrounded by vesicles
▪ Receives proteins from RER – modifies and packages them into vesicles
o Endoplasmic reticulum (ER)
▪ Attached to nucleus
▪ Synthesis, storage and transport of biomolecules
▪ Rough ER
• Main site of protein synthesis
• Proteins assemble into ribosomes attached to surface, then inserted
into ER lumen to undergo chemical modification
▪ Smooth ER
• No ribosomes
• Synthesis of fatty acids, steroids and lipids
• Detoxifies drugs in liver and kidney
• Specialised smooth ER in muscle stores Ca2+ - sarcoplasmic
reticulum
o Ribosomes
▪ Float in cytoplasm or attached to RER
▪ 80S ribosomes made of small (40S) and large (60S) subunits – S is
Svedberg unit relating to sedimentation rate
▪ Functions
• Translation – assemble amino acids into a specific protein based on
mRNA
o Cytoplasmic vesicles
▪ Secretory vesicles – proteins to be released from cell
▪ Storage vesicles – never leave cytoplasm
• Lysosomes
o Formed from breaking off of Golgi and merging with endosome
o Digestive system of cell – contain hydrolytic enzymes that
breakdowns down bacteria or old organelles
o Enzymes require low pH so lysosomes take up H+
• Peroxisomes
o Smaller than lysosomes
o Derived from ER
o Degrade long chain fatty acids and potentially toxic foreign
molecules
o Contain oxidase enzymes that produce H2O2 which is
converted to H2O and O2
o Peroxisomal disorders disrupt processing of lipids and neural
function by altering structure of nerve cell membranes
o Nucleus
▪ Nuclear envelop
3
, BHCS1002 Summary Notes
• Trialmellar appearance
• Nuclear lamina – intermediate filaments equivalents
▪ Nuclear pores
• Allow transport of RNA, ribosomes and proteins
▪ Nucleolus
• Synthesis of DNA, RNA and ribosomes
• No membrane
• Size correlates to activity of cell
▪ Chromatin
• In non-dividing cells, nucleus appears to be full of randomly scattered
granular material of chromatin
• Composed of DNA and associated proteins.
Genetic variation – important consequence of sexual reproduction, contributing to evolution
Darwin’s theory of evolution by natural selection involves three participants; principle of
variation, heredity and selection
Measuring genetic variation
• Within populations
o Polymorphism
▪ ‘Occurrence together in the same habitat at the same time of two or more
distinct forms of a species such that the rarest of them cannot be maintained
by recurrent mutation’
▪ Considered polymorphic if frequency of rare allele >1%
o Heterozygosity
▪ Average frequency of heterozygous individuals per locus
▪ Considers number of alleles at each locus
▪ Useful for differentiating populations when number of alleles per locus is low
o Nucleotide diversity
▪ Heterozygous or gene diversity average over all the nucleotide sites in a
gene/DNA stretch
▪ Usually, two nucleotides in any 2 copies of a gene from same species is the
same
▪ Values are typically very small
▪ Used to make comparisons between populations
o Segregating sites – number of variable or polymorphic nucleotide sites in a set of
homologous DNA sequences
o Haplotype number – number of haplotypes at a locus
• Between populations
o Genetic identity, I
∑𝑋1𝑌1
▪ Nei’s measure 𝐼 = √(∑𝑋12 ∑𝑌1^2)
o Genetic distance, D – measure related to genetic identity = -loge(I)
o Genetic diversity analysis – amount of genetic differentiation between populations
▪ FST = (HT – HS) / HT
▪ FST – Fixation index
• =0-0.5 => little genetic differentiation
• =0.05-0.15 => moderate
• =0.15-0.25 => great
• =0.25-1.0 => very great
▪ HT – total heterozygosity, HS – avg sample heterozygosity
Population genetics – study of genetic variation within a population
4
