Three foundations of biology

1st foundation: Evolution through natural selection

All life evolved from pre-existing life

Homology

Fossils

Fossils

Strong evidence for evolution

Increasing complexity towards higher strata, or as geological time increases.

Ontogeny recapitulates phylogeny

Development is a fast-action replay of ancestry.

Embryos of different species show similarities in the beginning and differences increase as they

grow.

Homology

Structures derived from a common ancestral feature, but do not necessarily serve the same

function.

Darwin’s observations

Variation in population leads to different levels of fitness for each organism.

Traits were passed to offspring through hereditary mechanisms.

Different fitness > fittest survive > reproduce > offspring inherits traits that assist in survival.

Competition for survival and reproduction drove the selection process.

Two-step process

Variability

Ordering that variability by natural selection

2nd foundation: Unity of biochemical processes

All organisms share the main biochemical reactions.

All organisms use nucleic acids (RNA/DNA)

All organisms use proteins as ‘hardware’ to carry out instructions.

3rd foundation: Cell theory

All known living things made up of one or more cells.

All living cells arise from pre-existing cells (by cell division).

The cell is the fundamental unit of structure and function in all living organisms.

Cells contain hereditary information passed on through cell division.

Relatedness of life

All organisms have genes (DNA).

DNA contains history of evolution.

Compare genes to define relationships.

Glossary

Ontogeny

developmental history of organism in its own lifetime.

Phylogeny

evolutionary history of a kind of organism.

Fossil

preserved evidence of life from a past geological age.

Ultrastructure

close detail of cell with all organelles visible.

Homology

state of similarity in structure or anatomical position, but not necessarily in function between different

organisms, thus indicating evolutionary origin.

Paralogy

genes that are homologous (derived from a common ancestor).

Prokaryotes vs eukaryotes

Domains of life

Capital B in ‘Bacteria’ distinguishes the domain.

Dependence on prokaryotes

Photosynthetic bacteria produce more than 50% of the earth’s free oxygen.

Nitrogen-fixing bacteria process about 70% of the biologically available nitrogen.

Diseases caused by Bacteria (domain) include:

TB

Leprosy

Pneumonia

Cholera

Syphilis

Gonorrhoea

Anthrax

Archaea are not known to cause disease.

Prokaryotic cells

Usually microscopic (1-10 m)

Single, circular chromosome (DNA)

Nucleoid is the zone in which the chromosome is found.

In bacteria, no proteins attached to DNA.

In archaea, histone proteins are attached to DNA.

Peptidoglycan (protein-sugar) cell wall – similar in archaea and bacteria.

Typical prokaryotic cell

Prokaryotes

(no nucleus)

Bacteria

Archaea

Eukaryotes

(with nucleus)

Animals

Plants

Fungi

Protists

Bacteria cells

Cell wall is made of peptidoglycan.

Gram positive (+) has one surrounding membrane, a cytoplasmic membrane (clear and vivid

colour as wall gets stained).

Gram negative (-) has two surrounding membranes, a cytoplasmic membrane and outer

membrane surrounding cell wall (pale colour as wall is covered).

Ribosomes

Present in all cells.

Composed of numerous proteins and several RNAs.

Site of translation – protein synthesis (mRNA to AA sequence).

Prokaryotic ribosomes are smaller than eukaryotic ribosomes.

Antibiotics

Some act on peptidoglycan cell wall, particularly gram +ve.

Others act on ribosomes, particularly gram -ve.

Flagellum

Prokaryotic flagellum

Motility appendage with a corkscrew (rotating shaft) action.

It is a long thin filament made of flagellin protein.

Extracellular structure.

After division, one daughter cell is without flagellum, so it will grow it.

Eukaryotic flagellum

Motility appendage with a beating (like a whip) action.

Consists of microtubules and dynein motors.

Analogous structure

Cell division

Prokaryotic division

Binary fission.

Constricting ring made of FtsZ protein pinches parent cell in two.

Divide every ~20 minutes.

Eukaryotic division

Mitosis and meiosis.

Use of microtubules in the spindle.

Feature of eukaryotic cells absent from prokaryotic cells.

Division of labour in the cytoplasm by compartmentalisation of organelles.

Nucleus and histone proteins.

Linear chromosomes.

Endomembrane system (ER, Golgi complex) – system of membranes inside the cell.

Cytoskeleton (microtubules, microfilaments, intermediate filaments) – gives and maintains shape,

whereas prokaryotes have a cell wall that defines shape.

Motor proteins and movement through cytoplasm – allows shape change.

Eukaryotic nucleus

Surrounded by nuclear envelope (double membrane).

Nuclear pores (75nm diameter) - RNA transcribed from DNA leaves nucleus through pores

(communication between nucleus and cytoplasm).

DNA in chromatin – long, linear strands covered by histones.

Different organisms have different number of chromosomes.

Nucleolus is subregion of nucleus where ribosomal genes are transcribed.

Chromosome is

copied and

attached to

membrane next to

each other.

Cell wall grows

between the

attachment

points.

Chromosome

attaches to the

membrane.

FtsZ protein

pinches cell in two.

Endomembrane system

Nuclear pores

Lined with a ring of proteins that control the movement of substances.

Pores are attached to the lamina (nuclear skeleton) that holds them in place.

Located at the site where inner membrane curls around to become the outer membrane. Evenly

spaced over the nuclear envelope. Membrane is continuous.

Controls traffic of proteins and RNA into and out of the nucleus.

Endoplasmic reticulum

ER (rough) is continuous with the nuclear envelope.

Consists of membrane cisternae, resulting in internal compartments and channels that are not

fixed.

Dynamic structure, changing in structure and function to reform compartments.

Rough ER – ribosomes attached to the ER.

Smooth ER – ribosomes are absent.

Vesicles containing materials (protein) “bleb off” and are transported to the Golgi complex.

Protein is made into the cisternal space and folding occurs there.

Intracellular membranes

Major functions:

Surface for biochemical reactions.

Compartmentalise to prevent mixing.

Provide transport for materials within the cell.

Golgi complex (apparatus)

Flattened sacs of membrane (cisternae) are called Golgi bodies.

Collection, packaging and distribution of molecules synthesised elsewhere in the cell.

All Golgi bodies are the Golgi complex.

Functional extensions of the ER.

Almost all polysaccharides in the cell are manufactured in the Golgi bodies. May be attached to

protein (glycoprotein) or lipid molecules (glycolipid).

“Zones” of the Golgi apparatus

‘Cis’ zone is closest to ER; receives vesicles from the ER.

‘Medial’ zone is in the middle.

‘Trans’ zone is closest to the plasma membrane; polysaccharides attach to vesicles that

bleb off, acting a tags.

Vesicles travel through Golgi zones by merging and “blebbing” off.

Cytoskeleton

Major elements of the cytoskeleton.

Actin filaments (microfilaments) (7nm)

Composed of actin protein.

Gelsolin (solubiliser that cuts actin filaments) controls filament assembly.

Microtubules (25nm)

Composed of tubulin protein.

13 individual protofilaments (tubulin dimers each made of one α- and one β-tubulin

monomer) that form a cylinder. LOOK UP PROTOFILAMENTS

Intermediate filaments (10nm)

Composed of vimentin protein.

Motor elements of the cytoskeleton

Actin filaments – myosin motors.

Muscle contractions and cytoplasmic streaming.

Myosin has a ‘walking’ action on actin filament.

Controlled assembly and disassembly of actin filaments alter cell shape.

Microtubules – kinesin (kinetic) and dynein (dynamic) motors.

Dynein slides one microtubule against another. If microtubules are fixed at one end,

result is curvature in movement. Basal body is the point where microtubules are fixed.

This structure is present in eukaryotic flagella; sliding causes a whip motion.

Kinesin moves vesicles along microtubules using a ‘walking’ motion.

It is similar to dynein, but not attached to another microtubule and is free.

Uses ATP

Microtubules disassemble by splitting and reassemble by closing at a seam.

Intermediate filaments are static.

Intra- and inter-cellular stabilisation.

Lipids

Lipids include fats, oils, waxes and steroids/sterols.

Function:

Energy storage and insulation.

Waxes for protective coatings.

Chemical messengers (steroids/sterols – 4 carbon ring molecules).

Structural components of membranes.

Lipid monomers:

Glycerol

Fatty acids

Reactive carboxyl end and neutral hydrocarbon tail attached.

Double bond in the carbon chain results in a kink.

They are primary components of membranes.

Levels of saturation depend on the number of double bonds in carbon chain.

No double bonds – saturated.

One double bond – (mono)unsaturated.

Many double bonds – polyunsaturated.

Fatty acids bond to glycerol through esterification, involving the formation of an ester bond.

Triglycerides

Composed of 3 fatty acids and 1 glycerol.

State as solid (fat) or liquid (oil) depends on the degree of unsaturation.

More unsaturated double bonds, closer packing is prevented. Fats have less double bonds, oils

have more double bonds.

Phospholipids

Composed of 2 fatty acids, 1 glycerol and 1 phosphate group.

The phosphate group attaches to C3 on the glycerol molecule.

Hydrophobic fatty acid tails and hydrophilic phosphate head result in [???] structure.

Hydrophobic repels water, while hydrophilic is attracted to water.

Phospholipids arrange in a bilayer. Hydrophobic tails interact with each other through

dispersion forces. Hydrophilic heads face water, forming H-bonds.

Head groups, such as inositol (an alcohol) and choline, can bind to the phosphate group changing

the properties of the phospholipid.

Membranes

All membranes are composed of a phospholipid bilayer. They also contain proteins, glycoproteins and

steroids.

Different membranes have different ancillary components. These determine function.

Selective barriers for the internal environment of the cell from the external environment.

Transport across membranes:

Diffusion

Net passive movement of molecules from a region of high concentration to one where

they are in a low concentration.

Down concentration gradient.

Small, non-polar (lipid soluble) molecules. Includes O2, CO2 and H2O.

Osmosis

Special case of diffusion for water.

Biological membranes are differentially permeable (control the entry and exit of

substances).

Movement of water through a differentially permeable membrane from a region of high

water potential to one of low water potential.

Osmotic concentration = solute concentration.

Hypoosmotic = hypotonic = low solute (osmotic) concentration

Hyperosmotic = hypertonic = high solute (osmotic) concentration

Water potential is the tendency of water to leave one place in favour of another.

Low water potential = high solute

High water potential = low solute

Osmotic potential

Greater solute concentration, more negative potential.

It is the pressure required to prevent movement of water into a solution

if it is separated from the water by a selectively permeable membrane.

Higher negative potential difference can push water up against gravity.

Varying concentration of solution and effect on plant and animal cells.

CONCENTRATION: HYPOTONIC ISOTONIC HYPERTONIC

ANIMAL CELL Lysis (haemolysis for RBCs)

Normal Crenation

PLANT CELL Turgid Cell stiffens but retains shape.

Normal Plasmolysis Cell body shrinks and pulls away from cell wall.

Plant cell wall prevents bursting; hence the cell is turgid.

Ciliates use contractile vacuoles to regulate water. They remove excess water caused by

osmosis in a freshwater environment.

Facilitated diffusion

Proteins embedded in the membrane facilitate diffusion.

Large, polar and/or charged molecules. Includes Na+.

Carrier proteins

Channel proteins

Closed when inactive.

Specific molecule can bind to it.

Protein channel opens to allow the specific molecules through.

Active transport

Involves the movement of substances against the concentration gradient.

It requires energy (ATP).

Used in ion pumps, such as sodium-potassium ion pump. They create potential

differences to move Na+ against the concentration gradient.

Coupled active transport

Symport - required substance travels along the concentration of another

molecule.

Antiport – required substance is pushed through while another is out.

Bulk transport

Endocytosis (in)

Phagocytosis

Engulfment of solid material.

Cell recognises the substance before beginning the process.

Phagosomes form when the material is engulfed.

These combine with lysosomes, forming secondary lysosomes.

Enzymes in lysosomes digest the material.

Pinocytosis

Engulfment of liquid.

An indentation is formed.

Membrane pinches to surround liquid.

Clathrin cytoskeleton forms under the membrane. It pulls the membrane and

facilitates a pinching action. The vesicle formed is coated by clathrin.

Exocytosis (out)

Bulk transport requires energy.

Proteins

Membrane proteins

Some are enzymatically active.

Structural role.

Restrict interdependent reactions to a limited space.

Self-recognition (glycoproteins).

Surface receptors.

Transport mechanisms as a selective barrier.

Types of proteins

Hardware – interpret genetic code.

Catalytic (enzymes) – direct reactions.

Structural – form cytoskeleton and connective tissue.

Regulatory – hormones.

Immunoglobulins – antibodies for immune defence.

Monomer: amino acid.

Each amino acid (α-amino acid) has four carbons bonded to a central atom.

Amino acid R groups

Some polar, but uncharged (hydrophilic).

Some charged (hydrophilic).

Some non-polar (hydrophobic).

Some form rings (proline).

Some have special properties, such as two cysteine AA forming disulfide bonds.

Polymer: polypeptide, then protein.

Condensation polymerisation of AA.

Peptide bonds between AA forms polypeptide.

Linear chains of AA (no branching).

Variable length and order of AA.

NH2- side is capped, more AA join on -COOH end.

Protein structure