BIOL10002

Summary Lecture Notes

Lecture 1 Introduction to Biology

1. Three foundations of biology
Evolution through natural selection
Unity of biochemical processes
Cell theory
2. First foundation of biology
Evolution through natural selection- Charles Darwin
 All life evolved from preexisting life
 Homology
 Fossils
Fossil record is strong evidence for evolution
Obverse increase complexity with passage of time
Ontogeny Recapitulates phylogeny—Development is a fast action
replay of ancestry
Webbing between fingers degenerate by programmed cell death to
free digits
Homology—derived from a common ancestral feature
Biogeography—also support evolution

3. Darwin’s 3 observation
 Individuals in a population vary----Fitness
 Pass on traits/fitness to offspring---Heredity
 Never enough resources---Competition for survival & reproduction
4. Evolution is a 2 steps processes
 Variability
 Natural selection---ordering that variability by natural selection
5. Second Foundation of biology
Unity of biochemical processes--- all organism share main biochemical
reactions
Example:
 All organism have genetic material—DNA—contains the instruction on
how that organism will develop
 Organism also have the hardware to carry out the instruction---
Proteins
6. Third Foundation of biology
Cell Theory
 All known living things are made up of one or more cells
 All living cells are arise from preexisting cells by division
 The cell is fundamental unit of structure and function
 Cells contains hereditary information –DNA—passed from cell to cell
 during cell division
7. Studying the evolution/relatedness of all life
 All organism have genes—DNA
 DNA contains a history of evolution
 Compare gene to define relationship
8. Cell morphology---2main types of cells
 Prokaryotes
 Eukaryotes
9. 3 major groups of organism
 Bacteria
 Eukarya
 Archaea

Lecture 2 Prokaryotes
1. Life depends on prokaryotes
 Archaea allow herbivores to break down the sugars in plants
 Bacteria in our intestines help to make essential vitamins
 Harmless Bacteria in our skin protect us from attack by other
invaders
2. Gut microbiology
Without gut bacteria – diseases
Very sick
Not develop properly
Mental illness
Suffer degenerate neurological illness
3. Prokaryotes are used in food production
Fermented food
Produced via the action of microbes
4. Life depends on prokaryotes
Bacteria:
 Generated 50% of earth free oxygen
 Proceed 70% biologically available nitrogen
5. Domain Bacteria can cause diseases
Legionnaire’s, typhus, Lyme disease, TB, gangrene, leprosy, meningitis,
pneumonia, cholera, dysentery, syphilis, gonorrhoea, anthrax
6. Domain Archaea
Are Not known to cause any diseases
7. Prokaryotic cells
 Usually microscopic (1-10μm)
 DNA is single, circular chromosome (‘nucleoid’)
 No proteins attached to DNA (Bacteria)
 Proteins (‘histones’) attached to DNA (Archaea)
Histones—attach to Archaea
  Wall (peptidoglycan), similar in Bacteria & Archaea
Bacteria—peptidoglycan
Achaea—pseudopeptidoglycan
8. Bacterial cells
 Cells typically have a wall (peptidoglycan)
 One surrounding membrane (Gram +) positive --- blue/ purple
 Two surrounding membranes (Gram -) negative---pink
9. Ribosomes
 All cells have ribosomes
 Small machines composed of numerous proteins and several RNAs
 Site of translation
 Take mRNA sequence and ‘translate’ it to a protein sequence
 Prokaryotic ribosomes are small (17-23nm)
 Eukaryotic ribosomes are larger (25-30nm)
 Bacterial ribosomes are different to eukaryotic ribosomes
 Sensitive to drugs like chloramphenicol, erythromycin and tetracycline
- antibiotics
 Antibiotics--- target the bacteria ribosomes and block the ribosome
translation pathway
10. Prokaryotic flagellum--- One of the two Rotating shaft design in biology
 Motility appendage
 Long thin filament
 Corkscrew action
 One of only two rotating shaft designs in biology
 Composed of flagellin protein
 Extracellular (not inside the cell membrane)
 6,000 rpm (similar to car engine) but often lot slower (~200 rpm) due to
drag & energy loss
11. Prokaryotic division--- Binary fission
Constricting ring pinches pareny cell into two
Circular DNA attach to the plasm membrane
Circular DNA replicate and grow apart then separate into two
12. Prokaryotes VS. Eukaryotes
 Prokaryotes are microscopic
 Eukaryotes can be large and multicellular
 Prokaryotes lack a nucleus
 Eukaryotic cells have a membrane bound nucleus
13. Prokaryotes = Bacteria & Archaea
14. Features of Eukaryotic Cells not seen in Prokaryotes
• Division of labour in the cytoplasm.
• Nucleus & histones
• Endomembrane system.
• Endoplasmic Reticulum. (ER).
 • Golgi complex.• Cytoskeleton.
• Microtubules.
• Microfilaments.
• Intermediate filaments.
• Motor proteins & movement
15. Features of the eukaryotic nucleus
 Surrounded by a double membrane or nuclear envelope
 Presence of nuclear (annular) pores (75 nm in diameter, text wrongly
says 9nm)
 DNA in long, linear strands covered with histones = chromatin
 Different organisms have different numbers of chromosomes
–Humans 46, Arabidopsis (cress )10
 Nucleolus = sub region of nucleus where ribosomal genes are
transcribed
 RNA transcribed from DNA leaves nucleus via pores and goes out into
the cell to be translated
16. Lokiarchaeota—Asgards
 Are new member in Domain Archaea
 Have cytoskeleton like Domain Eukarya
 Asgard Domain archaea might have endomembrane system
 Have structure like microfilaments
 Probably the closest living relative to the first eukaryotes

Lecture 3 Eukaryotes
1. Pores
 Pores lined with proteins
 Pore attached to lamina (nuclear skeleton)
 Pores evenly spaced over nuclear envelope
 Traffic of proteins and RNAs out of nucleus
 Traffic of proteins and RNAs into nucleus
 Pore is located at site where inner membrane curls around to become
outer membrane
2. Endoplasmic reticilum (ER) the heart of the endomembrane system
 Consists of membrane cisternae that ramify through the cytoplasm.
The result is internal compartments and channels.
 The ER is a dynamic structure, ever changing in structure and
function.
 If ribosomes are attached to the ER, it is called ROUGH ER.
 If ribosomes are absent, it is referred to as SMOOTH ER.
3. Major Function of Intracellular membrane
 Provide a surface for biochemical reactions.
 To establish a number of compartments to prevent mixing.
 To provide for transport of materials within the cell, from the cell to
its exterior, or from the cell to an adjacent cell.
4. Golgi complex
 Consists of flattened stacks of membrane or cisternae called Golgi
bodies.
 Collectively, all the Golgi bodies in a cell are the Golgi complex.
 Golgi bodies are functional extensions of the ER.
 The Golgi complex functions in the collection, packaging, and
distribution of molecules synthesize elsewhere in the cell.
 Almost all the polysaccharide in cells is manufactured within the Golgi
bodies.
 The polysaccharide may be attached to either protein or lipid
molecules in the Golgi bodies.
Polysaccharides on proteins may be used to distinguish between cells that
are self and non-self
5. The cytoskeleton
 Components of the cytoskeleton are not composed of membrane.
 Act as a form of scaffolding or as structural elements within the
cytoplasm of cells.
 Cytoskeletal components are associated with maintaining cell
shape.
 Involved in certain cell movements.
6. Major elements of the cytoskeleton
 actin filaments interact with myosin motors
controlled assembly & disassembly of actin filaments to alter shape
Assembly & disassembly of actin to create ameoboid cell movement
Eg. White blood cell pursuing & ‘neutralizing’ bacterial invaders
 microtubules interact with kinesin or dynein motors
 intermediate filaments are predominantly static
7. Actin filaments
 Interact with myosin motors
 Responsible for
 Muscle contractions
 Cytoplasmic streaming
Eg. Chloroplasts streaming in aquatic plant
8. Microtubules
 tubulin protein forms protofilament
 13 protofilaments form cylinder
9. Flagella movement
Eukaryotic flagella beat
prokaryotic flagella rotate
Eukaryotic flagellum consists of microtubules and dynein motors
•Dynein can slide one microtubule against another
•Microtubules are fixed at one end → curvature
Longitudinal and cross sections of a flagellum at different points to show
machine-like structure
Ciliates are unicellular eukaryotes covered in cilia (short flagella)
Ciliates swimming by waving their cilia (short flagella)
Kinesin can move vesicles along microtubules
10. The cytoskeleton
 Actin - myosin drives muscle contraction cytoplasmic streaming,
microvilli
 Microtubule - kinesin moves vesicles
 Microtubule - dynein drives cilia/flagella beating
 Intermediate filaments - intra- and inter-cellular stabilisation

11. DNP cause weight lost

DNP uncoupling oxidative phosphorylation->lead to an increase in
metabolic rate and fat metabolism.
DNP as a lipid soluble aromatic weak acid it can diffuse across the
mitochondrial intermembrane from the intermembrane space and into the
matrix. While doing so, DHP can transport protons across the membrane
and release the portion into the matrix. In essence this cancels the
chemiosmosis effect because it depleting the proton gradient. When this
happen, you have a shortage of protons for ATP synthase which results in
a shortage of ATP.

12. Cellular effect of DHP

When your body oxidizes sugar, fat or proteins, energy is produced.
Our body then needs to continue to burn more carbs, fats, and proteins at
a higher rate to make up for the shortage of ATP. When DNP transport a
proton across the membrane, heat is produced.

13. Erythropoietin
Erythropoiesis: Production of red blood cell which is part of
Haematopoiesis

EPO produced in kidney and liver (small amount) in response to

insufficient oxygen in the bloodstream.

EPO and erythropoiesis work together as a negative feedback cycle in

homeostatic response to keep tissue oxygen levels stable by controlling
the number of red blood cell circulating in the blood.

Go to High elevation and experience oxygen deficit, body will response by.
releasing EPO. This will increase red bold count and improve oxygen
carrying capacity and increase stamina and performance.

Usage of EPO lead to diseases: blood clotting and potential death due to
stroke and heart diseases also cause cerebral or pulmonary embolism and
 there is a synthetic form EPO can cause autoimmune diseases.

EPO also increase the body’s ability to buffer lactic acid. This would
reduce the lactic acid build up in the muscles which can occur if insufficient
oxygen is present in the muscle causing fermentation to occur rather than
cellular respiration.

14. Haematopoiesis
In Haematopoiesis, a few pluripotent haematopoietic stem cells in bone
marrow proliferate and give rise to all the mature cells found in blood and
lymphoid organs

15. Old red blood cells

Old red blood cells are less flexible
In the spleen, they are squeezed tightly in order to enter the storage area
in the spleen called sinuses ( act as reservoirs for the red blood cells).
When the old red blood cells are ruptured by this process, they are taken
up and degraded by macrophages.

16. Excretion (Ammonia in Fish VS. Urea and Uric acid)

Ammonia is toxic and must be either excreted rapidly or detoxified.
Ammonia is highly soluble in water and diffuses rapidly. So, in fish,
ammonia can diffuse in to the blood and then be lost to the water
environment by continuous diffusion across the gill membranes.

Because mammals are tidal breathers, the ammonia in their blood have to
be lost by diffusion across alveolar membrane. So, mammals detoxify
ammonia by converting it into urea or uric acid.

17. Terrestrial animals—advantages of excreting uric acid as nitrogenous

waste
Most terrestrial animals have to conserve water.
The advantage of excreting uric acid is that it can be precipitated out of
solution in the excretory system, enabling the reabsorption, and therefore
conservation.

18. Afferent and efferent arterioles

Afferent: bring blood into glomerulus at high pressure to support filtration.
Efferent: carry the remaining blood from the glomerulus to the capillaries
serving the renal tubules, where secretion and reabsorption of solution
occurs.

19. Composition of blood and urine different

Because of the processes of selective active reabsorption and secretion
 by the rental tubules.

20. Water and desert rat different in structure

Desert rat- longer loops of Henle and therefore longer rental medulla.
The desert rat has evolved under selective pressure to conserver water.
Produce a more concentration urine.
The longer the loop of Henle, the greater the concentration gradient can
be created in the renal medulla, so the desert rat should have longer loops
of Henle.