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Chinchilla Notes
Chapter 1: Cells
Chapter Overview
This introductory chapter goes in-depth into the anatomy of a cell, starting with
how it is studied. You will then learn about organelles that form the protoplasm
and endomembrane system, which will lay the foundation of understanding future
systems of the human body.
1.1 Cytology
A branch of biology that involves the structure of animal and plant cells, using
microscopes and employing the technique of cell fractionation
Microscopes
Light Microscope Scanning Transmission
Electron Electron Microscope
Microscope
Mechanism Visible light → Electron beam Electron beam →
sample → glass → scan the very thin slice of
lenses, which surface of the sample to study its
refract light and sample to study internal ultra-
magnify image it structure
Quality Resolution Much higher resolution that does not
decreases as decrease as magnification increases
magnification until to a very large degree
increases
Key Words
Magnification: Ratio of image to
real size/size of image divided by
size of object
Resolution: Clarity of image
Note: Commonly used unit, (μm)
10−6 m – micrometre
• All basic chemical and physiological functions are carried out inside cells
• The cell activity refers to the activities of subcellular structures within it
Prokaryotic vs Eukaryotic
Prokaryotic Eukaryotic
Both have outside boundary including plasma membrane
Both carry out all functions of life
Both contain DNA
Contains DNA in ring form without Contains DNA with proteins as
protein chromatin
DNA is free in the cytoplasm DNA is enclosed within a nuclear
membrane
Mitochondria absent Mitochondria present
1.3 Organelles
This section will categorise organelles into those that constitute the protoplasm,
the endomembrane system and others.
1.3.1 Protoplasm
• Organelles: Cell surface membrane, Cytoplasm and Nucleus
1.3.1.1 Cytoplasm
• Cytoplasm refers to all cellular matter within the cell membrane excluding
the nucleus, while the cytosol refers to the parts of the cell not held by
organelles
• Thus, cytosol is a subset of cytoplasm
1.3.1.2 Nucleus
• Components: Nucleolus2, Nucleoplasm, Nuclear Envelope
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Cytosol – A water-based solution found within cells
2
Nucleolus – Plural: Nucleoli
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Chinchilla Notes
• Functions:
o Controls cell activities and chemical reactions like cell growth, division
and repair
o Contains most of the DNA, which contains information used by
ribosomes to make structural and secretory proteins, as well as
enzymes
Nuclear Envelope
• Functions:
o Regulates passage of molecules like
mRNA in and out of the nucleus
through nuclear pores
o Separates chemical reactions in
nucleus from those in cytoplasm
Nucleoplasm
• Structure: Jelly-like material where nucleotides and enzymes are dissolved
• Function: Contains nuclear lamina, protein fibres that support the nucleus
and determines its shape
Nucleolus
• Functions: Produces ribosome subunits by using rRNA and proteins which
in turn synthesize proteins
1.3.1.3 Cell Surface Membrane
• Components:
o Lipids → phospholipids and cholesterol
o Proteins → intrinsic and extrinsic
o Carbohydrates → glycolipids and glycoproteins3
• Functions: Partial permeability4 controls substances entering or leaving the
cell
o Non-polar5 and hydrophobic substances and gases can pass through
o Polar substances such as charged particles can pass through transport
proteins
3
Glycolipids and glycoproteins – Carbohydrates bonded to lipids and proteins respectively
4
Do not write semi-permeable
5
Polarity – for a molecule to have a difference in electronegativity (You will learn more in Chemistry)
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Chinchilla Notes
Phospholipids
• Structure: Glycerol6 head with 2 hydrocarbon tails (fatty acids7) and 1
phosphate group
o The glycerol is connected to the hydrocarbon tails and phosphate group
via ester linkage
o Hydrophilic head and hydrophobic tails → amphipathic8
*Memorise the chemical formula of the hydrophilic head and ester linkage
Fatty Acids
• Saturated Fatty Acids – all carbons in
hydrocarbon tail are connected by
single bonds
• Unsaturated Fatty Acids → one or more
double bonds between carbons in hydrocarbon tail, creating kinks
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Glycerol – An alcohol with 3 carbons and 3 hydroxyl groups
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Fatty Acid – A long carbon skeleton with a carboxyl group at the end
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Amphipathic – To have both hydrophobic and hydrophilic regions
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Chinchilla Notes
Cholesterol
• Structure:
o Comprised of a sterol and an
alcohol
o Has a carbon skeleton with four
fused rings
• Functions:
o Plays a role in maintaining fluidity of cell membrane
o Precursor from which other steroids are synthesized
Phospholipid Bilayer
Cholesterol and phospholipids collectively form the bulk of the cell-surface
membrane, the phospholipid bilayer
• Formation:
o Due to watery internal and external environments of the cell
o Phospholipids spontaneously align to form a double-layer membrane, with
polar ends on the outside and non-polar tails inside
• Features:
o Mixture of saturated and unsaturated fatty acids
▪ More unsaturated fatty acids 9 and shorter fatty acid tails increase
fluidity, allowing the membrane to function
o Contains cholesterol, which maintain fluidity
▪ Warm temperatures – cholesterol restrains movement of phospholipids
▪ Cool temperatures – cholesterol maintains fluidity by preventing tight
packing of phospholipids
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Recall how unsaturated fatty acids solidify at lower temperature than saturated fatty acids
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Chinchilla Notes
Membrane Proteins
Embedded and attached to the phospholipid bilayer are membrane proteins,
which perform various functions. They can be classified as extrinsic or intrinsic.
• Structure: A collage of different proteins embedded in the fluid matrix10 of
the phospholipid bilayer
• Functions:
o Hormone Binding Sites (E.g. Insulin Receptor)
o Immobilized Enzymes
o Channels (Passive Transport) and Pumps (Active Transport)
o Cell Adhesion (tight joints between groups of cells in tissues and organs)
o Cell Communication (e.g. Receptors for neurotransmitters)
Peripheral/Extrinsic Proteins
• Structure:
o Attached to inner or outer membrane surface, never flipping from one side
to the other
o Slide around membrane very quickly and sometimes collide
• Function:
o Maintain cell shape and cell motility11
• Examples:
o Enzymes that catalyse reactions in the cytoplasm
o Glycoproteins which stick out from the surface of the membrane like
antennae and play a role in cell recognition12
Integral/Intrinsic Proteins
• Structure:
o Transmembrane proteins 13 penetrate the hydrophobic core and
completely span the membrane
o Have hydrophobic regions comprised of stretches of nonpolar amino acids
coiled into a structure called alpha helices
• Function:
o Keep the membrane stable with weak hydrogen bonds
• Examples:
10
Fluid Matrix – Tissue between cells where specialized organelles are embedded
11
Motility – The ability to move independently
12
Some act as antigens, which activates production of antibodies if a virus is detected
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Transmembrane Proteins – Not all intrinsic proteins are transmembrane proteins
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Chinchilla Notes
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Carrier and Channel Proteins are elaborated on in Chapter 2
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Rich amounts in gonads and adrenal glands
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Rich amounts in liver cells
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Rich amounts in muscle cells
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Lumen – Inside space of a tubular structure
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E.g. Carrier Proteins
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E.g. Lysosomes
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E.g. Hormones and Enzymes
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Chinchilla Notes
1.3.2.4 Vesicles
• Structure: Tiny spherical spaces enclosed by a membrane
• Types:
o Secretory vesicle – from Golgi apparatus, contains material to be released
from cell
o Lysosome – found in Amoeba and human macrophages23 that fuse with,
break down, engulf and ingest large molecules at low pH during
phagocytosis
▪ Large molecules – worn-out organelles within cell produce molecules
to be recycled during autophagy24 or bacteria
22
Golgi Apparatus – Remember to capitalize Golgi
23
Macrophage – A type of White Blood Cell
24
Autophagy – A catabolic mechanism involving self-degradation of dysfunctional components
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Elaborated on in Year 4 Chapter 6 - Genetics
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Elaborated on in Chapter 2
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Chinchilla Notes
1.3.3.1 Vacuole
• Structure: Enclosed by a partially permeable membrane (tonoplast)
• Function: Stores water and food in animals, cell sap in plants
o Cell sap contains dissolved substances like sugars, mineral salts and
amino acids
In summary, here is a section on how organelles are organised within a cell, and
how cells are organised in an organism.
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Found in Chapter 6, Plant Nutrition
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Found in Chapter 7, Plant Transport
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Found in Chapter 9, Respiratory System
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Found in Year 4 Chapter 3, Mitosis
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Chinchilla Notes
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Chinchilla Notes
• As the size of an organism increases, the surface area to volume ratio decreases
• Cells cannot be too large as their volume increases faster than their surface
area, and the cell cannot transport nutrients in and wastes our fast enough
• Cells cannot be too small as the organelles will not be able to fit and function
correctly
Sample Questions
Q: Why is it better to use iodine to observe plant cells and methylene blue to
observe animal cells? [2]
A: Iodine can be used to stain plant cells as it binds to the starch granules in the
cytoplasm and nucleus. For animal cells, methylene blue stains the nucleic acids
as it binds well to DNA and RNA, as they have a negative charge. This allows
the nucleus to be clearly seen under the microscope.
Q: What are the differences between a cell wall and cell surface membrane of an
animal cell? [3]
A: Firstly, cell wall is made of cellulose while cell surface membrane is made of
phospholipid bilayer. Secondly, cell wall is fully permeable while cell surface
membrane is partially permeable. Finally, cell wall is rigid with a fixed shape
while cell surface membrane is flexible to change shape as needed.
Q: Why can the plant’s cell surface membrane not be observed under normal
conditions? [2]
A: The cell membrane is thin and transparent and is pressed against the interior
of the cell wall.
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Chinchilla Notes
5. Lysosomes containing the modified substances are pinched off the Golgi
apparatus
6. The lysosome fuses with a phagosome (phagocytic vesicle) where microbes
are broken down at low pH
7. Digestive enzymes in the lysosome digest the microbes and the products are
absorbed by the cell
Q: Explain with examples how the inability of animals to synthesize organic food
results in the need for two tissues unique to animals. [2]
A: Firstly, intestinal epithelium is required to enable motility and coordinated
digestive and absorptive functions in the digestive system. Secondly, glandular
tissues in the epithelium of the stomach and small intestines secrete enzymes for
digesting food.
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Chinchilla Notes
Chapter 2: Transport
Chapter Overview
This chapter covers how different substances rely on different ways to be
transported, such as through diffusion, osmosis, active transport and facilitated
diffusion. The link to Chapter 1 lies in the description of channel and carrier
proteins, as well as the process of exocytosis, which is part of the endomembrane
system.
2.1 Diffusion
• Definition: Diffusion is the passive net movement of molecules or ions from
a region of higher concentration to a region of lower concentration, down the
concentration gradient
• Factors increasing rate of diffusion
o Smaller particles
o Thinner membranes and shorter distance between two regions → shorter
diffusion pathway
o Larger surface area
o Higher temperature → particles have more kinetic energy
o Higher solution concentration → steeper concentration gradient
2.2 Osmosis
Osmosis is a subset of diffusion that only involves movement of water molecules
• Definition: Osmosis is the passive net movement of water molecules from a
region of higher water potential to a region of lower water potential across a
partially-permeable membrane
• In U tube experiment, the side with initially higher concentration of sugar
eventually has a higher level than the other side, as water molecules pass down
concentration gradient
from the lower
concentration of sugar to
the higher concentration,
while the larger sugar
molecules cannot pass
through the pores in the
partially-permeable
membrane
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Chinchilla Notes
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The pressure exerted by the inelastic cell wall to prevent the cell from over-expanding is called turgor
pressure, which prevents further entry of water
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Chinchilla Notes
*Learn how to draw diagrams of the effects of different tonicities on plant and animal cells
Sometimes, molecules need a little help from carrier and channel proteins to pass
through membranes like the phospholipid bilayer. They can be seen as boats that
shuttle these molecules across an uncrossable river.
• Definition: The spontaneous passage of molecules and ions, bound to specific
carrier proteins across a biological membrane down the concentration
gradient
• Involves large (e.g. amino acids, sugar), polar (e.g. water) or strongly
charged molecules (Na+, Ca2+, K+ which cannot dissolve in phospholipid
bilayer
2.3.1 Channel Proteins
• Function: Open up pores along the membrane to allow entry or exit of
substances and are lined with polar groups which allow charged ions to pass
through
o Channel proteins are specific to only one type of ion
2.3.2 Carrier Proteins
• Function: Allow diffusion of larger polar molecules like sugars and amino
acids across the partially permeable membrane
o A molecule attaches to the carrier protein at its binding site, causing the
carrier protein to change shape, allowing the molecule to pass through the
membrane
There are two types of carrier proteins, simply distinguished by what triggers the
conformational change in the protein.
• In Facilitated Diffusion: Substrate attachment brings about conformational
change in protein
• In Active Transport: ATP32 brings about the conformational change in the
protein
2.4 Active Transport
• Definition: The movement of materials through a plasma membrane against a
concentration gradient, with energy from ATP molecules
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Adenosine Triphosphate (ATP) – an important source of energy in organisms
16
Chinchilla Notes
• Found in cells that have many mitochondria or have a high rate of respiration
• Factors:
o Temperature
o Oxygen concentration
o Presence of poisons such as cyanide
• Involved in:
o Absorption of amino acids in the small intestine
o Absorption of mineral salts by plant roots
o Excretion of urea by the kidney
2.5 Summary
Passive vs Facilitated Diffusion
Passive Diffusion Facilitated Diffusion
Reach equilibrium when concentrations are equal
Do not require energy from ATP
Can occur in either direction Faster in one direction
Rate depends on conc. gradient, similar Specific molecules diffuse
molecules diffuse at similar rate faster
Overall Comparsion
Diffusion Osmosis Facilitated Diffusion Active Transport
Passive processes – no respiratory energy is required Requires ATP
Involve movement of substances down concentration Against conc.
gradient gradient
Refers to any Refers only Refers to large or Refers to molecules
substance to water as strongly charged that need to be
regardless of solvent molecules that cannot transported against
state molecules dissolve in the the concentration
phospholipid bilayer gradient
- Requires p.p. Requires channel or Requires ATP and
membrane carrier proteins carrier protein
2.6 Endocytosis and Exocytosis
Sometimes, larger amounts of substances need to be taken up or released by cells,
resulting in the need for endocytosis and exocytosis.
• Definition: Exocytosis and endocytosis Active processes where the cell can
transport large quantities of material, into (endocytosis) or out of (exocytosis)
the cell with ATP
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Chinchilla Notes
2.6.1 Endocytosis
• Process - Cellular uptake of macromolecules and participate substances by
localised regions of plasma membrane the surround the substance and pinch
off to form an intracellular vesicle
• Examples of Endocytosis
o Phagocytosis (E.g. Macrophages and bacteria)33
o Pinocytosis (E.g. Uptake of nutrients by egg cells from follicles)34
o Receptor-Mediated Endocytosis (E.g. Cholesterol and iron bound to RBC)
- vesicles form from regions of cell membrane that contain specific
receptor molecules, which bind with specific target molecules called
ligands
2.6.2 Exocytosis
• Process – Recap to Chapter 1
• Examples of Exocytosis
o Secretion of insulin from Islets of Langerhans/glandular tissues in
Pancreatic Cells35
33
Recap to Chapter 1 in lysosomes
34
The same process as phagocytosis, but referring to liquids instead of solids
35
Elaborated in Chapter 5
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Chinchilla Notes
Chapter 3: Nutrients
Chapter Overview
This chapter describes the substances that allow organisms to carry out all
functions of life. You will learn about carbohydrates, fats, proteins and water, as
well as some ways to test for the presence these substances experimentally.
Plants Animals
Transport Mineral salts from roots to
Digested products from
leaves via xylem, food ileum36 to rest of body,
substances from leaves to rest
excretory products from cells
of plant to kidneys and hormones from
glands to body
Required Chemical reactions (as a Respiration38,
For medium), respiration, digestion photosynthesis39
(provides energy via
hydrolysis37)
Component Sweat (regulates body temp.), Cell sap – provides turgidity
In protoplasm, joint lubrication, for plant cells which keeps
tissue fluid and blood plant upright
3.2.2 Structural Features of Water
• Polar Covalent bonding – Electrons are shared unequally due to
electronegativity difference between oxygen and hydrogen
o Relevance – universal solvent for polar substances40
36
Ileum – A section of the small intestine, elaborated in Chapter 5
37
Covered later in the chapter
38
To be elaborated in Chapter 9
39
To be elaborated in Chapter 6
40
Polar substances include water and sugars, while non-polar substances include halogens and oils. Some
amino acids are polar while others are non-polar
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Chinchilla Notes
3.3 Macromolecules
Macromolecules constitute the majority of nutrient groups found in organisms.
In this segment, we will look at carbohydrates, proteins and lipids 42 and find out
how to test their presence.
• Macromolecules include carbohydrates, proteins and nucleic acids
• Macromolecules are also called polymers and consist of covalently bonded
monomers
Here are two reactions that involve the synthesis and breakdown of polymers,
summarizing those involving the macromolecules covered.
41
Important in transport of water in plants – Elaborated in Chapter 8
42
While lipids share many traits as polymers, their classification as polymers is debated. For simplicity, I
include them under macromolecules
43
Elaborated in Chapter 5
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Chinchilla Notes
3.3.1 Carbohydrates
*At minimum, note the shapes of the various monosaccharides pictured above
44
All three of the monosaccharides have the same chemical formula, just a different arrangement of atoms
45
Starch – long, straight chains of glucose molecules with only a few branches, stores energy in plant cells
46
Glycogen – highly branched, comprised of glucose molecules, stores carbohydrates in animals
47
Cellulose – straight chain of glucose molecules, structural carbohydrate in plant cell walls
48
Chitin – contains glucose molecules, component in exoskeletons of animals
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Chinchilla Notes
Observation Conclusion
Negative Yellowish-brown coloration Absent
Positive Blue-black coloration Present
Observation Conclusion
Negative Remains blue on heating Absent
Positive Green precipitate formed on heating Present in small
amount
Positive Yellow precipitate formed on heating Present in moderate
amount
Positive Orange-red precipitate formed on heating Present in large
amount
3.3.1 Lipids
• Lipids do not form polymers and are hydrophobic as they are non-polar
• Functions: Efficient source of energy, breaking down 1g of fats releases 32 kJ
of energy
o Insulating material beneath skin that prevents excessive heat loss
o Insolubility with water helps to reduce water loss from skin surfaces when
oils are secreted from glands in skin
o Component in cell membranes and hormones
o Solvent for fat-soluble vitamins like A, D, E, K
o Cushions organs
• Chemical Structure: Carbon, hydrogen, oxygen
• E.g. Steroids, phospholipids50 and triglycerides51
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Chinchilla Notes
Observation Conclusion
Negative Clear mixture obtained in ethanol Absent
Mixture remains clear when water is added
Positive Clear mixture obtained in ethanol Present
Mixture becomes cloudy white emulsion when water
is added and shaken
3.3.3 Proteins
• Functions: Essential for growth and repair of worn-out body cells
o Synthesizes enzymes and hormones
o Forms antibodies produced by white blood cells
o Maintains fluid and pH balance52
• Chemical Structure: Carbon, hydrogen, oxygen and nitrogen, sometimes
sulphur (differentiated by an R group)
o Peptide bonds between amino acids
• Deficiency Symptom – kwashiorkor – swollen stomach, cracked and scaly
skin
52
Proteins should not be broken down for energy as it is extremely inefficient
53
One component in heme groups is iron ions
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Chinchilla Notes
This section will differentiate between two ways in which proteins are broken
down – denaturation and hydrolysis54.
Denaturation
• Proteins can be denatured by heat, chemicals of unsuitable pH by breaking the
weak bonds linking the coils together
• Once this is done, the protein loses its 3D shape, involving the loss of the
function of the protein. This is usually irreversible55
Application of Hydrolysis
• To be absorbed by the body, proteins must be digested into polypeptides then
into amino acids by hydrolysis, as proteins molecules are too large to pass
through living cell surface membranes (Refer to Chapter 5)
• The resulting amino acids are simpler, smaller and soluble in water,
allowing them to diffuse through living membranes via facilitated diffusion to
be absorbed
• Once inside the cell, the amino acids can be linked up again to form proteins
within the cell
*Hydrolysis is NOT denaturation, as denaturation only involves a conformational
change while hydrolysis involves breaking down a substance into simpler forms
Observation Conclusion
Negative Mixture remains blue Absent
Positive Violet coloration observed Present
Note: For food tests involving solid samples, first prepare by masking, mixing
with distilled water, shaking, filtering and decanting, using the filtrate for the test
54
Hydrolysis is NOT denaturation, as denaturation only involves a conformational change in shape while
hydrolysis involves breaking down a substance into simpler forms
55
Elaborated on in Chapter 4
24
Chinchilla Notes
Chapter 4: Enzymes
Chapter Overview
Last chapter, we learnt about proteins. In this chapter, we learn about a special
type of protein, called enzymes, which were also cited to be involved in
hydrolytic and condensation reactions in Chapter 3. They will continue to be
prevalent, especially in Chapter 5, the Human Digestive System.
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Activation energy – the energy required for a reaction to occur
57
Free energy – the thermodynamic energy available for substances to do work
25
Chinchilla Notes
• When not all enzymes have a substrate tor react with, the substrate becomes
the limiting factor and the rate of reaction levels off
*Learn how to draw the induced fit and lock and key hypothesis
Condition Effect
Template Answer: Condition → ___ energy → enzyme and substrate
molecules collide ___ → ___ substrates bind to enzyme’s active site → ___
rate of r.
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Saturated – When all enzymes are occupied by substrate molecules
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Chinchilla Notes
Note: Optimal temperature is about 37℃, rate of reaction is doubled for every
rise of 10oC until the optimum temperature is reached. Enzymes are more
sensitive to pH than temperature. pH denaturation is reversible within a range.
59
Optimal pH Range varies from enzyme to enzyme. E.g. Salivary amylase has a neutral optimal pH range in
the mouth, while pepsin has an acidic optimal pH range in the stomach
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Chinchilla Notes
Sample Questions
Q: It has been found that fresh pineapple contains and enzyme that can be used
to make meat more tender. Explain why the pineapple should be placed on the
meat a few hours before, rather than during cooking. Also suggest how the
enzyme tenderises the meat. [4]
A: The protease found in the pineapple would have the active site altered and
denatured at high temperature, rendering it unable to break down proteins in the
meat for a tenderising effect. This also provides sufficient time for enzymes in
the pineapple to digest the meat proteins into smaller polypeptides. The enzyme,
protease, allows the large and insoluble proteins in the meat to bind to its active
site, forming an enzyme substrate complex and allowing the enzyme to process
the proteins and break down the polypeptide chains in the meat into small and
soluble amino acids, making the meat more tender and easier to chew.
Q: Can protease be used to wash a silk shirt? Why?
A: No. Silk is made of animal proteins which will be broken down by the protease.
Hence, silk shirts are usually dry cleaned.
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Chinchilla Notes
Chapter Overview
This is the first organ system you come across in the Upper Secondary Syllabus
and focuses heavily on the role of enzymes. In this chapter, you will learn the
various organs that constitute this system, their roles and how they work together
to break down the food we eat.
5.2.1 Mouth
Roles Ingestion, Secretion, Digestion
Anatomy pH 7, Teeth, Salivary Glands, Tongue, Epiglottis, Saliva
Mechanical • Teeth break up food by chewing, cutting and grinding food
Digestion into smaller pieces, creating higher SA:V ratio for salivary
amylase and mucin to act on
• Tongue pushes bolus60 to back to mouth for swallowing into
the oesophagus via the pharynx
• Epiglottis is a flap that prevents food from entering windpipe
60
Bolus – a ball of partially digested food
29
Chinchilla Notes
5.2.3 Stomach
Roles Secretion, Digestion
AnatomypH 2, Distensible muscular bag, smooth muscles, gastric glands,
gastric juice, pyloric sphincter
Mechanical • Smooth muscles chyme62, grinding food with digestive juices
Digestion and breaking down food into smaller pieces
Chemical • Pepsin in gastric juice – Proteins → polypeptides
Digestion • Renin in gastric juice – Soluble caseinogen → insoluble
(Enzymes) casein63 (curdling)
Other • Gastric juice also contains hydrochloric acid, which provides
Functions slightly acidic medium suitable for renin and pepsin
and Info
61
Peristalsis is not just seen in the oesophagus, but in the small and large intestines as well
62
Chyme – The liquefied acidic mixture of food in the stomach
63
Allows pepsin to act on milk proteins
30
Chinchilla Notes
64
Renin and pepsin are stored in inactive forms as they digest proteins, and could destroy the stomach lining
65
Recap to Chapter 3 for the monosaccharides that form disaccharides
31
Chinchilla Notes
66
To be elaborated in Chapter 8
32
Chinchilla Notes
5.2.5 Liver
The liver, along with salivary glands, pancreas and gall bladder, is considered an
accessory organ. The information under ‘assimilation’ is not just for the liver, but
for all nutrients absorbed, converting them into a form to be used by the body.
Roles Assimilation
Assimilation Glucose
• Excess converted to glycogen, stored in liver, converted
back into glucose when body needs energy and blood sugar
is low
• Further excess stored as fats in adipose tissue
• Used in cellular respiration
Fats
• Partially stored in adipose tissue
• Used in synthesis of cell membrane or stored under skin to
store energy and provide insulation
• Used in cellular respiration if glucose and glycogen is used
Amino Acids
• Used to synthesize proteins, enzymes and hormones for
growth and development
• Excess amino acids broken down and deaminated in liver to
form urea and glucose
Functions 1. Regulates blood glucose concentration67
67
Elaborated on in Chapter 11
33
Chinchilla Notes
2. Produces bile
3. Stores iron by breaking down haemoglobin from destroyed
RBCs to be stored as iron ions or used in bile pigments
4. Deaminates excess amino
acids, converting amino
groups into urea to be
excreted in urine
5. Synthesizes proteins (e.g.
albumins, globulins)
6. Regulates blood amino
acid levels in blood
7. Converts blood into
harmless substances (e.g.
ammonia to urea)
8. Produces cholesterol and
special proteins to transport fats around body
*Learn the chemical formula of amino acids and how its parts are broken
down
Sample Questions
A: 1. Liver deaminates excess amino acids and converts the carbon component
into glucose. 2. Liver synthesizes proteins like albumins to form amino acids. 3.
Liver converts excess glucose into glycogen and stores it.
Q: Why would the removal of the gall bladder lead to the inability to digest
food properly?
34
Chinchilla Notes
A: The gall bladder stores bile which emulsifies fats from large fat globules to
small fat droplets, increasing surface area to volume ratio for Pancreatic and
Intestinal lipase to act on. Without the gall bladder, there would be lower
surface area of fats for the lipase to act on, leading to incomplete digestion of
fats.
Q: Why are obsess people often treated by removing part of their small intestine
to lose weight?
A: Shortening the small intestine reduces digestion and absorption of fats into
the lymphatic vessels, helping the obese person to lose weight.
Q: How does the digestive system provide necessary conditions for digestion of
food?
A: The digestive system has specific pH to provide optimum condition for the
enzymes to function.
35
Chinchilla Notes
Chapter Overview
In this chapter, we will go into greater detail on the way plants make their own
food as autotrophs 68 , via photosynthesis. We will also cover the internal and
external features of plants that enable the plant to get the raw materials required
for photosynthesis.
6.1 Photosynthesis
Note that photosynthesis is split into two parts – the light dependent and the light
independent stage.
• Reaction: 12H2O + 6CO2 → C6H12O669 + 6H2O + 6O2 (with light energy and
chlorophyll)
o Light Dependent: 12H2O → 6O2 + 24H + ATP
o Light Independent: 6CO2 + 24H → C6H12O6 + 6H2O
6.1.1 Chloroplasts
• Structure:
o Double membrane outer chloroplast envelope
o Extensive system of internal membranes
called thylakoids70
o Stroma, a colourless fluid containing many
enzymes surrounding the grana71
*Learn how to draw. In diagram, draw grana as stacks of
horizontal lines. Include double membrane and stroma as well
68
Autotroph – an organism that can make its own food
69
C6H12O6 - glucose
70
Thylakoids – have an intense green colour due to chlorophyll.
71
Grana – Multiple stacks of thylakoids (1 stack – granum)
36
Chinchilla Notes
• Not very abundant due to low concentration in the air (0.03%) and is thus
often the limiting factor for photosynthesis
• Controlling variables:
o De-starch the plant by placing it in a dark room for 2 days
o Remove CO2 by using soda lime/potassium hydroxide
o Provide CO2 by using sodium hydrogen carbonate
• For iodine extraction, boil the leaf to disrupt the cell membrane and soften
the cuticle and cell wall, helping to make the cell more permeable to iodine.
• Putting the leaf in ethanol extracts the green chlorophyll and makes
coloration results more prominent
72
Not like animal species, but a chemistry term for substances composed of identical molecular entities, or
parts
37
Chinchilla Notes
• Used immediately by plant cells for cellular respiration and form cellulose
cell walls
• Excess is converted into sucrose and transported to storage organs as starch
or stored as starch in leaf for respiration at night
• Used to form proteins to synthesize new protoplasm, where glucose reacts
with nitrates to form amino acids in leaf → form proteins
• Used to form fats for storage to be used in the future for cellular respiration
and for synthesis of new protoplasm
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• Day: Stoma open to allow carbon dioxide to diffuse in, water and oxygen
diffuse out, allowing photosynthesis to occur
o Increase in potassium ion concentrations in guard cell by active transport
o Increase in glucose concentrations in guard cell by light-independent stage
of photosynthesis
o Water potential lowered, water diffuses into guard cells by osmosis
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o Guard cells become swollen and turgid; thicker inner cell wall of guard
cell cannot stretch while the thinner outer cell wall stretches and pulls
open to stoma
• Night: Stoma closed to reduce gases diffusing in and out of leaf/under hot
and dry conditions to prevent excessive loss of moisture
o No sunlight → no photosynthesis occurs → no glucose produced
o No high potassium ion concentrations by active transport into guard cells
→ no osmosis → water potential stays unchanged
o Guard cells remain flaccid; stoma remains closed
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Chapter Overview
In the previous chapter, we discussed how plants obtain nutrition through
photosynthesis. Plants also absorb water containing various minerals they need
to survive. This chapter will cover the various methods with which they transport
these nutrients, namely root pressure, capillary action and transpiration pull for
water and translocation for products of photosynthesis.
The transport of water in plants can be easily understood in three parts – entry
into the plants via the roots (root pressure), up the stem through the xylem
(capillary pressure) and leaving the plant through the stoma in the leaves
(transpiration pull)
Movement of Water
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to other regions of lower water potential – other inner cells, allowing the water
to enter the xylem vessels and up the plant
• Root cells that surround the xylem vessel actively pump ions into the xylem
vessels, lowering the water potential in the xylem and creating a water
potential gradient
• This allows water to enter the xylem by
osmosis, creating increased pressure which
pushes the water column upwards
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Structure of Phloem
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Source Organs – the sites of production or release of sugars (can also be storage organs during winter, not
just leaves)
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Water is drawn out of surrounding cells and into the sieve tube
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Phloem sap – the mixture of water and food materials
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Sink Organs – the sites of sugar delivery
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Cortex – a form of storage tissue
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Chapter Overview
Humans require a special transport system as more of substances like oxygen is
required to sustain life, compared to unicellular organisms that rely on passive
and slow processes like diffusion. In this chapter, we will cover the mechanism
of the human circulatory system. Note that all diagrams of heart are mirror image.
Misunderstanding will mess up this whole chapter!
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Single Circulation – E.g. Fish
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Double Circulation – E.g. Humans and other mammals
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Pericardium – A two-layered membrane with fluid to reduce friction acting on a beating heart
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Atrioventricular valves – Tricuspid valve on right, bicuspid valve on left
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Everting – Sort of like an umbrella in the wind
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Coronary Sinus – a collection of veins that open to the right atrium
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*The graph shape for left and right chambers are similar, just that pressure in
left side is higher for the systemic circuit
8.2.4.3 Regulation of Cardiac Cycle
• Sinoatrial (SA) node: Acts as pacemaker in the right atrium that sends out
electrical signals to initiate the contraction of both atria every cycle,
controlling the basic heart rate
o Influenced by nervous and non-nervous system, hormones (adrenaline
increases firing rate), body temperature and exercise
• Atrioventricular (AV) node: Upon receiving signal from SA node at right
atrium, 0.1 second delay to allow atria to empty completely then sends out
another electrical signal, initiating ventricular contraction
o The second electrical signal is conducted by heart apex and ventricular
walls by specialized muscle fibres
(bundle branches and Purkinje
fibres)
• E.g. Increased demand for oxygen
for cell respiration and for getting rid
of increased level of accumulated
carbon dioxide in blood stream
during exercise is chemically sensed
by the medulla, part of the brainstem
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o Medulla sends signal to cardiac nerve then SA node to increase heart rate
appropriately. After exercise, the level of carbon dioxide decreases
o Medulla sends signal to vagus nerve84 then SA node to decrease heart rate
to normal levels
8.3 Blood Vessels
Artery Capillary Vein
84
Cardiac and vagus nerves are cranial nerves, which mean that they transmit nerve signals directly to the
brain. You will learn more about them next year in the Nervous System
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Arteriole – small branches in arteries leading to capillaries
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Venule – small branches in veins leading out of capillaries
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Endothelium – a thin membrane that lines the heart and blood vessels
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8.4 Blood
Component88 Function Features
Plasma (55% Transports dissolved mineral Pale and yellow, 90% water,
of Blood) salts, soluble proteins, food 10% transported substances
and excretory products, gases
and hormones
Red Blood To carry 98% of oxygen (the To carry oxygen:
Cells/ rest is carried by plasma) • Circular, flattened,
Erythrocytes Made in bone marrow, has biconcave to increase
(5-6 lifespan of 3-4 months, SA:V ratio
• Contains haemoglobin89
3
million/mm ) destroyed by spleen and the
haemoglobin is broken down • No nucleus or
at the liver mitochondria to minimise
use of oxygen and
maximise space for
haemoglobin
• Can become elastic and
bell-shaped to squeeze
through capillaries
White Blood Short lifespan of several days, • Colourless, no
Cells (5000- produced by stem cells in haemoglobin, irregularly
3
10000/mm ) bone marrow shaped, has nucleus
To fight diseases (details on • Can change shape, move
types below) and squeeze through
capillary walls
Platelets Not true cells, lifespan of 6 • Membrane-bound
(250000- days fragments of cytoplasm
3
400000/mm ) Blood clotting (process below) from bone marrow cells
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Blood composition can be determined by using the centrifuge covered in Chapter 1
89
Haemoglobin – comprised of 4 protein globin chains centered around a heme group
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Chinchilla Notes
*To analyse blood type compatibility, only consider the effect of the
recipient’s plasms on the donor’s RBCs
For example, since type O has no antigens, it is compatible with all blood types,
as the antibodies will have nothing to react with. Thus, O is a universal donor
8.4.2 Types of White Blood Cells
Lymphocytes Phagocytes
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8.4.4 Immunisation
• Induces antibody production in human body by injecting dead or weakened
forms of a pathogen into bloodstream to become resistance against infections
• The immune system may also reject transplanted organs or tissues, destroyed
by lymphocytes. This can be prevented by using a genetic match, immune-
suppressive drugs for life or X-ray radiation on bone marrow and lymphatic
system
8.5 Summary of Circulatory System
Deoxygenated blood pours into right
atrium via vena cava → Enters right
atrium, right ventricle which contracts
and pumps cells through the pulmonary
artery to the lungs where diffusion of
oxygen in and carbon dioxide out
occurs → Oxygenated blood enters left
atrium through pulmonary vein, enters
left atrium and left ventricle →
Oxygenated blood is pumped to
different parts of body through aorta,
reaches organs via arteries and enters
capillaries, where dissolved food
substances and oxygen from blood diffuse into tissue fluid and metabolic waste
products and carbon dioxide diffuse from cells into tissue fluid, then blood →
deoxygenated blood carried by veins and vena cava back to right atrium and cycle
repeats
*Hepatic refers to the liver, renal refers to the kidney and pulmonary refers to the
lungs
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Fluid has different names depending on where it is found – fluid in blood is called plasma, fluid surrounding
cells is tissue fluid and fluid in the lymphatic system is called lymph
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Sample Questions
Q: Suggest how increasing the number of RBCs adapts a person to living at
4000 metres
A: At 4000 metres, the air pressure and conc. of atmospheric oxygen is lower.
The body cannot obtain sufficient oxygen to maintain its metabolic rate. Thus,
the body produces more RBCs to acclimatize to the lower concentration of
oxygen. This increase means more oxygen can now be transported to the tissue
cells / unit time
Q: Suggest how training at 4000 metres could improve athlete’s performance at
sea level
A: Training at 4000m will increase the number of red blood cells in their bodies
due to acclimatization. Back at sea level, with the increase in RBCs, the athlete
will be able to transport more oxygen to the muscle tissues per unit time. Thus,
with more oxygen molecules, more energy is released during aerobic respiration
for the athlete to perform.
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Chapter Overview
Transport of gases such as carbon dioxide and oxygen was a feature in the
previous chapter about the circulatory system. In this chapter, we look at how
these gases are inspired and expired by the human body, as well as an more
comprehensive view of how these gases are transported by blood.
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Yeast are both aerobes and anaerobes
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Ribs move upwards and outward; Ribs move downwards and inwards,
sternum moves up and forward sternum moves down to original
position
Volume in thoracic cavity increases Volume in thoracic cavity decreases
Air pressure in lungs causes it to Lungs compressed and decrease in
expand to fill up enlarged thorax, volume, causing air pressure to
causing air pressure to decrease increase
Atmospheric pressure is higher than Air pressure within lungs now higher
pressure within lungs, air enters lungs than atmospheric pressure, air forced
out
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Sample Questions
Q: What is the adaptive significance of hyperventilation?
A: Hyperventilation reduces the amount of carbon dioxide in the blood,
balancing the carbon dioxide and oxygen levels and maintaining constant pH in
the blood
Q: Essay - Suggest why sprinters get 80% of their energy from anaerobic
respiration and 20% from aerobic respiration, and vice versa for long distance
runners
A: Sprinters run for a short distance thus they need a lot of energy in a short period
of time but long-distance runners run for a long time and thus they need sustained
release of energy for a long period of time. Aerobic respiration is more efficient
and releases more energy compared to anaerobic respiration for the same amount
of glucose. However, there is a limit to the supply of oxygen that the body can
provide for aerobic respiration. When there is a lack of oxygen, but energy is still
required, the body switched to anaerobic respiration. During anaerobic respiration,
the body incurs an oxygen debt. When lactic acid concentrations build up in the
muscles, fatigue and muscular pains will result and the runner will not be able to
run anymore. The runner will need to rest to repay the oxygen debt and remove
lactic acid build-up in the body. For the case of the sprinter, he undergoes 80%
anaerobic respiration and 20% aerobic respiration as anaerobic respiration is able
to provide extra boost of energy to run as fast as he can during that short distance.
For the case of the long-distance runner, he undergoes 20% anaerobic respiration
and 80% aerobic respiration as he needs to minimize the production of lactic acid
by anaerobic respiration so he can continue to run for a long distance
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Chapter Overview
In this chapter, we will cover the human excretory system, and how different
waste products are eventually expelled in urine. In addition, we will also touch
on the dialysis machine, and describe how it can replicate several functions of the
excretory system to treat those with kidney failure.
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o Blood Vessels
▪ Renal artery branches into many arterioles → divides into mass of blood
capillaries called the glomerulus → leaves renal corpuscle and enters
kidney tubule → unites to form venules and leaves as the renal vein
o Renal/Malpighian corpuscle
▪ Glomerulus is surrounded by Bowman’s capsule and separated by the
partially permeable basement membrane
▪ Basement membrane that wraps around glomerular blood capillaries
and has small pores to filter water and small molecules
o Proximal convoluted tube
▪ Site of selective reabsorption
▪ Has many mitochondria to provide ATP
for active transport
▪ Microvilli to increase surface area for
reabsorption
o Others: Distal convoluted tube, loop of
Henle, collecting duct
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Divalent ion – an ion with charge of 2+
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Note: the inside of the dialysis is a very long coiled tubing, which gives sufficient
time for sufficient diffusion of toxins out of the blood and increases surface area
to volume ratio. The dialysis fluid flows in the opposite direction to the blood
flow to maintain concentration gradient for removal of waste products.
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Partially-permeable tubing to replace the function of the basement membrane
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Chinchilla Notes
Chapter Overview
The excretory system in the last chapter is one of the many ways the human body
maintains a relatively constant internal environment and keeps us alive. These
mechanisms fall under homeostasis, and includes control of variables from
temperature to blood water potential.
11.1 Introduction to Homeostasis
• Definition: Homeostasis is the maintenance of a relatively constant internal
environment within a narrow range in an organism despite significant
changes in external environment
o Aspects of this environment can include body temperature, body fluid
water potential, body fluid glucose levels and body fluid pH among others
• Mechanism: Negative feedback
o Definition: Negative feedback is a form of regulation in which
accumulation of an end product slows down the process and change in a
variable triggers a response that counteracts the initial change
• The general process of homeostasis is as follows:
o Stimulus (any change in factors stated above) → detected by receptor at the
site of the organ → signal sent to control centre (brain) → effector (cell that
responds to the stimulus) → automatic corrective mechanism → once the
optimal internal environment is achieved, negative feedback is sent to the
receptor to stop the mechanism
11.2 Response to Changes in Glucose Concentration
Rise in Glucose Conc. Fall in Glucose Conc.
Stimulus Blood glucose levels rises Blood glucose levels falls
above normal levels (e.g. after below normal levels (e.g. after
consuming starch/sugar) fasting or exercise)
Receptor Beta cells of Islets of Alpha cells of Islets of
and Langerhans in pancreas Langerhans in pancreas
Effector stimulated stimulated
Automatic Islets of Langerhans secretes Islets of Langerhans secretes
Corrective more insulin which is more glucagon, which is
Mechanism transported by blood and liver transported by blood and liver
muscles → permeability of muscles → glucagon
cell surface membrane to stimulates conversion of
glucose increases → liver and stored glycogen to glucose,
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o Granular layer consists of living cells that move upward from Malpighian
layer and become the cornified layer eventually
o Malpighian layer contains skin colour pigment and protects it from harmful
ultraviolet rays. It
continually divides to form
upper cell layers
• Arterioles are controlled by
nerves for vasodilation and
vasoconstriction95
• Hair follicles are hollow tubes
through the epidermis and
dermis and are controlled by
hair erector muscles which
contract to cause hair to stand and form goose bumps. It is provided with
nutrients and oxygen by hair papilla, as mass of tissue with blood capillaries
and nerves
• Sweat glands, tightly coiled tubes, are connected to the sweat pore via the
sweat duct and facilitate the removal of urea
Using these features of skin, the body can regulate heat gain and loss with the
aforementioned corrective mechanisms, along with the following:
• Heat Gain - Aerobic tissue respiration, distribution of heat via blood, eating,
shivering and exercising, conduction, convection and radiation96
• Heat Loss - Conduction, convection and radiation, faeces, urine, exhalation
of air
Sample Questions
Q: Explain the significance of maintaining core body temperature.
A: Excess heat must be removed from the body as one could die of overheating
or enzyme denaturation
Q: Why does heat production increase during exercise?
A: The body releases energy to supply muscle cells which undergo rapid
contractions and kick off metabolic processes. Aerobic and anaerobic respiration
is exothermic, and an increased rate of respiration to release more energy heats
up blood circulating through the muscles, increasing body core temperature
95
Only use the terms “vasodilation” and “vasoconstriction” for arterioles in skin
96
Conduction, convection and radiation – include them in all answers regarding heat change for homeostasis
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Chinchilla Notes
Diagrams to Draw
• Chapter 1
o Animal and Plant Cell
o Phospholipid Bilayer with Cholesterol, Unsaturated and Saturated Fatty
Acids
o Ester Linkage Chemical Structure
• Chapter 2
o Effect of Hypotonic and Hypertonic Solutions on Plant and Animal Cells
• Chapter 4
o Enzyme Lock and Key Hypothesis
o Enzyme Limiting Factors Graphs
• Chapter 5
o Deamination of Amino Acids
o Small Intestine Villi with Lacteal and Blood Vessels
o Peristalsis
• Chapter 6
o Photosynthesis Limiting Factors Graphs
o Chemical Equations for Light Dependent and Independent Reactions
o Leaf Cross Section
o Guard Cells and Chloroplast
• Chapter 7
o Dicotyledonous Root and Stem
• Chapter 8
o Identify Parts of Human Heart
o RBC and WBC
o Capillary, Vein, Artery Cross Section
• Chapter 9
o Aerobic and Anaerobic Equations
• Chapter 10
o Kidney
• Chapter 11
o Skin Structure
References
• Year 3 ACS Biology Slides
• Brent Cornell. (n.d.). Retrieved from https://ib.bioninja.com.au/
• Khan Academy. (n.d.). Retrieved from https://www.khanacademy.org/
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