BIOLOGY NOTES

Module 1

Gifty Varghese
 TABLE OF CONTENTS

TOPIC 1-1 CELL BASICS ......................................................................................................................... 2

TOPIC 1-2 OBSERVING CELLS ................................................................................................................ 4

TOPIC 1-3 DRAWING CELLS................................................................................................................... 5

TOPIC 1-4 CELL ORGANELLES ................................................................................................................ 5

TOPIC 1-5 THE FLUID MOSAIC MODEL .................................................................................................. 7

TOPIC 2-1 DIFFUSION AND OSMOSIS .................................................................................................... 8

TOPIC 2-2 CELL FUNCTION – ENDOCYTOSIS AND EXOCYTOSIS .............................................................. 9

TOPIC 2-3 SURFACE AREA TO VOLUME RATIO .............................................................................. 10

TOPIC 2-4 ENERGY AND MATTER REQUIREMENTS .............................................................................. 11

TOPIC 2-5 WASTE REMOVAL .............................................................................................................. 12

TOPIC 2-6 PHOTOSYNTHESIS AND RESPIRATION ................................................................................ 13

TOPIC 2-7 ENZYMES ........................................................................................................................... 15

TOPIC 2-8 ENZYME ACTIVITY .............................................................................................................. 16

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 INQUIRY QUESTION: WHAT DISTINGUISHES ONE CELL FROM ANOTHER?

TOPIC 1-1 CELL BASICS

examining a variety of prokaryotic and eukaryotic cells

Cell Theory states:

1. All living thing are made up of cells
2. The cell is the basic unit of structure and function in living things
3. All cells are produced from existing cells

BASIC STRUCTURES OF THE CELL

Classifying Cells

CHARACTERISTICS OF PROKARYOTES
¶ Dispersed freely
¶ Single, circular chromosome in the nucleoid
¶ Small circular pieces of double stranded DNA that floats in the plasmids
¶ Cell wall for protection from the environment, covered with a capsule
¶ Flagella, pili and fimbriae allow motility.
¶ Some pili can transfer genetic information

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 Bacteria
• Diverse metabolic systems
• Exists in moist, low-salt, moderate temperature environments with an abundance of organic material
• Obtain energy from processes such as photosynthesis or chemosynthesis
• Decomposers
• Used in industrial processes

Archaea
• Exists in extreme conditions
• Made of lipids, membrane is fluid and semi-permeable

Eukarya
Þ Unicellular Þ 4 kingdoms: Protista, Fungi, Plantae and
Þ Multicellular Animalia
Þ Reproduce sexually or asexually Þ All have: Nucleus, membrane bound organelles
and mitochondria

COMPARING PROKARYOTIC AND EUKARYOTIC CELLS

TOPIC 1-2 OBSERVING CELLS
Describe a range of technologies that are used to determine a cell's structure and function

Cytology: study of cells

MICROSCOPES

It's importance in the history of medicine and our understanding of disease should not be underestimated. It opened up an
entire spectrum of new knowledge and continue to be vital in science.

Simple Microscope: one lens

Compound Microscope: multiple lens (eyepiece and objective)
Magnification: change in apparent size

Light Microscope: uses light to magnify objects

Resolution: distinguishing between two objects that are very close in
distance

Note: Total magnification = ocular lens x objective lens

Electron Microscope: uses beams of electrons to magnify objects

gives more detail than light microscope, cells magnified are not living

Scanning Electron Microscope (SEM): Transmission Electron Microscope (TEM):

• electrons bounced off the sample coated in gold • passing beam of electrons through an ultrathin
• Outer structure in 3D section
• image is 2D

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TOPIC 1-3 DRAWING CELLS
Drawing scaled diagrams of a variety of cells

TOPIC 1-4 CELL ORGANELLES

Comparing and contrasting different cell organelles and arrangements
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TOPIC 1-5 THE FLUID MOSAIC MODEL
Modelling the structure and function of the fluid mosaic model of the cell membrane
Cell Membrane
ð Encloses the contents of the cells ð Maintains the environment inside the cell
ð Controls the movement of substances ð Recognises and communicates with other cells

Extracellular Fluid
¶ Cells draw in nutrients from the extracellular fluid to maintain their stability and function

Unicellular Organisms
• Fluid is the external environment hence they can't control it and will die if it changes significantly
Multicellular Organisms
• Fluid is within their body
• Possess a protective outer layer hence less affected by changes in the environment

THE FLUID MOSAIC MODEL

Proteins, carbohydrates and cholesterol floating in the bilayer (hence

fluid-mosaic)

MEMBRANE PERMEABILITY
Þ Hydrophobic layer prevents water soluble molecules from passing
Þ Proteins however, act as a passage to allow some (not all) from passing
= selective permeability

Permeability: the state or quality of a material or membrane that causes it to allow liquids or gases to pass through it.

Low permeability: High Permeability:

Charged Particles Non-charged Particles
Large Particles Small Particles
Water Soluble Lipid Soluble
Oxygen, Carbon Dioxide, Water

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 INQUIRY QUESTION: HOW DO CELLS COORDINATE ACTIVITIES WITHIN THEIR INTERNAL E
ENVIRONMENT AND THE EXTERNAL ENVIRONMENT?

TOPIC 2-1 DIFFUSION AND OSMOSIS

Conducting a practical investigation modelling diffusion and osmosis

DIFFUSION
Diffusion: the intermingling of substances by the natural movement of their particles
• Particle movement from an area of low concentration to high concentration
• Slow process
• Particles move across concentration gradient: does not require energy

OSMOSIS
Osmosis: a process by which molecules of a solvent pass through a semi-permeable membrane from a less concentrated
solution into a more concentrated one.

• Net diffusion of water molecules across a semi-permeable membrane

• Molecules move across the membrane until the concentration of water molecules is the same on both sides

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TOPIC 2-2 CELL FUNCTION – ENDOCYTOSIS AND EXOCYTOSIS
examining the roles of active transport, endocytosis and exocytosis

ACTIVE AND FACILITATED TRANSPORT

• Diffusion and osmosis are examples of passive transport because they do not require the input of
energy to occur
• Active transport involves the cell using energy to move particles across membranes

COMPARING FACILITATED DIFFUSION AND ACTIVE TRANSPORT

Cells also expend energy to move larger quantities of fluids or large molecules across their membranes:
• endocytosis: taking in membrane bound ‘packets’ of molecules
• exocytosis: expelling membrane bound ‘packets’ of molecules

ENDOCYTOSIS

ENDOCYTOSIS CAN OCCUR IN 3 WAYS:

• PHAGOCYTOSIS: taking in solid material using extensions
of the cell membrane
• PINOCYTOSIS: taking in dissolved material by engulfment
• RECEPTOR-MEDIATED ENDOCYTOSIS: pinocytosis
that uses protein molecules embedded in the cell membrane to
recognise and take in specific substances

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 EXOCYTOSIS

A membrane-bound vesicle containing secretory proteins or

waste material can fuse with the cell membrane, releasing its
contents into the environment; this is called exocytosis. the
membrane of the vesicle becomes part of the cell membrane; the
cell membrane is constantly being recycled by both exo and
endocytosis.

Topic 2-3 SURFACE AREA TO VOLUME RATIO

relating the exchange of materials across membranes to the surface-area-to-volume ratio,
concentration gradients and characteristics of the materials being exchanged

Substances that enter cells must travel from the outside environment across the surface of the cell and then diffuse
inwards until they reach the centre of the cell.
• If a cell has a large volume, the organelles in the centre of the cell are further from the outside

SA : V Ratio: calculated by dividing the total surface area of the shape by its total volume

WAYS OF INCREASING SA:V RATIO

! CELL COMPARTMENTALISATION
It allows cells to have separate areas with the right conditions for various cellular reactions, this allows eukaryotes to be
bigger as it
- Reduces the amount of exchange that has to happen across cell membrane; the exchange happens
across the membranes of the organelles instead
- Increases the total area of membranes in the cells overall; allowing room for more transport proteins or
membrane-embedded enzymes

! FLATTENED SHAPE
As a cell increases in volume, the distance between the centre to the membrane of the cell increases.
The flattened shape results in a:
- Greater surface area for the same volume but a shorter distance from centre to membrane

! CELL MEMBRANE EXTENSIONS

Extensions is effective if the cell only requires a large surface area in a specific region; examples include:
- Microvilli in the internal wall of the intestines and Root Hairs in the root cells of plants that increase the
absorption of water via diffusion

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TOPIC 2-4 ENERGY AND MATTER REQUIREMENTS
suitable forms of energy, including light energy and chemical energy in complex molecules
matter, including gases, simple nutrients and ions

ENERGY REQUIREMENTS
Organisms can be divided into groups depending on the way they obtain their energy needs:

MATTER REQUIREMENTS
Cells require matter in order to grow and reproduce including:
Inorganic Compounds:
- Simple molecules without carbon atoms
- Cells need these compounds to synthesis the complex molecules they need to
function and survive.
- Typically sourced from the environment

Water: transport medium in cells, most cellular processes take place in watery environments. Also, a reactant
Oxygen: produce energy such as cellular respiration
Carbon Dioxide: all organic compounds in cells are ultimately made with Carbon Dioxide. Enters through photosynthesis by
plants.
Nitrogen: essential part of proteins and nuclei acids. Enters food chain through nitrates which are taken up by plants; the
nitrogen cycle.
Minerals: required for the structure and function of organisms, e.g. calcium for bones.

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Organic Compounds:
- Complex molecules that contain carbon and hydrogen
- They make up the structure of the cell or take part in cellular processes

• Carbohydrates: energy source and structural component, e.g. glucose

• Lipids: Major component of cell membranes, energy storage in the form of fats and oils
• Proteins: Polymers of amino acids with specific structures with important functions including, enzymes,
hormones, carrier proteins in membranes and antibodies.
• Nucleic Acids: Carries genetic information as well as instructions for making proteins

Structural organic molecules such as coenzymes, cofactors and vitamins bind to proteins for proper function. Lipid soluble
molecules can be manufactured or stored by the body. Water soluble ones cannot be stored and so have to be obtained by
the organism’s diet.

TOPIC 2-5 WASTE REMOVAL

removal of wastes

Excretion: removal of substance that once formed part of an organism’s body, occurs largely in the kidney
Egestion: removal of undigested food from gut via anus

By-products of cellular processes must be removed as they can affect normal functioning:
- Carbon Dioxide: build up cause acidity
- Water: regulated to ensure the right concentration of solutes and adequate pressure
- Nitrogenous Waste: e.g. ammonia is toxic

For Unicellular organisms – wastes diffuse out of the cell into the environment (passive removal)
For Multicellular organisms – passive removal is too slow due to organism’s SA:V ratio and requires active transport and
sometimes a chemical change to waste product.

Autotrophs
Plants produce wastes called by-products that can be used by other organisms
- CO2 and H2O are released via stomates in the leaves
- Nitrogen is stored in the plant until death
- Plants in high salt areas need to excrete salt to maintain osmotic balance e.g. mangrove plants
- Aquatic plants release wastes directly into the water

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 Heterotrophs
Produce wastes from breaking down carbohydrates, lipids, proteins and nucleic acids. These wastes cannot be used by the
body and can be toxic.
- CO2 dissolves into blood, then goes to lungs or gills and released through exhalation
- H2O is regulated by the kidneys and removed via the bladder
- Nitrogenous Wastes created by the liver, regulated by the kidneys and removed via the bladder

TOPIC 2-6 PHOTOSYNTHESIS AND RESPIRATION

investigate the biochemical processes of photosynthesis, cell respiration and the removal of
cellular products and wastes in eukaryotic cells

PHOTOSYNTHESIS
It is the initial pathway by which energy enters the ecosystems. It
converts inorganic carbon to organic carbon.

STAGES
1. Light Dependent phase
• Occurs in sunlight; splits water into hydrogen and oxygen gas to produce ATP
2. Light Independent phase
• Can occur in the dark; uses ATP to combine hydrogen and carbon dioxide to produce glucose

STRUCTURES FOR TRANSPORT OF MATERIALS

Stomates
- Open and close to allow gas exchange, close to prevent the leaf from drying out
- Usually located on the underside of leaves; regulated by solute concentration in guard cells
Root Hairs
- Large surface area to absorb water from the soil
Xylem
- Dead tissue located on the inside of stems that draws water and minerals upwards to the leaves by capillary
action
Phloem
- Living tissue located outside the stem transporting water and nutrients upwards and downwards

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 CHLOROPLAST STRUCTURE LEAF STRUCTURE

CELLULAR RESPIRATION
A chemical reaction that occurs in living cells; uses glucose and
oxygen to produce usable energy, with Carbon Dioxide formed as
waste

- Energy is held in glucose bonds, when broken, energy is released carried by ATP

o ATP: Adenosine triphosphate

o Stores chemical energy
o When energy is available ADP collects it
o When energy is required ATP supplies it

AEROBIC RESPIRATION
1. Glycolysis
• Splits glucose into Pyruvate

2. Kerb’s Cycle
• Uses Pyruvate to charge up the batteries NADH and FADH2

3. Electron Transport Chain

• Uses power from the batteries to pump protons out past the mitochondrial membrane

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TOPIC 2-7 ENZYMES
conduct a practical investigation to model the action of enzymes in cells

Many chemical reactions occur too slowly on their own to keep us alive. Hence, enzymes are used to control chemical
reactions and speed it up without requiring heat (heat can damage live tissue). Enzymes are made with Ribosomes within the
cell.

Terminology:
Catalyst: any substance that speeds up a chemical reaction but remains unchanged
at the end of the reaction.

Enzyme: a large molecule made up of one or more folded up protein chains plus a
non-protein part called co-factor (inorganic- Mg, Fe) or co-enzyme (organic-
vitamins). Enzymes are produced by living things and speeds up chemical reactions
that take place in the body; thus, known as biological catalysts.

Substrate: A molecule upon which an enzyme acts; the enzyme either breaks down
(catabolic) the substrate into simpler substances or joins (anabolic) the substrate to other molecules.

ENZYME SPECIFICITY
The folded shape of the enzyme is essential as it creates an active site.
The active site physically fits the shape of the substrate; this means other molecules will not be able to fit in the enzyme so
it will not be affected.
This is called enzyme specificity as enzymes only act on the specific substrate(s) that fits.
When an enzyme and substrate fit together, it is called an enzyme-substrate complex.

CATALYTIC ACTIVITY
Enzymes are catalysts; they can be reused. This means that only a small amount of enzyme is needed for a chemical
reaction to occur quickly.

Activation Energy: the minimum amount of energy that reactant molecules must possess in order to form products.
Enzymes lower the activation energy needed to start a reaction.

ENZYME-SUBSTRATE INTERACTION MODELS

Lock and Key Model: enzyme = lock; substrate = key
The substrate and enzyme must fit together exactly, or the reaction will not take
place (less accurate).
Induced Fit Model: enzyme’s active site will change shape once the substrate binds to
it. It’s flexible and changes shape to fit substrate exactly (more accurate).

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TOPIC 2-8 ENZYME ACTIVITY
investigate the effects of the environment on enzyme activity through the collection of primary
or secondary data

! Enzymes need good working conditions

Enzymes regulate biochemical reaction; they control metabolism through the catalysis at every step of a biochemical
pathway.
They depend on the right conditions to work properly:
- pH
- Temperature
- Enzyme and Substrate Concentration

ENZYMES AND PH

• Enzymes depend on the active sites being able to fit the substrate they act on; it is formed through the folds in
the protein
• Most enzymes are only folded correctly in a small pH range
• Drastic changes in pH can cause the enzyme to become folded incorrectly and thus be unable to accommodate its
substrate and so no reaction occurs.

ENZYMES AND TEMPERATURE

• Increasing the temperature of a chemical reaction tend to speed up the reaction.

• However, in enzyme-substrate reactions, high temperatures may cause the enzyme to denature

Denaturation: loss of the 3D structure of the protein and is usually irreversible. The enzyme changes its active site, and so
will permanently not be able to fit the substrate and form a reaction.

• Reducing the temperature tends to slow down a

chemical reaction as the reactant particles slow down
• In enzyme-substrate reactions, the 3D structure of the
enzyme become less flexible and thus cannot change its
shape and so will not fit the substrate to form a
reaction

This process does not disrupt the chemical bonds and so heating
it up to optimum temperature will cause a reverse to occur and it
will continue to work.

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 ENZYMES AND SUBSTRATE CONCENTRATION

Concentration: measure of how many particles of a

substance there are in a given volume

• If concentration of an enzyme is high compared to substrate; the reaction will occur quickly as there are many
active sites available to act on the substrate
• If the concentration of enzyme is low compared to substrate; the reaction proceed more slowly as there are
limited active sites available to act on the substrate

o Enzyme activity can be changed by molecules that inhibit or bind to the active site, preventing the substrate from
binding; thus, stops the enzyme from working.

Competitive inhibitors: binds directly to the active site and blocks the substrate from binding

Non-Competitive inhibitors: binds to another part of the enzyme but changes the shape of the active site

Feedback inhibitors: the product of the biochemical pathway is the inhibitor of the enzyme; as the amount builds up, it begins
to bind to the enzyme stopping its activity

As a result, products stop binding to the enzyme and is removed, which then increases the enzyme activity

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