Yr 11 Biology notes Module 1-

Cells as the basis of life

Cell varieties
Metalanguage-

 Cells- basic structural unit of all living things

 Prokaryotic- unicellular cells with organelles that are not membrane bound
 Eukaryotic- unicellular or multicellular that contain membrane-bound organelles
 Organelles- subcellular fluid structures that have specific functions within the cell
Common cell structures-

 Cell membrane- separates the interior of the cell from the outside environment
 Zygote- first ever cell
 Cytoplasm- consists of cytosol which is made up of water and contains ions, salts and organic
molecules
 DNA- carries hereditary information, directs the cell’s activities, and is passed from parent to
offspring
 Ribosomes- organelles responsible for the synthesis of proteins

a) plant cell
b) animal cell
c) bacterial cell

Types of plant cells

 - Root hair
- Epidermal cell
- Phloem cell
- Xylem cell
Types of animal cells-
- Red blood cells
- White blood cells
- Nerve cells
- Muscle cells

Prokaryotic- Usually unicellular and are overall smaller and less complex compared to eukaryotic
cells. This provides cells with a large surface area relative to the volume allowing for efficient uptake
and release of materials and quick replication

- Organelles are not membrane bound

- Divided into two domains- bacteria and archaea
- DNA is in circular shape and contain plasmids
- Smaller
- Cell size 0.1-0.5 micrometres
- Unicellular
- E.g., cyanobacteria

Bacteria-

 Microscopic, single celled organisms

 Diverse metabolic systems- can obtain energy from sunlight (photosynthesis) or by reducing
inorganic compounds (chemosynthesis)
 Cell walls are made up of peptidoglycan
 Gram positive- thick layer- purple, e.g., Staphylococcus
 Gram negative- thin layer- pink, e.g., cyanobacterium
Archaea-

 Microscopic, single celled organisms

 Includes extremophiles which can live in extreme conditions e.g., high temperatures
 Methanogenesis is unique to archaea
 Cell membrane is composed mainly of lipids which can form a structure that remains fluid
and selectively permeable over a wide range of temperatures
Eukaryotic- Cells are much large than prokaryotic. Organisms can be unicellular and multicellular,
and cane reproduce sexually and asexually.

- Eukaryotic cells have a cell (plasma) membrane that surrounds the cell’s cytoplasm
and internal (non-plasma) membranes that form specialised compartments (cell
compartmentalisation)
- Membrane bound structures are called organelles
- Nucleus is present
- DNA is in a linear shape and is found in the nucleus
- Larger by up to 10 times
- Cell size 10-100 micrometres
- Unicellular and multicellular
- E.g., humans

Compartmentalisation-
Benefits-

 Allowing enzymes and reactants for a particular cellular function to be close together in high
concentrations and at the right conditions
 Allows processes that require different environments to occur at the same time in the same
cell
 Makes the cell less vulnerable to changes in its external environment
Cell theory-
Cells prokaryotic and eukaryotic
Pro- bacteria and archaea
Eukaryotes- plant, animal, fungi, and Protista
Organelles-
Nucleus-

 Surrounded by a double-layered nuclear membrane

 Contains most of the genetic material, which is formed in linear chromosomes composed of
DNA and proteins
 Nucleolus is inside the nucleus and is composed of proteins, DNA, and RNA, and is where
ribosomes are assembled
Ribosomes-

 Composed of proteins and ribosomal rRNA and are the sites of protein synthesis. They
translate the sequence of amino acids specified into the mRNA into proteins
 Consists of 2 subunits which are different eukaryotes and prokaryotes
 Can be found either free in the cytosol, or bound to endoplasmic reticulum

Endoplasmic reticulum-

 A network of intracellular membranous sacs and tubules. Can be rough or smooth

 Rough- ribosomes are attached. Found in cells that actively produce and export proteins
 Smooth- no ribosomes attached. Contains enzymes involved in the synthesis of molecules
other than proteins. Found in steroid-secreting cells
Golgi apparatus-

 A stack of flattened, smooth membrane sacs. Each sac forms a vesicle to transport the
proteins for modification for use by the cell of for transportation out of the cell
Lysosomes-

 The cell recycling units- specialised vesicles that digest unwanted matter
 Forms when transport vesicles from the Golgi apparatus fuse with each other
 Can perform endocytosis or exocytosis
Mitochondria-

 Contains DNA in the matrix

 Plays an important role in cellular respiration converting the chemical energy in organic
molecules (from food) into energy that cells can use
 Large SA of inner membrane provides numerous sites for chemical reactions
Chloroplast-

 Possesses DNA
 Involved in photosynthesis. They trap light energy, which is used to split molecules into
hydrogen and oxygen
Vacuoles-

 Membrane bound, liquid-filled space that stores enzymes and other organic and inorganic
molecules
 Animal- small, temporary
 Plant- single, large, permanent- provide structural support
Plastids-

 Involved in the synthesis and storage of different chemical compounds

 Contains DNA. Not in animal cells
Can be
- Chloroplast
- Leucoplasts
- Chromoplasts

Cell wall-

 Rigid structure that surrounds the cell membrane of plant cells, fungal cells, and some
prokaryotic cells
 Composed mainly of cellulose
 Provides support, prevents expansion, and allows water and dissolved substances to pass
freely through it
Cytoskeleton-

 Composed of microtubules and filaments. Supports the structure, allows cells to move
and transport organelles and vesicles within the cell
Centrioles-

 Present in eukaryotes. Involved in cell division and the formulation of cell structures
Cilia and flagella-

 Hair-like structures on the surface of cells. Involved in the movement of the cell of things
around the cell
Cytoplasm-

 A jelly like substance made of mainly water, salt and amino acids
Comparison of smooth ER and rough ER-
The rough ER has ribosomes connected to it whereas the smooth ER doesn’t. In the rough ER
ribosomes produce proteins, whereas in the smooth ER lipids are made.
Compare the pair-
Membrane bound organelles- none in prokaryotes, many with specialised structures and functions
in eukaryotes
Nucleus and DNA- prokaryotic cells have a single circular chromosome and plasmids. Eukaryotic
cells have linear chromosomes in the nucleus
Cell wall and membranes- prokaryotic cells have peptidoglycan, eukaryotes have carbohydrates
Size- eukaryotic cells are 10 times larger than prokaryotic cells
Structural hierarchy-

 Molecules  organelles  cells  tissues  organs  organ systems  organism

Technology
Metalanguage-

 Cytology- the study of cells

 Total magnification- ocular lens magnefication x objectification lens magnification
 Micrometres- unit of measurement- 1000um = 1mm
 Typical cell lengths-
- Bacteria: 0.1-1.5um
- Plant: 10-100um
- Human: 8-60 um
- Parmecium: 150um

Preparations and mountings-

 Whole mounts- the whole organism is placed directly on the slide, and are used for thin
structures such as very small organisms
 Smears- used for cells suspended in fluid (e.g. blood), or cells that have been scraped from a
surface
 Sections- very thin slices of specimens prepared by embedding the specimen in parrafin wax,
using a slcing instrument called a microtone to cut sections of just one layer of cells
Drawing conventions-
Drawings should be:

 Large and simple, two dimensional pencil drawings

 Have rule lines where possibl
Guidelines-

 Draw the whole diagram

 Don’t draw in a circle
 Do not sketch or shade; simple clear lines
 Include labels outside the drawing that do not cross, no arrowheads
 Include a scale bar or state the magnification
Light microscopy-

 Can be used to view living cells in colour

 Uses visible light and a system of lenses to magnify images
 Cells need to be prepared and mounted on glass slide
 Light travels through specimen and into the lens system
 Two types of light microscopy include fluorescence and confocial microscopy
Flourescence microscopy-

 Used to examine cells, cellular structures or any floating flourescing material with flourescent
molecules
 Filters allow the light emmited by the flourescing molecules to be seen against a black
background
 Flourescent dyes (markers) can be added to cells that do not contain flourescent molecules
 Allows scientists to visualise structures and materials inside cells that are usually too small to
view
 They can also target and detect particular proteins, and diagnose disease
Confocal microscopy-

 Allows scientists to obtain ‘optical sections’ of a cell or tissues, stained with markers, without
actually sectioning or slicing the cells
 High resolution (high quality) images of thin sections of a specimen are obtained
 Laser light is passed through the lens to provide highly focused light onto a tiny part of the
specimen. A slow scan produces an optical section
 3D images can be created with expensive software, despite being time consuming

Electron microscopy-

 Uses an electron beam rather than light to view objects, increasing the detail of structures
 Image has a much higher resolution and a great depth of field than an image from a light
microscope
 Produces only black and white images that are coloured later to highlight important features
Types of electron microscopy-

- Transmition electron microscopy (TEM)-

Electron beams travel through an ultrathin section (less than 100nm thick) of a
specimen. Very fine details of cellular structures can be seen
Specimes is chemically fixed to stop the structures from collapsing, and then
dehydrated with alcohol. This is then imbedded in a plastic resin, sectioned and
stained
- Scannning electron microscopy (SEM)-
 The electrons are bounced off a specimen that has been coated with an extremely
thin layer of gold. This gives a high-resolution picture of the surface features, but
cannot show internal detail
Autoradiography-

 A method of light and electron microscopy that can identify specific organelles or the location
of molecules within a cell or tissue
 The tissue is treated with a labelled, radioactive substance which is emitted to produce a high-
resolution image
 Tissue sections are stained to locate the cellular structures seen in the image
Synchrotron-

 A large particle accelerator which allows structures to be viewed at the atomic scale
 Can produce an extremely intense beam of radiation in a wide range of wavelengths
 The light produced allows us to see matter at the atmoic scale e.g., nanosecond behaviour of
protein molecules

Fluid Mosaic Model

Metalanguage-

 Hydrophobic- water hating

 Hydrophillic- water loving
 Active transort- requires energy
 Passive transport- no energy required
 Diffusion- movement of any types of molecules from high to low concentration
 Osmosis- movement of a solvent, through a semipermeable membrance
 Concentration gradient- the gradual change in the concentration of solutes present in a
solution between two regions

Cell structure-

 Each cell is surrounded by the cell (or plasma) membrane which regulates the flow of
substance in and nout of the cell
 Helps maintain and environment within the cell that differs from the external environment
 Differentially or selectively permeable; only certain substances can cross it
 Cell membrane- 40% lipid, 60% protein
Fluid mosaic model-

 Proposed by S.J Singer and Garth . L Nicholson in 1972

 Bilayer of phosphoid molecules with other molecules (proteins, carbohydrates and cholestrol)
scattered throughout the bilayer
 Impermeable to water-soluble particles, ions and polar molecules; the movement of these
molecules are controlled by protein channels
 The fluidity of the membrane allows individual phospholoid molecules to move about within
the layers
 Fluidity of the membrane is affected by temperature, cholestrol and the phospholipid
composition and structure
 Entrance into the cell depends on
- Size
- Electron charge (Na+ Cl-)
 Lipid solubility

Functions of cell membrane-

Proteins-
  Provide selective water channels to enable water-soluble particles and ions to travel through
the cell membrane
 Catalyse reactions associated with the cell membrane
 Communicate with the external environment and other cells
 Bind with other cells
 Additionally: transport, enzyme activity, signal transduction, cell to cell recognition,
attachment to the cytoskeleton and extracellular matrix
Phospholipid- long chain fatty acid of a phosphate head

Active transport-

 Specific carrier proteins in the membrane bind with the molecules and carry them through the
membrane
 Requires expenditure of energy
 Substrate molecules activate protein-carrier molecules that allow previously excluded
molecules to enter the cell
 Low to high concentrations
 Against concentration gradient
Passive transport-

 No energy is required
 Water, oxygen, carbon dioxide and other small ions and molecules can diffuse freely through
all cell membranes
 High to low concentration
 Along the concentration gradient
Diffusion-

 Passive movement of molecules from a region where the concentration of those molecules is
high to a region where the concentration is low
 It is a passive process that occurs because there is a concentration gradient
Factors affecting diffusion-

- Concentration: the greater the difference in concentration gradient, the faster the rate
of diffusion
- Temperature: the higher the temperature, the higher the rate of diffusion
- Particle size: the smaller the particles, the higher the rate of diffusion
Facilitated diffusion- movement through channel proteins in the membrane, down the concentration
gradient

 The membrane transport proteins are specific for particular particles, so transport is selective
 Transport is simpler by rapid diffusion the transport proteins can become saturated (fully
occupied) as the concentration of the transported substances increases
 The transport of one particle may be inhibited by the presence of another particle that uses the
same transport protein
 No energy is required
Osmosis- the net diffusion of water molecules across a semipermeable membrane. The water moves
from a diluted to a concentrated solution along its own concentration gradient

Endocytosis-

 Large molecules are transported across a membrane

 The molecules are enclosed in a vacuole or vesicle formed by the membrane, and then
discharged on the other side
Types of endocytosis-
- Pinocytosis
- Phagocytosis
- Receptor-mediated

Exocytosis-
the process by which substances such as antibodies, neurotransmitters and enzymes that have
important functions elsewhere and waste products, in the organism need to be removed
Solution concentrations-

 Isotonic- a solution of equal concentration to the cell

 Hypotonic- a solution with a lower concentration than a cell
 Hypertonic- a solution with a higher concentration than a cell

Villi- where nutrients is being digested in the small intestine with folded to increase surface area

Substances that must leave the cell are waste such as urea, uric acid, and excess carbon dioxide

Surface area to volume ratio

Metalanguage-

 Ratio- how much of one thing compared to another

 Surface area- a measure of the total area that the surface of the object occupies
 Volume- the quantity of three-dimensional space enclosed by a closed surface
Surface area to volume ratio-

 The area of the surface membrane affects the rate at which nutrients can enter the cell, as well
as the rate which wastes can leave
 As the cell grows, its needs are greater, but the rate of exchange of materials with its
surroundings falls
 As the cell increases in size, the surface to area to volume ratio decreases
 As a cell increases in volume, the distance from the centre of the cell to the cell membrane
also increases. The rate of chemical exchange from the centre of the cell to the surrounding
environment may become too low to maintain the cell
Increasing the cell surface to volume ratio-
Three ways of changing the cell surface to volume ratio without changing the cell volume are:

 Cell compartmentalisation- creates more space for membrane-bound enzymes to increase

activity in the cell
 A flattened shape- creates a larger SA: V to allow a higher rate of exchange through the
membrane. Also reduces the distance the substance needs to be transported to and from the
cell membrane
 Cell membrane extensions: e.g., microvilli and root hairs

Processes and requirements

Metalanguage-

 Heterotroph- feeding on something different, consume other organisms, includes all animals
and fungi
- Animal cells do not contain chloroplasts and must obtain the substances they need
from their external environment
 Autotroph- self feeding
- Plant cells which contain chloroplast are able to produce their own nutrients by
photosynthesis
- Make their own organic compounds from inorganic compounds
- Also called producers
- Fundamental to the existence of all organisms

Chemical compounds-
Inorganic- without C atoms, with only one or two C atoms

 Water- important solvent and transport medium

 Oxygen- needed for energy supply
 Carbon dioxide- source of C for organic molecules
 Nitrogen- key atom in amino acids
 Minerals important for building enzymes and vitamins
Organic compounds- contains C and H atoms

 Carbohydrates- energy sources and structural compound

 Lipids- cell membranes and energy storage
 Proteins- composed of amino acids, enzymes, hormones, part of the cell membrane
 Nucleic acid- carrying genetic information of the cell, DNA and RNA
Energy-

 ATP- Adenosine triphosphate

 Universal carrier of energy
 High-energy bonds between the inorganic phosphate groups can be broken to release energy
  ADP- Adenosine diphosphate – can readily combine back with a phosphate to form an ATP
molecule again

Photosynthesis-

 Can only occur if plant cells can obtain carbon dioxide, water and light from their external
environment
 Occurs in the chloroplast. These contain chlorophyll, (green pigment) molecules which
absorb energy from sunlight
 Other pigments can assist in absorbing different wavelengths of light
Stage 1; Light dependant reactions

- Chlorophyl captures solar energy and uses it to

produce ATP
- Water is split into hydrogen ions and oxygen gas
- Occur in the thylakoid membranes (grana) of the
chloroplast
Stage 2; Light independent reactions

- Produce glucose, water and ADP

- The ATP made in stage 1 provides energy for
the dark reactions which combine carbon
dioxide and hydrogen ions to form glucose and
water
- Occurs in the stroma (fluid part) of the
chloroplast
Organic has carbon and hydrogen

Rate of photosynthesis-
  Light intensity- light dependant reactions cannot occur with low light intensity. As light
intensity increase, the rate of photosynthesis will increase until a certain point before
plateauing
 Carbon dioxide concentration- when no CO2 is available, photosynthesis will not occur.
When CO2 becomes available, photosynthesis will increase until a certain point before
plateauing
 Temperature- affects the functioning of enzymes that catalyse reactions of photosynthesis

Respiration-
Use glucose and oxygen to produce usable energy, with carbon dioxide formed as waste.
Occurs in the cytosol and mitochondria of cells

Transformation of chemical energy stored in organic compounds into a usable form of

energy, stored in the bonds of ATP

 Stage 1: Glycolysis- splits glucose into two parts and does not require oxygen –
occurs in the cytosol of a cell
 Stage 2: Aerobic or anaerobic respiration- depending on the presence of oxygen
Aerobic vs Anaerobic respiration-

 Both enable the maintenance of energy stores

 Aerobic respiration produces almost 20 times the number of ATP molecules produced by
glycolysis alone
 Anaerobic respiration is crucial to continue the generation of ATP by glycolysis for very short
periods of time or when there is not enough oxygen available for aerobic respiration
Removal of waste-

 As cells function, they produce substance from their metabolism that are no longer useful to
them
 Accumulation of waste substance can prevent cells from functioning properly. These waste
substances need to be removed to ensure balance is maintained
 Passive- Osmosis of water molecules; simple diffusion of oxygen, carbon dioxide, ammonia,
and alcohol; facilitated diffusion of urea, glucose, and ions
 Active- urea, toxins and ions being removed against their concentration gradient via
endocytosis and exocytosis
Cyano bacteria started producing oxygen
2 major biochemical processes that cells carry out are:

 Photosynthesis (in autotrophic cells)

The process by which plants utilise energy, usually from the sun, which is trapped by
chlorophyll. It uses this energy to break apart water and carbon dioxide molecules, and build
them up into oxygen, energy storing glucose molecules and water molecules
Light energy Light energy
Carbon dioxide + water  glucose+ oxygen = 6C)2 + 6 H2O  C6 H 12 O6
Chlorophyll Chlorophyll
  Respiration (in all living cells)
All organisms break down glucose as a source of energy to drive cellular metabolism
Glucose can either be broken down in the presence of oxygen (aerobic cellular respiration) or
in the absence of oxygen (anaerobic cellular respiration). Different products and amounts of
energy are released in each of these processes.
- Anaerobic formula
Glucose  ethanol + carbon dioxide +adenosine triphosphate
C6H12O6  2CH3CH2OH + 2CO2 + 2ATP
- Aerobic formula
Glucose + Oxygen 
Removal of wastes-

 Autotrophs-
- Most waste is by-products
- No specialised excretory organs
- Low metabolic rate = almost no true waste
 Heterotrophs-
- Cells break down and replace carbohydrates, lipids, nucleic acids, and proteins that
cannot be used by the body
- More complex excretory structures and processes are required

Removal of waste systems- Organs and systems

 Liver- prepares various substances for excretion. Detoxifies harmful chemicals and breaks
down amino acids to release ammonia, which is converted into urea
 Kidneys- excretes waste after performing filtration, reabsorption, and active secretion.
Performed by functioning units called nephrons

Enzymes
Metalanguage-

 Enzyme- special large proteins

 Optimum- conditions under which enzymes perform at their best
 Catalyst- substances that accelerate the rate of any chemical reaction without themselves
being changed
 Denaturation- the loss of the characteristic 3D shape of a protein which prevents functioning
of the enzyme and is irreversible
 Substrate- molecule upon which enzyme acts
 Cofactor- any extra ion of molecule that works with an enzyme
Enzyme-
Special large proteins that regulate organisms and maintain the rate of its chemical activity

 Specificity- different enzymes acts as catalysts for different biochemical reactions by binding
to a specific type of molecule, called a substrate
 Catalytic power- enzymes do not make reactions occur that would not occur on their own
 Catalyse repeated reactions- they are not consumed when they catalyse reactions
Characteristics-

 Made of proteins
  Catalysts, because they control the rate of chemical reaction
 Remain unchanged at the end of the reaction
 Needed only in small amounts
 Highly specific- one enzyme for one type of reaction
 Work best under certain optimum conditions
 May need coenzyme to help functioning
Enzyme Activity-

 Provide the surface or active site for reaction to take place

 The substrate molecule binds to the active site, creating enzyme substrate complex. This
binding induces a temporary change in shape of the enzyme as induced fit
 A chemical reaction occurs, and the substrate is changed. The product of products are then
released and the enzyme returns to its original form
 When temperature, pH and the concentration of the substrate are optimal, enzyme activity is
at its highest, the rate of reaction is at its fastest, and the biochemical pathway is operating at
maximum efficiency

Factors that affect enzyme activity-

 pH- enzymes work best at a certain level of acidity: any variation above or below those levels
reduces their rate of activity. Extreme pH will alter or denature them which is a permanent
change, and the enzyme can no longer catalyse the reaction
 temperature- most enzymes work best at a certain temperature (37 C in mammals), and the
speed of reaction they are catalysing decreases is the temperature varies from its level
 concentration- an increase in substrate concentration will increase the rate of reaction until all
enzyme active sites are occupied.