Year 11 Biology chapter 1

YEAR 11 BIOLOGY

Protista

Have a cell wall

Don' t have chloroplasts

Have membrane bound nucleus and organelles

All other eukaryotes that are not classified - leftovers

Technologies that are used to Determine a Cell's Structure and Function

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Cytology is the study of cells. - use a variety of tools and techniques to study cells

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Modern techniques include light and electron microscopy - understand structure and functioning of cells

Resolution is the ability to distinguish two objects as distinct

Light Microscope

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Uses light and lenses to magnify the images

Advantages: can be used to view living cells in colour

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The cell needs to be prepared and mounted on a glass slide, which is then placed on the stage. Light travels through the specimen and can be viewed through the eye piece or through a digital means Can be used to view large organelles such as the nucleus, chloroplasts, mitochondria and plant vacuoles

• Common specimen preparation methods:
  Whole Mounts - place whole organism directly under the slide; used for thin structures; usually under a dissecting microscope
  Smears - used to for cells suspended in fluid; where they have been scraped off the surface

• Sections - thin slices of specimen, prepared by embedding the specimen in wax; cut sections of just one layer of cells

Electron Microscope

• An electron microscope uses an electron beam and it produces

a narrow beam of electrons which is maintained by

the electromagnetic lenses

The electron is absorbed, scattered or passes through it to create an image It has a higher resolution and a greater depth of field than in a light microscope But the organisms need to be dead The images are in black and white but can be coloured later

• Transmission Electron Microscopy (TEM)
  The electron beam travels through a thin section of specimen

• Scanning Electron Microscope (SEM)
  Electrons are bounced off a specimen which is coated in a thin layer of gold

High resolution picture of surface, but no internal detail (3D surface view)

Investigate a variety of prokaryotic and eukaryotic cell structures including different organelles and arrangements, scaled diagrams and the fluid mosaic model of the cell membrane:

Cell Organelles and their Arrangement

• Light microscope can be used to identify the main structures in eukaryotic cells -

• More complex organelles within a eukaryotic cell can only be viewed through the electron microscopes

• Organelles: Structure and Function
  NUCLEUS - surrounded by a double membrane (phospholipid bilayer) called the nuclear membrane

• Contains DNA

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What distinguishes one cell from another?

Investigate different cellular structures

Classifying a Variety of Cells

• Cells are the basic structural units of all living things

There are two types of cells: prokaryotes and eukaryotes

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• Taxonomy or classification breaks down the levels and categorises the cells

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Domain is the highest rank followed by kingdom, phylum, class, order, family, genus, species

As you go down the classification the more specific and less inclusive the

KINGDOM

categories become

Extremophile - live in very harsh environmental

The three-domain system!

Eukarya:

Archaea

Bacteria and Archaea are prokaryotic cells, Archaea are more closely related to Eukarya than

ORDER

FAMILY

The six-kingdom system

tended

Protista:

Plantae

Fungi

Animalia

GENLA

SPECIES

Examining a Variety of Prokaryotic Cells

Prokaryotes are organisms made up of only one cell

• The cells are very simple in structure - they have no membrane bound DNA (no nucleus) and no membrane: bound organelles

• They have a folded cell membrane and the cytoplasm has scattered ribosomes (structures made of RNA and protein involved in protein synthesis

• The genetic material inside the are called genophores - irregular circular DNA chromosomes; they can also have plasmids which are small rings of double stranded DNA

• Some cells also have a tail like structure called a flagellum which assists in their movement while others have pili (small hair-like projections) surrounding the external membrane

Bacteria

• Bacteria is made up of prokaryotes

• They are extremely adaptable and can live in most environments

• Need little oxygen to live as they can extract energy and fix carbon. They obtain energy through photosynthesis or chemosynthesis

• They are decomposers that break down various organic matter

• Most are harmless but may cause disease in some organisms - cholera, typhoid

Archaea

• A very specialised cell that is restricted to particular environments - these are usually extreme environments

• They do not require a lot of oxygen and sunlight known as extremophiles

• Halophiles - Archaea that are found in salt concentrated areas - Dead Sea and Great Salt Lake

• Thernophiles - Require high temperature for growth - areas of volcanic activity, hot springs, geysers and hydrothermal vents

Examining a Variety of Eukaryotic Cells

• Eukaryotic cells are much larger and more complex

• They have membrane bound organelles - diversification

• Both unicellular and multicellular forms which can reproduce sexually and asexually

Eukaryotic

Cells

Features and Characteristics

Animalia

Plantae

Fungi

Have membrane bound nucleus and organelles

Does not have a cell wall or large vacuole

Have membrane bound nucleus and organelles

Have a cell wall, large vacuole and chloroplasts Have membrane bound nucleus and organelles

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Fluid inside is called nuclear sap

Contains genetic material (DNA), assisting in cell replication, growth and repair and other activities

• NUCLEOLUS - dark stained area in it
  Site of ribosome production and nucleic acid

• GOLGI BODY - membrane bound sac,

• It is responsible for modifying, storing, processing and packaging substances for secretion

• CELL MEMBRANE - a single bilayer with proteins and lipids

• It controls what enters and leaves the cell

• CYTOPLASM - fluid component, made 90% of water and it is the site of all chemical reactions

• CYTOSKELETON - interlinking filaments and tubules in the cytoplasm which hold it in place and maintain the

shape

• MITOCHONDRIA - surrounded by a double membrane, where the inner membrane is folded to increase surface area
  It is the site of cellular respiration, giving the cell energy (ATP molecules)

• LYSOSOMES - membrane bound vesicle that contains enzymes and proteins
  It is responsible for digesting and breaking down cellular waste and foreign material

• CENTRIOLE - small structures of microtubules found in animal cells
  Involved in mitosis (spindle fibres)
  ENDOPLASMIC RETICULUM - system of membranous sacs

and tubules connected to the nucleus

• Rough ER - have ribosomes binding to it - produces and transports proteins

• Smooth ER - no ribosomes - synthesises lipids

• Used for communication between nucleus and cell cytoplasm and protein synthesis

• CHLOROPLAST - surrounded by a double membrane. Two lipid bilayers

• Contains complex system of membranes called thylakoids which contain chlorophyll

• Thylakoids are stacked up together to make

granum

• This is where photosynthesis happens

• CELL WALL - external structure in plant cells which is made of cellulose; providing the cell with support (semi-permeable)

• VACUOLE - membrane bound, which is filled up with fluid; gives support and in plant cells acts as storage

• FLAGELLUM - external structure which helps in the movement (single celled organisms)

• RIBOSOME - a structure made of RNA and protein and is found free floating in cytoplasm or attached to ER

• It is the site of protein synthesis

Drawing Scaled Diagrams of a Cell How to correctly use a Microscope

• Set the microscope appropriately

• Turn the revolving nosepiece so that is the lowest objective lens is in position

• The lamp needs to be turned on and the diaphragm may need to be adjusted

• Place the specimen on the stage and hold it using the stage clips

• Lower the objective lens using the coarse focus knob

• Then use the fine focus knob to refine the detail of the image

Examining the Size of the Cell

• A light microscope has two lenses: the eye piece and the objective lens

• To calculate the total magnification: total magnification = occular lense x objective lense

• The size of the cell can be estimated by working out the diameter of the field of view - the area that you can see

• To work out the size divide the number of cells you can see in the field of view by the dimeter of the field of view

field of view (mm)

- = length of each cell (mm)

number of cells

1000um = 1mm

The Structure and Function of the Fluid Mosaic Model of the Cell Membrane The Purpose of the Cell Menbrane

• Different substances are needed by the cell in the intracellular fluid and needs to be removed by the cell into the extracellular fluid - this happens via the cell membrane

• Examoles of things needed include oxygen, carbon dioxide, sugar, acids, water and salts

• Substance leaving the cell include wastes such as urea, excess carbon dioxide or other secretions like mucus or hormones

• It also controls the passage of water in and out

• It is semi permeable or selectively permeable meaning it is able to determine which molecules may enter or exit The Fluid Mosaic Model

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Structure of the Fluid Mosaic Model

• Lipid Component

The cell membrane is made of a phospholipid bilayer. Each layer is made up of on phospholipid which has a head and The phosphate head is hydrophilic meaning it attracts water and the fatty acid tail is hydrophobic, repelling water

• Protein Component

Molecules are scattered throughout the lipid layer where some are only on the surface and other penetrate through the whole layer forming channels

These channel proteins allow some molecules to pass through the membrane.

• Other proteins are fixed in place - channel proteins and others move around - peripheral proteins

• Some act as pores, form active transport systems or channels

• Carbohydrate Component

Usually linked to the proteins forming glycoproteins which assist cell recognition

• Cholesterol

Gives extra stability to lipids and allows to expand and contract the membrane as required

Function of the Fluid Mosaic Model

• Water soluble molecules have difficulty entering the membrane whereas lipid soluble molecules do not (hydrophobic and hydrophilic head and tail) making the membrane semi-permeable

Neutral molecules like COz and O2 have high permeability

Water moves through the hydrophilic pores

• Larger molecules move through the proteins through facilitated diffusion and are 'carried'

Chapter 2 - Cell Function

How do cells coordinate activities within their internal environment and the external environment?

Investigate the way in which materials can move into and out of cells

Cell Permeability

• Permeability of the cell membrane refers to its ability to allow the cell to exchange liquids and materials between the cell's internal environment and the external environment

• Movement both in and out is essential for the functioning and survival of the cell for molecules needed and wastes and communications

• The cell membrane is selective or semi-permeable

• It is able to choose what goes through to the cell based on the characteristics of the molecule and its interaction with the cell membrane.

Diffusion

• Diffusion is a process where particles in a solution move from an area of high concentration to an area of low concentration through a concentration gradient

• It is a passive process and does not require energy

• Simple diffusion and facilitated diffusion are both passive where molecules move along the concentration gradient

Simple Diffusion

• Solute molecules can only diffuse if the membrane is permeable to them - there would be constant movement

• The molecules will cross from an area of high concentration to low concentration

• It then achieves evenly spread particles. At this point movement still happens but the same number of particles move in an out, thus having no net movement

• Solute: the substance dissolved in a given solution

• Solvent: the substance in which the solute is dissolved in

Facilitated Diffusion

• The phospholipid bilayer is impermeable to some particles; however, channel proteins allows some particles to pass through and

• The molecules still move along the concentration gradient, but the movement is just assisted by the proteins

• The transport is for specific particles; it is more rapid than simple diffusion and no energy is required

• Channel Proteins:

• Like pores which open and close to allow the molecule to pass through

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Usually used in the passage water-soluble polar particles

• Carrier Proteins

It binds with the molecules, causing the protein to change shape to transport it, it then returns to its original shape.

Osmosis

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Osmosis is the movement of water molecules from an area of high concentration to an area of low concentration through a selectively permeable membrane

• It does not require any energy and is thus passive The Effect of Solute Concentration on Osmosis

• Water concentration is affected by the number of solutes dissolved in it

• The higher the concentration of solute, the lower the water concentration

• Water therefore also in osmosis moves from an area of low solute concentration to an area of high solute concentration

• Different solutions can be described differently based on their solute and solvent concentrations

• ISOTONIC SOLUTION: the water concentration and solute concentration are equal - in equilibrium

• HYPERTONIC SOLUTION: the solution with a higher concentration of solute

-This means that there is low concentration of water inside the cells, and higher concentration outside meaning that water moves into the cell

• HYPOTONIC SOLUTION: low concentration of solute, meaning high concentration of water molecules

• This means that the water will move outwards

Osmosis in Cells

• If cell has a higher solute concentration than the water, the water will move into the cell if the cell is able to expand (hypotonic environment)

ANIMAL CELLS: results in expansion of until the cell membrane bursts open - lysed

• PLANT CELLS: the cellulose wall is only slightly elastic, as the incoming water stretches it, it exerts an opposing force - wall force. If these two forces of the water and the wall are equal then the cell will be in a state of turgor, which gives the plant support

If the cell has a lower solute concentration than the water, the water will leave the cell until it begins to shrink (hypertonic

environment)

• ANIMAL CELLS: the cell contents leave the cell until it becomes shrivelled and breaks down - no longer function

• PLANT CELLS: also loses the cell contents and the membrane will shrink, leaving a gap between the cell wall - plasmolysis

- these are unable to provide sufficient support causing the plant to wilt

Active Transport

Transport of Small Molecules

• Active transport is the movement of molecules from an area of low concentration to an area of high concentration which requires

• It usually requires a carrier protein that can move molecules using ATP energy against the concentration gradient

• Active Transport is faster than passive transport

Transport of Large Molecules - Endocytosis (Enter the Cell)

• Endocytosis occurs when particles larger than individual molecules need to enter the cell

• The cell takes in new materials by forming vesicles from the cell membrane

• A small area of the membrane sinks inwards to from a pocket and the substance becomes enclosed within in it

The vesicle then transports the substance to wherever it is required in the cell

Phagocytosis: when solid particles are engulfed by the membrane

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• Pinocytosis: when the cell membrane engulfs liquid with dissolved molecules

Receptor Mediated Endocytosis: protein reception on the membrane respond to certain molecules, triggering the engulfment of it (pinocytosis)

Transport of Large Molecules - Exocytosis (Exiting the Cell)

• Exocytosis occurs when large molecules need to exit the cell and the vesicle membrane comes in contact with the cell membrane and fuses together.

• The substance inside the vesicle is released

The vesicle membrane becomes a permanent part of the cell membrane

Examples: hormones, proteins or foreign matter

Factors that affect the Efficiency of Movement of Materials across the Cell Membrane Surface Area to Volume Ratio

• Surface Area: the part of the object that is exposed to the surroundings

• Volume: the amount of space an object occupies

• Surface Area to Volume Ratio: a fraction that compares SA: V

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When diffusion or transport occurs, the substances move from the external environment to the cell until they reach the centre

• The surface area of the cell membrane affects the rate of exchange that is possible between the cell and its environment

• Larger cells need a greater amount of nutrients and wastes, but they also have greater volumes. This means that the organelles al further away from the cell membrane

• If a cell increases in size, its volume increases at a faster rate than the surface area, and the SA: V decreases The smaller or flatter the cell the greater the efficiency to exchange matter due to a large surface area to volume ratio This is the reason why most cells are microscopic, in order to maintain that perfect SA:V ratio. If cells get too big, then the volume of the cell will increase more than the surface area reducing the cell's efficiency. Once it reaches a too big state, the cells divide Investigate the biochemical process of photosynthesis, cell respiration and the removal of cellular products and wastes in eukaryotic cells

Investigate cell requirements including matter (gases, simple nutrients and ions), suitable forms of energy, and the removal of

wastes

Organic Matter

• Organic compounds that are chemical substance that are synthesised by living things and contain carbon and hydrogen

Carbohydrates

• Made up of carbon, hydrogen and oxygen atoms

• Monosaccharides are simple sugars of single units (Glucose)

Disaccharides are sugar made of two units (Sucrose)

Polysaccharides are complex polymers made of many units (Starch)

• Uses

Monosaccharides and Disaccharides are quick sources of energy and are used in cellular respiration

Polysaccharides like starch are a source of energy in plants; cellulose forms the structural part of cell walls and glycogen is a form of stored energy in plants

Lipids

• Made up of carbon, hydrogen and oxygen atoms

• Have an oily, greasy or waxy consistency and are insoluble in water and water repellent

• Made of a glycerol head and a fatty acid tail

Uses

Forms the cell membrane with hydrophobic and hydrophilic properties, regulating movement of substances Biological fuels storing lots of energy

Form a waxy waterproof coating for leaves, protecting it

Proteins

Made up of carbon, hydrogen, oxygen and nitrogen atoms

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Made up of long chains of amino acids - polypeptides joined by peptide bonds

• The sequence and arrangement of the 20 amino acids determines what protein it is

• Uses

Form the structural components like protoplasm and tissues for bones, hair and nails

• Also, a structural part of cell membrane and regulates the movement of substances across the membrane

• Some proteins are enzymes and help control and maintain chemical reactions of the cell

Nucleic Acids

Made up of carbon, hydrogen, oxygen, nitrogen and phosphorus

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Made up of repeating units called nucleotides which make RNA which make double stranded DNA

Nucleotides are made up of a simple sugar, a phosphate and a nitrogenous base

Uses

DNA has genetic information that controls the cells Responsible for transmitting inheritance, important during cell division

• RNA is found in the nucleus and cytoplasm and is associated with the ribosome

• It is involved in the production of the proteins

Simple Nutrients

• Include all vitamins

• Vital for cell function

• Some a water soluble while others are fat soluble

• A deficiency in vitamins or lack of can lead to many diseases

Inorganic Matter

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Inorganic compounds are found in both living and non-living things and are not synthesises by living things

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Gases

E.g. carbon dioxide and oxygen

Carbon dioxide is used by plants for photosynthesis and is released as waste from respiration

• Oxygen is necessary for cellular respiration to produce energy and is released as a product of photosynthesis

Mineral Salts

• Includes chlorides, nitrates, phosphates and carbonates

• Assist in chemical reaction, helping enzyme function

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Used for the synthesis of body tissues like calcium for bones, iron for blood

Sodium and chloride ions assist in water balance and ensure functioning of cell membrane, nerve and muscle cells

Water

• Makes up 90% of liquid in cell

• Water is a transport medium in cells and is an important solvent when most chemical reactions occur

• Is used to regulate the temperature

Energy

Autotrophs

• Autotrophs make their own food form inorganic compounds - producers and use the process of photosynthesis to produce their own food

• They trap energy from the sunlight and convert it into chemical energy, which is stored in glucose. This takes place in the chloroplasts

Chloroplasts contained stacks of flattened membranes called grana. Each granum has thylakoids which contain chlorophyll

• Carbon dioxide, chlorophyll, water and light are essential for photosynthesis to occur

The chlorophyll (green pigment) captures the light

Reactions take place in the stoma

Non-green plants have other pigments to absorb the light

• Photosynthesis is a complex biochemical process which is represented through the equations

carbon dioxide + water → glucose + oxygen + energy

6C02 + 6H20 → C6H1206 + 60г

• There are a series of many chemical reaction that take place for photosynthesis to occur

1. Light-Dependent Phase (Photolysis)

• Involves the splitting of water using light energy which is captured by the chlorophyll

• The energy is able to excite an electron which may either

Split the water into hydrogen gas and oxygen which joins with another oxygen atom to form oxygen gas; the hydrogen atoms will be used in the light independent phase

• Or it may be used to form adenosine triphosphate (ATP) which provides the cell with the energy it needs

2. Light Independent Phase

• Involves using carbon dioxide to make sugar - carbon fixation. This process does not require chlorophyll and no light

• The hydrogen atoms are carried to the stroma

• Carbon dioxide needed for this reaction is absorbed from the air

• Hydrogen atoms and the carbon dioxide combine to form glucose (energy rich)

• The ATP from previous process gives this process enough energy and is incorporated into the new product

Heterotrophs

• Heterotrophs obtain organic compounds by consuming other organisms - called consumers

• They must undergo the process of cellular respiration to release energy

• Cellular respiration takes place in the mitochondria of all living things

• The glucose is broken down in the presence of oxygen producing carbon dioxide and water and releasing energy

• Energy is stored as ATP molecules (adenosine triphosphate)

• Energy in the form of ATP is released as heat from the process and is used for cell functions

• The role of respiration is to remove oxygen from the air and provide energy to the cell

1. Glycolysis

• The glucose molecule is split into pyruvate molecules

There is a net gain of 2 ATP molecules

2. Aerobic and Anerobic Respiration

• When oxygen is available respiration occurs in the mitochondria and converts ADP to ATP. The two pyruvate molecules are broken down into carbon dioxide, water and 34 ATP molecules

Anaerobic Respiration occurs when there is an insufficient supply of oxygen, the pyruvate ferments.

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This process occurs in the cytoplasm and produces no ATP molecules. This process prevents the accumulation of pyruvate in cell

The pyruvate molecules are converted into lactic acids or carbon dioxide and alcohol

Waste Removal

Removal of waste products is essential, and any accumulation can disrupt metabolism and result in cell death

• Wastes include

Carbon dioxide from respiration

Nitrogenous wastes from the breakdown of proteins

• Excess salts

Build-up of pyruvate molecules in plant cells

Eukaryotic cells have organelles that are specialised in processing and removing wastes

These are called lysosomes - small vesicles filled with digestive enzymes. They fuse with waste products and then recycled in the cell or removed via the cell membrane through exocytosis

Conduct a practical investigation to model the action of enzymes in cells

Investigate the effects of environment on enzyme activity through the collection of primary or secondary data

Role of Enzymes in Metabolism

• Metabolism refers to the sum of all the chemical processes occurring within a living cell or organism

• Enzymes are biological catalysts which speed up the chemical reactions without a change in temperature

• The reactants need to be supplied with enough energy in order for the bonds to break and the reaction to occur. The minimum amount of energy required to start the reaction is called the activation energy.

• The role of enzymes is to lower the activation energy required to start a reaction

Properties of Enzymes

Chemical Composition

• Enzymes are protein molecules - which are made up of long chains of amino acids joined by peptide bonds

• The chains formed are called polypeptide chains

• Enzymes are globular proteins which have polypeptide chains folded into a specific 3D shape

• The surface has a specific shape and is called the active site.

• The molecule on which an enzyme acts is called the substrate

• An enzyme fits together with a substrate at the active site, forming an enzyme-substrate complex, allowing for the reaction to proceed

• The shape of the active side must not be altered, otherwise the enzyme will not work Specificity

• Enzymes are substrate specific meaning that only a particular enzyme can work on one particular substrate molecule (shape of active site needs to match the shape of the substrate molecule/s

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Catabolic Reaction: breaks down the substances that release energy

• Anabolic Reaction: produce larger molecules from smaller substances - requires and input of energy

Models of Enzyme Activity

Models have been used to explain how the substrate binds at the active site to form the enzyme-substrate complex

1. Lock and Key Model

• Suggests that the enzyme active site and substrate is like a key fit into a lock

• It suggests that the active site is rigid and specific to the shape of the substrate

2. Induced Fit Model

• The model suggests that the active site is not rigid

The binding of the substrate to the active site allows the shape of the enzyme to change so that it can fit more tightly around the substrate

Factors Affecting Enzyme Activity

Temperature

• Proteins and enzymes are sensitive to temperature and any changes affect their functioning

• The optimum temperature refers to the temperature where there is a greatest rate of reaction, where the enzyme can work most effectively.

• Usually as temperature increase, the rate of reaction increases as the particles move more rapidly allowina for more successful

• At high temperature though, the globular shape of the enzyme breaks down: permanently alterina the active site, causing the

enzyme to denature

• At very high temperatures, the enzymes are permanently denatured

• At lower temperatures, the rate of reaction is slow as the particles have less kinetic energy. They are not denatured.

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PH

Each enzyme has it own pH range where it functions most efficiently

Anything outside the optimum pH range will alter the shape of the enzyme causing it to slow down or stop functioning

• Extreme of pH causes enzymes to denature

Substrate Concentration

The concentration of enzyme and substrate affects the rate of reaction

• An increase in concentration increase the rate of reaction until all available enzymes are used

• The reaction occurs over a shorter period of time

The point where the reaction will be happening at its maximum is called saturation point, where all enzymes are occupied Increasing the concentration beyond the saturation point will not increase the rate of reaction