NCEA Level 2 Biology Cells

Enzymes

Biological catalysts made up of proteins, which means they speed up reactions. Without them reactions would occur too slowly to sustain life. They are not changed in the process, and can be used over and over again. Every reaction in a cell has its own enzyme - enzymes are specific to their reaction

Structure of enzymes

An enzyme acts on a molecule called the substrate and binds at its active site. Enzyme activity depends on the enzyme's shape and its active site (the binding site for the substrate), and each enzyme is specific to its substrate

How enzymes work

Enzymes increase the rate of reaction by lowering the activation energy barrier and allow molecules of relatively low energy to take part in reactions at body temperature

Lock and key mechanism

The fit between the substrate and the active site of the enzyme is exactly like how a key fits into a lock (very precisely). A temporary structure called the enzyme-substrate complex is formed

Induced fit

Some proteins can change their shape. When a substrate combines with an enzyme it induces a change in the shape of the enzyme. The active site is then moulded precisely to fit the substrate

Factors which affect enzymes

Temperature, pH, enzyme and substrate concentration

How temperature affects enzyme activity

1.. When the temperature is too low, the kinetic energy is not enough and there are few or no collisions between enzymes and substrates. Therefore, the enzyme is inactivated

2. As the temperature increases, more kinetic energy is provided so there are more collisions between enzymes and substrates. Therefore more enzyme-substrate complexes are formed and enzyme activity increases

3. At 40 degrees, enzyme activity is at its maximum (optimum temperature)

4. From 40 to 80 degrees, the temperature is too high and the shape of the active site is altered. Therefore the enzyme is denatured and enzyme activity decreases

How pH affects enzyme activity

Different enzymes have different optimum pHs, and don't work at extreme pHs. The pH affects the properties of the active site so the substrate can no longer bind

How substrate concentration affects enzyme activity

As the substrate concentration increases, the rate of reaction increases because more substrate molecules can collide with enzyme molecules, so more reactions will take place. At higher concentrations the enzyme molecules become saturated with substrate, so there are few free enzyme molecules, so adding more substrate won't make much difference

How enzyme concentration affects enzyme activity

As the enzyme concentration increases, the rate of reaction increases because there are more enzyme molecules available to catalyse the reaction

Enzyme inhibitors

Molecules that prevents enzymes from working. They bind to an enzyme, but not at its active site, changing the shape of the active site so that it can no longer fit the substrate. For example:

- Cyanide (a poison) inhibits the working of one of the enzymes involved in respiration

- Heavy metals such as lead and mercury combine with inactive enzymes in the cells of the nervous system, leading to serious effects

Co-factors

Many enzymes can't work on their own, but need an additional non-protein substance or co-factor for them to work. For example, Haemoglobin (an enzyme) needs iron (Fe) as a co-factor

Transport across cell membranes

Cells need to move materials across the cell membrane to obtain nutrients for energy, growth and repair, get rid of excess materials and metabolic wastes, exchange gases (usually CO2 and O2) and take in water, minerals and food

Cell membrane

A boundary that separates the contents of the cell from the surrounding environment and controls movement in and out of the cell. It is composed of a phospholipid bilayer in which protein molecules are embedded and carbohydrates extend out. The phospholipid molecules are arranged with their hydrophilic (water loving) 'heads' outwards and their hydrophobic (water fearing) 'tails' facing inwards. The cell membrane is semi-permeable (very selective, only lets small molecules diffuse easily)

Passive transport

No energy (ATP) is required for the molecules to move into or out of the cell. Examples are diffusion and osmosis

Diffusion

The movement of molecules from an area of high concentration to an area of low concentration through a semi-permeable membrane. The difference between the two areas is called the concentration gradient. For example, oxygen diffusing into blood across alveoli in the lungs

Factors that affect the rate of diffusion

- The size of the molecules (small move faster)

- The temperature (warm moves faster)

- The state of matter diffusing (gases move faster than liquids, solids don't diffuse)

- The steepness of the concentration gradient

Facilitated diffusion

Transport molecules help (facilitate) certain molecules to pass through the cell membrane. This is a passive process and does not require the use of ATP. For example, when glucose passes into the liver

Types of transport proteins

Channel proteins and carrier proteins

Channel proteins

Allow charged substances (usually ions) to diffuse across membranes. Most channels can be gated (opened or closed) allowing the cell to control entry and exit of ions

Carrier proteins

Have a binding site for a particular solute. The substance will bind on the side where it is at high concentration and be released where it is at low concentration

Osmosis

The movement of water molecules from an area of high concentration to an area of low concentration through a semi-permeable membrane

Solute

Substance being dissolved e.g. salt

Solvent

Substance doing the dissolving e.g. water

Hypotonic solutions

Solutions with a lower solute concentration and a higher water concentration, causes animal cells to swell and may burst (lysis), creates turgor pressure in plant cells which is important for plants to maintain an upright position

Hypertonic

Solution with a higher solute concentration and a lower water concentration, causes cells to shrink (net movement of water is outward), causes plasmolysis in plant cells (cell membrane pulls away from cell wall and the plant wilts)

Isotonic

Solutions of equal solute concentration

Osmoregulation in animal cells

Because animal cells have no cell wall, they burst (lyse) if water moves into them, and if water moves out they shrivel. Single-celled organisms such as paramecium, amoeba and euglena have a constant problem of water flowing into their cells (by osmosis, passive transport, high concentration of water from the surrounding water to a low concentration in the organism) as they live in a hypotonic environment. They overcome this osmoregulation problem by having contractile vacuoles, using active transport (pumping water from a low concentration in the cell to a high concentration in the surrounding water) to remain isotonic

Osmoregulation in plant cells

There is a large vacuole in the centre of plant cells. If this loses water the cells are plasmolysed (the cytoplasm and cell membrane pull away from the cell wall, the cell becomes floppy). If there is a slight loss of water pressure the cell is said to be flaccid and the plant will wilt. When water passes into the vacuole, the cell swells until it is turgid, which is the best state for plants. The cell is prevented from bursting by the cell wall

Active transport

Movement of molecules from an area of low concentration to an area of high concentration. This is against a concentration gradient and requires energy (ATP). A cell with a high rate of active transport has large numbers of mitochondria. Methods are:

- Active transport (pumping)

- Vesicles

Pumping

Active transport is the pumping of substances across a membrane by a protein pump molecule. The protein binds a molecule of the substance to be transported on one side of the membrane, changes shape, and releases it on the other side

Vesicles

Large molecules (such as proteins, polysaccharides and nucleotides) and even whole cells are moved in and out of cells by membrane vesicles

Endocytosis

The transport of membranes into a cell. Materials are enclosed by a fold of the cell membrane, which then pinches down to form a closed vesicle

Pinocytosis

When the materials and the vesicles are small (such as a protein molecule) the process is known as pinocytosis (cell drinking)

Phagocytosis

If the materials are large (such as a white blood cell ingesting a bacterial cell) the process is known as phagocytosis (cell eating)

Exocytosis

The transport of materials out of a cell. It is the exact reverse of endocytosis

Cellular respiration

Respiration is required by all cells to produce ATP energy required for essential life processes. Chemical energy in the form of glucose is converted into chemical energy in the form of ATP and heat energy. It involves both the cytoplasm and the mitochondria, and cells with higher energy demands will have more mitochondria

Requirements and products of respiration

Requirements are food molecules (especially glucose), enzymes, ATP and oxygen (unless it's anaerobic respiration). Products are CO2 and water (waste products) and ATP energy. In anaerobic respiration, the waste products are lactic acid, or CO2 and ethanol

Respiration equation

Mitochondria

Mitochondria are the powerhouse of the cell. They produce ATP energy for the cell to use in the carrying out of essential life processes

Structure of mitochondria

They have 2 membranes, the inner and the outer. The inner membrane is organised into layers called cristae that increase the surface area of the inner membrane to allow a higher transport rate of reactants (e.g. hydrogen ions and oxygen) and products (e.g. carbon dioxide and water). The matrix contains enzymes which speed up the breakdown of glucose products into carbon dioxide and water

ATP

Adenosine triphosphate - its third phosphate bond is a high energy bond which carries energy. When it gives up this energy for a body process it loses a phosphate and becomes ADP (adenosine diphosphate).

Storing energy: ADP + P -> ATP

Releasing energy: ATP -> ADP + P

Steps of cellular respiration

1. Glycolysis (2 ATP)

2. Krebs Cycle (2 ATP)

3. Electron transport chain (34 ATP)

Total yield per glucose molecule is 38 ATP

Glycolysis

Occurs in the cytoplasm and needs 2 ATPs to get started. Glucose is converted to 2 pyruvate molecules, which releases 4 ATPs and 2 hydrogen atoms, meaning the net gain is 2 ATPs and 2Hs

Krebs Cycle (citric acid cycle)

Only occurs in aerobic respiration in the mitochondrial matrix.

1. Two pyruvate molecules are transported through the mitochondrial membrane to the matrix

2. The pyruvate molecules are then converted into Acetyl Co-enzyme A molecules and carbon dioxide

3. Acetyl CoA is broken down in the Krebs cycle into carbon dioxide, hydrogen atoms and 2 ATP

It takes 2 turns of the Krebs Cycle to oxidise 1 glucose molecule

Electron Transport Chain

Only occurs in aerobic respiration in the inner mitochondrial membrane (cristae).

1. Hydrogen from the Krebs Cycle produces high energy electrons which pass along a chain of proteins on the cristae

2. As the electrons pass along the respiratory chain they lose their high energy to produce 34 ATPs

3. At the end of the process hydrogen joins with oxygen to form water

Anaerobic respiration

Also called fermentation, occurs when there is not a lot of oxygen available. It produces very little energy, as only the glycolysis stage will occur and involves only the cytoplasm. 1 glucose molecule is only partially broken down to form 2 ATP and waste products. It is affected by temperature. It can be harmful (e.g. lactic acid can make you feel sick) or help (e.g. with making bread rise or make yoghurt sour

Anaerobic pathways

1. Glucose -> 2 lactic acid (C3H6O3) + 2 ATP

- happens in muscle cells when they run out of oxygen

- happens in bacteria that make yoghurt and cheese

2. Glucose -> 2 ethanol (C2H6O) + 2CO2 + 2 ATP

- happens in some bacteria and yeast

- happens in the production of vinegar

- happens in some organisms that live in swamps, estuarine mud, in the guts of animals

Aerobic respiration

Very efficient, needs oxygen to occur. It is enzyme driven and these enzymes are located in the cytoplasm. 1 glucose is completely broken down to carbon dioxide and water. It releases a lot of energy (38 ATP per molecule of glucose). It involves both the cytoplasm and the mitochondria, and is affected by oxygen demand

Factors affecting respiration

- Oxygen supply (sufficient supply needed)

- Temperature (low=slow, increasing temp=increased rate, high=denatured enzymes)

- Body's energy demands (high energy demand needs increased)

Respiration in exercise

During heavy exercise initially the muscles carry out aerobic respiration as there is lots of oxygen therefore large amounts of ATP is produced and energy released. As exercise continues the oxygen supply cannot keep up with demand and some pyruvate will remain in the cytoplasm and convert to lactic acid, causing muscles to cramp. Near the end of exercise respiration will be largely anaerobic due to less oxygen being supplied to muscles than is needed

Slow twitch muscle

Slow twitch fibres have a good blood supply, which ensures that they receive a large amount of oxygen, which allows them to work for a long time before becoming fatigued. They have a large number of mitochondria, which provide them with an almost limitless amount of energy. Combined with their large blood supply, slow twitch muscle fibres are ideally suited to long, endurance type activities. Aerobic respiration is used for a longer time at a slower rate

Fast twitch muscle

Fast twitch fibres have a relatively poor blood supply, which results in relative blood restriction, so fast-twitch fibres tend to fatigue much faster than the better oxygenated slow-twitch fibres. They also have considerably fewer mitochondria which also makes them fatigue much faster. Fast twitch muscle fibres are good for rapid movements like jumping or sprinting. They contract quickly but tire fast as they consume lots of energy. Aerobic respiration is used for a shorter time at a faster rate

Photosynthesis and requirements for it

Photosynthesis is a process by which plants manufacture their own food using sunlight, carbon dioxide and water. It occurs in the chloroplast.

Requirements:

- carbon dioxide (CO2) from the atmosphere

- water (H2O) from the soil or atmosphere

- light, usually as solar radiation from the sun

Products of photosynthesis

Products:

- glucose (carbohydrates)

- water (H2O)

- oxygen (O2)

Glucose is stored as starch in the plant, enzymes break the starch back into glucose to provide the plant with energy so it can grow, repair and carry out life functions

Photosynthesis equation

Chloroplast

Contains chlorophyll which is inside thylakoids (disks stacked up to form stacks called grana). Grana are joined by lamella. Stroma is the clear fluid filling the chloroplast

Adaptations of chloroplast

- Chloroplasts are small so there can be many chloroplasts in each cell and they have a large SA:V ratio so CO2, O2, glucose and water can diffuse easily

- They are located near the cell wall so it is easy for light and CO2 to diffuse in

- They have a double membrane - the outer membrane surrounds the stroma and the inner membrane is folded to increase the surface area for light absorption

- The stroma is clear so it does not block sunlight, and contains enzymes for the light independent phase to happen

- The grana contain enzymes for the light phase to occur and have a large SA for maximum absorption

Chlorophyll

A pigment that absorbs red and blue light, but reflects green light (which is why plants appear green to our eyes). It is required for photosynthesis to occur

Autotrophic

Because plants can 'manufacture' their own energy directly, they are self-suffient and can survive independently of other living things (autotrophic)

Heterotrophic

All other forms of life, such as humans, animals, insects and bacteria depend on other living things for sustenance (heterotrophic)

Phases of photosynthesis

1. Light dependant phase (requires light to occur)

2. Light independent phase (does not depend on light for energy)

Light dependent phase

Takes place in the thylakoids, only during daylight hours. The chlorophyll absorbs light to split water into hydrogen and oxygen (released as a waste product), and charge up ADP to ATP (energy)

Light independent phase

A cyclic process that occurs in the stroma of the chloroplast, takes place at any time. This combines hydrogen (from the light phase) with carbon and oxygen (from CO2) to make glucose (C6H12O6). ATP from the light phase provides the energy

Factors affecting photosynthesis

- light quality, intensity and duration

- carbon dioxide concentration

- temperature

- water availability

- chlorophyll concentration

How light quality affects photosynthesis

Chlorophyll will only react to certain wavelengths of light. Light in the blue and red wavelengths are most necessary for photosynthesis

How light intensity affects photosynthesis

Plants react differently to different levels of light. Some plants are more sun-loving while others prefer the shade. However, as a general rule the brighter the light the more efficient the photosynthetic process

How light duration affects photosynthesis

The longer the day, the longer the light duration, the more photosynthesis can take place and the more a plant can grow

How carbon dioxide concentration affects photosynthesis

The higher the carbon dioxide concentration, the faster the rate of photosynthesis is. Greenhouse owners sometimes release carbon dioxide gas into greenhouses to increase plant growth

How temperature affects photosynthesis

Plants react differently to different temperatures. Some plants like high temperatures while others prefer lower temperatures. However, as a general rule the higher the temperature the more efficient the photosynthetic process (with the exception of low light conditions)

How water availability affects photosynthesis

Plants that suffer from a lack of water will experience a slowing of photosynthetic activity. Stomata open and close by guard cells and rely on water moving in and out to open and close. If there is no water then no CO2 or water can enter therefore there will be a decrease in photosynthesis and therefore impaired growth of the plant

How chlorophyll concentration affects photosynthesis

Chlorophyll is required for photosynthesis and the more chlorophyll, the faster the rate of photosynthesis

Structure of a leaf

Cuticle: A waxy, waterproof layer which cuts down the water lost by evaporation and protects against parasitic fungi

Upper epidermis: A single layer of cells that are transparent and contain no chloroplast allowing light to pass straight through

Palisade layer: Made up of palisade cells which contain chloroplasts, where most of the photosynthesis takes place

Vein: Contains tubes called the xylem and phloem. The xylem brings water and salts to the leaf for photosynthesis. The phloem transports the dissolved foods away

Spongy layer: consists of irregularly shaped cells with large air spaces between them allowing gas exchange (diffusion) between stomata and photosynthesising cells

Lower epidermis: contains lots of tiny holes or pores called stomata at regular intervals which allow gases to diffuse in and out of the leaf

How leaves are adapted for photosynthesis

- High surface area: volume ratio of leaves (thin and flat so more sunlight can be absorbed)

- Arrangement of leaves (spread out so sunlight can hit as many leaves as possible)

- Epidermis is thin and transparent (to allow more light to reach the palisade cells)

- Thin cuticle made of wax (to protect the leaf without blocking out light)

- Palisade cell layer at top of leaf (to absorb more light)

- Spongy layer (air spaces allow carbon dioxide to diffuse through the leaf, and increase the surface area)

- Palisade cells contain many chloroplasts (to absorb all the available light)

DNA

- A chemical that contains the genetic code

- It is double stranded and twisted into a spiral, a shape called a double helix

- Made up of two long chains of sub-units called nucleotides (sub-units of DNA made up of a 5-carbon sugar called deoxyribose, a phosphate group and a nitrogenous base)

Genes and alleles

A gene is a section of DNA that codes for a particular characteristic. Different genes code for different characteristics. Alleles are alternative forms of a gene that code for the same characteristic. The allele on each chromosome may be the same or different

How do genes work?

Each unique gene has a unique sequence of bases. The order of bases determines which amino acids are produced which determines the protein made which makes up the traits or characteristics

DNA replication

- Cells must divide for growth, replacement of cells and for reproduction

- When cells divide they must get an exact copy of DNA, therefore the DNA must make a copy of itself (replication)

- The replication of DNA is called "semi-conservative" as the two new DNA double helixes contain one strand of the original DNA and one new strand

DNA replication steps

1. The hydrogen bonds between the bases start to break with the help of an enzyme

2. The two strands unzip and unwind to expose the unpaired bases

3. Phosphate and sugar join up to form the 'sides' of the new strand

4. New nucleotides that match to the exposed bases assemble alongside in a 5' to 3' direction, and hydrogen bonds bind them together with an enzyme.

5. The two DNA molecules wind up and achieve double helix shapes. Each molecule is half 'old' material, half 'new' (semi-conservative)

Factors that affect DNA replication

- Because this process is controlled by enzymes, any factor that affect enzymes will affect the rate - temperature, amount of nucleotides present (substrate), amount of enzymes present

- Plants grow more in spring (cells divide more) because its warm with unlimited resources for all cell processes including DNA replication

- Animals grow more at certain stages of their life cycle e.g. foetus

Cell cycle

1. G1 (gap 1): normal cell functions occur as well as cell growth

2. S (synthesis): DNA replicates, producing two copies of each chromosome

3. G2 (gap 2): the cell continues to prepare for mitosis and cell division

4. M (mitosis): duplicate copies of the chromosomes are created and the nucleus divides into 2, each with identical genetic material

5. C (cytokinesis): the cell's cytoplasm divides and 2 genetically identical daughter cells are formed

Mitosis

- A type of cell division needed for growth, repair and replacement of cells

- Occurs everywhere in the body

- Produces 2 new cells, identical to the parent cell and with the same number of chromosomes

Mitosis steps

1. Chromosomes shorten, fatten and become visible

2. Each chromosome divides to form two chromatids and the nuclear membrane disappears

3. The chromatids line up across the middle of the cell and a spindle forms (strings of protein)

4. The chromatids are pulled apart by the spindle; they are now called chromosomes. They are pulled to either end of the cell

5. The parent cell starts to split in 2 and new nuclear membranes are formed

6. 2 cells are formed, each with the same number of chromosomes of the parent cell

Factors affecting the rate of mitosis

- stage of life

- availability of nutrients

- location of cells

- environmental factors

How stage of life affects the rate of mitosis

The rate of mitosis is very high when organisms are undergoing growth and repair. For example:

- during the early years of development (infancy/childhood and puberty related growth spurts in humans, the breaking of dormancy and germination in plants)

- seasonal growth in plants

- following damage to the organism when repair of the tissue is necessary

How availability of nutrients affects the rate of mitosis

Replication is slowed or prevented if vital nutrients are not available

How location of cells affects the rate of mitosis

Specific areas of an organism may have a higher rate of mitosis where most growth or replacement of cells is occurring, such as root/shoot tips, hair follicles, bone marrow, skin cells, mucus membranes etc

How environmental factors affect the rate of mitosis

The processes of mitosis and DNA replication involve enzymes. Therefore the rate of mitosis and DNA replication are affected by factors that affect enzymes - temperature, pH, substrate and enzyme concentration