Year 11 Biology Term 1

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Prokaryotic Cell

A unicellular organism that lacks a nucleus and membrane bound organelles.
Archaea and Eubacteria
0.1-5 micrometer
Single circular chromosome in cytoplasm area called nucleoid.
Non-essential genes - plasmids.
Smaller ribosomes found in cytoplasm.
Rigid cell wall outside plasma membrane
Capsule - sticky outer coating to cling to surfaces.
Short projections - pili, long projections - flagella
Asexual reproduction, chemosynthesis, aerobic and anaerobic respiration, horizontal gene transfer.

Eukaryotic Cell

Protista, Fungi, Plantae, Animalia are the four kingdoms.
All multicellular organisms are eukaryotic.
Membrane bound organelles and nucleus.
Adaptable cell shape depending on function.
Eukaryotic DNA - multiple linear chromosomes.
Phospholipid Bilayer
Cell walls (if applicable) are made of carbohydrates (unlike prokaryotes)
Plant CW - cellulose, Fungi CW - Chitin.
All carry respiration. Plants - photosynthesis, Fungi - fermentation,
Reproduction - Animal + some plants - sexual, fungi, some plants, protists - asexual.

Eubacteria

Cell wall of peptidoglycan, cell membrane - phospholipid bilayer, common in moist, low salt environments of moderate temperatures.

Archaea

Extremophiles,
Main circular chromosome with two smaller, extra-chromosomal elements.
No cell wall peptidoglycan
Contain phytanyl in the phospholipid bilayers.

Cell theory states

All living things are made up of cells, cells are the basic units of structure and function in living things, new cells are produced from existing cells

The Light Microscope

Passes a focused beam of light through the specimen, passing through the objective lens, up to the ocular lens (eyepiece) and into the eye You multiply the magnification of the objective and ocular lenses Light Microscopes have a maximum resolution of about 1500x.
Resolution - describes the ability of a lens to distinguish two points.
Light Microscopes can be used to view both living an dead specimens
Stains can be used to highlight parts of the cell

Whole mount

A specimen to be observed with a microscope that is an intact object, either living or dead, and can be an entire intact organism or a small part of a large organism.

Smear

Cells suspended in fluid being viewed on a light microscope

Sections

Thin Slices of Specimens.

Electron Microscope

Uses a beam of electrons as a source of energy. Two types - TEM and SEM.|
Electron Microscopes do not transmit colour

TEM

Requires a thin specimen to allow the passing of electrons Magnetic lenses condense and focus the electrons onto a fluorescent screen where it can be viewed.
Modern TEM have a 1 000 000x magnification and a resolution of 0..0001 micrometres.
The electron beam must travel in a vacuum, and specimens must be dehydrated and therefore dead.

SEM

The specimen is coated with a thin layer of metal and the electrons are deflected, allows a 3D image to be produced.

Staining

Stains and dyes used to highlight biological tissue structures, enhance contrast, define and example bulk tissues, cell populations, or highlighting specific organelles.
Example - Methylene blue reacts with DNA to visualise the location of the nucleus.

Autoradiography

Use of X-ray or photographic film to detect radioactive materials.
Radioactive tracer - chemical compound where one or more atoms have been replaced by a radioisotope. This allows the path that the atom takes from reactant to product to be followed, and the products formed to be analysed.

Main Function of Cell Organelles

Synthesis and processing of cellular materials, storage, energy transformations, structure, movement, breakdown/recycling of waste/foreign materials.

Endosymbiotic Theory

Suggests that membrane bound organelles originated when smaller prokaryotes were consumed, creating a co-dependent set of organisms.
Evidence - Chlorpolasts and Mitochondria are surrounded by a double membrane and

Nucleus

A large spherical organelle which contains DNA in the form of Chromosomes which determine the cell characteristics and control its activity. Its rich in nucleoproteins (nucleic acid + protein)

Nuclear Membrane

Semi-permeable membrane which is perforated which allows large molecules like RNA to enter and exit the Nucleus.

Nucleolus

Found in the nucleus which contains the genes for RNA synthesis and is also the site for ribosome production.

Cytoplasm

A jellylike fluid inside the cell in which the organelles are suspended. It contains water, dissolved nutrients, and mineral ions.

Cell Membrane

Selectively permeable barrier between the cell and the environment, which allows some molecules to move in and out of the cell.

Cell Wall

A rigid wall made of cellulose, located outside of the cell membrane, providing structural support.

Mitochondria

Small oval shaped organelle surrounded by a double membrane. The inner membrane is folded into cristae (to increase surface area). Enzymes on the membrane catalyse ATP production via respiration. Contains DNA.
The matrix of the cell is the "free" space.

Ribosomes

Small sites of protein synthesis inside the cytoplasm. Attatched to the E.R or suspended in cytosol.

Endoplasmic Reticulum

A series of membranous sacs that produce lipids, carbohydrates, proteins, providing a transport path within the cell. May be surrounded by Ribosomes (or not).

Golgi Body

Stacked, flattened, vesicles called cisternae. Chemically modify, store, package, and distribute substances.
Can be in any eukaryotic cell, but mainly so in cells involved in secretion.

Lyosome

Contains about 40 enzymes which are involved in solid waste processing.

Chloroplast

A green, disc shaped organelle enclosed by a double membrane. The inter membrane called the lamella, is modified into sacs called thylakoids. Stacks of thylakoids are called grana, which increase the surface area. The grana are embedded into the stroma. Chloroplasts contain DNa, ribosomes and chlorophil, therefore being the site of photosynthesis.

Vacuole

Membrane bound storage sites for water and waste. When part of an animal cell, they are small and numerous.

Microtubules

TIny hollow tubules which control the shape of the cell and its movement.

Cytoskeleton

Microtubules of a protein called tubulin and filaments of protein named actin. Supports the cell structure, allows movement, and helps transport organelles and vesicles within the cell.

Centrioles

Pair of small cylindrical structures composed of microtubules. Involved in cell division and formation of pili/flagella.

Cilia and Flagella

hairlike structures that extend from the surface of the cell, where they assist in movement. Arrangement of microtubules.

Microns (micrometers)

a cellular measurement equal to one thousandth of a millimeter.

The Cell Membrane (ID)

Every cell is surrounded by a membrane.
Forms boundary and separates the cell from the external environment.
Regulates the passage of molecules.
Cell recognition and communication with other cells.
Extracellular fluid - the area outside the cell. In unicellular organisms, this is the environment, meaning that changes in the environment can rapidly affect their survival. Multicellular organisms control the composition and are less affected by the changes in environment. They can control pH, salt, water, oxygen, CO2, glucose, and nitrogenous waste concentrations.

The Phospholipid Bilayer

Phospholipids are comprised of glycerol and two fatty acid tails, as well as a phosphate group. They are arranged in a double layer, with a POLAR HYDROPHILIC outside, and a NON-POLAR HYDROPHOBIC inside. Relatively impenetrable to water soluble particles, ions, large polar molecules. Only non-polar molecules (O2, CO2), and very small materials can pass through.

Cholesterol

Lipid made of four fused carbon rings, fit within phospholipids and disturb the close packing. Regulates membrane stability and permeability.

Proteins (Cell Membrane)

Comprise 50% of the mass and are responsible for many properties.
Key functions: Connect and join cells together, may be enzymes, allow substance transport, cell identification/recognition, shape and motility, and are receptors for peptide hormones.

Integral Protein

Permanently attatched to the membrane and span across the bilayer.
Channel proteins are integral proteins that allow ions or other small molecules across the membrane.

Peripheral Proteins

are temporarily attached to one side of the membrane.

Carbohydrates (Cell Membrane)

Attach to proteins to form glycoproteins, or to membrane lipids to form glycolipids.
Forms, along with proteins, the glycocalyx (used for cell recognition, protection and adhesion)..

Fluid-Mosaic Model

Cell membranes appear to be able to form, reform and change.
Fluidity - individual phospholipid molecules and some proteins can move about.
Capacity for proteins to move allows them to carry out functions.

Active vs Passive transport

Active needs energy; passive does not.
Active transport requires ATP and can go against the concentration gradient.

Diffusion

Net movement of particles of a substance from a region of higher concentration to a region of lower concentration.

Osmosis

Semi-permeable membrane limits the diffusion of the solute. To compensate, there is a net movement of water from the area of LOW CONCENTRATION TO HIGH CONCENTRATION.
Osmotic pressure - pressure causing water to move along the gradient.
Water often moves through special protein channels called aquaporins.

Solvent

A liquid substance capable of dissolving other substances

Solute

A substance that is dissolved in a solution.

Hypotonic

The environment is less concentrated than the cytosol of the cell.
Plant cells become turgid (swell up to fit the wall) and Animal cells lyse (burst open)

Isotonic

Equal concentration outside and inside cell, leading to a normal animal cell and a flaccid plant cell.

Hypertonic

More concentrated environment than in cell, leading to a shriveled animal cell and a plasmolysed plant cell. This leads the cell membrane to separate off of the cell wall and can lead to death of the cell.

Simple Diffusion

A net particle movement down a concentration gradient, when particles can move through the membrane easily.

Facilitated diffusion

Particles are too large or charged meaning they cannot pass through the membrane. They move through integral proteins instead,

Channel Proteins

Water filled channel in the membrane, allows water soluble or polar molecules. as well as some ions to pass through the membrane.

Carrier Proteins

Have a specific binding site and constantly flip so that the site is alternately open to opposite sides of the membrane.
The substance will release to an area where there is a lower concentration.

Protein Pumps

Actively pump molecules from one side of the membrane to the other. Different pumps are for different molecules. The pumps binds to a molecule and uses energy to change shape, releasing it on the other side.
Ions, amino acids, glucose, and other products of metabolism move across the membrane using protein pumps.
Sodiam Potassium pump is an example, pumping 3sodium ions out for two potassium molecules in.

Vesicles

Allow the bulk transport of large molecules (such as polysaccharides, proteins, and nucleotides)

Endocytosis

Materials are enclosed by the cell membrane and then taken in. Enzymes digest the membrane and the contents are abhasorbed.

Pinocytosis

Cell engulfs extracellular fluid which includes molecules like sugar and proteins.

Phagocytosis

Cell engulfs large solids.
Example - white blood cell eating a bacteria

Receptor-mediated endocytosis

Protein receptors of the cell bind to specific molecules which trigger the engulfment of a substance.

Exocytosis

Transport of materials out of a cell.

Surface Area to Volume Ratio

A cell needs to feed its volume through its surface area. As volume increases, the ratio of surface area to volume decreases. Cells also need materials to diffuse to the center, which takes longer if a cell is larger. Therefore, smaller cells are more efficient.

When cells reach a certain size, it divides by mitosis to maintain a favourable SA:V ratio. Big volumes can be supported if the cell is flat or a long tube, or with projections on the surface.

Concentration Gradients

Number of solute molecules that can be found within a given volume of solvent. Greater CG (difference between high and low solute concentration in a solvent) -\> greater diffusion rate.

Polarity (Factors Affecting the Exchange of Materials Across Membranes)

Non-Polar means molecules without a charge. Non-polar molecules are hydrophobic and can dissolve in the fatty acid chains. This means they can easily penetrate the plasma membrane. Examples are gases like CO2 and non-polar hormones.
Polar molecules (with a charge) are hydrophilic and can dissolve in water. They do not diffuse across the bilayer easily. The bilayer is virtually impenetrable to ions, surrounded by a cage of water. Water soluble molecules such as non-polar ones have to use active transport such as protein pumps to get through.

Temperature (Factors Affecting the Exchange of Materials Across Membranes)

Diffusion rate is affected by temperature due to kinetic theory.

Solubility of particles (Factors Affecting the Exchange of Materials Across Membranes)

Lipid soluble substances easily diffuse through the membrane, and cross the membrane much faster than water-soluble substances.

Size of particles (Factors Affecting the Exchange of Materials Across Membranes)

Smaller the particles, faster rate of diffusion. Small molecules can slip between the phospholipids by diffusion. For example, oxygen is only two atoms.

Protoplasm

The entire cell contents, including the cytoplasm, nucleus.

Organic Compounds

have a structure based on carbon-carbon and hydrogen-carbon bonds. Atoms are linked to form carbon chains or rings.. Examples include carbohydrates, proteins, lipids. Many organic molecules are polymers, which are made by linking monomers.
Organic compounds, primarily glucose, are used for respiration.

Inorganic Compounds

Do not have a structure based on carbon rings/chains. Examples: Calcium, water, etc.

Phototrophs

use photoreceptors to capture energy from sunlight and turn it into chemical energy.

Chemotrophs

use organic molecules such as glucose or inorganic chemicals such as hydrogen sulfide for energy.

Autotroph

an organism that is able to form nutritional organic substances from simple inorganic substances such as carbon dioxide.

Heterotroph

an organism deriving its nutritional requirements from complex organic substances.

Carbohydrates

Made of Carbon, Oxygen, and Hydrogen arranged in rings. They are broken down into glucose during digestion, and used in respiration to release energy, and provide structure and support for the cell.

Monosaccharide, Disaccharide, Polysaccharide

Monosaccharide: simple sugars (fructose, glucose, galactose)
Disaccharide: two simple sugars bonded (sucrose, lactose)
Polysaccharide: many carbohydrates joined together, such as starch.

Lipids

Carbon, Hydrogen, and Oxygen arranged in chains. Lipids are usually composed of triglycerides, a glycerol head with 3 fatty acid tails.

They are used to store energy, serve as a structural component, and as hormones.

Protein

A three dimensional polypeptide chain, where the polypeptides are made of amino acids. They contain Nitrogen, Oxygen, Carbon, Hydrogen, Phosphorus, and Sulphur.

Polypeptides

A chain of amino acids (about 75 or more) that are linked together with peptide bonds.

amino acids

They are building blocks of proteins (monomers), there are about 21 in the human body.

nucleic acids

Contain Carbon, Oxygen, Hydrogen, Nitrogen, and Phosphorus. They are made of large chains of nucleotides, the monomers of nucleic acids.
They store and transmit genetic information.

DNA vs RNA

Deoxyribose sugar vs. ribose sugar, thymine vs. uracil , DNA has a double helix structure with nucleotides in the middle, and RNA has a single strand and does not contain thymine.

Vitamins

Vitamins are essential in small quantities to promote normal metabolism/growth, an example of their use is them being cofactors of enzymes.

Photosynthesis in Autotrophs

Photosynthetic autotrophs capture light energy and convert it into glucose, stored in complex organic compounds that are passed through the ecosystem.

Carbon Dioxide + Water -\> Glucose + Oxygen
Light Energy
6CO2+6H20 -\> C6H12O6 + 6O2

Chloroplast Structure

Composed of outer membrane, inner membrane, and thylakoid system. The inner membrane is impermeable and filled with a liquid called stroma.

The stroma contains a single circular chromosome composed of DNA, ribosomes, and numerous enzymes.

The grana are stacks of small discs called thylakoids, where chlorophyll is made.
Thylakoid - smallest units
Grana - stacks of those units
Lumen - narrow aqueous mixture inside the thylakoid.

Light dependent reactions

Takes place in presence of light, requires water, light and chlorophyll to produce ATP. Light energy is trapped by the photoreceptor in the green pigment and is used to energise the surface of the lamellae or the thylakoid stacks.

Light independent reactions

The reaction in which glucose is made, uses ATP & NADPH to change carbon dioxide into glucose, takes place in the stroma, doesn't need sunlight to work.

Factors affecting rate of photosynthesis

Light intensity - more light makes faster reaction until upper limit is reached.
CO2 Levels - as it increases, photosynthesis will increase until an upper limit.
Temperature - enzymes in photosynthesis are sensitive and photosynthesis only happens in a narrow temperature range.
Availability of chlorophyll - more green plants have higher photosynthesis.

Cellular Respiration in Eukaryotic Cells

Glucose most be broken down chemically and the energy released is in the form of adenosine triphosphate. This breakdown is called Respiration.

Aerobic Respiration vs Anaerobic Respiration

Aerobic - requires oxygen, complete breakdown of glucose into CO2 and H2O. 15x more efficient.
Anaerobic does not require oxygen and breaks down glucose into lactic acid or alcohol and carbon dioxide. Example is yeast fermentation.

Aerobic respiration equation

Glucose + Oxygen -\> Carbon Dioxide + Water + ATP
C6H12O6 (aq) + 6CO2 -\> 6CO2 (g) +6H2O + 38 ATP

Aerobic respiration occurs in about 50 steps with many different enzymes.

ATP

High energy phosphate bonds store large amounts of chemical energy.
It is Adenosine linked to 3 phosphate groups, and in the 3rd bond, there is the energy stored. When the energy is released, the ATP breaks the bond to become ADP, going back to the Mitochondrion to be recharged.

The Structure and Function of Mitochondria

Respiration occurs in the mitochondria.
Mitochondria are composed of an inner and outer membrane. The outer membrane is like a string, while the inner membrane folds over many times to create layers known as cristae.
Fluid in Mitochondria is called matrix.
Outer membrane is porous, so ions and small uncharged molecules can move through the membrane proteins. The inner membrane is a tight barrier which can only get past using transport proteins.
Cristae - main sites of ATP synthesis.
Matrix - site for DNA replication, protein biosynthesis, enzymatic reactions.

The Removal of Cellular Products and Wastes

For small molecules, diffusion allows waste to be eliminated.
Lyosome - contains enzymes to break down cellular waste.
Vesicles may also store waste, including ingested material from endocytosis. Lyosomes bind with vesicles and digest the matter.
Exocytosis may be used to remove large scale waste products.

Enzymes

Biological catalysts, control the rate of chemical reactions. Made of proteins, Acts on a substrate to break it down or synthesize something more complex. Lowers the amount of activation energy needed for a chemical reaction to occur.
Made of chains of amino acids to form polypeptides which together make enzymes.
Each enzyme has specific enzyme-substrate interactions.
LAK, IF are the two types of enzyme substrate models. Basically, enzymes fit the two substrates together and chemical reactions occur.

pH (Factors affecting enzyme activity)

a logarithmic scale, 0 is acidic, 14 is basic
Enzymes only tolerate a narrow range of pH, with a deviation distorting the active site and denaturing the enzyme.

Temperature (Factors affecting enzyme activity)

As temperature increases, enzyme activity increases until after an optimum. This is when the enzyme activity declines due to denaturisation, or a change in shape of the enzyme.

Amount/Concentration of Substrate (Factors affecting enzyme activity)

Large amounts of substrate will increase enzyme activity until all active sites are filled, when the reaction stabilises.

Enzyme Concentration (Factors affecting enzyme activity)

Level of enzyme present affects the rate of reaction (more means faster generally)

Salt (Factors affecting enzyme activity)

Ions can interfere with intermolecular forces within enzymes.