OCR A-Level Biology Module 2: Foundations in Biology PDF

OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.1 Cell structure Learners should be able to demonstrate and apply their knowledge and understanding of:...

OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.1 Cell structure Learners should be able to demonstrate and apply their knowledge and understanding of: (a) The use of microscopy to observe and investigate different types of cell and cell structure in a range of eukaryotic organisms. (b) The preparation and examination of microscope slides for use in light microscopy. (c) The use of staining in light microscopy. (d) The representation of cell structure as seen under the light microscope using drawings and annotated diagrams of whole cells or cells in sections of tissue. (e) the use and manipulation of the magnification formula. (f) The difference between magnification and resolution. (g) The ultrastructure of eukaryotic cells and the functions of the different cellular components. (h) Photomicrographs of cellular components in a range of eukaryotic cells. (i) The interrelationship between the organelles involved in the production and secretion of proteins. (j) The importance of the cytoskeleton. (k) The similarities and differences in the structure and ultrastructure of prokaryotic and eukaryotic cells. OCR A-Level Biology Module 2: Foundations in biology Use of microscopy in determination of cell structure Optical and Electron Microscopes There are two types of microscopes used when studying cells: Optical (light) microscopes and electron microscopes. Optical (light) microscopes Electron microscopes 1. Uses a light to form the image 1. Uses electrons to form an image. 2. Has a maximum resolution of about 2. Has a higher resolution than optical 0.2 micrometres (μm). You cannot microscopes to give a more detailed view organelles that are smaller than image (and can be used to view all 0.2μm - including ribosomes, the organelles). endoplasmic reticulum and 3. Maximum resolution of about lysosomes. Mitochondria may be 0.0002 micrometres (μm) - about visible but not clear. You can see the 1000 times higher than optical. nucleus. 4. Maximum useful magnification of an 3. Maximum useful magnification of electron microscope is about x optical microscopes is about x 1,500,000. 1500. Types of microscopes Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Scanning or Transmission Electron Microscopes There are two basic types of electron microscopes: transmission electron microscope (TEM) and the scanning electron microscope (SEM). Transmission electron microscopes Scanning electron microscopes (TEMs) (SEMs) 1. Uses electromagnets to focus a 1. Scans a beam of electrons over the beam of electrons, which is specimen that knocks off electrons transmitted through a specimen. that are gathered in a cathode ray 2. The densest parts of the specimen tube to form an image. absorb more electrons, which makes 2. The images show the surface of the them look darker. specimen and can be 3D. 3. TEMs produce a high resolution 3. Good for use on thick specimens. image to see internal structure of 4. SEMs give a lower resolution image organelles. than TEMs. 4. They can only be used on thin specimens. Viewing specimens under an optical microscope Step-by-step instructions for preparing a temporary mount of a specimen on a slide: 1. Pipette a drop of water onto the slide and use tweezers to place a thin section of the specimen on the drop. 2. Add a drop of stain to highlight objects in the cell (e.g. eosin for cytoplasm, iodine in potassium iodine solution for starch grains in plant cells). 3. Add a cover slip (square of clear plastic) to protect the specimen. Stand the slip upright on the slide and tilt and lower it until the specimen is cover - making sure not to get any air bubbles under. OCR A-Level Biology Module 2: Foundations in biology Preparing inputs for light microscopy One of the most commonly used microscopes is the brightfield microscope for which the specimens are prepared by fixation and/or staining. Components of a typical brightfield microscope Image Source: cnx.org The specimens can be fixed on the slide by the following methods: 1. Heat-fixation by using a slide warmer. 2. Heat-fixation by holding a specimen a slide with a smear over a microincinerator. 3. Chemical fixation by using chemical agents like acetic acid, ethanol, methanol, formaldehyde (formalin), and glutaraldehyde which denature proteins, stop biochemical reactions, and stabilise cell structures in tissue samples. OCR A-Level Biology Module 2: Foundations in biology Preparing inputs for light microscopy Staining of samples is often used in light microscopy to identify various components of a cell. In simple staining, a single dye is used to emphasise particular structures in the specimen which imparts the same color to all the organisms in a specimen. Types of simple staining Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Preparing inputs for light microscopy Staining of samples is often used in light microscopy to identify various components of a cell. Differential staining employs more than one dye to impart different colors to different organisms in a specimen. Types of differential staining Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Outputs from a microscope Light microscopy as well as electron microscopy produce images, which can be deciphered to the construction of the cellular level. Images produced by each of these vary and can be used as needed. Treponema pallidum spirochetes as seen under dark field microscope, bright field microscope, and scanning electron microscope Image Source: cnx.org Components of cells (with labelling) as observed under microscope Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Magnification and Resolution To see cells and the organelles found within them, you need to use a microscope. Microscopes produce a magnified image of a cell sample, but the resolution is equally important. Magnification Resolution Magnification is how much bigger the The resolution is how detailed the image image appears than the specimen sample is. The better the resolution, the better the is. It’s calculated using this formula: microscope is able to distinguish between two points that are close together. magnification = size of image If a microscope cannot separate two objects, more magnification will not help size of real object to see them. Magnification example Your magnified image is 15mm wide and the actual size of the cell is 0.015mm. What is the magnification? magnification = 15 ÷ 0.015 = x 1000 magnification If no scale bar is given, use the formula actual size = image ÷ size magnification. If you are given the size of the image and the size of the sample in different units in your exam you will need to convert them into the same units before using the formula. You also need to be able to rearrange the formula and look for the units required in the answer. Converting between units cm x10 mm x1000 μm x1000 nm OCR A-Level Biology Module 2: Foundations in biology Eukaryotic Cells and Organelles Cells are the basic building block of life. Living organisms are classified into one of five kingdoms. The biggest division is between the cells of the prokaryote kingdom (the bacteria) and those of the other four kingdoms (animals, plants, fungi and protoctists), which are all eukaryotic cells. Prokaryotes or Eukaryotes 1. Prokaryotic organisms are prokaryotic cells (single-cell organisms) and eukaryotic organisms are made of eukaryotic cells. 2. Both cell types contain organelles, which are parts of cells, and each organelle has a specific function. The structure of eukaryotic cells Here are some general diagrammatic representations of plant and animal cells, and some of the structures (organelles) within them. We need to learn how the structures outlined in the specification are adapted to do their job. A typical animal cell Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology The structure of eukaryotic cells A typical plant cell Image Source: cnx.org Algal and fungal cells Algal cells are similar to plant cells with the same organelles, including a cell wall and chloroplasts. Fungal cells are also very similar but have have two key differences: ○ Their cell walls are made of chitin and not cellulose. ○ They don’t have chloroplasts because they don’t photosynthesise. Algae carry out photosynthesis like plants but they can be single-celled or multicellular. Fungi include yeast and mushrooms. OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Below is a big list of organelles, including their structure and function. You will need to know all of these for your exams. Most organelles are surrounded by membranes - don’t confuse a diagram of an organelle as a diagram of a whole cell. They are only parts of cells. Cell Membrane (Plasma Membrane) Structure of a cell membrane Image Source: cnx.org This membrane is found on the surface of animal cells and just inside the cell wall of other cells. It’s made mostly of lipids and protein. The cell membrane regulates the movement of substances into and out of the cell. Receptor molecules on the membrane allow it to respond to chemicals like hormones. Nucleus This is the largest organelle that is surrounded by a nuclear envelope, which contains many pores. The nucleus contains chromosomes made from protein-bound linear DNA and one or more structures called nucleolus. The nucleus controls cell activity through transcription of DNA, which contain instructions to make protein. The pores allow substances (i.e RNA) to move between the nucleus and the cytoplasm. The nucleolus Structure of a nucleus makes ribosomes. Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Mitochondrion Structure of a cell membrane Image Source: cnx.org This is an oval or rod-shaped organelle that has a double membrane. The inner membrane is folded to form structures called cristae. Inside is the matrix, which contains enzymes involved in respiration. Mitochondrion is the site of aerobic respiration where ATP is produced. They are found in large numbers in very active cells and require a lot of energy. Chloroplast Chloroplast is a small, flattened structure found in plant and algal cells. Surrounded by a double membrane with membranes inside called thylakoid membranes. These stack up to form grana. Grana are linked together by lamellae which are thin, flat pieces of thylakoid membrane. Chloroplast is the site where photosynthesis takes place. Some parts of that process happen in the grana, and others happen in the stroma, which is a thick liquid found in chloroplasts. Structure of a chloroplast Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Golgi Apparatus Structure of golgi apparatus Image Source: cnx.org A series of fluid filled, flattened membrane sacs. Vesicles are often seen at the edges of the sacs. The Golgi apparatus (or Golgi body) processes and packages new lipids and proteins. It also makes lysosomes. Golgi Vesicle This is a small fluid-filled sac (see diagram above) found in the cytoplasm. It is surrounded by a membrane and is produced by the Golgi apparatus. The vesicle stored lipids and proteins made by the Golgi apparatus and then transports them out of the cell through the cell-surface membrane. Lysosome Structure of lysosome Image Source: cnx.org These are small, round organelles surrounded by a membrane and with no clear internal structure. Lysosome is a type of Golgi vesicle. They contain the digestive enzymes lysozymes. The enzymes are kept separate from the cytoplasm by the membrane and can be used to digest invading cells or break down worn out components of the cell wall. OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Ribosome The smallest and most numerous of the cell organelles, ribosomes either float free in the cytoplasm or are attached to the rough endoplasmic reticulum. It’s made up of proteins and RNA, is not surrounded by a membrane and is the site where proteins are made. Structure of ribosome Image Source: cnx.org Rough Endoplasmic Reticulum (RER) This is a system of membranes that enclose a fluid-filled space. The surface is covered with ribosomes. RER folds and processes the proteins that have been produced at the ribosomes. Smooth Endoplasmic Reticulum (SER) Very similar to rough endoplasmic reticulum, except that no ribosomes are present. SER synthesises and processes lipids. Structures of rough and smooth endoplasmic reticulum Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Cell Wall The cell wall is a rigid structure that surrounds cells in plants, algae and fungi. It’s made mainly of the carbohydrate cellulose in plant and algae cells. In fungi, the cell wall is made of chitin. Its primary function is to support cells and prevent them from changing shape. Structure of cell wall Image Source: cnx.org Cell Vacuole A membrane bound organelle found in the cytoplasm of plant cells. It contains a weak solution of sugars and salts called cell sap. The membrane surrounding plant cell vacuoles is called the tonoplast. They help to maintain pressure inside the cell and keep it rigid. The vacuole is also involved in isolating unwanted chemicals in the cell. Structures of rough and smooth endoplasmic reticulum Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Cytoskeleton Eukaryotic cells have an internal cytoskeleton made of microfilaments, intermediate filaments, and microtubules. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored. Structure of cytoskeleton Image Source: cnx.org Two short, identical microtubule structures called centrioles are found near the nucleus of cells. A centriole can serve as the cellular origin point for microtubules extending outward as cilia or flagella or can assist with the separation of DNA during cell division. The microfilament is a thinner type of cytoskeletal filament responsible for muscle contraction. An intermediate filament is a filament intermediate in thickness between the microtubules and microfilaments. Intermediate filaments, in conjunction with the microtubules, are important for maintaining cell shape and structure. Structure of cytoskeletal ‘cables’ intermediate filaments Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Organelles and Their Functions Prokaryotes and Eukaryotes Prokaryotic organisms are prokaryotic cells (single-cell organisms) and eukaryotic organisms are made of eukaryotic cells. Both cell types contain organelles, which are parts of cells, and each organelle has a specific function. Prokaryotic cells are smaller and simpler than eukaryotic cells. Bacteria are a good example of prokaryotic cells. Difference between the structures of eukaryotic and prokaryotic cells Image Source: cnx.org OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.2 Biological molecules Learners should be able to demonstrate and apply their knowledge and understanding of: (a) How hydrogen bonding occurs between water molecules, and relate this, and other properties of water, to the roles of water for living organisms. (b) The concept of monomers and polymers and the importance of condensation and hydrolysis reactions in a range of biological molecules. (c) The chemical elements that make up biological molecules. (d) The ring structure and properties of glucose as an example of a hexose monosaccharide and the structure of ribose as an example of a pentose monosaccharide. (e) The synthesis and breakdown of a disaccharide and polysaccharide by the formation and breakage of glycosidic bonds. (f) The structure of starch (amylose and amylopectin), glycogen and cellulose molecules. (g) How the structures and properties of glucose, starch, glycogen and cellulose molecules relate to their functions in living organisms. (h) The structure of a triglyceride and a phospholipid as examples of macromolecules. (i) The synthesis and breakdown of triglycerides by the formation (esterification) and breakage of ester bonds between fatty acids and glycerol. (j) How the properties of triglyceride, phospholipid and cholesterol molecules relate to their functions in living organisms. (k) The general structure of an amino acid. (l) The synthesis and breakdown of dipeptides and polypeptides, by the formation and breakage of peptide bonds. (m) The levels of protein structure. (n) The structure and function of globular proteins including a conjugated protein. (o) The properties and functions of fibrous proteins. (p) The key inorganic ions that are involved in biological processes. OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.2 Biological molecules Learners should be able to demonstrate and apply their knowledge and understanding of: (q) How to carry out and interpret the results of the following chemical tests: Biuret test for proteins. Benedict’s test for reducing and non-reducing sugars. Reagent test strips for reducing sugars. Iodine test for starch. Emulsion test for lipids. (r) Quantitative methods to determine the concentration of a chemical substance in a solution. (s) i) The principles and uses of paper and thin layer chromatography to separate biological molecules / compounds. ii) Practical investigations to analyse biological solutions using paper or thin layer chromatography. OCR A-Level Biology Module 2: Foundations in biology Water Water is an important constituent of the tissues. Typically about 60% of the water we take in comes from drinks, 30% from food and the remaining 10% is metabolic water (a byproduct of respiration). Water as a Solvent Water is made up of hydrogen ion and hydroxyl ions. It is dipolar in nature thus it attracts both positively and negatively charged ions towards it. It is a universal and a very important solvent in all living organisms. 70% of the human body weight is water. Ions can dissolve in water present in the blood and can be transported to various parts of the body. Water molecules are charged, with the oxygen atom being slightly negative and the hydrogen atoms being slightly positive. These opposite charges attract to each other, forming hydrogen bonds than bind water molecules loosely together. Charged or polar molecules such as salts, sugars, amino acids dissolve readily in water and so are called hydrophilic ("water loving"). Uncharged or nonpolar molecules such as lipids do not dissolve so well in water and are called hydrophobic ("water hating"). Hydrogen bonds are formed between an atom (usually hydrogen) with a slight positive charge (denoted d+) and another atom (usually oxygen or nitrogen) with a slight negative charge (denoted d–). Because hydrogen bonds are weak they can break and form spontaneously at the temperatures found in living cells without needing enzymes. When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Water Can Resist Changes in Temperature Hydrogen bonds between water molecules can absorb a lot of energy. This means that water has a high specific heat capacity - it takes a lot of energy to heat it up. Water has a specific heat capacity of 4.2 J g-1 °C-1, which means that it takes 4.2 joules of energy to heat 1g of water by 1°C. This unusually high heat capacity means that water does not change temperature very easily. The constant temperature is useful for living organisms because it means water doesn’t experience rapid temperature changes. Water is a good habitat as the temperature underwater is likely to be more stable than on land. Water inside organisms is also fairly stable - which helps them to maintain a constant internal body temperature. Strong cohesion between water molecules Cohesion is the tendency of molecules within a substance to “stick together”. Water molecules are very cohesive because they are polar hydrogen bonds. A strong cohesion helps water to flow, which is useful for transporting substances - for example the xylem (tube-like transport cells) in plants relies on water being pulled up. Cohesion also gives the water a high surface tension, allowing small organisms like pond skaters and other insects to “walk” on the surface of a pond. Density and freezing properties Water is unusual because its solid form is less dense than its liquid form. Below 4°C the density of water starts to decrease. Ice floats on water and insulates the water below it, reducing the chances of large bodies of water completely freezing and increasing the chances of life. Changes in density of water with temperature set up ocean currents, which circulate nutrients. Photosynthesis Water is used in photosynthesis, so it is responsible for the production of glucose. This in turn is used in the synthesis of many chemicals. OCR A-Level Biology Module 2: Foundations in biology What are monomers? Monomers are small, identical or similar molecules, that can be joined together to make larger molecules called polymers. What are polymers? Polymers are large molecules which are formed by joining many identical or very similar monomers together. A polymer with monomer units A and B Image Source: Wikipedia Monomers: Key monomers to learn Nucleic acids, amino acids, α&β glucose, fructose, fatty acids and glycerol are all examples of monomers. Isomers are molecules with the same molecular formula but different molecular arrangement. DNA and RNA nucleotides A nucleotide is made up of three components: 1. A nitrogenous base 2. A pentose sugar 3. One or more phosphate groups Two types of pentose sugar are found in nucleotides: Deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose but it has an H instead of an OH at the 2’ positions. OCR A-Level Biology Module 2: Foundations in biology Nucleotide (DNA and RNA) monomers Nucleotide (DNA and RNA) monomers Image Source: Wikipedia OCR A-Level Biology Module 2: Foundations in biology Glucose Glucose is a hexose sugar (a monosaccharide) which has six carbon atoms in each molecule. The two types of glucose are alpha (α) and beta (β). They are isomers, which means they have the same molecular formula, but the atoms are connected in a different way. The two types of glucose have the functional group reversed, as shown in the diagrams on the right Image Source: cnx.org Other important monomers Below are examples of fructose and amino acids - two important monomers. Structures of fructose (left) and a functional unit of amino acid (right) Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Polymers: Key polymers to learn The three main polymers you need to know: Carbohydrates: monomers are joined by glycosidic bonds. Proteins: monomers are joined by peptide bonds. Lipids: monomers are joined by ester bonds. Glycosidic bond Glycosidic bond in sucrose Image Source: cnx.org Peptide bond Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released. Structure of peptide bond Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Ester bond Triacylglycerol is formed with an ester bond by the joining of three fatty acids to a glycerol backbone in a dehydration reaction. Three molecules of water are released in the process. Formation of ester bond Image Source: cnx.org Types of reactions in biological molecules Two most common types are: (a) Dehydration (condensation), (b) Hydrolysis. OCR A-Level Biology Module 2: Foundations in biology Monosaccharides and Disaccharides Carbohydrates only contain the elements carbon, hydrogen and oxygen. They provide energy to the body, particularly through glucose - a simple sugar. Carbohydrates have the formula (CH2O)n where n is the number of carbons in the molecule. Monosaccharides You need to know the structure of the three main monosaccharides: glucose, fructose, and galactose. Structures of some monosaccharides Image Source: cnx.org Disaccharides Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. This is a condensation reaction, which involves the removal of a molecule of water (H2O). Glucose molecules join together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule, it is called a 1-4 glycosidic bond. Bonds between other carbon atoms are possible, leading to different shapes, and branched chains. Three common disaccharides: Sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose). OCR A-Level Biology Module 2: Foundations in biology Disaccharides Structures of some disaccharides Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Polysaccharides: Cellulose, starch and glycogen A long chain of monosaccharides that are linked by glycosidic bonds are known as a polysaccharide - poly meaning many. Cellulose structure Cellulose is a polymer of β glucose - it’s made of long, unbranched chains of beta-glucose. Condensation reactions link carbon atom 1 to carbon atom 4 on the next β glucose. The glucose subunits in the chain are oriented alternately upwards and downwards. The consequence of this is that the cellulose molecule is a straight chain rather than curved. Structure of cellulose Image Source: cnx.org The cellulose chains are linked together by hydrogen bonds to form strong fibres called cellulose microfibrils. Because of those fibres, the tensile strength of cellulose provides structural support for the cells (e.g. the cell walls) and prevents plant cells from bursting - even under very high (water) pressure. OCR A-Level Biology Module 2: Foundations in biology Starch structure Cells get their energy from glucose. Plants store excess glucose as starch. When a plant needs more glucose for energy, it will break down that starch to release the glucose. Starch is a mixture of two polysaccharides of alpha-glucose - amylose and amylopectin. Amylose is a long, unbranched chain of α-glucose. The angle of the glycosidic bonds give it a coiled, cylinder-like structure. This compact structure is good for storage because more glucose can be stored in a small space. Amylopectin is a long, branched chain of α-glucose. It has side branches which allow the enzymes that break the molecule down to access glycosidic bonds easily - meaning the glucose can be released quickly. Since starch is insoluble, water cannot enter the cells by osmosis - which makes it very good for storage. Condensation reactions link carbon atom 1 to carbon atom 4 on the next α-glucose. All the glucose molecules in starch can be orientated in the same way. The consequence of this is that the starch molecule is curved, rather than straight and the size of the molecule is not fixed. OCR A-Level Biology Module 2: Foundations in biology Amylose and Amylopectin Structure of amylose and amylopectin Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Glycogen structure Glycogen is the main energy storage material in animals and is made by some fungi too. It’s a polymer made from repeating glucose sub-units and varies in size, typically consisting of 30,000 units. Animals store excess glucose as glycogen - another polysaccharide of alpha-glucose. In humans, it is stored in the liver and some muscles. It’s used in cells where large stores of dissolved glucose would cause osmotic problems. Glycogen has a similar structure to amylopectin but it has a lot more side branches. These extra branches mean the stored glucose can be released very quickly - something that is very important in animals. As a result of the branches, glycogen is very compact which makes it very good for energy storage. Glycogen does not affect the osmotic balance of cells - i.e. cause too much water to enter them. Structure of glycogen Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Lipids Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. The main complex lipid types are triglycerides and phospholipids. Hydrophobic: water fearing, non-polar molecules, lipid soluble. Hydrophilic: water loving, polar molecules, water soluble (not soluble in lipids). Lipid Classification Lipids complex simple Triglycerides Phospholipids Waxes Steroids Terpenes Triglyceride Formation Triglycerides are commonly called fats or oils. Triglycerides are insoluble in water. They are made of one molecule of glycerol and 3 fatty acids attached to it. Glycerol is a small, 3-carbon molecule with three alcohol groups. (C3H8O3). Glycerol is common to all triglycerides and so the properties of the fats depend on the nature of the fatty acids. They are used for storage, insulation and protection in fatty tissue (or adipose tissue) found under the skin (subcutaneous) or surrounding organs. They yield more energy per unit mass than other compounds so are good for energy storage. Fatty Acid Glycerol Fatty Acid Fatty Acid hydrocarbon “tail” of fatty acids OCR A-Level Biology Module 2: Foundations in biology Formation of Triacylglycerols (triglycerides) Fats are also called triacylglycerols or triglycerides because of their chemical structure. Formation of Triglycerides (triglycerol) Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Phospholipids Similar to triglycerides, but a phosphate group in place of one fatty acid chain. The phosphate head is hydrophilic and polar (water soluble). Two non-polar hydrophobic "tails" (the fatty acid chains). They are the main components of the cell membranes also known as plasma membranes. When mixed with water, phospholipids form droplet spheres with the hydrophilic heads facing the water and the hydrophobic tails facing each other. This is called a micelle. Alternatively, they may form a double-layered phospholipid bilayer. This traps a compartment of water in the middle separated from the external water by the hydrophobic sphere. This naturally-occurring structure is called a liposome, and is similar to a membrane surrounding a cell. Fatty Acid phosphate group Glycerol Fatty Acid hydrocarbon “tail” of fatty acids Formation of Phospholipid Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Steroids Steroids have a fused ring structure. They are also hydrophobic and insoluble in water. Hence these are clubbed with lipids. All steroids have 4 linked carbon rings and several of them, like cholesterol, have a short tail. Many steroids like cholesterol also have the OH functional group, which puts them in the alcohol classification. Cholesterol is the most common steroid. Cholesterol is mainly synthesized in the liver and is the precursor to many steroid hormones such as testosterone and estradiol. It is also the precursor to vitamin D. Cholesterol is also the precursor of bile salts, which help in the emulsification of fats and their subsequent absorption by cells. It is necessary for proper functioning of the body. It is involved in cell-to-cell communication. Glycerol Structure of cholesterol Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Amino acids and proteins Amino Acid General Structure Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached. Structure of amino acid Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Proteins Proteins are one of the most abundant organic molecules in living systems. Amino acids are the monomers that make up proteins. Amino acids are so-called because they have both amino groups and acid groups, which have opposite charges. All living things share a bank of only 21 amino acids. Each amino acid has different properties, and this in turn means that proteins can have a wide range of properties. Peptide formation between two amino acids Polypeptides are formed via condensation reactions between the amine group of one amino acid and the carboxyl group of another. A molecule of water is released during reaction. The bonds formed between amino acids are called peptide bonds. The reverse reaction happens during digestion. The sequence of amino acids in a polypeptide is determined by the sequence of the genetic code on mRNA being translated in the ribosomes. Peptide formation between two amino acids Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Formation of Proteins The shape of a protein is critical to its function. An enzyme, for example, can bind to a specific substrate at site known as the active site. If that active site is altered because of changes to the protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape, you need to know the four levels of protein structure: Primary, secondary, tertiary and quaternary. Primary Structure The unique sequence of amino acids in the polypeptide chain is its primary structure. Primary structure of proteins Image Source: cnx.org Secondary Structure This is a result of protein folding, and consists of a few basic motifs that are found in all proteins. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The two most common secondary structure motifs are the α-helix and the β-pleated sheet, but it does not have to be either of these The α-helix is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure. OCR A-Level Biology Module 2: Foundations in biology Formation of Proteins Secondary structure of proteins Image Source: cnx.org Tertiary Structure Further folding of the secondary structure. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. There are three kinds of bonds involved: Hydrogen bonds, which are weak. Ionic bonds between R-groups with positive or negative charges, which are quite strong. Sulphur bridges - covalent S-S bonds between two cysteine amino acids, which are strong. Tertiary structure of proteins Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Formation of Proteins Quaternary Structure In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Examples of this association of several polypeptides include: Collagen - a fibrous protein of three polypeptides (trimetric) that are supercoiled like a rope. Hemoglobin - a globular protein with four polypeptide chains (tetrameric). Insulin - two polypeptide chains (dimeric) held together by disulfide bond. Quaternary structure of proteins Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Formation of Proteins The four levels of protein structure summarised The four levels of protein structure Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Inorganic ions in biological processes An inorganic ion is one which does not contain carbon (with a few exceptions) There are inorganic ions in cells and each has a specific role. Hydrogen (H+) pH is calculated based on the concentration of hydrogen ions (H+). The more H+ present the lower the pH level and the more acidic the environment is. Enzyme-controlled reactions are affected by pH. Iron (Fe2+) Haemoglobin is a large protein that carries oxygen around the body in red blood cells It’s made of four polypeptide chains - each with an iron ion in the centre. The iron ion is a key component that binds to the oxygen in haemoglobin. When oxygen is bound, the Fe2+ ion temporarily becomes an Fe3+ ion until oxygen is released. Calcium (Ca2+) As calcium phosphate it provides a hard, strong, insoluble matrix in bones and teeth in mammals. Required for blood clotting in mammals. As calcium pectate in plant cell walls, it forms a matrix in which cellulose fibres lie. Involved in the transmission of action potentials from one neuron to another in muscle contraction. Sodium (Na+) Helps glucose and amino acids cross cell membranes. A molecule of glucose or an amino acid can be transported into a cell across the cell-surface membrane alongside sodium ions (Na+). This is known as co-transport. Potassium (K+) Constantly pumped into cells by active transport in exchange for sodium ions. Important in the transmission of nerve impulses. Magnesium (Mg2+) Forms part of the chlorophyll molecules in plants. Important for the absorption of light energy to drive the reactions of photosynthesis Chloride (Cl-). Moved out of cells lining the lungs and digestive system to provide a low water. potential outside the cell causing water to follow so mucus is not thick and stiff (failure of this mechanism causes cystic fibrosis). Nitrate (NO3-) Used to produce amino acids and proteins from the carbohydrates made in plants by photosynthesis. Phosphate (PO43-) Used in production of nucleic acids (DNA and RNA) production of ATP (energy currency of cells) and phospholipids, which are essential in cell membranes. OCR A-Level Biology Module 2: Foundations in biology Chemical tests to detect biological molecules Biuret test for proteins Biuret test for proteins Image Source: cnx.org The test solution needs to be alkaline, so you first need to add sodium or potassium hydroxide solution. Next you add a few drops of copper sulfate solution. If protein is present, the solution turns purple. If there is no protein, it will remain blue. Benedict’s test for reducing and non-reducing sugars Sugar is a general term used to describe monosaccharides and disaccharides. All sugars can be classified as either reducing or non-reducing. Testing for reducing sugars Reducing sugars include all monosaccharides (e.g. glucose) and some disaccharides (e.g. maltose and lactose). Add Benedict’s reagent (which is blue) to a sample and heat it in a water bath that boils the mixture for 5 minutes. If the test is positive, it will form a coloured precipitate (solid particles suspended in the solution). The higher the concentration of reducing sugar, the further the change of colour goes. You can use this to compare the amount of reducing sugars in different solutions. A more accurate way, though, is to filter the solution and weigh the precipitate. The colour of the precipitate changes from: None Trace Low Moderate High OCR A-Level Biology Module 2: Foundations in biology Chemical tests to detect biological molecules Benedict’s test for reducing and non-reducing sugars Sugar is a general term used to describe monosaccharides and disaccharides. All sugars can be classified as either reducing or non-reducing. Testing for reducing sugars Benedict’s test Image Source: cnx.org Testing for non-reducing sugars If the result of reducing sugars is negative, there may still be non-reducing sugar present in the solution. To test for a non-reducing sugar (like sucrose) you first need to break them down into monosaccharides. Take a fresh sample of the solution and either heat it with diluted hydrochloric acid or hydrolyze using enzymes. You can then neutralise it with sodium hydrogencarbonate. Once you have done these, you can continue the Benedict’s test in the same way you would for a reducing sugar. If the test is positive, it will form the coloured precipitate just the same as for a reducing sugar. If the test is negative, the solution stays blue and it means the solution does not contain any sugar (either reducing or non-reducing). OCR A-Level Biology Module 2: Foundations in biology Chemical tests to detect biological molecules Iodine Test for Starch Whenever you want to experiment on the digestion of starch and need to know if there is any left, you need the iodine test. The test is very simple. Just add iodine dissolved in potassium iodide solution to the test sample. If there is starch present, the sample changes from brown-orange to a dark blue-black colour. “Iodine is dissolved in potassium iodide” and not just iodine alone. Emulsion Test for Lipids Emulsion Test for Lipids Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Chromatography in separation of biological molecules Thin Layer Chromatography A common and effective use of TLC in in the isolation of amino acids. Amino acids have different R groups, which means they will have different solubilities in different solvents and can be separated by thin layer paper chromatography. A container is filled to a depth of 2cm with a suitable chromatography solvent. The container is sealed and left to allow the solvent to saturate the atmosphere. This is important because solvent must not evaporate from the chromatogram as it is running. A strip of chromatography paper has a pencil line drawn on it slightly more than 2cm from the bottom and small crosses are drawn on it to indicate where to add the amino acids. It is important not to touch the paper as there are amino acids on your fingers. A spot of amino acid is applied to a cross on the line using a capillary tube; the spot must not exceed 2mm in diameter. The spot is dried with a hairdryer and another is applied over the top. This is done until a small but concentrated dot of amino acid has been built up on the cross. The nature of the amino acid is indicated by writing in pencil below the spot. This is repeated until each amino acid dot has been added. The strip of chromatography paper is placed in the container, making sure that the solvent doesn’t splash above the line. The solvent is drawn up the paper by capillary action but does not evaporate from it due to the saturated air around it. The amino acid was be carried by the solvent and each will travel at different speeds. When the solvent has nearly reached the top the paper is removed and a line is drawn to show where the solvent has reached, this is the solvent front. The chromatogram is dried in a fume cupboard and then sprayed with ninhydrin spray. When the chromatogram dries, the amino acids will appear as purple spots at different distances up the chromatogram. The distance each spot has traveled from the center of the cross to the center of the spot is measured, call this D1. The distance the solvent front has traveled from the cross is measured, call this S. The Rf value can then be calculated as Rf = D1/ S Each amino acid will have a unique Rf value and as the Rf values for all amino acids are known they can be identified knowing the Rf value. OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.3 Nucleotides and nucleic acids Learners should be able to demonstrate and apply their knowledge and understanding of: (a) The structure of a nucleotide as the monomer from which nucleic acids are made. (b) The synthesis and breakdown of polynucleotides by the formation and breakage of phosphodiester bonds. (c) The structure of ADP and ATP as phosphorylated nucleotides. (d) i) The structure of DNA (deoxyribonucleic acid). ii) Practical investigations into the purification of DNA by precipitation. (e) Semi-conservative DNA replication. (f) The nature of the genetic code. (g) Transcription and translation of genes resulting in the synthesis of polypeptides. OCR A-Level Biology Module 2: Foundations in biology The structure of a nucleotide The basic structure of a nucleotide is made up of three components: 1. A pentose sugar (made with 5 carbon atoms) 2. A nitrogenous base 3. A phosphate group The basic structure of a nucleotide Image Source: cnx.org Nucleotides Join Together and Form Polynucleotides Formation of a polynucleotide Image Source: cnx.org A polynucleotide is a polymer of nucleotides. Both DNA and RNA form polynucleotides. Nucleotides join via a condensation reaction between the phosphate group of one nucleotide and the sugar of another. This forms a strong, covalent, phosphodiester bond (which consists of the phosphate group and two ester bonds). This chain of sugars and phosphates is known as the sugar-phosphate backbone. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. OCR A-Level Biology Module 2: Foundations in biology The structure of ATP and ADP ADP and ATP as phosphorylated nucleotides Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology The structure of DNA DNA is made of two polynucleotide chains in a double-helix structure. Two DNA polynucleotide strands join together by hydrogen bonding between bases. Each base can only join with one particular partner - this is called complementary base pairing. Adenine always pairs with thymine (A-T) and cytosine always pairs with guanine (C-G), which means there are always equal amounts of adenine and thymine in a DNA molecule and equal amounts of cytosine and guanine. Two hydrogen bonds form between A and T and three hydrogen bonds form between C and G. This complementary base pairing ensures that replication of DNA is accurate (it will also ensure accurate transcription of the genes for protein synthesis). Individually these H bonds are weak and allow the DNA to be separated so replication and transcription can occur. Two antiparallel polynucleotide strands twist in opposite directions to form the DNA double-helix. This double strand is important as each strand can act as a template in replication, a semi conservative process, meaning that the DNA is copied accurately. The structure of DNA Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology DNA Replication DNA has an incredible ability to replicate itself. It copies itself before cell division, so that each new cell has the full amount of DNA. This is called semi-conservative replication because half the strands in each new DNA molecule come from the original DNA molecule. By doing this, it ensures genetic continuity between generations of cells (the cells produced by cell division will inherit their genes from parent cells). The DNA replication process 1. The enzyme DNA helicase breaks the hydrogen bonds between the base pairs on the two polynucleotide DNA strands. This unwinds the helix to form two single strands. 2. Each original single strand acts as a template for the new strand. Complementary base pairing means that free-floating DNA nucleotides are attracted to their base pair - A with T and C with G. 3. Condensation reactions join the nucleotides of the new strands together using the enzyme DNA polymerase as the catalyst. Hydrogen bonds form between bases on the original and new strands. 4. Each new DNA molecule contains one strand from the original DNA molecule and one new strand. The DNA replication process Image Source: cnx.org Meselson and Stahl showed that DNA is replicated using the semi-conservative method by using two isotopes of nitrogen (DNA containing nitrogen) - heavy nitrogen ( 15N) and light nitrogen (14N). OCR A-Level Biology Module 2: Foundations in biology Nature of the genetic code Due to the degenerate nature of the genetic code, not all base substitutions cause a change in the sequence of encoded amino acids. ▸The genetic code is degenerate. ▸It means more possible combinations of codons are present than number of amino acids (20 amino acids and 64 possible triplets or codons). ▸As a result, some amino acids are coded by more than one codon, e.g. tyrosine can be coded for by UAU or UAC. ▸So, all base substitutions do not change the sequence of encoded amino acids. Genetic code for translating mRNA codons to amino acid Image Source: cnx.org Primary Structure of Protein The unique sequence of amino acids in the polypeptide chain is its primary structure. Primary protein structure Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology Transcription and translation of genes Gene expression is a complex series of processes in which the information coded in the gene is translated into a useful and functional product such as proteins that dictates the function of the cells. In the process of gene expression DNA is converted to RNA and then RNA is converted to protein. This is also known as central dogma of life. Three main processes in gene expression are: 1. Transcription – The conversion of DNA to mRNA with the help of RNA polymerase and transcriptional factors is known as transcription. 2. Post-transcriptional Modifications – In this process, mRNA is modified to produce mature RNA. It involves: i. Splicing ii. Addition of a cap at 5’ site iii. Addition of a poly A tail at 3’ site 3. Translation – Conversion of mature RNA into protein is known as translation. Central Dogma Image Source: cnx.org OCR A-Level Biology Module 2: Foundations in biology The structure of molecules of messenger RNA (mRNA) and of transfer RNA (tRNA). ▪ RNA is ribonucleic acid. It is single stranded and have uracil as base instead of thymine present in DNA. ▪ It is formed from ribose sugar, bases and phosphates. ▪ There are various types of RNA such as, mRNA, tRNA, rRNA, siRNA, snRNA and many more. ▪ Messenger RNA (mRNA): It is made during transcription from DNA. It has single polynucleotide strand. ▪ Three adjacent bases form a group in mRNA, which is known as codons or triplets. ▪ Transfer RNA (tRNA): It is involved in translation. ▪ It is also single polynucleotide stranded but bends to form cloverleaf-like structure. ▪ This special shape is maintained by the hydrogen bonds between specific base pairs. ▪ They have specific triplets made at one end by specific bases, known as anticodon, which actually recognises the codon on mRNA. ▪ At another end they carry amino acids binding site where it carries amino acids through ribosomes according to the codons on mRNA. Structure of mRNA and tRNA Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Transcription as the production of mRNA from DNA and the role of RNA polymerase in joining mRNA nucleotides. Transcription is the first stage of protein synthesis. 1. At the initial point of a gene, RNA polymerase attaches to the DNA double-helix. 2. Hydrogen bonds between bases of DNA breaks to uncoil a segment of DNA thus exposing some of the bases. 3. Among the two strands of DNA, one is used as template for making mRNA copy. 4. Free RNA nucleotides are arranged beside exposed bases of DNA by RNA polymerase. 5. The base pairs of DNA pairs up with free RNA nucleotides following complementary base pairing. 6. Then these RNA nucleotides are joined by RNA polymerase forming RNA molecule. 7. Now RNA polymerase moves along the length of DNA to make a whole mRNA. 8. Once RNA polymerase completes its moving through DNA, it again recoils by forming the lost H-bonds. 9. RNA polymerase stops at a certain place in DNA called stop signal and finally detaches from DNA. 10. mRNA will come out of the nucleus through nuclear pores in eukaryotes and further steps of protein synthesis take place in cytoplasm. Steps in transcription Image Source: OpenStax CNX OCR A-Level Biology 3.4.2 DNA and protein synthesis Translation as the production of polypeptides from the sequence of codons carried by mRNA. Translation is the second phase of protein synthesis which takes place in cytoplasm with the help of ribosomes both in prokaryotes and eukaryotes. 1. The mRNA, ribosome and tRNA all come together. 2. Ribosome attaches to mRNA and amino acids are carried by transfer RNA (tRNA) near to ribosomes. 3. tRNA molecule carrying amino acids and anticodon pairs with the first codon of mRNA. 4. Then second tRNA molecule attaches itself to mRNA in same manner. 5. A peptide bond is formed between amino acids on two different tRNA molecules. The first tRNA molecule leave its amino acid at this point. 6. This process continues till ribosome reaches the stop codon on mRNA, thus producing a chain of amino acids (polypeptide or protein). 7. The polypeptide chain moves away and leaves behind ribosome and thus translation completes. Translation Image Source: OpenStax CNX OCR A-Level Biology 3.4.2 DNA and protein synthesis Role of ribosomes, tRNA and ATP 1. Ribosomes: The two units of ribosome joined to form a cleft like structure where mRNA attaches itself. Also it moves along the length of mRNA facilitating the base pairing of mRNA and tRNA. 2. tRNA: It has two roles. It base pairs with codons of mRNA complementarily with its anticodon. Also it carries amino acids specific to the codons on mRNA. 3. ATP: It provides energy for the bond formation between tRNA and amino acid. Relation of base sequence of nucleic acids to amino acid sequence in polypeptides 1. Three bases of DNA form complementary three bases of one mRNA. 2. Those three bases (base triplet) of one mRNA is a codon and that codon codes for one amino acid. 3. Therefore, if base sequence of a nucleic acid (DNA or mRNA) is known, then amino acid sequence can be taken out. 4. If amino acid sequence of a protein is provided, then from that, base sequence of nucleic acid can be taken out. Genetic code sequence diagram Image Source: OpenStax CNX OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.4 Enzymes Learners should be able to demonstrate and apply their knowledge and understanding of: (a) The role of enzymes in catalysing reactions that affect metabolism at a cellular and whole organism level. (b) The role of enzymes in catalysing both intracellular and extracellular reactions. (c) The mechanism of enzyme action: (d) i) The effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity. ii) Practical investigations into the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme activity. (e) The need for coenzymes, cofactors and prosthetic groups in some enzyme-controlled reactions. (f) The effects of inhibitors on the rate of enzyme controlled reactions. OCR A-Level Biology Module 2: Foundations in biology Enzymes Enzymes are biological catalysts. Enzymes come up a lot in biology because they make reactions work quickly. They increase the rate of reactions by lowering the activation energy. Enzymes catalyse metabolic reactions at both a cellular level (for example, respiration) and for the organism as a whole (for example, digestion in mammals). They can affect structures in an organism. For example, enzymes are involved in the production of collagen - an important protein in the connective tissue of animals. Enzymes can also affect organism functions, like respiration. An enzyme action can be intracellular (within the cells) or extracellular (outside the cells). Enzymes have an active site, which is a specific shape. It’s part of the enzyme where the substrate molecules bind to. Role of enzymes in catalysing both intracellular and extracellular reactions The macromolecules or large molecules are broken down or hydrolysed by the enzyme called hydrolases. Hydrolases are enzymes which help in splitting up of a molecule by adding water and the process is hydrolysis. Examples of Hydrolases: digestive enzymes like amylase, lipase, protease etc. Digestion of carbohydrates through a series of enzymatic reactions Image Source: OpenStax CNX Aerobic respiration constantly generates reactive oxygen species (ROS), byproducts that must be detoxified. The enzyme catalase converts one such ROS hydrogen peroxide to water and oxygen according to the reaction: 2H2O2 → 2H2O+O2 OCR A-Level Biology Module 2: Foundations in biology The mechanism of enzyme action Lock and Key Model For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model suggested that the active site has a rigid shape and that only a substrate with the correct complementary shape can bind to the active site. However, this has its limitations. Lock and Key Model of enzyme action Image Source: OpenStax CNX Scientists soon realised that this lock and key had limitations. In particular: It does not easily explain how activation energy is lowered. It does not easily explain the role of competitive inhibitors. It does not easily explain the role of non-competitive inhibitors. Current research supports a more refined view called induced fit. The induced fit model is a better mechanism to explain enzyme activity. OCR A-Level Biology Module 2: Foundations in biology Induced Fit and Enzyme Function The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the transition state of the substrate. This ideal binding maximises the enzyme’s ability to catalyze its reaction. Induced-fit model of enzyme action Image Source: OpenStax CNX According to the induced-fit model, both enzyme and substrate undergo dynamic conformational changes upon binding. The enzyme contorts the substrate into its transition state, thereby increasing the rate of the reaction. Advantages of the induced fit model Can explain how the activation energy is lowered, the stretching and distorting of bonds or causing the closer orientation of reactive groups. Explain how non-competitive inhibitors can bind to a region away from the active site and change its shape so that substrate can no longer bind to the active site. Explains how competitive inhibitors can bind to the active site or other molecules with similar shapes to the substrate. OCR A-Level Biology Module 2: Foundations in biology Factors Affecting the Rate of Enzyme Activity Now you know what enzymes are and how they work, you need to understand the factors that affect their activity. Temperature Increase in temperature increases kinetic energy. so more enzyme substrate complexes form. High temperatures cause denaturation, due to the breaking of breaking of bonds holding the tertiary structure together (H bonds/disulphide bridges/ionic bonds). Active site altered (changes shape) substrate cannot bind, no enzyme substrate complexes form. pH Deviations from the optimum pH cause a decrease in enzyme activity. Small deviations change the charge at the active site and affect the binding of the substrate. Larger deviations can cause the hydrogen and ionic bonds holding the tertiary structure together to change and the enzyme denatures, meaning enzyme substrate complexes can no longer form. OCR A-Level Biology Module 2: Foundations in biology Factors Affecting the Rate of Enzyme Activity Enzyme Concentration As enzyme concentration increases so will the rate: As there are more enzyme substrate complexes forming. At very high concentrations of enzyme the rate remains constant as substrate becomes the limiting factor Add more enzyme will cause rate to increase again. Substrate Concentration As the substrate concentration increases, the rate 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 doesn't make much difference. OCR A-Level Biology Module 2: Foundations in biology Factors Affecting the Rate of Enzyme Activity Enzyme Activity can be inhibited Enzyme activity can be prevented by enzyme inhibitors. These are molecules that bind to the enzyme that they inhibit. Inhibition can be either competitive or noncompetitive. Inhibitors prevent the binding of substrate to active site; therefore fewer enzyme-substrate complexes formed, reducing the rate of their reactions. They are found naturally, but are also used artificially as drugs, pesticides and research tools. COMPETITIVE INHIBITORS They have a similar shape to that of the substrate molecules. They compete with the substrate molecules to bind to the active site, but no reaction takes place. Instead of a reaction, they block the active site so no substrate molecules can fit in it. The level of activity inhibited depends on the relative concentrations of the inhibitor and the substrate. High concentration of the inhibitor means it will take up nearly all of the active sites and hardly any substrate will get to the enzyme. With a lower concentration, the chances of the substrate getting to an active site before the inhibitor increase. So, increasing the concentration of a substrate will increase the rate of reaction - up to a point. NON-COMPETITIVE INHIBITORS They bind to the enzyme away from its active site. This causes the active site to change shape so the substrate molecules cannot bind to it. They don’t “compete” with the substrate molecules to bind to the active site because they are different shapes. Increasing the concentration of substrate doesn’t affect the reaction rate - enzyme activity is still inhibited. OCR A-Level Biology Module 2: Foundations in biology Competitive and Noncompetitive Enzyme Inhibitors Diagram showing the difference between competitive and noncompetitive enzyme inhibition Image Source: cnx.org Competitive and noncompetitive inhibition affect the rate of reaction differently. Competitive inhibitors affect the initial rate but do not affect the maximal rate, whereas noncompetitive inhibitors affect the maximal rate. OCR A-Level Biology Module 2: Foundations in biology Competitive and Noncompetitive Enzyme Inhibitors Metabolic pathways are a series of reactions catalyzed by multiple enzymes. Feedback inhibition, where the end product of the pathway inhibits an upstream step, is an important regulatory mechanism in cells. Inhibition of pathway Image Source: cnx.org End product inhibition/allosteric effectors The activity of some enzymes is controlled by certain molecules binding to a specific regulatory (or allosteric) site on the enzyme, distinct from the active site. Different molecules can inhibit or activate the enzyme, allowing sophisticated control of the rate. Only a few enzymes can do this, and they are often at the start of a long biochemical pathway. They are generally activated by the substrate of the pathway and inhibited by the product of the pathway, thus only turning the pathway on when it is needed. OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.5 Biological membranes Learners should be able to demonstrate and apply their knowledge and understanding of: (a) The roles of membranes within cells and at the surface of cells. (b) The fluid mosaic model of membrane structure and the roles of its components: (c) i) Factors affecting membrane structure and permeability. ii) Practical investigations into factors affecting membrane structure and permeability. (d) i) The movement of molecules across membranes. ii) Practical investigations into the factors affecting diffusion rates in model cells (e) i) The movement of water across membranes by osmosis and the effects that solutions of different water potential can have on plant and animal cells. ii) Practical investigations into the effects of solutions of different water potential on plant and animal cells. OCR A-Level Biology Module 2: Foundations in biology Cell Membrane Also known as the plasma membrane, the cell membrane is a semi-permeable area in a cell that separates the interior components of the cell from the extracellular matrix. Ions and organic molecules can selectively pass through the membrane. Transport of material across the cell membrane is important in the operation of the cell. The cell membrane is composed of a lipid bilayer with some proteins embedded in it. The hydrophobic tails of the lipid components of the membrane is placed in the middle of the bilayer, protected from the polar extracellular and interstitial fluids. Aside from the proteins, cholesterol molecules are also embedded in the cell membranes. It maintains the fluidity of the membrane and increases its stability. Cell Membrane Image Source: OpenStax CNX Functions of Cell Membrane 1. Separation between the extracellular fluid and the internal components of the cell. 2. Communication with other cells. 3. Recognition of external substances. 4. Structural support. 5. Transport of materials. OCR A-Level Biology Module 2: Foundations in biology One of the important functions of the cell membrane is facilitating the transport of materials from the outside to the inside of the cells, or vice-versa. Transport of materials is accomplished via a number of possible mechanisms. These include: Simple diffusion. Facilitated diffusion. Osmosis. Active Transport. Co-transport. The type of transport is dependent on the concentration difference of the extracellular matrix and the interstitial fluids, the type of compound being transported, and energy requirement for the transport. Simple diffusion ‒ Diffusion, also called passive transport, is the movement of particles from an area with higher concentration to an area of lower concentration. ‒ This is the primary mode of transport for small molecules and gases like oxygen and carbon dioxide. It is important that these two gases readily diffuse through the membrane because oxygen is needed by the cells for metabolism, and carbon dioxide need to be expelled by the cell for eventual release to the environment. Simple diffusion Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Facilitated diffusion ‒ Facilitated diffusion is the spontaneous transport of material across the cell membrane via membrane proteins embedded in it. ‒ The transport is dependent on the interaction of material and the channel or carrier protein. ‒ This type of transport is particularly important in moving large polar molecules and ions that cannot readily diffuse via simple diffusion. ‒ The main difference between carrier and channel proteins is carrier proteins are not open readily to both intracellular and extracellular environments, while a channel protein is open to both. ‒ In carrier proteins, binding sites are present where molecules to be transported can bind. The protein then undergoes conformational change eventually opening the protein molecule to the other side of the cell membrane. Eventually, the solute molecule is released to the other side of the membrane. ‒ Channel proteins interact weakly with the material to be transported. If the channel is open, specific solutes can freely pass through them. Facilitated diffusion Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Active transport ‒ This is the type of transport where solute is transported from an area of lower concentration to an area of higher concentration. ‒ This type of transport is needed to accumulate solute in a specific area where cellular metabolic process may occur. ‒ Active transport may be classified as either primary or secondary active transport. Primary active transport requires energy in the form of ATP for the transport of material. Secondary active transport, on the other hand, uses an electrochemical gradient for the transport of material to occur. ‒ An example of active transport is the transport of potassium and sodium ions through the sodium potassium pump. An electrochemical gradient is present because of the imbalance in the concentration of positive charges across the membrane. ATP provides the energy needed to produce conformational change for the eventual release of the ions to the other side of the membrane. Sodium - Potassium Pump Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Osmosis ‒ This is the type of transport where water molecules (solvent) diffuse through the membrane down its concentration gradient. ‒ In the process of transport, the concentration in both sides of the membrane is equalised. ‒ This type of transport occurs when there the solute concentrations are not equal, and water molecules have higher tendency to diffuse than the solute molecules. ‒ Depending on the condition of the extracellular environment, different things can happen to the cell. If the cell is exposed to an isotonic environment (same concentration inside and outside the cell), the movement of water into and out of the cell occur at the same rate. If the cell is exposed to a hypertonic environment (outside of the cell has higher solute concentration than the inside), the cell will shrivel because of loss of water. If the cell is exposed to a hypotonic environment (inside of the cell has higher concentration than outside), the cell take up more water and becomes bloated and will eventually burst. Osmosis in Red Blood Cells Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Co-transport ‒ This is the type of transport where two substances are simultaneously transported across a membrane. ‒ This is a specific type of secondary active transport. ‒ This is facilitated by symporters, which can transfer two substances in the same direction. An example of a symporter is the sodium-glucose symporter. It uses the sodium ions to move glucose into the cell. The flow of sodium ions through the symporter provides the needed energy for the glucose to move also through the symporter. Co-transport Image Source: Wikimedia Commons OCR A-Level Biology alevelbiology.co.uk Module 2: Foundations in biology SPECIFICATION 2.1.6 Cell division, cell diversity and cellular organisation. Learners should be able to demonstrate and apply their knowledge and understanding of: (a) The cell cycle. (b) How the cell cycle is regulated. (c) The main stages of mitosis. (d) Sections of plant tissue showing the cell cycle and stages of mitosis. (e) The significance of mitosis in life cycles. (f) The significance of meiosis in life cycles. (g) The main stages of meiosis. (h) How cells of multicellular organisms are specialised for particular functions. (i) The organisation of cells into tissues, organs and organ systems. (j) The features and differentaton of stem cells. (k) The production of erythrocytes and neutrophils derived from stem cells in bone marrow. (l) The production of xylem vessels and phloem sieve tubes from meristems. (m) The potential uses of stem cells in research and medicine. OCR A-Level Biology Module 2: Foundations in biology The Cell Cycle The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. A series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produces two identical (clone) cells. The cell cycle Image Source: OpenStax CNX Mitosis vs Meiosis 1. Mitosis is the type of cell division which produces two daughter cells that are identical from the parent cell. 2. Meiosis is the type of cell division which produces daughter cells that is not identical to the parent cell, and contains half the amount genetic material as the parent cell. (This will be covered in more detail later) Regulation of the Cell Cycle By External Events Both the initiation and inhibition of cell division are triggered by events external to the cell. The reason may be a simple factor like death of a nearby cell. It can also be a major factor like release of growth-promoting hormones, such as human growth hormone (HGH). A lack of HGH can inhibit cell division, resulting in dwarfism, whereas too much HGH can result in gigantism. Crowding of cells can also inhibit cell division. Another factor that can initiate cell division is the size of the cell. Due to the growing size, a cell becomes inefficient due to its decreasing surface-to-volume ratio. Hence, the division occurs. OCR A-Level Biology Module 2: Foundations in biology Regulation of the Cell Cycle Regulation at Internal Checkpoints The G1 Checkpoint: At the G1 checkpoint, cell size and protein reserves are assessed. Determines whether all conditions are favourable for cell division to proceed. Growth factors, play a large role in carrying the cell past the G1 checkpoint. Additionally, check for genomic DNA damage is done at the G1 checkpoint. The G2 Checkpoint: The most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged. On detection of damage, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA. The M Checkpoint: It determines whether all the sister chromatids are correctly attached to the spindle microtubules. Regulation of the cell cycle Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Stages of Mitosis The diagram below shows the processes involved in mitosis. You need to learn what happens in each step and how daughter cells that are identical to the parent cells are produced. Stages of Mitosis Image Source: Openstax cnx OCR A-Level Biology Module 2: Foundations in biology Prophase During the prophase, the nuclear membrane of the cell breaks down forming small vesicles. In the process, the nucleolus disintegrates. The centrosome that have been duplicated in the G2-phase separates. They start to move towards opposite poles of the cells. Mitotic spindles extend between the centrosomes, pushing them further apart when the microtubules lengthen. Chromosomes become visible, which is composed of two chromatids joined together at the centromere. Prophase Image Source: The Biology Corner Prometaphase ‒ This the second stage of the mitotic cycle where remnants of the nuclear envelope disappears. ‒ Protein structures called kinetochores appear. ‒ Microtubules that emerges from the centrosome lengthen to reach the chromosomes and attach to the kinetochore. ‒ Proton motors associated to microtubules arrange the chromosomes towards the center of the cell. ‒ Prometaphase ends when all the kinetochore microtubules have attached to their kinetochore. Prometaphase Image Source: Wikimedia Commons OCR A-Level Biology Module 2: Foundations in biology Metaphase This is the third stage of the mitotic cycle. This is when the centromeres of the chromosomes line up in an imaginary line equidistant (at equal distances) to the two centrosome poles called the metaphase plate. This is facilitated by the counter effect of the pull of the two opposing kinetochore microtubules. Metaphase Image Source: The Biology Corner Anaphase ‒ This is the fourth stage of the mitotic cycle. ‒ This is when the the centromere splits, dividing the chromosome into two sister chromatids. ‒ Each chromatid moves to opposite poles of cells when the mitotic spindle shortens. Anaphase Image Source: Wikimedia Commons OCR A-Level Biology Module 2: Foundations in biology Telophase This is the fifth stage of the mitotic cycle. The mitotic spindle disappears during telophase and the chromosomes uncoil to form diffuse chromatin. A nuclear membrane forms around the daughter chromosomes present in both ends of the cell. Telophase Cytokinesis Image Source: The Biology Corner Image Source: OpenStax CNX Cytokinesis This is the final step in cellular division. This is when physical separation of cytoplasmic materials occur in the parent cell. For animal cells, a cleavage furrow is produced by having the actin filaments pull the equator of the cell inwards, forming the fissure called a cleavage furrow. The cleavage furrow continually develops eventually dividing the cell in two. For plant cells, a cell plate is produced by having Golgi vesicles come together at the position of the original metaphase plate separating the two sets of chromosomes. The cell plate continually grows until it reach the cell walls. New cell walls are then produced from the contents of the vesicle. OCR A-Level Biology Module 2: Foundations in biology The process of meiosis 1. Two nuclear divisions result usually in the formation of four haploid daughter cells from a single diploid parent cell. 2. Genetically different daughter cells result from the independent segregation of homologous chromosomes. 3. Crossing over between homologous chromosomes results in further genetic variation among daughter cells. Total process of meiosis Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Stem Cells 1) Different cell types, each having a specialised function, make up the multicellular organisms. These include muscle cells, liver cells, WBC, RBC etc. 2) The origin of these specialised cell types is from a reservoir called stem cells. 3) Stem cells are like a reservoir, i.e. they are unspecialised cells which can develop into different specialised cells. 4) Every multicellular organism has stem cells. 5) Human stem cells are located in early embryos (which can develop into all the types of cells in a human) and also in some parts in adults (which have a limited range of development). Cell Differentiation The division of stem cells is followed by specialisation - a process called differentiation. From bone marrow to blood cells - the process of cell differentiation in erythrocytes The erythrocyte lifecycle Image Source: OpenStax CNX OCR A-Level Biology Module 2: Foundations in biology Stem cells in medical research for curing diseases A range of diseases arise from deformities in specialised cells. Hence, the scientists are researching the possibility of utilising the stem cells to generate the specialised cells that can replace damaged cells. Neurological disorders like Alzheimer’s and Parkinson’s both of which are related to the death of nerve cells in the brain, can be cured by newly generated cells. Stem cell research also paves the way for understanding developmental biology and stages of development and also in understanding the nature of cancer cells and finding the cure. Specialised cells - Neutrophil A neutrophil is a phagocytic cell that is attracted via chemical messenger from the bloodstream to infected tissues. These are like military reinforcements that are called into a battle to hasten the destruction of the enemy. The neutrophil is the primary pathogen-killing cell of the inflammatory process of the innate immune response. Neutrophil granulocyte migrates from the blood vessel to the matrix, secreting proteolytic enzymes, and envelop bacteria through phagocytosis Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Specialised cells - Epithelial cells Epithelial cells are the cells forming the outermost layer on the surfaces of organs. These have a membrane at their base and joined by interlinking cell membranes. Ciliated epithelia are the ones having cilia to brush away the particles. Squamous epithelia are extremely thin, which allows diffusion of gases in a smooth manner. Types and functions of epithelial cells Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Specialised cells - Sperm cells Sperm cells are the cells in males to carry forward the sexual reproduction. The flagella help these to swim towards the egg (female sex cell), mitochondria supplies the required energy while the acrosome contains the enzymes which help to penetrate the surface of the egg. Structure of a sperm cell Image Source: Wikimedia commons Specialised cells - Palisade cells These are the main site for photosynthesis on a leaf surface. These contain the most number of chloroplasts, absorb a lot of sunlight and let the carbon dioxide easily diffuse into the active site for photosynthesis. Structure of a palisade cell Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Specialised cells - Root hair cells These are designed to absorb water and minerals from the soil. A very thin and permeable cell wall and the large surface area allows the inflow of water and necessary ions. Extra mitochondria is housed in cytoplasm to provide the extra energy for the process of absorption. Tip of the root with root hair cells Image Source: cnx.org Specialised cells - Guard cells Since plants need to open their stomata to allow gas exchange, there should be a mechanism by which the plants can control the loss of water. This is solved by the presence of guard cells. Guard cells become swollen when water enters them. This swelling causes the stomata to open. When the plant gets dehydrated, the guard cells lose the water and as it becomes flaccid, the stomatal pore closes. Guard cells in action Image Source: Wikimedia commons OCR A-Level Biology Module 2: Foundations in biology Organisation of cells into tissues, organs and organ systems The constitution of multicellular organisms comp