CAPE BIOLOGY UNIT ONE MANUAL (by Sperwin Zinger) MODULE ONE - CELL AND MOLECULAR BIOLOGY THIS MODULE CONTAINS FOUR TOPICS: 1. ASPECTS OF BIOCHEMISTRY 2. CELL STRUCTURE 3. MEMBRANE STRUCTURE AND FUNCTION 4. ENZYMESTOPIC 1: ASPECTS OF BIOCHEMISTRY Your body is comprised of numerous elements, ‘which make also combine to form molecules. These include macronutrients such as carbohydrates (such as starch and glucose, required for release of ATP), proteins (which are used for growth and repair of cells and also to Why are water molecules attracted to each other? form hormones) and fats (used for as an energy store). However, the molecule that comprises the majority of the human body (more than 70% of @ cell’s mass) is WATER. First, observe the molecular structure of water. Water consists of two hydrogen atoms COVALENTLY bonded to one oxygen atom. This means that electrons are shared between them. Party Nepte a memes oxygen “om On the diagram, you will observe the symbol 8 (delta), and a symbol for +ve or ve charge. In this case, the ONYGEN has the negative charge and the HYDROGEN atoms have the positive charge. Water itself is electrically balanced or ‘NEUTRAL, However, there is uneven distribution of these charges in the structure, This is called a DIPOLE, This allows weak electrical attraction between the water ‘molecules, which results in COHESION and the ability to undego MASS FLOW. They also result in HYDROGEN BONDS, which are essential for many biological molecules. Property of Water | What Allows This Temp. regulation Iis high specific heat capacity and ability to evaporate easily “Universal” solvent | Its tiny charges attract other molecules of ions to form bonds. Allows mass flow Its H-bonds produce cohesion and surface teasion. Suitable for excretion, Assists buffers Its neutral pH allows H ions or OH ions to be absorbed by proteins. Reactivity Used in hydrolysis reactions during digestion and in photosynthesis.What exactly are CARBOHYDRATES? Carbohydrates are organic molecules that comprise a ratio of carbon, hydrogen and oxygen. They are comprised of at least one sugar unit. However, they can be linked together to form increasingly complex molecules. Type of carbohydrate | Number of units | Examples MONOSACCHARIDE | One Glucose, fructose, ribose, galactose, glyceraldehyde DISACCHARIDE Two Maltose, sucrose, lactose POLYSACCHARIDE |More than two | Starch, glycogen, cellulose, chitin MONOSACCHARIDES are the simplest A pentose such as ribose has a value of *5* and carbohydrate and cannot be further hydrolysed. is written as CsH1,0Os. However, modifications They are written with the general formula occur, such as deoxyribose having one less (CH.O),. The ‘n’ depends on the type of sugar. oxygen atom, so deoxyribose is written as For example, a hexose sugar (e.g. glucose) has a CsHOs value of “6°, so glucose is written as CF:05. As previously mentioned, giucose is a HEXOSE, which means it has a six-membered ring consisting of five carbons and one oxygen. Observe the straight-chain and ring structures of glucose below. ° H on \/ Beta- " slucose’s »CH,OH 7 ring — Oy Hoy 04 structure HAI la is similar “KO on H 1 oH f but H and = watt | yg 10H topo swapped H OH A : — OH Straight chain onl. Ring structure of alpha-glucose. structure of *CH,OH aipha-glucose. Tt can be observed thatthe 6th carbon atom in the ring structure does not exist as part of the ring structure. Asa result ofthis, glucose tends to alternate between its ring and its chain form, This is why there are two different types of glucose (alpha and beta)How are DISACCHARIDES formed then? As previously mentioned, a DISACCHARIDE forms when two monosaccharide molecules are bonded. ‘When this linkage occu, itis known as a GLYCOSIDIC bond. These types of bonds are very strong. One common example of a disaccharide is SUCROSE, which we commonly know as the sugar that is sweet (such as in sugar cane), ‘pat two monosaccharides combine to form sucrose? That would be an ALPHA GLUCOSE anda BETA FRUCTOSE. What is notable about sucrose is that when it undergoes enzyme breakdown, sucrose yields two glucose molecules. However, one of those molecules has been reformed from fructose. Here ave their ring structures: CH,OH ‘CH_OH wi H Re CH.OH OH Beta-fructose. Carboa-1 ofthe alpha glucose will now bond with the Carbon-2 of beta-fuctose, This is thus called a 22 lycosidisbond, A CONDENSATION reaction removes a water molec inthe process ‘Now observe the structure of SUCROSE: Sucrose js used for cHOH HOH transport instead of 5 e 4 H glucose because itis much more complex, OHH HOW more energy-efficient on ‘CHOH and not as reactive as 7 glucose HOH OH OH glucose fructose sucrose What is the difference between a REDUCING and NON-REDUCING sugat In O’ levels you would've leamed that Benedict's solution can be used to test for reducing sugar. However, the addition of HYDROCHLORIC ACID and then SODIUM HYDROXIDE was needed for non-reducing sugars. This is because disaccharides such as sucrose have a glycosidic bond that prevents Benedict's reageant from reacting with it. The HCI is needed to break that glycosidic bond and the NaOH is needed to neutralize the HCLNOW WHAT ABOUT POLYSACCHARIDES: A polysaccharide can contain thousands of sugar molecules and can be quite large and complex. As a result, they are insoluble, Not all of them are arranged in long chains, however. Some of them form, compact spirals, Polysaccharide nutrients such as starch must be hydrolysed before they can be absorbed through the small intestine and into the bloodstream. We'll be looking at three main polysaccharides: Polysaccharide | Function Misceltaneous short notes STARCH. Energy reserve in plants | A mixture of two polymers, AMYLOSE and after photosynthesis. | AMYLOPECTIN. Stored in PLASTIDS, which form grains. Never found in animal cells. Digested by AMYLASE, GLYCOGEN | Energy reserve in animals. Easier to break down into glucose. Usually found in the LIVER and in MUSCLES. CELLULOSE | Found in cell walls Used for structural support. Abways has a straight structure. Very strong due to thousands of hydrogen bonds. Large bundles of them are called FIBRES. Difficult for animals to digest. Amvlose Cellulose Now let’s be more specific about these molecul Amylose forms a spiral from many a-glucose molecules. Its held together by H-bonds that form between -OH groups attached to C-1 of each unit HOH HoH CHOH chaow 0, 0. 0, 0, OH Oe H ° °. ct ° oH oH on Glycogen is also made of many a-glucose molecules and are linked through a 1-4 glycosidic bonds with a 1-6 branches. enon own GLYCOGEN 11-4 glycosidic bond‘© Cellulose is also made up of thousands of B- glucose molecules. Cellulose molecules form a straight structure instead of a spiral or branches. As said, their bonds are extremely strong due to the multitude of hydrogen linkages. The type of bonds in cellulose are B 1-4 glycosidic bonds between the glucose molecules. This is what it makes it INSOLUBLE and sturdy to provide structural support in cell walls. The ring structure combines many different glucoses. However, each alternating glucose molecule is INVERTED. Observe the structure below. Notice how each successive one is ‘flipped’. Hon u,oH Hon | 8 on on ® O°? HoH cu,on Hon cH,04 The table below will provide a summary of all of this complex information. Feature Amylose Glycogen Cellulose Sugar unit a-glucose a-glucose Brghucose Overall shape Linear and spiral Linear, spiral, branches | Only linear Solubility in water Insoluble or very low | Insoluble or very low | Insoluble Glycosidie bond type | a 1-4 a 1-4anda 1-6 pis H-bonds Within Within Within and between Location Starch grains, plastids | Animal liver cells Cell walls, REMINDERS ABOUT BREAKING AND FORMING BONDS ‘© Breaking a covalent bond is called a HYDROLYSIS REACTION, while formation of the bond is called a CONDENSATION REACTION. © Hydrolysis reactions use a water molecule during the breakdown of polymers into monomers ‘Condensation reactions release a molecule during the formation of a bond. If that molecule is ‘water, this is known as a DEHYDRATION reaction. ‘+ Examples of dehydration reactions include the formation of SUCROSE (from glucose & fructose) and the formation of a DIPEPTIDE molecule from two amino acids. ‘+ Hydrogen bonds form between water molecules. HYDROXYL groups (-OH) form hydrogen bonds because hydrogen is slightly +ve and oxygen is slightly -ve. Dipole or polar molecules are fiyarophilie while non-polar motecules (without dipoles) are tropbiobie,WHAT ARE LIPIDS AND TRIGLYCERIDES? Lipids have a similar chemical structure to carbohydrates. The main difference is that they contain a uch higher proportion of HYDROGEN. They also tend to be insoluble in water. The main lipids that you would have previously leared of are fats and oils, which are used as energy reserves in the body and also used to provide insulation for organs, Fats are broken down by the enzyme LIPASE A TRIGLYCERIDE is comprised of thiee fatty (secreted by the pancreas). This results in the acids attached to a glycerol molecule. They are formation of FATTY ACIDS AND insoluble in water and are HYDROPHOBIC. GLYCEROL. These fatty acids can be classified ‘meaning that they are not attracted to water. The as either saturated or unsaturated (more on fatty acids contain a -COOH, which is called 2 this Tater), CARBOXYL group. These carboxyl groups react with the -OH groups of glycerol. This forms a very strong covalent bond called an ESTER BOND. Thus, think of the glycerol as the ‘backbone’ of the triglyceride structure. Observe the detailed structure of a glycerol molecule and a triglyceride below: yt EE EEL, rity crete —— : ' LIL, emo i OLE LLL. apt L. Glycerol Fatty Acids Triglyceride Molecul You should also get familiar with how itis represented in simpler diagrams: Ester a ° In triglycerides, ener Fatty acid | allthe Catoms are bonded to H, which makes it a yield more energy Glycerol Haagen upon breakdown, o” than carbs.SO WHICH FATS ARE ‘BAD? Triglycerides are an energy reserve and are stored in tissues in humans called ADIPOSE tissue, Accumulation of excess adipose tissue will eventually lead to OBESITY, Studies of fat are constantly yielding new information and show that fats act almost like endocrine organs, affecting hormonal secretion and metabolism. The cells shown are called ADIPOCYTES. “White far’ cells have a much higher concentration of triglycerides than ‘brown fat” cells. White fat Brown fat Brown fat cells tend to have a high concentration of mitochondria, which regularly ‘burn’ off the energy reserves, As previously stated, fatty acids are typically classified into two types: saturated and unsaturated. What is the main difference between these two? A SATURATED fat molecule has its © An UNSATURATED fat molecule has last carbon atom bonded to three hydrogens. Thus, it has been ‘saturated” with hydrogen, This is usually referred to as the “bad! fat, as it forms a dense structure that can contribute to the build-up of LDL (low- density lipoprotein) cholesterol, leading to coronary heart disease. Saturated HHH HH HH HH ‘c-G-G-G-¢-¢-¢-G-¢-C-H oT Weddhanaa 4 at least one carbon atom double-bonded to another, reducing the amount of hydrogen that is holds. Observe below to see that it causes a slight bend in the linear structure. Imagine that this bend prevents the fat from packing too tightly and contributing to arterial plaque build-up. EXTRA NOTE: Another type of ‘bad’ fat is called TRANS fat. Trans fats are formed when oils are artificially made semi-solid during artificial hydrogenation. Hydrogenation involves the insertion of gases through oils to solidify them. This affects the bonding linkages. Examples of such foods that have contained ‘rans fats in the past are margarine and shortening, and certain fast foods. They have since been banned.WHAT IS A PHOSPHOLIPID? Observe the diagram shown, It shows a phospholipid bilayer (which forms the plasma membrane). Imagine a triglyceride where one of its fatty acids has been replaced by a PHOSPHATE group. (On the diagram, you'll notice that the phosphate heads’ are HYDROPHILIC while the “fatty Erracehr Hyerepie head QUO, wees racer Phosphetid bayer NOTE: The reason the ‘head’ is attracted is because it has a negative charge. This is attracted to the positive charge of the Iuble. H atoms on the water molecule. The ‘head’ is water acid? tails are HYDROPHOBIC. If you recall hydrophobic means they are not attracted to Water molecules. Hydrophilic means they are attracted. So in water, they form this “bilayer” structure, Without this structure, cells would not be able to keep their organelles together. Glycerol H -C-H Fatty acid side chains | Q Phosphate H~ C- O-@ | g H-C-0-€ @ SS u WHAT ARE PROTE} AND AMINO ACIDS? ‘You will recall from 0" Level Biology that proteins are mainly used for cellular growth and repair in the body. They also form a entire roster of other molecules in the body, including enzymes and hormones. An amino acid is single unit and many of these combine to form a protein, just like with monosaccharides and polysaccharides i 9 H—N—C—C—OH Amino: | Carboxyl Group Group Side Chain Observe the structure. There is a central carbon atom connected to FOUR otter groups. These include: An AMINO group (NH) ACARBOXYL group (COOH) A HYDROGEN (#) atom. Another group or chain of amino acids, which is represented as “R’ Amino acids can bond with each other during condensation reactions. The linkages formed are very strong covalent bonds called PEPTIDE BONDS. ‘When this occurs, a H atom joins with an OH to form a water molecule,WHAT IS A POLYPEPTIDE? Protein synthesis occurs in the RIBOSOMES of the cells. As previously said, condensation reactions occur when amino acids are bonded, which produce water molecules When many of these amino acids are linked by peptide bonds, the chain itself is called a POLYPEPTIDE. These polypeptide chains eventually come together to form structures of protein, 10 The chains can be non-linear in shape, For example, HAEMOGLOBIN (found in the red blood cells) has four polypeptides connected in a coiled structure. ‘When polypeptide chains are broken, a water molecule is consumed during a hydrolysis reaction, An example of this would be when PEPSIN digests proteins in the stomach. Observe the linkage between two amino acids to form a dipeptide molecule: amino acid a Itcan be seen that the PEPTIDE BOND forms between the C and N after the dati ceaction, There are 20 amino acids. They may be hydrophilic groups) that contain ring structures are hydrophobic. Leu or hydrophobic. Only the ones with side chains (‘R” Here are a few examples of amino acids. Serine — Used in the synthesis of components in the brain cell membranes and neurones, — Involved in increasing lean muscle mass. Valine — High levels are associated with insulin resistance and diabetes, ‘Tryptophan — Converts to serotonin, which affects mood and sleep - Aspartic acid — Contributes to the formation of urea.cr HOW ARE PROTEINS ARRANGED? Recall that proteins are comprised of amino acid units which form polypeptide chains. The way in which these are sequenced can occur in multiple levels of increasing complexity in proteins, resulting in what are known as the primary, secondary, tertiary and quaternary structures. Structure Diagram Notes Primary A sequence of a chain of amino acids. - Determined by a gene. ~ The sequence of amino acids on the chain determines the type of protein. Secondary ~y ¢ = Occurs when the amino acid sequences are linked by weak hydrogen bonds. - The bond occurs between an O in the CO group and the H of the -NH: group. ~ Can be a helix or B pleated sheet. Tertiary ‘Haem group ret Apna ~ Occurs when multiple secondary structures fold together. - Four types of bonds involved: Hydrogen, Disulphide, Ionic and Hydrophobic Interaction. ~ May have separate PROSTHETIC groups attached to it such as haem in HAEMOGLOBIN ~ Also forms the structures of ENZYMES. Quaternary ~ The highest level of complexity for proteins. ~ The example depicted is Ha@miOglobif, which consists of numerous secondary and tertiary structures, as well as FOUR HAEM groups. ~ The role of haemoglobin is to transport oxygen, ‘When the oxygen binds to a haem group, uptake is made easier by the other three." - Haemoglobin is a GLOBULAR protein, as opposed to COLLAGEN which is a FIBROUS protein. * Haemoglobin’s structure will change any time an O; molecule is bound to the haem group. The results in what is called a conformational change and protein ‘folds’, allowing quicker binding of each successive O; molecule. This is referred to as positive cooperativity.HOW ARE PROTEINS BONDED? 12 There are four main types of bonds that help form the linkages that hold protein molecules in shape. Name of Bond | Strength of | Can be broken b How It Oceurs Bond Hydrogen Weak. High temperatures and Slightly negative and positive changes in pH. molecuiles become attracted (2. Hand 0) Tonic Strong. Changes in pH. Forms between R groups that have full positive and negative charges. Disulphide Strongand _| Reducing agents Forms between the R groups of covalent. cysteine, an amino acid. Hydrophobic Very weak. | Not considered a bond. But | Forms between R groups which Tuteraction can denature in high heat. | contain only C and H atoms. WHAT IS COLLAGEN? HOW IS IT DIFFERENT FROM GLOBULAR PROTEINS? Collagen is a protein found in our bodies that is mainly used for STRUCTURAL SUPPORT. It can be found in areas such as cartilage, bones and tendons. Due to its structural role, its insolubility in water and its repeating sequences, itis referred to as a FIBROUS protein. This contrasts with GLOBULAR proteins, such as Hemme BlObid, AGRIBOIES and SAVAGES, which partake in chemical reactions. are often soluble in water and the primary structures usually have specific shapes instead of repeated sequences. As can be seen in the molecular structure, it consists of THREE polypeptide chains. These form three helical strands, which intertwine and are held together by HYDROGEN bonds. These collagen molecules form cross-links and form FIBRILS, which form bundles known as FIBRES. BRP ‘Amino Acid > > S Ss Collagen Collagen Molecule Fiber ‘The following are some roles of globular and fibrous proteins: - Egg GIOBUIAE) — Lowers activation energy to catalyze certain chemical reactions. - KEIR TERE — Forms protective layers and filaments, such asin hair and nail - BANGTEBUTER — Converts glucose to glycogen for storage inthe cel - ati) ~ lows ee ry to organs such as the lungs and bladder.13 TEST FOR REDUCING AND NON-REDUCING SUGARS Examples of reducing sugars include GLUCOSE, MALTOSE and FRUCTOSE, while an example of a non-reducing sugar is SUCROSE. The solution needed to test for both of these is called BENEDICT’S SOLUTION, a blue liquid that contains eopper(ID spits Upon heating, Cu? is reduced to Cu and forms copper (I) oxide in the presence of reducing sugar, which forms a BRICK RED precipitate Trace amounts of sugars results in a GREEN colour. FOR NO REDUCING SUGARS: Recall that sucrose has a GLYCOSIDIC bond. To break this bond, heat the solution with dilute HCI and then neutralize with SODIUM HYDROXIDE. This GLUCOSE and FRUCTOSE from the sucrose. TEST FOR STARCH Starch is a polysaccharide that is comprised of amylose and amylopectin. The test for starch presence involves the addition of IODINE SOLUTION IN POTASSIUM IODIDE (KI). The iodine is able to bind to the helical structure of amylose and produce the BLUE-BLACK, colour. EMULSION TEST FOR LIPIDS Recall that lipids are hydrophobic and are thus INSOLUBLE in water. To test for the presence of lipids, ETHANOL is first poured into the sample. The lipid molecules will dissolve in the ethanol. WATER is then added. The hydrophobic lipid molecules begin to disassociate from the solution and form an opaque milky white layer of droplets that float to the top called an EMULSION. ll yield TEST FOR PROTEINS Proteins have linkages called PEPTIDE bonds (between the C and N of adjacent amino acids). BIURET reagent is used to test for proteins, which contains copper (I) sulphate and potassium hydroxide, ‘When BIURET reagent is added, the copper ions produce a PURPLE colour. Distiled water —_ Cloud Sample + emulsio 95% ethandTOPIC 2: CELL STRUCTURE 14 DIFFERENCES BETWEEN LIGHT AND ELECTRON MICROSCOPES Characteristic Light Microscope Electron Microscope Max, Magnification | x 1400 x 300,000 Type of lens used Glass Electromagnets ‘Type of radiation used Visible light Electron beams Colour Image will appear in colour. Image will be in black and white. Preparation of specimen Living cells and tissues are used. Non- living tissues may be used if they are mounted on a slide in a transparent liquid. Only non-living and dehydrated cells are used. They are cut very thinly and placed in a vacuum. Staining of specimen Cells absorb many different coloured stains Cells and organelles absorb heavy metals. Viewing of specimen By eye or projection on a screen. Electrons fall onto a fluorescent screen. Main advantages - Much more affordable than electron microscopes. - Slides can last for a very long time. - Little tisk of distortion while viewing. - Much higher resolution - Much higher magnification Main disadvantages - Much lower resolution - Much lower magnification - Expensive, requires expertise - Specimen deteriorates during viewing (unlike slides) - High risk of distortion Two types of electron microscopes 1. SEM (Scanning Electron Microscope) 2. TEM (Transmission Electron Microscope) SEM usually observes the surface of an specimen hile TEM is used to observe a very thinly cut section of specimen, supported on grids.45 ULTRASTRUCTURE OF CELLS Recall that light microscopes have a much lower resolution and magnification than electron microscopes. Photomicrographs therefore are unable to clearly show all of the organelles present in the structures of the animal and plant cells. When an electron microscope is used to view the structure, the visible image is called an ULTRASTRUCTURE. vacuole cell membrane nucleolus ucteat ‘membrane > nucleus chromatin ‘ytoplasm mitochondria Smooth cell membrane mitochondrion nucleus cytoplasm chloroplast Structure of undifferentiated plant cell under light microscope endoplasmic reticulum. Rough endoplasmic reticulum Polyribosomes Nuclear pores J Plasma membrane Vacuole j— Ribosomes Mitochondrion Golgi body ram of the ultrastructure of an animal cellCell wall Middle lamella Plasmodesma ram of ultrastructure of a plant cell ‘TABLE SHOWING DIFFERENCES BETWEEN ANIMAL AND PLANT CELLS Organelle or Structure Animal Cells Plant Celts Chloroplasts Chloroplasts and any plastids are absent. | Present in photosynthetic cells. Cell wall and Cell wall and plasmodesmata are absent. | Present in cells, usually containing plasmodesmata cellulose, pectin or lignin. Vacuole ‘Small, temporary vacuoles. Large, permanent vacuoles surrounded by tonoplast. Centrioles ‘Usually present. Centrioles are absent, Waste removal Digestion by lysosomes. ‘Vacuoles move to plasma membrane Sugar storage Stored in glycogen granules. Statch grains (in amyloplasts) Cilia and flagella Present in some (e.g. sperm, respiratory epithelium) Mostly absent.7 Organelle or | Diagrams Notes Structure Nucleus - The nucleus contains long nuclear membrane Dna, nuclear membrane ona nucleos clear pore molecules of DNA called CHROMOSOMES, which is made up of threads called CHROMATIN. ~ The nucleus is surrounded by a pair of membranes known as NUCLEAR ENVELOPE. - The nuclear envelope has tiny openings called NUCLEAR PORES, which allow movement of ATP and RNA. - The NUCLEOLUS contains ribosomal RNA or :RNA, which helps with PROTEIN SYNTHESIS. ~ Two types of cells that don’t have Mitochondrion Inner membrane cites ate intermemraal ~ Mitochondria are the site of AEROBIC RESPIRATION in both plant and animal cells. - This mostly occurs in the tiny folds of the inner membrane called the CRISTAE. - Several chemical reactions also ‘occur in the MATRIX, Chloroplast Lipid Gran (Pe ot Takis) GGranumia_ Starch grain (Grew has) vvertoa Srcton Chloroplast envelope - Chloroplasts are sites of PHOTOSYNTHESIS -Ithas a double membrane, like mitochondria - Sacs called THYLAKOIDS contain cilorophyll necessary for the light-dependent reactions, while light-independent reactions occur in the STROMA. ~ Stacks of thylakoids are GRANA.