Grade 12 Biochemistry Unit PDF

UNIT 1 BIOCHEMISTRY Cell Structures Biochemistry  Cell Membrane Also known as the plasma membrane Protects the cell Determines what can enter and exit the cell  Cytoplasm Gel-like substance that holds all organelles in cell  The Mitochondria...

UNIT 1 BIOCHEMISTRY Cell Structures Biochemistry  Cell Membrane Also known as the plasma membrane Protects the cell Determines what can enter and exit the cell  Cytoplasm Gel-like substance that holds all organelles in cell  The Mitochondria The Powerhouse of the cell. Cigar-shaped organelle characterized by the folding inner membrane called the CRISTAE Make ATP - energy carriers Two membranes - inner and outer Has its own DNA (mDNA) and ribosomes - self-replicates – mDNA: contains genes important for specific functions (ie. making enzymes) Mitochondrial DNA (mDNA)  Endoplasmic Reticulum Interconnected tubes – Begin at nucleus Type 1: Rough endoplasmic reticulum (ER) – Ribosomes attached to make look “rough” – Protein synthesis occurs here Type 2: Smooth ER – Lipid synthesis occurs here R.E.R. S.E.R.  Nucleus Control centre; isolates DNA Has a Nuclear envelope – 2 lipid bilayers with pores to let things in and out Nucleolus – Inside nucleus – Where some proteins and RNA built; ribosomes made Chromosomes – Chromatin – Sister Chromatids – Genetic information/traits  Golgi Body Final processing of proteins Formation of vesicles Packages and secretes (gets rid of) waste Golgi Body and Vesicles  Vesicles Lysosomes - animal cells – Contain enzymes – “Digestive system of the cell” Peroxisomes – Smaller than lysosomes – Also contain enzymes – Breakdown fatty acids and toxins Lysosomes  Chloroplast – Double membrane – Stroma (fluid inside) – Photosynthetic synthesis of ATP (traps sun’s energy and makes food)  Vacuole – Storage (food and water)  Cell Wall Wraps around the plasma membrane Protects and physically supports Found in: – Plant cells – Protistans – Fungi  Centrioles Helps the cell to divide  Cytoskeleton Interconnected system of protein fibers – Cell shape – Stabilize position of organelles – Movement Types of cytoskeletal proteins – Microtubules – Microfilaments – Intermediate filaments  Flagella and Cilia Same basic structure – Ring of 9 pairs of microtubules surrounding a central pair  Flagella and Cilia Cilia – Short hair-like projections on outside of cell used for movement Flagella – Long whip-like tail on outside of cell used for movement  Bacteria Prokaryotic – DNA clustered in one region of cytoplasm Smallest and simplest cells Cell wall Ribosomes Flagella No cytoskeleton  Water Biochemistry Polar Covalent Molecule Water is formed through covalent bonds (two non-metals) Polar molecule Oxygen has a high electronegativity (strong pull on electrons) Hydrogen has a low electronegativity (weak pull on electrons) Properties of Water 1. Cohesion 2. Adhesion 3. Universal Solvent 4. High Specific Heat Capacity 5. High specific heat of vaporization 6. Highest Density at 4 degrees Celsius Cohesion Cohesion ○ Refers to the attraction of water molecules to each other ○ Molecules can form H-bonds with each other ○ Cohesion creates SURFACE TENSION ○ Surface tension causes water to form spherical droplets and allows it to support small objects, like a scrap of paper Surface Tension Surface tension is the ability of a liquid to “push back” on something. COHESION causes surface tension. Surface tension is due to the molecules at the surface having stronger hydrogen bonds Water molecules are surrounded only on one side at the surface, and the H-Bonds are therefore stronger Adhesion Attraction of water molecules to other types of molecules Adhesion enables water to “climb” upwards against gravity For example, capillary action causes water to move up the xylem tubes in plants Universal Solvent Polar substances that dissolve in water are: ○ Miscible - forming a homogeneous mixture when added together. ○ Hydrophilic - molecules are polar or charged molecules that are strongly attracted to water Non-polar substances that do NOT dissolve are: ○ Immiscible - incapable of being mixed to form a homogeneous ○ Hydrophobic - molecules are nonpolar molecules that are not strongly attracted to water. Example: Dissociation of NaCl Each ion becomes surrounded by water molecules attracted to it. This is why the salt seems to vanish in the water. The sodium chloride molecules have been split into ions, or dissolved, by the water molecules. Salt and other substances that dissolve in water are said to be “water soluble.” High Specific Heat of Vaporization Heat Capacity Specific heat is how much energy is required to heat a substance - water needs a LOT of energy to be heated, so WATER HAS A VERY HIGH SPECIFIC HEAT CAPACITY. To heat things you need to make the molecules move faster. It is hard to make water molecules move fast because its hydrogen bonds keep the molecules stuck High Specific Heat of Vaporization Water’s high specific heat capacity helps to moderate air temperature around large bodies of water. This moderation of temperature helps organism maintain a constant body temperature. Density Solid water is less dense than liquid water. As water molecules cool below 0 degrees Celsius, they form an ice water lattice. The hydrogen bonds keep the water molecules spread apart, reducing the density so that it is below the density of water. For this reason, fish and other aquatic organism survive in winter because water freezes from the top down. Practice Make a chart summarizing the thermal, cohesive and solvent properties of water. Include examples of how these properties apply in real contexts (eg. Why does water travel upwards in a plant?) List and describe the significance of water to living organisms. (ie. What features/properties of water make it important?) Extra reading posted on Google Classroom Hydrocarbons Biochemistry Important Molecules in Biochemistry As mentioned before, the key compounds we will be studying this semester are: Organic; composed mostly of carbon, hydrogen, oxygen and other elements like phosphorus, sulfur, and nitrogen Molecular compounds with covalent or polar covalent bonds The Chemicals of Life Carbon atoms attach to themselves in many ways with bonds (carbon atoms can have 4 bonds attached to them - bonding capacity). Molecules made of carbon can be straight chained, branched or form ring structures. Molecules that contain only carbon and hydrogen atoms are called hydrocarbons, and are the main component of many types of fuel (such as diesel, gasoline, propane, etc). Bonding Capacity Bonding Capacity Bonding Capacity - Carbon!! Tetravalent (4 bonds) Can form single, double and triple bonds Can form long chains, sheets, and rings with other atoms Can bond with many other atoms/atom groups (aka functional groups) Bonding Capacity - Carbon!! Tetravalent (4 bonds) Can form single, double and triple bonds Can form long chains, sheets, and rings with other atoms Can bond with many other atoms/atom groups (aka functional groups) Hydrocarbons - contain only C and H Saturated Hydrocarbons: Alkanes Methane CH4 Hexane C6H14 Ethane C 2H 6 Heptane C7H16 Propane C3H8 Octane C8H18 Butane C4H10 Nonane C9H20 Pentane C5H12 Decane C10H22 Unsaturated Hydrocarbons Alkynes Alkenes Functional Groups Biochemistry Functional Groups Organic compounds usually comprise a carbon skeleton with reactive or functional groups attached. Functional groups are a group of atoms that affect the function of a molecule by participating in chemical reactions. Usually ionic or strongly polar, necessary for chemical reactions. Have definite chemical properties that they retain no matter where they occur. Functional Groups Some of the important functional groups in biological molecules include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids. R, also known as R-group, is an abbreviation for any group in which a carbon or hydrogen atoms is attached to the rest of the molecule. Hydroxyl Group -OH H H Hydroxyl Features: Consists of an O atom group joined by a single covalent bond H C C OH to an H atom. H H Properties: Polar, hydrophilic, highly reactive Organic molecules containing hydroxyl groups are alcohols. Structural formula of ethanol, shown Found in carbohydrates, proteins, as a straight chain (top) and a space filling model (bottom). nucleic acids, lipids Carboxyl Group -COOH H O Features: Consists of a central C atom joined by covalent bonds to two O and OH H C C Properties: ○ Ionized to release H+ (Donate H+), H OH ○ Since carboxyl group can release H+ ions into a solution, they are considered acidic - Carboxylic acids One valence electron on the carbon is available for bonding to another atom so that the carboxyl group In this acetic acid molecule, the can form part of a larger molecule. carboxyl group is highlighted. Found in amino acids, fatty acids and some vitamins Carbonyl Group -CO H H O Features: Composed of a central C atom H C C C Propanal is an example of an joined to an O atom by a double bond. aldehyde. H H H Properties: Polar/Hydrophilic If the carbonyl group occurs at the end of H O H a carbon molecule it is called an H C C C H aldehyde. If the carbonyl group occurs H H within the carbon compound Acetone is an example of it is called a ketone. a ketone. Found in carbohydrates, nucleic acids Amino Group -NH2 H O H Feature: Consists of one N atom attached by Amino covalent bonds to two atoms of H. C C N group Properties: HO H H ○ Charged accepts H+ to form NH3+ Glycine (above, and space filling model below) is the ○ Since amino groups can remove H+ from simplest amino acid solutions, they are considered basic ○ Hydrophilic A lone valence electron on the nitrogen is available for bonding to another atom. Amino Group - NH2 (cont’d) Organic molecules containing amino groups are called amines. Since amino groups can remove H+ from solutions, they are considered weak bases. The amino group is common to all amino acids, which in turn are the building blocks of proteins. Found in amino acids and urea in urine (from protein breakdown); proteins and nucleic acids Phosphate Group -PO4 O H Features: Composed of one P atom OH OH bound to four O atoms. H C C C O P O– Properties: ○ Charged, ionizes to release H+ H H H O– ○ Since phosphate groups can The phosphate group of this glycerol phosphate molecule release H+ ions into solutions, is shown in red. they are considered acidic. Phosphate Group -PO4 Organic molecules containing phosphate groups are called organic phosphates The phosphate group is one of the three components of nucleotides and often attached to proteins and other biological molecules. Found in nucleic acids Sulfhydryl Group -SH H H OH Features: Consists of a S atom HS C C C bonded to an H atom. H NH2 O Properties: Polar The sulfhydryl group in the amino acid cysteine is shown here in red. Organic molecules containing sulfhydryl groups are called thiols. Involved in protein structures Helps to bind ribosomes Found in proteins Practice Question Fructose is a common sugar you’ve probably come into contact with in your life. What functional groups can be found in a fructose molecule? Practice Question Leucine is an amino acid that plays an important role in muscle development. What functional groups can be found in leucine molecule? Practice Complete the summary table on Functional Groups. Practice identifying functional groups found in organic compounds. Extra resources posted on GC (videos, readings, etc.). Important Reactions in Biochemistry Biochemistry Important Reactions in Biochemistry Redox Dehydration synthesis Hydrolysis Neutralization Redox Reaction You can recognize redox reactions by following the flow of electrons… Something will LOSE ELECTRONS and become OXIDIZED Something will GAIN ELECTRONS and become REDUCED The combination of those is a Reduction-Oxidation, also known as a Redox reaction. Redox Reaction Redox Reaction Because the two reactions are paired up, we call the compound that is being oxidized the reducing agent (because it is responsible for the reducing the other compound). We call the compound that is being reduced the oxidizing agent (because it is responsible for the oxidizing the other compound). Redox Reactions Redox Rxn → involves the transfer of electrons from one atom to another – An electron transfer between substances always involves one losing electron(s) and one gaining electron(s) Oxidation → the process of losing electrons Reduction → the process of gaining electrons (LEO the lion goes GER) Reducing Agent → substance that loses electrons Oxidizing Agent → substance that gains electrons Redox Reaction Example The simplest example of a Redox reaction is an ionization like the one shown below. Redox Reaction Example In this reaction, what is being oxidized? What is being reduced? Which is the reducing agent? Which is the oxidizing agent? Redox Reaction Example Oxidized; Reduced; Reducing Agent Oxidizing Agent Redox Example This is also a Redox reaction… In covalent compounds like this, the electrons aren’t entirely “lost” but rather, they become more closely bound to a different nucleus. The electrons are represented by the blue dots. See if you can track how they are shifting and why we would say the methane is being oxidized and the oxygen reduced. Helpful Rules to Follow: Oxidation Reactions: Reduction Reactions: Addition of oxygen atoms to Removal of oxygen atoms a substance from a substance Removal of hydrogen atoms Addition of hydrogen atoms from a substance to a substance Loss of electrons from a Addition of electrons to a substance substance Try this… Determine which species is oxidized and which species is reduced in the following chemical equation: Try this… Determine which species is oxidized and which species is reduced in the following chemical equation: C6H12O6 is oxidized in the Cellular Respiration reaction above. O2 is reduced in the Cellular Respiration reaction above In Summary... Redox Rxn → involves the transfer of electrons from one atom to another – An electron transfer between substances always involves one losing electron(s) and one gaining electron(s) Oxidation → the process of losing electrons Reduction → the process of gaining electrons (LEO goes GER) Reducing Agent → substance that loses electrons Oxidizing Agent → substance that gains electrons Electron Carriers Electron shuttles: carry high-energy electrons between compounds in biochemical pathways Can be easily reduced or oxidized Example: Nicotinamide adenine dinucleotide ○ NAD+ - oxidized ○ NADH - reduced Electron Carriers Neutralization Reaction Dehydration Synthesis Hydrolysis  Introduction to Biological Molecules Biochemistry B3.2 describe the structure of important biochemical compounds, including carbohydrates, proteins, lipids, and nucleic acids, and explain their function within cells  Biological Molecules Macromolecules: large molecules composed of repeating subunits The subunits are called MONOMERS  Biological Molecules Four major classes: carbohydrates, lipids, proteins, and nucleic acids 102  Polymer Monomer Carbohydrates Monosaccharides Lipids Fatty acids + glycerol Proteins Amino Acids Nucleic acids Nucleotides  How Macromolecules are Formed Dehydration Synthesis (Condensation Reaction) Two subunits link together through the removal of a water molecule. Dehydration synthesis is an anabolic reaction that absorbs energy. Anabolic Reaction - a reaction that produces large molecules from smaller subunits  How Macromolecules are Broken Down Hydrolysis Reaction Two subunits break apart through the addition of a water molecule. Hydration synthesis is a catabolic reaction that releases energy. Catabolic Reaction - A reaction that breaks macromolecules into smaller subunits  Choice Board Use the following resources to complete the macromolecule summary sheet attached on Google Classroom. We will be going through each macromolecule together in the the coming classes. Read: Synthesis of Macromolecules, Biological Molecules Watch: Amoeba Sisters, Crash Course Carbohydrates Biochemistry Unit Learning Goal: B3.2 describe the structure of important biochemical compounds, including carbohydrates, proteins, lipids, and nucleic acids, and explain their function within cells After this lesson I can: ❏ Outline the structure of carbohydrates ❏ Explain the role carbohydrates play in organisms ❏ Identify and differentiate between monosaccharides, disaccharides and polysaccharides Molecules Monomers - a small molecule that can bind chemically to other molecules (building blocks). Polymer - a large molecule that is formed when monomers link together chemically in a chain. Macromolecules - complex molecule composed of repeating units of smaller molecules covalently linked together.  Carbohydrates source of energy necessary to build various biological molecules Structure of Carbohydrates The Carbohydrates/Saccharides are divided into 3 chemical groups: 1. Monosaccharides (simple sugars) - alpha glucose, beta glucose, galactose, fructose 2. Disaccharides (double sugars) - sucrose, maltose, lactose 3. Polysaccharides (complex sugars) - starch, glycogen, cellulose, chitin Carbohydrates A carbohydrate is a large biological molecule consisting only of carbon (C), hydrogen (H) and oxygen (O). The general empirical formula is (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 “Carbo” = carbon and “hydrate” = water Name often ends in -ose Functional Groups in Carbohydrates Carbonyl group Hydroxyl group Role of Carbohydrates Energy Source Carbohydrates broken down to mainly glucose are the preferred source of energy for our body, as cells in our brain, muscle and all other tissues directly use monosaccharides for their energy needs. Monosaccharides are directly absorbed by the small intestine into the bloodstream, where they are transported to the cells in need. Role of Carbohydrates Membrane Carbohydrates Structural role as a physical barrier Participate in cell recognition ○ Cell surface markers for cell-to-cell identification and communication Role of Carbohydrates Structural Support Different carbohydrates, particularly those in the form of polysaccharides, contribute to the building of cellular structure. In plants particularly, cellulose creates a solid wall around the plant cells, giving the plant its structure. Role of Carbohydrates Biochemical Synthesis As carbohydrates break down, they release carbon atoms. These serve as the raw material for much of an organism's biochemistry, as the carbon can then join with other chemicals in the body. Monosaccharides Monosaccharides are simple carbohydrates that consist of 1 monomer subunit. Many contain 6 Carbon atoms, 12 Hydrogen atoms, 6 Oxygen atoms (isomers) Energy source, building blocks (monomer) Most monosaccharide names end with the suffix -ose. Monosaccharides Monosaccharides include: 1. Glucose - produced during photosynthesis 2. Fructose - in fruit 3. Galactose - in milk 4. Ribose 5. Deoxyribose  C6H12O6 Monosaccharides Monosaccharides Describe the difference in structure between Glucose and Galactose… Glucose Galactose  Describe the difference in structure between Glucose and Galactose… All are ISOMERS – same chemical formula, but different arrangement of atoms ∴ different shapes and physical and chemical properties Monosaccharides Glucose is an important source of energy a.k.a. blood sugar Fructose is commonly found in fruits and known as fruit sugar. Galactose is found in milk products Ribose and Deoxyribose are sugar component of DNA (C5H10O5 & C5H10O4) Monosaccharides Scientists classify monosaccharides based on … 1. The position of their carbonyl group 2. The number of carbons in the backbone. Monosaccharides Monosaccharides can be distinguished by their carbonyl group. Glucose, fructose and galactose are isomers, meaning they have the same chemical formula, (C6H12O6) but a different atom arrangement. Monosaccharides Monosaccharides can be distinguished by the number of carbons. For example, Ribose and Deoxyribose are a Pentose Sugar - 5 carbons Glucose is a Hexose Sugar - 6 carbons In Solutions Monosaccharides form a ring structure when dissolved in water The hydroxyl group on carbon 1 can end up either above or below the ring α-glucose - below the ring β-glucose - above the ring Dry State Monosaccharides are linear in a dry state How does ring formation happen? Alpha and Beta Glucose Formation  Glucose can exist in 2 forms: α-glucose β-glucose ⦿ -OH group on carbon 1 ⦿ -OH group on carbon 1 points downwards points upwards Disaccharides Disaccharides are formed when two monosaccharide molecules join in a dehydration reaction (or condensation reaction) to form a glycosidic bond - in the process an H2O molecule is removed. Disaccharides are used as energy storage and as building blocks for larger molecules. Disaccharides Some important disaccharide molecules include: 1. Sucrose - table sugar 2. Maltose - grain sugar 3. Lactose - milk sugar The types of disaccharides formed depends on the monomers involved and their form (alpha or beta) Sucrose = glucose + fructose Lactose = glucose + β-galactose Maltose = α-glucose + α-glucose Polysaccharides Unbranched A long chain of monosaccharides linked by glycosidic bonds is a polysaccharide (poly- = “many”). Branched The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides Primary examples of polysaccharides include: 1. Starch 2. Glycogen 3. Cellulose Starch and glycogen are examples of storage for carbohydrates. Cellulose and chitin are examples of structural complex carbohydrates. Polysaccharides Disaccharides and polysaccharides can be broken down into smaller simpler sugars via hydrolysis. ○ A chemical reaction using water to break bonds to form two or more new substances Starch (found in plants) 2-6 thousand glucose molecules bonded together forming amylose (unbranched, coiled α-glucose chain) or amylopectin (branched α-glucose chain) Both types twist into coils – making them insoluble in water Storage molecules used by plants The glucose made through photosynthesis can be stored as a starch polymer Starch Glycogen (found in animals) Glycogen is the storage form of glucose in humans and other vertebrates and is comprised of monomers of glucose. Stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen breaks down to release glucose. α-1,4 (linear) and α-1,6 (branched) Glycogen (found in animals) Cellulose Structural component of plant cell walls that provides support Straight chain of β- glucose monomers with β1-4 linkages Linkages cause inversion of every other monomer Form bundles of fibres (H-bonds between cellulose molecules form bundles with high tensile strength) Cellulose Chains of beta-glucoses monomers Humans are unable to digest cellulose because we lack the enzymes in our digestive systems to Hydrogen Bonds break down the bonds within cellulose The linear shape of cellulose allows it to interact with water Chitin Exoskeleton of insects and crustaceans contains a glucose-like monomer with a nitrogen group at C-2 Difference between alpha and beta… QUIZ YOURSELF… Carbohydrates CARBOHYDRATE FACT: IN A YEAR, THE AVERAGE PERSON EATS 423 LB OF VEGETABLES, 271 LBS OF FRUIT AND 20 LBS OF RICE. WHICH OF THE FOLLOWING ELEMENTS ARE FOUND IN CARBOHYDRATES? a. Carbon, Hydrogen, and Nitrogen b. Carbon, Hydrogen, and Oxygen c. Hydrogen, Oxygen, and Nitrogen d. Calcium, Hydrogen and Oxygen WHICH OF THE FOLLOWING ELEMENTS ARE FOUND IN CARBOHYDRATES? b. Carbon, Hydrogen, and Oxygen WHY ARE CARBOHYDRATES IMPORTANT FOR LIFE? Provide short-term energy for the cell Main reactant in cellular respiration THIS MONOSACCHARIDE IS THE MOST COMMON SUGAR. WHICH SUGAR IS IT? GLUCOSE C6H12O6 Two monosaccharides joined together are called… DISACCHARIDES Name the reaction that forms disaccharides? Dehydration Synthesis MANY MONOMERS JOINED TOGETHER ARE CALLED…? Polysaccharides  POLYSACCHARIDES STARCH GLYCOGEN Storage of Short term energy storage in humans glucose in Broken down in plants liver and muscle cells when energy POLYSACCHARIDES GLYCOGEN POLYSACCHARIDES STARCH WHAT AM I? Glucose WHAT AM I? Fructose WHAT AM I? Sucrose IDENTIFY THE NAME OF EACH LABEL A-D A. Glucose Molecule B. Fructose Molecule C. Hydroxyl group NAME THE TYPE OF REACTION SHOWN Dehydration Synthesis (or condensation reaction) Lactose Intolerance Lactase is an enzyme that breaks down the glycosidic bond in lactose Although almost all babies are born with the ability to produce lactase, some people lose that as they get older These people are said to be lactose intolerant  Lipids Biochemistry Unit Learning Goal: B3.2 describe the structure of important biochemical compounds, including carbohydrates, proteins, lipids, and nucleic acids, and explain their function within cells After this lesson I can: ❏ Outline the structure of lipids ❏ Explain the role lipids play in organisms ❏ Identify and differentiate between different types of lipids ❏ Explain the significance of saturation Lipids - RicochetScience Lipids Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules. Like carbohydrates, lipids contain carbon, hydrogen, and oxygen, but in lipids, the proportion of oxygen is much smaller (1:2:very few) Lipids are the body’s main form of stored energy, plasma membranes, hormones Functional Groups in LIPIDS hydroxyl carboxyl Biological Roles of Lipids Shock Absorbant Fat absorbs shocks. Organs that are prone to bumps and shocks (e.g. kidneys) are cushioned with a relatively thick layer of fat Biological Roles of Lipids Metabolic Water Lipids are a source of metabolic water. During respiration, stored lipids are metabolized for energy, producing water and carbon dioxide. Biological Roles of Lipids Insulation Stored lipids provide insulation in extreme environment. Increased body fat levels in winter reduce heat losses to the environment. 1. Most Common Fat: Triglycerides Fat molecules are also called triacylglycerols or triglycerides Made up of a glycerol backbone + three fatty acid tails In the human body, triglycerides are primarily stored in specialized fat cells called adipocytes (adipose tissue) Glycerol Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty Acids Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached Triglyceride Formation Glycerides are formed when the hydroxyl group on glycerol bonds with the carboxyl group on fatty acids (dehydration synthesis) Bond is called ester linkage and the process is known as esterification Ester Linkages (Esterification)…creates an C-O-C bond Saturated Saturated fatty acids - all available bonds are filled with hydrogen (only single bonds between carbons) ○ Solid at room temperature (hydrogens packed closely together- allows for more LDF forces to form) Monounsaturated Monounsaturated fatty acids contain one C-C double bond (hydrogen is removed) Bent hydrocarbon chains do not fit closely together, not allowing as many LDF forces to form Polyunsaturated Polyunsaturated fatty acids contain more than one C-C double bond ◦ tend to be liquid at room temperature as double bonds cause kinks in the structure and prevent molecules from packing together Hydrogenation Hydrogenation - hydrogen atoms are added to double bonds in unsaturated triacylglycerols Forms trans form rather than the cis form Trans Fat vs Cis Fat Arrangement of atoms in Cis - chains of carbon atoms are on the same side of the double bond, resulting in a kink. Arrangement of atoms in Trans - Hydrogen atoms are on the opposite side of the double bonds of the carbon chain, making the fat molecule straight. Due to the larger bend, the cis isomers cannot line up Cis vs Trans 2. Phospholipids Phospholipids make up the lipid bilayer of cell membranes, an important structural feature of cells. 2. Phospholipids Phospholipids are made up of a Glycerol + two hydrophobic fatty acids + hydrophilic phosphate group 2. Phospholipids Phospholipids Bilayer - phosphate heads facing the water and their tails pointing towards the inside 2. Phospholipids If a drop of phospholipids is placed in water, it may spontaneously form a sphere-shaped structure known as a micelle - hydrophilic phosphate heads face the outside and the fatty acids tails face the interior of this structure. 3. Steroids Steroids is a lipid composed of a 4 carbon ring + OH functional group Also called sterols due to hydroxyl group on one or more rings They do not contain any fatty acids! Considered lipids because they are hydrophobic and insoluble in water. 3. Steroids Examples: cholesterol, testosterone, estrogen, vitamin D Sterol Lipid Role Keeps cell membrane fluid in cold temperatures and Cholesterol maintains structure and rigidity in warm temperatures Testosterone Male sex hormone Estradiol Female sex hormone Progesterone Female sex hormone Cholesterol Cholesterol is a steroid that is essential for animal cell membranes and converts into a number of compounds. High cholesterol levels contribute to atherosclerosis (build up in/on artery walls), which can lead to heart attacks and strokes 4. Waxes fatty acids linked to alcohols or carbon rings nonpolar - hydrophobic pliable consistency - forms waterproof coating barrier against water loss and infection keeps birds dry and bees busy (forms honeycombs/beeswax)!  4. Waxes ▶ Diversity of structures ▶ Usually long carbon-based chains ▶ Solid at room temp 4. Waxes ▶ Produced in plants and animals In Plants ▶ Carnauba wax ▶ Coats surface of leaves preventing water loss and repels insects 4. Waxes In Animals ▶ Earwax, beeswax ▶ Present on the skin, fur and feathers of many animals Summary Lipids vs. Carbohydrates What is fat? - TED-Ed  Proteins Biochemistry Unit Learning Goal: B3.2 describe the structure of important biochemical compounds, including carbohydrates, proteins, lipids, and nucleic acids, and explain their function within cells After this lesson I can: ❏ Outline the structure of proteins (primary, secondary, tertiary and quaternary) ❏ Explain the role proteins play in organisms ❏ Identify amino acids ❏ predict product of amino acid reactions Proteins - Bozeman Science Protein Overview Involved in almost everything cells do They make up gelatin, hair, antibodies, spider webs, blood clots, egg whites, tofu, fingernails… Proteins are made up of amino acids At the atomic level, all proteins are made up of carbon, hydrogen, oxygen, nitrogen and sometimes sulphur. Protein can be obtained from both animal and plant Protein and DNA The genetic information in DNA codes for producing specific proteins and NOTHING ELSE These proteins then go on to accomplish all life processes Functions of Proteins Enzymes are biological catalysts that speed up chemical reactions in the body Hormones - regulate physiological processes, such growth and development, metabolism, reproduction. Functions of Proteins Antibodies - proteins that bind like a lock-and-key to the body's foreign invaders — whether they are viruses, bacteria, fungi or parasites. Protein Carriers - Transport materials through cell membranes and through the body (e.g. hemoglobin carries O2 and CO2 throughout mammalian bodies) Structural - Keratin found in hair and fingernails, fibrin helps blood clot, and collagen forms the protein portion of bones, skin, ligaments & tendons Amino Acids Proteins are made up of a combination of amino acids folded into a 3D shape. Shape determines protein function. Every amino acid has the same structure - consists of a central carbon atom bonded to an amino group (-NH2), carboxyl group (-COOH), and a hydrogen atom. The difference lies in the R group - R group gives the amino acid distinct properties. Functional Groups in Amino Acid Proteins There are 20 different amino acid R groups (side group) ○ 9 amino acids are essential (consume in our diets) ○ 11 amino acids are non-essential (our bodies create them) The R Groups determine the properties of the amino acid and the protein Side groups may be polar or nonpolar, acid or base The sequence and number of amino acids ultimately determine Nonpolar Amino Acids Polar Amino Acids Acidic and Basic Amino Acids Acidic Amino Acids possess a carboxyl group on their R-Group Basic Amino Acids possess an amino group on their R-Group Protein Structure Amino acids are the monomers that make up proteins The bonds that hold amino acids together are called peptide bonds Peptide bonds are formed by a dehydration synthesis reaction. Occurs between amino group of one amino acid and the carboxyl group of an adjacent amino acid Protein Structure Draw the structural diagram to represent the peptide bond that forms between serine and alanine. Protein Structure Draw the structural diagram to represent the peptide bond that forms between serine and alanine. This structure is called a dipeptide (two amino acids joined by a peptide bond) Proteins Structures As more amino acids are added, it becomes a polypeptide A polypeptide is a peptide that is greater than 50 amino acids in length A protein consists of one or more polypeptides that are folded into a precise 3-dimensional shape; only after folding occurs is the protein able to function. Hydrolysis Reaction Protein Structures Protein Structure The unique amino acid sequence of a protein is reflected in its unique folded structure. This structure, in turn, determines the protein's function. Proteins have up to 4 levels of structures, each giving them different characteristics to the overall protein: 1. Primary Structure 2. Secondary Structure 3. Tertiary Structure Primary Structure The primary structure of a protein is the unique linear sequence of its amino acid in each polypeptide chain. Changing even a single amino acid in the primary structure will alter the overall structure of the protein or destroy its biological function. Secondary Structure The secondary structure folds and coils as the polypeptide chain grows Formed by H-bonds between O atoms of a carboxyl group (partially -) and H atoms of an amino group (partially +) Two types ○ α helix ○ β pleated sheets Tertiary Structure In the tertiary structure, the polypeptide chain undergoes additional folding due to side chain (R-group) interactions. Quaternary Structure Two or more polypeptide chains come together to form a functional protein, such as in collagen and hemoglobin. Denaturation Denaturation involves the breaking of many of the weak bonds (e.g., hydrogen bonds), within a protein molecule that are responsible for the highly ordered structure of the protein. See animation and summarize your findings. Denature Heat, pH and salt concentration can break hydrogen bonds - changing the structure of your protein Change in structure = change in function Practice Complete the Protein Worksheet also posted on Google Classroom Optional: complete the summary Proteins handout posted on Google Classroom Nucleic Acids Biochemistry Unit Learning Goal: B3.2 describe the structure of important biochemical compounds, including carbohydrates, proteins, lipids, and nucleic acids, and explain their function within cells After this lesson I can: ❏ Outline the structure of nucleic acids (including DNA vs RNA, pyrimidine vs purine bases) ❏ Explain the role nucleic acids play in organisms ❏ Describe antiparallel directionality in DNA strands Nucleic Acid Nucleic Acids serve as the assembly instructions for all proteins in living organisms. Two types of Nucleic Acid exists: 1. DNA - Deoxyribonucleic acid 2. RNA - Ribonucleic acid Nucleic Acid 1. DNA - Deoxyribonucleic acid ○ stores hereditary information that is responsible for inherited traits in all eukaryotes and prokaryotes and in many viruses 3. RNA - Ribonucleic acid ○ there are different forms of RNA involved in protein synthesis in all cells Functional Groups in Nucleic Acids Phosphate Hydroxyl Amino group group group Nucleotides All nucleic acids are polymers of units called nucleotides (monomer). A nucleotide consists of 3 components: 1. Pentose sugar - 5 carbon ring-shaped sugar 2. Phosphate group (PO43-) 3. Nitrogenous base - ring of carbon and nitrogen atoms Nucleotide In nucleotides, each nitrogenous base links covalently to a pentose, either deoxyribose or ribose. Nucleotide The two sugars differ only in the chemical group that is bound to the 2’ carbon; deoxyribose has an -H and ribose has an -OH group. Nucleotide DNA contains deoxyribose sugar RNA contains ribose sugar Nucleic Acid There are two general types of nitrogenous base: 1. Pyrimidine Bases 2. Purines Bases Nucleic Acid 1. Pyrimidine Bases ○ Pyrimidine bases are single organic rings. ○ The three pyrimidine bases are uracil (U), thymine (T), and cytosine (C). Nucleic Acid 2. Purines Bases ○ Purine bases are two-ringed organic structures ○ The two purine bases are adenine (A) and guanine (G) From Nucleotides into Polymers Phosphate-Sugar Backbone Nucleotides are linked together by covalent bonds between phosphate of one nucleotide and sugar of next. These monomers that are linked through phosphodiester bonds become the phosphate-sugar From Nucleotides into Polymers The Nucleic Acid Ladder Hydrogen bonds form between specific nitrogenous bases forming the double-stranded DNA molecule. The nitrogen bases form the stairs and are DNA Structure From Nucleotides into Polymers From Nucleotides into Polymers From Nucleotides into Polymers Base Pairing in DNA ○ Guanine forms 3 hydrogen bonds with cytosine ○ Adenine forms 2 hydrogen bonds with thymine Antiparallel Strands in DNA DNA strands run antiparallel to each other; this means they are oriented in the opposite direction relative to the sugar phosphate backbone. 5 PRIME (5’ end) - The phosphate end antiparallel structure of DNA 3 PRIME (3’ end) - The DNA In a DNA chain, each nucleotide contains: ○ Deoxyribose ○ Phosphate group ○ Nitrogenous bases (A, T, G or C) Double stranded Found in the nucleus of the cell Stores hereditary information RNA In an RNA chain, each nucleotide contains: ○ Ribose ○ Phosphate ○ Nitrogenous bases (A, U, G or C) Single stranded Integral part of protein synthesis (transfers DNA msg outside of nucleus) Summary: Nucleic Acids - Bozeman Science Practice Complete Nucleic Acid Review questions posted. Complete questions from textbook excerpt on proteins and nucleic acids (#1-10). Practice using Quiz Yourself - Proteins and Nucleic Acids. Enzymes Biochemistry Enzymes Enzymes are biological catalyst - speed up a chemical reaction without being consumed by the reaction. Each enzyme has a unique 3-Dimensional shape, and this shape determines which reaction it catalyzes. Enzyme Structure The Substrate is the reactant (chemical) that the enzyme acts on when it catalyzes a reaction. The Product is the end chemical produced The substrate binds to a region on the surface of the enzyme known as the Active Site - Enzyme Structure Enzyme Structure Enzyme Structure The enzyme and the substrate shape match each other exactly Enzymes are specific as only one enzyme acts on only one substrate Once the substrate is catalyzed, the enzyme takes its original form and can be used again … Types of Reactions Types of Reactions 1. Degradation Reaction (“breaking down”) 2. Synthesis Reaction (building up) Degradation Reaction  Degradation Reaction Substrate Enzyme Product Hydrogen Peroxide Catalase Oxygen & Water Starch Amylase Maltos Maltose Maltase Glucose Protein Pepsin Peptides Peptides Protease Amino Acids Fats Lipase Fatty Acid & Glycerol Synthesis Reaction Synthesis Reaction Lock and Key Model The substrate and enzymes active site are complementary shapes Induced Fit Hypothesis Active site sort of fits substrate Once substrate binds, functional groups of various amino acids react and shift, allowing the enzyme to change its shape to better accommodate the substrate How Does it Work The enzyme provides a site that the substrate can attach to so they are correctly aligned and can easily be broken down Enzymes also lower the activation energy (EA) required Activation Energy The energy that is required to ‘kick start’ a chemical reaction Heat is often the ‘kick start’ a reaction needs, however if too much heat is applied, the proteins in the body will denature. Enzymes speed up the rxn by decreasing EA while keeping the temperature stable so the proteins are not How Does it Work How Does it Work Note that enzymes do not change the overall reaction - they speed up the reaction, allowing for more collisions and a greater number of products Factors Affecting Enzyme Activity Factors that affect enzyme activity include: 1. (Enzyme or Substrate) Concentration 2. Temperature 3. pH Enzyme & Substrate Concentration Enzyme Concentration: Increasing enzyme concentration will speed up the reaction, as long as there is substrate available to bind to. Once all of the substrate is bound, the reaction will no longer speed up, since there will be nothing for additional enzymes to bind to. Enzyme & Substrate Concentration Substrate Concentration: Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate Enzyme & Substrate Concentration Temperature As temperature increases the enzyme activity increases. The temperature that the enzymes works best at is called its Optimum (or Optimal) Temperature If the temperature is too high, the enzymes active site changes shape. When the enzymes active site has changed shape, the enzyme, is said to be denatured, and it will no longer Temperature pH Enzymes work best within a range of pH depending on the type of enzyme. The pH that the enzymes works best at is called its Optimum pH If the pH is too high, the enzymes active site changes shape (denatured) What is the optimum pH of this enzyme ? pH Enzyme Activators Enzyme activators are molecules that bind to an enzyme and turn them on in a chemical reaction Types of enzyme activators include: 1. Cofactors 2. Coenzymes Enzyme Activators Cofactors are inorganic non-protein group that binds to an enzyme and are essential for catalytic activity Most often, metals (iron, copper, zinc and manganese) are cofactors Coenzymes are organic, non-protein molecules that act like cofactors. Act as electron transport carriers during biochemical pathways (NAD+) Both cofactors and coenzymes can bind to either the substrate or Enzyme Activators Enzyme Inhibitors Enzymes need to be regulated to ensure that levels of the product do not rise to undesired levels; this is accomplished by enzyme inhibition Enzyme inhibitors are molecules that binds to an enzyme and turn them off in a chemical reaction. Types of inhibitors include: 1. Competitive Inhibitors 2. Non Competitive inhibitors Enzyme Inhibitors Reversible and irreversible inhibitors are chemicals which bind to an enzyme to suppress its activity. Irreversible inhibitors permanently bind to an enzyme Reversible inhibitors are chemicals that transient bind to an enzyme either to an active site (competitive inhibitor) or to another site on the enzyme (non-competitive inhibitors) Enzyme Inhibitors Competitive Inhibitors are so similar to an enzyme’s substrate that they can bind to the active site and block the normal substrate. Non-competitive Inhibitors bind to the enzyme at an allosteric site (not the active site) and cause a conformational change in the enzyme, preventing the normal substrate from binding. Enzyme Inhibitors Allosteric Control of Enzyme Activity The allosteric site is a binding site on an enzyme that binds regulatory molecules; either activate or inhibit, or turn off, enzyme activity. These molecules bind the allosteric site and change the conformation, or shape, of the enzyme. Allosteric regulation is the regulation of one site of a protein binding to another site on the same protein. Allosteric Regulation In allosteric inhibition the active site changes shape when an inhibitor binds to an allosteric site. Allosteric Regulation In allosteric activation the activators may bind to allosterically controlled enzymes to stabilize its shape and keep all active sites available. Feedback Inhibition See animation Feedback inhibition occurs when there is a sequence of chemical reactions that are forming a common product in the end When the product travels back and inhibits an earlier enzyme in the reaction (competitively or non-competitively) the pathway is interrupted and no more product is Feedback Inhibition Feedback Inhibition Uses of Enzymes Enzymes are being used in industry and in medicine for MANY different purposes. Name ONE way enzymes are being used. Choose a SPECIFIC enzyme and summarize its commercial/industrial use in 2-3 sentences. Modelling Enzymes Use Modelling Clay to show a visual representation of each of the following: Enzyme Substrate(s) Active Site Enzyme-Substrate Complex Competitive Inhibitor (what happens to the enzyme and substrate?) Non-Competitive Inhibitor (what Cell Membranes Unit 1: Biochemistry Cell Membrane A semi-permeable barrier that protects the internal metabolic environment of the cell and filters what goes in and out. The current model of cellular membranes is the fluid mosaic model: “the idea that a biological membrane consists of a fluid phospholipid bilayer, in which proteins are embedded and flow freely.” Nelson Biology 12, 2012 Fluid Mosaic Model Functions i. Controls what enters and exits the cell to maintain an internal balance called homeostasis ii. Separates intracellular fluid (ICF) from extracellular fluid (ECF) iii. Provides protection and support for the cell Components of the Cell Membrane 1. Phospholipid 2. Cholesterol 3. Membrane Proteins 4. Glycolipids 5. Glycoproteins Phospholipid Bilayer Lipid Bilayer - 2 layers of phospholipids a. Phosphate head is polar and hydrophilic b. Fatty acid tails nonpolar and hydrophobic c. Proteins, carbohydrates and other lipids embedded in membrane Phospholipid Bilayer polar hydrophilic heads nonpolar hydrophobic tails polar hydrophilic heads Cholesterol Membrane Proteins Proteins determine membrane’s specific functions cell membrane & organelle membranes each have unique collections of proteins Membrane proteins: a. Peripheral Proteins b. Integral Proteins Membrane Proteins 1. Peripheral Membrane Proteins a protein on the surface of the membrane may not interact with the hydrophobic core of the membrane held to membrane surfaces by non covalent bonds (hydrogen and ionic bonds) Examples include, cell surface identity marker, enzymes, attaching to cytoskeleton structures Membrane Proteins 2. Integral Membrane Proteins A protein that is embedded in the lipid bilayer have at least one region that interacts with the hydrophobic core of the membrane most are transmembrane protein which means they span the entire bilayer transport proteins Channels and pumps Role of Membrane Proteins Role of Membrane Proteins 1. Transport Proteins - move molecules and ions across the membrane 2. Enzyme Activity - act as a catalyst in chemical reactions but are fixed in place in the membrane 3. Triggering Signals - molecules (hormones) bind to it, and trigger a cell response (cell-cell communication) 4. Attachment and recognition - acts as an ID tag so other cells can recognize it (glycoprotein) Glycolipids and Glycoproteins Glycolipids - any membrane lipid that is bound to a carbohydrate Glycoprotein - a membrane component that contains a sugar or carbohydrate bound to an amino acid Both play a role in cell recognition and cell-cell interactions  Chloride ions attract Cystic Fibrosis sodium ions High ion concentration attracts water by osmosis One example of why properly functioning membrane proteins are a big deal!  By the end of the lesson you should be able to answer the following: 1. Explain why the fluidity of the bilayer is an important property. 2. Describe the factors that affect membrane fluidity. 3. Explain the importance of cholesterol in cell membranes. 4. Differentiate between integral proteins and peripheral proteins. 5. Describe the various functions of membrane proteins. Cell Transport Biochemistry Unit Cell Transport Cell transport is the transport of molecules and ions in and out of the cell through their plasma membranes. Cell Transport There are 2 Types of Transport: 1. Passive Transport - does not require energy to move molecules across the membrane 2. Active Transport - requires the input of energy (ATP) to move molecules across the membrane Passive Transport Passive transport is regulated by a concentration gradient and accounts for much of the movement of water, ions and many types of molecules into and out of the cell. Does NOT need energy (ATP) Passive transport is driven by Diffusion - the movement of molecules from an area of high concentration to an area of low concentration until molecules are evenly distributed. Passive Membrane Transport Factors that Determine the Rate of Diffusion 1. The steepness of the concentration gradient. The bigger the difference between the two sides of the membrane the quicker the rate of diffusion. 2. Temperature. Higher temperatures give molecules or ions more kinetic energy. Molecules move around faster, so diffusion is faster. Factors that Determine the Rate of Diffusion 3. The surface area. The greater the surface area the faster the diffusion can take place. This is because the more molecules or ions can cross the membrane at any one moment. 4. The type of molecule or ion diffusing. Large molecules need more energy to get them to move so they tend to diffuse more slowly. Non-polar molecules diffuse more easily than polar molecules because they are soluble in the non-polar phospholipid tails. Factors that Determine the Rate of Diffusion 3 Types of Passive Membrane Transport 1. Simple Diffusion 2. Facilitated Diffusion 3. Osmosis Simple Diffusion The ability of small and non-polar substances to move across a membrane unassisted. ○ O2 ○ CO2 ○ non-polar steroid hormone ○ non-polar drugs ○ small, uncharged molecules (H2O, glycerol) Simple Diffusion Facilitated Diffusion The facilitated transport of ions and polar molecules through a membrane Molecules and ions enter the cell via protein complexes Movement is still driven by diffusion based on a concentration gradient across the membrane; no energy needed Once equilibrium is reached, there is no longer a concentration gradient; facilitated diffusion Facilitated Diffusion Facilitated diffusion is carried out by integral membrane proteins called transport proteins There are 2 types of transport proteins: 1. Channel Proteins 2. Carrier Proteins Facilitated Diffusion: Channel Proteins are a hydrophilic pathway in a membrane that enables water and ions to pass through Facilitate the transport of ions such as Na+, K+, Ca2+ and Cl- Voltage-gated meaning that they switch between open, closed and intermediate states Facilitated Diffusion Carrier Proteins also form passageways through the lipid bilayer Each carrier protein binds to a specific solute Facilitate the transport of glucose molecules and certain amino acids Carrier protein changes shape, allowing solute to move from one side of the membrane to the other. Facilitated Diffusion Osmosis Like solutes, water can diffuse passively across a membrane Osmosis is the passive diffusion of water across a membrane Water always diffusion from an area of lower solute concentration (high water concentration) to an area of greater solute concentration (low water concentration) Osmosis In living cells, the inward or outward movement of water by osmosis causes cells to swell or shrink Hypotonic: the property of a solution that has a lower solute concentration than another solution Hypertonic: the property of a solution that has a higher solute concentration than another solute Isotonic: the property of a solution that has the same solute concentration as another solution Types of Solutes Types of Solutes Managing Water Balance Managing Water Balance Cells in an Isotonic Solution There is no NET movement of water Water flows across the membrane equally, in both directions Volume of cell is stable problem: none Managing Water Balance Cells in a Hypotonic Solution Less solute outside the cell than inside the cell NET water movement is INTO the cell Result: ○ Animal cells LYSED or bursts ○ Plant cells become TURGID because cell membrane is pushed against cell Managing Water Balance Cells in a Hypertonic Solution More solute outside the cell than inside the cell NET water movement is OUT of the cell Result: ○ Animal cell is SHRIVELED/DEHYDRATE ○ Plant cells undergo PLASMOLYSIS, where the cell membrane pulls away from the cell wall, making the plant feel flaccid Active Transport The movement of substances across a membrane against a concentration gradient. Movement occurs from a region of lower concentration to a region of higher concentration. The term “active” refers to the fact that the cell has to expend energy in the form of ATP to pump molecules across a membrane. Primary Active Transport All primary transport pumps move positively charged ions (such as H+, Ca+, Na+ and K+ across a membrane Examples of primary active transport include: 1. Proton Pump (H+ pump) 2. Sodium Potassium pump 3. Calcium Pump Primary Active Transport Transport Summary Exocytosis and Endocytosis Eukaryotic cells can export and import larger molecules by two mechanisms: 1. Endocytosis - moves proteins, large molecules or even whole cells from the exterior of a cell into the cytosol 2. Exocytosis - moves proteins and waste materials from the cytosol to the exterior of a cell Both endocytosis and exocytosis require energy Exocytosis There are two types of Endocytosis 1. Pinocytosis 2. Phagocytosis ○ bulk-phase ○ cell eating endocytosis ○ taking in large, ○ cell drinking solid particles ○ taking in extracellular fluid Bulk-phase Endocytosis or Pinocytosis Phagocytosis Cell engulfs bacteria, parts of dead cells, viruses or other foreign particles This pathway is performed by macrophage which is a type of white blood cell that helps fight Cell Transport - Amoeba Sisters To Do: Start studying for unit test…