Exploring The Essential Concepts of Biochemistry

Unit 1: Biochemistry Importance of Water: – Water is polar and forms hydrogen bonds with other water molecules Universal Solvent: ● – Dissolves more substances than any other ● – Solutes dissolve into the spaces between the molecules High Heat Capacity: – Ensures temperature regulation and homeostasis ● – Water requires large amounts of energy to heat it up, and it retains heat very well once it has been warmed ● – Release of sweat helps expel a source of warmth from the body Cohesion and Adhesion: ● – Cohesion is two water molecules bonded together (hydrogen bond) ● – Adhesion is a water molecule bonding with another substance Lower Density as Solid than as Liquid: – Once water reaches below 4oC, the amount of hydrogen bonds continues to increase; it creates a more structured lattice of water molecules which lowers the density of the water – Helps to spread the weight of the water out, giving it buoyancy 1 Types of Molecules: Organic Inorganic ● – Contains carbon, oxygen, hydrogen, nitrogen; carbon is the basis of all life ● – Larger in size ● – Complex structures containing rings or long chains ● – Eg. Glucose, Haemoglobin, DNA, Starch ● – Usually doesn’t contain carbon (if it does it doesn’t have hydrogen or is simple) ● – Smaller in size ● – Simple structures containing 2 to 10 atoms ● – Eg. Carbon dioxide, Oxygen gas, Sodium chloride, Calcium phosphate Molecules: ● – A large, complex, molecule (eg. protein, DNA) ● – Polymer: a molecule composed of smaller, repeating components (individual strand of DNA) ● – Monomer: the smallest repeating portion of a polymer (eg. nucleotide) Dehydration Synthesis: ● – Also known as condensation ● – When a water molecule is removed, it forms a new bond as a hydrogen and a hydroxyl, creating two new and longer polymers Hydrolysis: – When a water molecule is formed (from a hydrogen and hydroxyl), it breaks bonds and forms longer polymers Functional Groups: ● – Functional groups are the active sites on molecules ● – Responsible for determining the chemical and physical properties of a molecule 2 Group Chemical Formula Chemical Structure Hydroxyl OH Alcohols, carbohydrates Carboxyl COOH Fatty acids and amino acids Carbonyl C=O Lipids Amino NH​2 Amino acids Phosphat e PO​4 Phospholipids, nucleic acid Part of molecules 3 Carbohydrates: – Carbohydrates are used for storing energy (glucose), providing structure (cellulose), cell identification and communication – Monosaccharides are the monomers of carbohydrates; similar ring-like structure, building block of all carbohydrates – Found in foods like bread, pasta, fruit, vegetables Glucose: – The difference between glucose alpha and glucose beta is that on C1​​, the hydrogen and the hydroxyl are flipped ● – Alpha glucose: hydrogen on top ● – Beta glucose: hydroxyl on bottom ● – Galactose: C4​​has the hydroxyl on top and hydrogen on the bottom Dehydration Synthesis: ● – Water molecules are being removed, which forms new bonds and creates longer polymers ● – In carbohydrates, monosaccharides are joined together to form a disaccharide to form a ether bond – An ether bond is formed by the removal of water from two hydroxyl groups – One water molecule is removed when a disaccharide is formed Disaccharide Reactions: ● – Glucose + Glucose = Maltose + Water ● – Glucose + Fructose = Sucrose + Water ● – Glucose + Galactose = Lactose + Water Polysaccharides: Molecule Monomer Location Function of molecule Starch Alpha glucose Plants Glucose storage in plants Glycoge n Alpha glucose Liver and muscle cells Glucose storage in animals Cellulos e Beta glucose Plant cell walls Structural support for plant cells Lipids: Function of Lipids: – Used for long-term energy storage (triglycerides), cushioning, protection, vitamin absorption ● – Used to make cell membranes (phospholipids) ● – Used to make hormones (steroids) ● – Used to make waterproof coatings (waxes) Glycerides: – A bond between glycerol and one fatty acid – Diglyceride has one glycerol and two fatty acids, triglyceride has three – Carboxyl and hydroxyl are responsible for combining a glycerol to a fatty acid by creating one water molecule (two if diglyceride, three if tri…) – Forms an ester bond Saturated and Unsaturated Fatty Acid: Types of Fats: Fatty Acids: – Essential fatty acids are lipids that can’t be produced in the body and therefore must be consumed; they’re found in linoleic acid and omega 4 Molecule Bonding Physical State Example Saturated Fatty Acid Only single bonds between atoms Solid at room temperature Butter, meat, cream, cheese Unsaturated Fatty Acid One or more double Liquid at room bonds between temperature carbon atoms Vegetable oil, fish, nuts, avocados Molecule Monomer Units Location Triglycerides Glycerol and three fatty acids. Used for long-term energy storage in plants and animals Glycerol, two fatty acids, phosphate group Cell membranes (phospholipid bilayer); phospholipids have a polar head (hydrophilic) and nonpolar tails (hydrophobic) which causes them to form layers Phospholipid s Synthesized from cholesterol, composed of four carbon-based rings Cholesterol in the cell membranes Steroids Don’t contain glycerol or fatty acids, but they’re hydrophobic Estrogen and testosterone (sex hormones) – Trans-fatty acids are unsaturated fatty acids that have undergone hydrogenation in order to become saturated and solid at room temperature ● – The body can’t dispose of trans-fatty acids properly so it sits in the body ● – Hydrogenation is the process of breaking the double carbon bonds in unsaturated acids so that they only contain single bonds and can bond with more hydrogen to become saturated Proteins: – Found in foods like meat, tofu, eggs, nuts Function: ● ● ● ● – Structure components of all cells (support, movement, transport) – Enzymes (catalysts in chemical reactions) – Regulators of cell processes (hormones, gene control) – Defense from disease (antibodies) Amino Acids: ● – Amino acids are the monomers of all proteins – There are twenty different varieties of amino acids, differing only by their R groups – R-groups are side chains that affect bonding and make each amino acid unique from one another ● – When two amino acids undergo dehydration synthesis, they produce a dipeptide and one water molecule – Held together by a peptide bond of the amino and carboxyl functional groups Protein Structure: ● – Primary: the order of amino acids ● – Secondary: Alpha helix or beta-pleated sheet ● – Tertiary: Bends and kinds in secondary structure due to interaction of R groups ● – Quaternary: two or more polypeptide chains join together to make a globular-shaped structure Essential Amino-Acids: – These are proteins that are needed by the body but can’t be synthesized in it – Non-essential amino acids can be produced in the body Complete Protein Foods: – A complete protein food contains all 9 essential amino acids; it doesn’t require you to eat any other food in order to reach this full balance 5 6 Nucleic Acid: – Includes DNA, RNA and adenosine triphosphate (ATP) Functions: ● – DNA: makes up genetic material, making instructions for proteins ● – RNA: involved in making proteins ● – ATP: energy used for the cell (created in the mitochondria through cellular respiration) Nucleotide: ● – Monomer unit for all nucleic acid ● – Composed of sugar, phosphate group, and nitrogen base (adenine, thymine, guanine, cytosine) ○ – Adenine and guanine are similar in shape, as are thymine and cytosine ○ – Adenine and thymine bond through a double hydrogen bond ○ – Guanine and cytosine bond through a triple hydrogen bond DNA and RNA: Adenosine Triphosphate (ATP): ● – Composed of three phosphate groups, one ribose (sugar) and one nitrogen base ● – Dehydration synthesis of ATP from ADP + P uses energy since bonds are created (endergonic reaction) ● – Hydrolysis of ADP + P from ATP releases energy since bonds are broken (exergonic) reaction Enzymes: Biochemical Reaction: – Process that changes biochemical substances into others DNA RNA ● – Double-stranded helix ● – Composed of deoxyribose sugar ● – Contain nitrogen bases of adenine, cytosine, guanine and thymine ● – Single-stranded helix ● – Composed of ribose sugar ● – Contain nitrogen bases of adenine, guanine, cytosine and uracil ● – Reactant: starts the chemical reaction ● – Product: result from the chemical reaction Catalyst: ● – Substances that speed up chemical reactions without being consumed in the reaction ● – Enzymes are protein catalysts that reduce the activation energy required in biological reactions – Orient molecules towards each other or apart so that they can synthesize/decompose by using less energy Exergonic Reaction: – There’s a net-release of energy during the chemical reaction – Energy is consumed during the activation of the reaction, but more energy is released during the process of breaking bonds Endergonic Reaction: – There’s a net-input of energy into the chemical reaction – Energy is absorbed so the reaction can occur, with some being released after the formation of bonds Functioning of Enzymes: ● – Enzymes lower activation energy by reducing the amount of energy needed for the reactants to come together and react ● – Bind substrates tightly and specifically to an active site on the enzyme – Forms an enzyme-substrate complex – Products are released from the active site, allowing the enzyme to continue catalyzing additional reactions Influences on Enzymes: – Have optimal temperatures and pH – Any changes to these conditions will change the shape of the enzyme, altering the shape of the active site and their ability to catalyze reactions – Denaturation can be caused by heat, extreme cold, change in pH, chemicals ● – Bonding between R-groups is disrupted (eg. hydrogen bonds are disrupted in acidic environments since [H+​​] is high, meaning additional hydrogen are bonded to molecules) ● – Secondary, tertiary, and quaternary structures are modified ● – Protein loses its 3D shape and becomes non-functional Enzyme Inhibition: – Competitive Inhibitors: Substances that compete with a substrate for a spot on the enzyme’s active site (eg. CO bonds stronger to haemoglobin than oxygen does). 7 – Noncompetitive Inhibitors: Substances that attach to a binding site on an enzyme other than the active site; results in change of the enzyme’s shape and its loss of affinity for substrate Allosteric Regulation: ● – Allosteric Site: Receptor sites, located far away from the active site, which binds substances that inhibits or stimulates an enzyme’s activity ● – Allosteric Activator: substance that binds to an allosteric site on an enzyme and stabilizes the protein conformation that keeps all the active sites available for their substances ● – Allosteric Inhibitor: A substance that binds to an allosteric site on an enzyme and stabilizes the inactive form of the enzyme ● – Feedback Inhibition: When a product of a sequence of reactions inhibits an enzyme that catalyzed it in an earlier reaction ● – Cofactors: Non-protein components that are needed for some enzymes to function (often ions, et Zn+​2​, Mn+​2​) ● – Coenzymes: Organic nonprotein cofactors that are needed for some enzymes to function (eg. NAD+​​from vitamin B​3)​ Cell Structure and Organelles: Cell Wall: ● – Not vital to cells (not all cells have them, eg. animal cells) ● – Responsible for determining cell shape, controlling turgor pressure (outward water pressure), adds strength to cell ○ – High turgor pressure (turgid) is when the cell walls are pushed out and the cell is filled with water ○ – Low turgor pressure (flaccid) is when the cell walls shrivel with little water inside the cell ● – Cell walls are composed of cellulose (β glucose) in plants, chitin in fungi and protists, glycoprotein in bacteria Cell Membrane: ● – Protects the cell from the outside environment, keeps cell contents in place, controls which substances can enter and exit the cell ● – Phospholipids: ○ – Hydrophilic, polar head (phosphate and glycerol) ○ – Hydrophobic, nonpolar tails (fatty acids) ○ – Form a phospholipid bilayer 8 – Proteins: ● – Float around within or on the surface of the membrane ● – Used for structural support, surface binding sites for molecules (eg. hormones), recognition sites for cell to cell communication and interaction, transport molecules through the membrane, transport electrons and protons within the membrane – Glycocalyx: ● – Carbohydrate chains attached to proteins (glycoproteins) ● – Used for recognition and communication of proteins, site for cell to cell attachment – Cholesterol: – Keeps the phospholipids stable and retains the membrane’s shape; too much cholesterol makes the membrane solid, too little makes it liquid Nucleus: ● – Region of the cell containing the genetic information ● – Nucleolus – A dense area within the nucleus containing RRNA (ribosome RNA) and proteins; ribosomes are produced here – Nuclear pore: – Openings in the nuclear membrane allowing for the passage of molecules in and out of the nucleus – Chromatin: – Stringy material made of proteins and DNA that takes up the majority of the nucleus – Chromosomes: – Condensed chromatin; condenses into chromosomes shortly before cell division begins – DNA is important since it contains all the instructions to make proteins Ribosomes: ● – Microscopic spheres attached to the endoplasmic reticulum or free-floating in the cytoplasm ● – Protein factories: make primary protein structures by stringing amino acids together Endoplasmic Reticulum: – Twisting network of canals and sacs extending through the cytoplasm and connecting the cell membrane to the nuclear membrane 9 ● – Rough Endoplasmic Reticulum: ○ – Has ribosomes attached to it ○ – Produces, modifies, and transports proteins ● – Smooth Endoplasmic Reticulum: ○ – No ribosomes on it ○ – Produces lipids (cholesterol and phospholipids) and steroid hormones Golgi Apparatus: ● – Sacs of membranous plate-like bags which produce vesicles (sacs) ● – Produce and store cellular secretions (eg. fighting off infections) ● – Many proteins and lipids undergo final processing in the golgi complex – Apparatus helps to fold molecules into final shape completing tertiary and quaternary structures (eg. attaching cofactors to enzymes) Lysosomes: – Membrane-bound sacs that are used for digestion of various structures within the cell – Have acidic environment and hydrolytic enzymes to help digest foreign cells, damaged organelles, macromolecules Mitochondria: ● – Site of aerobic cellular respiration (converts sugar energy into adenosine triphosphate, ATP) – Sugar + O​2​→ CO​2​+ H​2O​+ ATP ● – ATP is used by other organelles and cell processes for energy ● – Mitochondrial Structures: ○ – Cristae: site of chemical reactions using embedded proteins ○ – Matrix: mitochondria cytosol (liquid portion of cytoplasm) ○ – Mitochondrial DNA: self replicating organelle, producing its own unique proteins Chloroplasts: ● – Found only in green and photosynthetic organisms ● – Convert sunlight to energy via photosynthesis – CO​2​+ H​2O​→ C​6H​​12O​​6​+ O​2 ● – Chloroplast Structures: ○ – Stroma: chloroplast cytosol ○ – Lamella: membrane that attaches inner chloroplast structures ○ – Thylakoid disc: have a specialized membrane for photosynthesis ○ – Grana: stack of thylakoid discs (connected by lamella) ○ – Chloroplast DNA: self-replicating organelle 10 Cilia and Flagella: ● ● ● ● – Made of protein fibres – Used for locomotion – Cilia: short and numerous on cell surface – Flagella: long and usually few in numbers on cell surface Cytoskeleton: – Structures that give the cell its shape and help organize its parts – Provide a basis for movement and cell division (allows for organelles to move along them) – Made of filamentous proteins ● – Microtubules: anchor organelles ● – Actin filaments: contract muscle cells Vacuoles: ● – Fluid-filled sac ● – In protozoa, vacuoles perform functions such as storage, ingestion, digestion, excretion, and expulsion of excess water ● – In plants, the large central vacuole help regulate water: turgor pressure is controlled by vacuole Theory of Endosymbiosis: ● – Explains the origin of eukaryotic cell organelles like mitochondria and chloroplasts ● – Works were advanced by Lynn Margulis in the 1960s Passive Transport: – The movement of molecules through the cell membrane without the use of cellular energy Diffusion: – Process by which particle move naturally from areas of high concentration to areas of low concentration until the dynamic equilibrium is reached – Moving with the concentration gradient 11 ● – Molecules are in constant motion (until equilibrium) ● – Small molecules are capable of passing through the phospholipids in the cell membrane(eg.O​2,​CO​2,​H​2O​,alcohol,smalllipids) ● – Rate of diffusion ○ – Concentration of particles (increased concentration increases the rate of diffusion) ○ – Temperature of particles (increased temperature increases the rate of diffusion) ○ – Pressure (increase in pressure increases the rate of diffusion) ○ – Agitation (increase in agitation increases the rate of diffusion) Osmosis: ● – The diffusion of water through a semipermeable membrane ○ – Solute: dissolved substance (eg. sugar) ○ – Solvent: able to dissolve things (eg. water) ○ – Solution: mixture of solvent and solute ● – Types of membranes: ○ – Impermeable: nothing can move across it ○ – Semi-permeable: only some molecules can cross it (eg. cell membrane) ○ – Permeable: any molecules can pass through it Types of Solutions: ● – Hypertonic Solution: The solution surrounding the cell has a higher concentration of solute than the cell’s cytoplasm, causing water to leave the cell ● – Hypotonic Solution: The solution surrounding the cell has a lower concentration of solute than the cell’s cytoplasm, causing water to enter the cell ● – Isotonic Solution: The concentration of the solute is the same on the inside and the outside of the cell Turgor Pressure: – The rigid cell wall of the plant prevents it from bursting when it’s filled with water, causing outward water pressure called turgor pressure – Plant cells full with water are called turgid Plasmolysis: – When plant cells are placed in a salt solution, the cells shrink, resulting in plasmolysis Facilitated Diffusion: – Some molecules are too large or are hydrophilic so they cannot pass through the phospholipid bilayer (eg. glucose) – Transport proteins assist in getting these molecules through the cell membrane – Transport occurs within the concentration gradient (no energy is required) 12 Active Transport: – The movement of molecules through the cell membrane against the concentration gradient using transport ions – Movement from low concentration to high concentration ● – Requires the use of cellular energy (ATP) ● – Transport proteins are highly selective (eg. Na+​​and K+​​pump) Endocytosis: – Transports materials into the cells by the means of vesicles – Energy is required ● – Cell engulfs the materials by folding a portion of its membrane around it ● – Types of endocytosis: 1. Phagocytosis: movement of large and whole molecules into the cell’s interior 2. Pinocytosis: transport of liquids into vesicles inside the cell 3. Receptor-mediated endocytosis: molecules bind to receptors on the cell’s surface and are folded into vesicles within the cell ● Exocytosis: ● – Transport of macromolecules (eg. hormones) out of a cell by means of vesicles made by the Golgi complex ● – Energy is required 13