Biochemistry Unit Test Review PDF

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In depth organized review with diagrams that I made in order to prepare and study for the Biochemistry Unit Test in Academic level Grade 12 Biology. ...

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Biochemistry Unit Test Structure and Function of Cells and Cell Organelles Organelle Cell Wall

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Function Protects the cell and gives it it’s shape Non-living and one component is cellulose Has pores that allow substances to pass through Only in plant cells

Cell Membrane

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Endoplasmic Reticulum

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Nucleus

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Nuclear Membrane

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Controls what goes in and out of the nucleus

Chromatin (Chromosomes)

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Long, thin strings that’re coiled (tangled) Contain DNA An area of chromatin that contains special RNA used to make ribosomes Where photosynthesis takes place Contains chlorophyll Powerhouse of the cell Provides all the energy (ATP) The jelly-like substance where the organelles are found Mostly water Completes the packaging of proteins and other macromolecules from the endoplasmic reticulum

Nucleolus Chloroplast

Cytoplasm

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Golgi Bodies

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Mitochondrion

Lysosomes

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Ribosomes

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Vacuole

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Centriole Extracellular Matrix

Microfilaments

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Controls what goes in and out of the cell (e.g. O2 and H2O move freely) Allows certain substances to travel through these channels. Rough: synthesize proteins. Smooth: help package macromolecules. The control center of the cell and contains the blueprint that determines your genetic makeup.

Where food and foreign substances are digested When the cell gets old or malfunctions, it breaks down the entire cell. Only in animal cells Makes the proteins needed for all kinds of purposes (e.g. structure, hormones, enzymes, etc.). Where water is stored (large in plants and smaller in animal cells) Also temporary storage of food or waste products Found in pairs of microtubules Important in cell division Material between cells that holds the tissues together, usually made of scaffolding proteins like collagen Smaller than microtubules Made from repeating actin subunits Responsible for cell movement and changes in shape and make muscle contraction possible.

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Microtubules

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Part of the cytoskeleton

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Small, tube assemblies of protein made from repeating tubulin subunits Help maintain cell’s internal structure and move organelles and cytoplasm using molecular motors Part of the cytoskeleton Double membrane that separates the contents of the nucleus from the cytoplasm Gaps in the nuclear envelope that allow substances to move in and out of the nucleus. Contains cholesterol and proteins Surrounds cell and enables it to communicate with its neighbors and detect and respond to changes in the environment

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Water • • • • • •

Nuclear Envelope

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Nuclear Pore

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Plasma Membrane

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Most abundant molecule in any cell. Carries dissolved molecules. Raw material in cell reactions. Lubricant between organs, tissues, and cells. Polar molecule, allowing water molecules to attract to one another at room temperature to form a liquid. Importance: o Liquid over wide temperature range. o Dissolves most substances involved in living processes. o Changes temperature gradually. o Expands when frozen, so it floats.

Carbon • Forms up to 4 stable bonds with other atoms. • Most abundant. Organic Compounds • Molecules with C and H, but can have O, N, P, and S. • Carbon is in all chemicals of life, except water. • Organic chemistry is the chemistry of carbon compounds. • Principle Organic Compounds o True Polymers: Carbohydrates, Proteins, Nucleic Acids o Not True Polymers: Lipids Functional Groups • A group of atoms that affects the function of a molecule by participating in chemical reactions (since carbon bonds are stable and don’t react as easily). • They’re usually ionic or polar (interact with water). • On large molecules like macromolecules, they interact and form different types of bonds.

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Group Hydroxyl (Alcohol)

Chemical Formula -OH

Carboxyl (Acid)

-COOH

Amino (Only Proteins)

-NH2 -NH3+

Sulfhydryl (Only Proteins)

-SH

Phosphate (Protein, DNA)

-PO4

Carbonyl – Aldehyde

-COH

Carbonyl – Ketone

-CO-

Chemical Structure

Chloe Popov Bond Types • Ester Linkage o Found in fats (ex., triglyceride). o Functional Groups: Alcohol and acid. o Condensation reaction forms the linkage.

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Glycosidic Linkage o Found in carbohydrates (sugars). o Functional Groups: 2 carbohydrates or alcohols. o Condensation reaction forms the linkage.

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Peptide Linkage o Found in proteins (Polypeptides). o Functional Groups: Amino and carboxyl, or 2 amino acids. o Condensation reaction forms the linkage.

*** A LINKAGE IS NOT A FUNCTIONAL GROUP BECAUSE THEY AREN’T THE ACTIVE SITE WHERE THE CONDENSATION REACTION OCCURS ***

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Chloe Popov Biochemical Reactions • Condensation Reactions – Anabolic o Builds macromolecules. o Creates covalent bond between monomers to make a polymer. o Involves the removal of H from the functional group of one monomer and the removal of an OH from the functional group of another monomer. o Produces water. o They absorb energy (endothermic/endergonic) – making bonds.

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Hydrolysis Reactions – Catabolic o Reverse of Condensation. o Breaks down macromolecules into monomers. o Water is used to break the covalent bond holding monomers together. o Gives off energy (exothermic/exergonic) – breaking bonds.

Carbohydrates • Most common organic material on Earth. • Have C, H, O, in a 1:2:1 ratio (CH2O)n. • Function: o Energy (glycogen, starch). o Building material in plants (cellulose). o Cell surface markers (identification and communication). • 3 Groups of Carbohydrates: o Monosaccharides Single sugar. Distinguished by carbonyl group and number of atoms in carbon backbone. Can be aldose or ketose – *** FOCUS ON HEXOSE ***

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o Oligosaccharides *** DON’T NEED TO KNOW SPECIFIC ONES, JUST KNOW THEY’RE THIS TYPE OF SACCHARIDES*** 2-3 monosaccharides attached by covalent glycosidic linkages. Bonds made by condensation reactions. 2 monosaccharides together = disaccharide.

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o Polysaccharides Several 100-1000 monosaccharides held by glycosidic linkages. Polymers of simple sugars. Functions: • Energy storage. • Structural Support. Examples: • Glycogen – insoluble energy storage in animals. • Cellulose – cellulose microfibrils inter wind to form cellulose fibres in plants. • Chitin – structural support in many organisms (ex., exoskeleton of insects).

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Lipids • Have less OH bonds, more non-polar CH bonds than carbohydrates. • Unable to dissolve in water because mostly non-polar. • Fats are not true polymers. They can be attracted to each other by Van der Waals forces but don’t form chains of monomers. • Trans fats are unsaturated fats that are straight instead of bent, which is bad for you. • Use: o Energy storage. o Cell membrane (phospholipid bilayer). o Chemical signalling (hormones). • Types: o Fats (our foods). Usually triglycerides (3 fatty acids and a glycerol molecule – ester linkage). Saturated (as many H bonds as possible, single bonds) or unsaturated (not as many bonds). Unsaturated fats tend to bend at double bond, reducing Van der Waals attraction and forming liquids at room temperature. Have at least one double bond. Polyunsaturated is a fatty acid with more than one double bond. Saturated fats tend to be solid at room temperature because they can fit close together since their chains are straight.

o Phospholipids. Glycerol and 2 fatty acids and a phosphate group (chief component of cell membranes). In water, phospholipids become oriented with their hydrophobic tails as far from the water as possible. They form a sphere or bilayer. Most lipids are non-polar but phospholipids have a non-polar tail and a polar phosphate group head.

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9 Will spontaneously form a bilayer in water or aqueous environment.

o Steroids (hormones). Ex., cholesterol: essential component of membrane and nerve tissue. It is the raw material for the making of vitamin D (sunlight converts it to vitamin D) and other steroid hormones.

o Waxes (plants). Long chain fatty acids attached to alcohols or carbon rings. Hydrophobic and pliable. Cell Membrane Structure • Functions: o Transport materials in and out of the cell. o Provides a barrier around the cell. o Allows cell recognition. • A bilayer; composed mainly of phospholipids (polar hydrophilic head, non-polar hydrophobic tail).

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“Fluid Mosaic Model” Phospholipid bilayer. Protein molecules embedded. o Integral proteins (extends to whole membrane). o Peripheral proteins (on top). Cholesterol: o Keeps membrane rigid at high temperatures. o Keeps membrane fluid at low temperatures. o Decreases membrane permeability. Carbohydrate chains: o Serve as an indicator. o Glycolipids and glycoproteins. THESE PROVIDE A MEMBRANE ‘FINGERPRINT’ WHICH HELPS CERTAIN HORMONES/PROTEINS KNOW THEY’RE WORKING ON THE RIGHT CELL. These membranes are semi-permeable/selectively permeable (controls entrance/exit of all nutrients to maintain homeostasis) and fluid. Most organelles are covered with a membrane like such.

Proteins • True Polymers made of Amino Acids. • Most diseases are caused by a protein not functioning properly. • Most proteins require more than 1 polypeptide. • Function: o Structural (ex., keratin – hair and fingernails, collagen, muscle tissue). o Enzymes. o Immunoglobins (antibodies). o Transport (ex., hemoglobin). • Structure: o Primary Structure: Sequence of amino acids (sequence determined by nucleotide sequence in DNA). DETERMINES FINAL SHAPE, ALL OTHER STRUCTURES.

Chloe Popov o Secondary Structure: Coils and folds (ex., d-helix, B-pleated sheets). Caused by primary sequence (ex., non-polar amino acid with a polar amino acid repel and cause a bend. o Tertiary Structure (Further Folding): Hydrogen bonding, disulfide bridges, hydrophilic or phobic interactions. o Quaternary Structure: 2 or more subunits (polymers). Amino Acids • Not a protein, but a component of one. • KNOW: Alanine, Glycine, Cysteine. • 8 essential ones that the body can’t synthesize, and needs to get from diet. • Can form Optical Isomers/Enantiomers.

Macromolecules Lab – Positive and Negative Tests • Benedict’s Reagent (+ orange = sugars) (- blue = no sugars). • Lugol’s Solution (+ black = starch) (- orange = no starch). • Biuret Reagent (+ purple = proteins) (- blue = no proteins). • Brown Paper (+ oily, greasy film when dried = fats) (- no film = no fats).

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Osmosis Lab • Gained mass = hypotonic. • Same mass = isotonic. • Lost mass = hypertonic. Solutions • Everything in an organism is a solution (a solute dissolved in solvent). • The solvent is always water, for a cell. Solutes are usually sugars, salts, ions, or ATP. Concentration Gradients • Concentration gradient is maintained/controlled by the cell. The cell works to ensure there’s more solute on one side of the cell membrane.

4 Main Factors Affecting Solute Molecules 1. Size of molecule (small molecules move easier). 2. Charge of molecule (neutral molecules can pass through phospholipid bilayer easier). 3. Concentration Gradient of Solute Molecule Across Cell Membrane (always easiest to move a solute molecule from high concentration to low). 4. Distance (harder to move to the inside of a large cell. a. In small cell the area > volume of the cell. b. In large cell the area < the volume of the cell. 3 Main Transport Methods 1. Passive transport (no energy). • Diffusion • Osmosis i. Solvent water molecules move from an area of high water concentration to low across a semipermeable cell membrane. ii. Solutes can’t pass through the membrane. iii. Direction of osmosis water flow depends on the concentration of waters on both sides of the membrane and the inability of the solute molecules to pass the membrane.

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• Facilitated diffusion 2. Active Transport (energy needed). • Molecules moved against concentration gradient. • Energy supplied by molecule of adenosine triphosphate (ATP) which is hydrolysed to adenosine diphosphate (ADP), releasing energy. • Sometimes energy is supplied by an electrical gradient if ions are involved. • Ex., sodium-potassium pump.

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3. Bulk Membrane Transport (cell membrane engulfing other large molecules). 1. Endocytosis: The cell membrane folds in trapping some extra-cellular material and forming a vesicle. The vesicle breaks from the cell wall and the contents are processed by the cell. i. Pinocytosis (Cell Drinking): Small vesicle formed, only fluid and small particles ingested. ii. Phagocytosis (Cell Eating): Larger vesicle forms around small particle of matter like bacteria cell, used by many protists to get food. • Sometimes specific receptor molecules control what particles are engulfed.

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15 2. Exocytosis i. Reverse of endocytosis and used when cell wants to export material. ii. A vesicle containing material produced in cell fuses with cell membrane. iii. Cell contents are expelled into extracellular fluid. iv. Important for hormones that are transported in the blood like insulin from the pancreas.

Sodium Potassium Pump 1) Start the NaK Pump a. 3 Na+ ions from the ICF attach to a special transmembrane enzyme protein. b. An ATP molecule is hydrolyzed providing energy. 2) Pushing out the Na a. Energy released by the ATP causes the enzyme protein to change shape and push out the 3 Na+ ions to the ECF against the concentration gradient (low to high). 3) Moving the K a. 2 K+ ions enter the enzyme protein from the ECF. b. The protein changes shape and discharges them to the ICF. c. There’s a more positive charge outside the cell. d. This ionic charge difference pulls water out of the cell and keeps it from swelling and breaking.

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Enzymes in Biochemical Reactions • Metabolism o Anabolic (synthesis): Require energy to be added as bonds are formed. o Catabolic (decomposition): Release energy as bonds are broken.

2 Laws of Thermodynamics 1) Energy can’t be created or destroyed but can be changed from one form to another. 2) When energy is changed from one form to another, some energy is lost as heat. 1) Exothermic • Release energy from bonds. • Product molecules are smaller than reactant molecules. • Ex., cellular respiration.

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2) • • •

Endothermic Energy is stored in bonds of molecules. Product molecules are larger than reactant molecules. Ex., photosynthesis.

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Gibbs Free Energy: the energy available for chemical reactions (ΔG). The hydrolysis of sucrose to glucose and fructose is exergonic so the free energy is negative (=-29 kJ/mol). Forming sucrose is endergonic (=+29 kJ/mol).

Enzymes • Cells are challenged to make chemical reactions go quick at body temperature. • The best way to speed up reaction is increase temperature, but cells will die if too hot so they use enzymes to solve this. • They increase efficiency. • They put stress on bonds making the reaction go faster. • How they work: o They lower the activation energy. o Every chemical reaction between molecules has breaking and making bonds. o The initial energy needed to start a chemical reaction is called the activation energy (Δ𝐸𝐴 ). o Activation energy is usually supplied in the form of energy (heat) from the surroundings or from ATP. o Adding activation energy brings reactants to the high energy transition state. o Using an enzyme means the transition state is reached with less activation energy.

Induced Fit Model of Enzyme Action • The reactant that an enzyme acts on is called the substrate. • The enzyme binds to its substrate, forming an enzyme-substrate complex. • The active site is the region on the enzyme where the substrate binds. • The induced fit of substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction. How Enzymes Lower Activation Energy 1) Orienting substrates correctly. 2) Straining substrate bonds. 3) Providing a favourable microenvironment (ex., pH). 4) Covalently bonding to the substrate.

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Factors Influencing Enzyme Action

1) Environmental Factors (ex., temperature and pH) I. Each enzyme has an optimal temperature and pH at which it can function. II. Wrong temperature or pH can denature an enzyme (enzyme protein’s shape is destroyed).

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2) Cofactors and Coenzymes I. Cofactors are non protein inorganic enzyme helpers. II. Coenzymes are organic cofactors. 3) Enzyme and Substrate Concentration (which affects the saturation of the active site) I. Increasing enzyme concentration means the rate of reaction increases. II. Increasing substrate concentration increases the rate of reaction until all the enzyme active sites are in use. This is the point of saturation.

4) Inhibitors I. II. III. IV.

Competing with substrates for the active site. Make sure enzymes are working when we really need them. Competitive inhibitors bind to the active site of an enzyme, competing with the substrate. Non-competitive inhibitors (allosteric regulation) bind to another part of an enzyme, causing it to change shape and make the active site less effective.

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A lot of poisons are competitive inhibitors.

Allosteric Regulation I. Describes cases where an enzyme’s function is affected by the binding of a regulatory molecule at a different site than the active site. II. May either inhibit or stimulate an enzymes activity. III. Usually end product of long series of reactions that make a metabolic pathway inhibits an enzyme near the beginning of the pathway. IV. When the product concentration is high, the chemical reactions leading to the product are slowed down.

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Feedback Inhibition

Definitions Amylose: Starch with the simplest structure. Anabolic Reaction: A type of metabolic reaction that uses small molecules to build up a larger one (making bonds) and uses up energy. ATP: Energy transfer and transport molecule of the cell. Biochemistry: The study of chemical reactions within cells and molecules and processes involved in these reactions. Catabolic Reaction: A type of metabolic reaction that uses larges molecules that break down into smaller molecules (breaking bonds) and gives off energy. Cellulose: Polysaccharide that’s the chief component of plant cell walls. Chemical Bond: Force that holds atoms together in a molecule. Chitin: Polysaccharide found in insect exoskeletons. Covalent Bond: Bond formed when 2 atoms share electrons.

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Dehydration: A reaction which serves to synthesize polymers. Denaturation: Change in 3D shape of the protein caused by temperature, pH, ionic concentrations, etc. Diffusion: Movement of molecules from a high concentration to low concentration to...