Biology HL Unit 1 (Water, Carbohydrates, Lipids: A1.1, B1.1)

Definition of Life

• Ability to reproduce (sexual/asexual)

• Must be made of cell(s)

• Must have a way to get rid of waste products (sweat, respiration, digestion)

• Must have a life cycle (stages of growth/development)

• Ability to do cellular respiration

• Gas exchange (aerobic/anaerobic respiration)

• Maintaining homeostasis/ responding to stimuli

• Able to take in (photosynthesis/cellular respiration)/ utilize energy (metabolism)

Living

Currently alive

Once living

Was alive, but is not at present time

Nonliving

Never living

Covalent bond

A bond between atoms in which pairs of electrons are shared (within a molecule)

Hydrogen bond

• A weak attractive intermolecular (between two molecules) force.

• A H atom in a molecule is attracted to an electronegative atom (oxygen, nitrogen, fluorine) in a different molecule.

• Accounts for unique properties of water.

Polar molecule

A molecule with an unequal distribution of electric charge. The ends are slightly positive or negative. (Ex. water)

Cohesion

The force by which individual molecules of the SAME type attract and associate (stick together)

Adhesion

The force by which individual molecules stick to surrounding materials and surfaces.

Surface tension

The property of the surface of a liquid that allows it to resist an external force, due to the cohesion between water molecules (hydrogen bonding).

Viscosity

A fluid’s resistance to flow, affected by temperature

Hydrophilic

Materials and substances with an affinity for water

Hydrophobic

Materials and substances that are repelled by water. Insoluble in water. Non-polar substances. Ex. all lipids

Capillary tubes

Channels with a very small internal diameter. Soil has many vertical, thin channels in which plant tubes are located.

Capillary action (aka capillarity)

The tendency of a liquid to move up against gravity when confined within a narrow tube (capillary)

Solute

Dissolved molecule or ion in a solution

Solvent

A liquid in which another substance (solute) can be dissolved

Buoyancy

The ability of any fluid to provide a vertical upwards force on an object placed in or on it.

Thermal conductivity (k)

The measure of how easily heat flows through a specific type of material.

Specific heat capacity

The amount of energy required to raise the temperature of 1 kg of a substance by 1 degree C.

Goldilocks zone (aka the ‘habitable zone’)

The area around a star where the temperature isn’t too hot or cold for liquid water to exist on the surface of surrounding planets.

Enzymes

Biological molecules that increase the rate of chemical reactions by lowering the activation energy needed.

Carbonaceous chondrites

Meteors with water incorporated into their mineral structure. Hydrogen isotope ratio similar to Earth’s seawater.

Carbon

• All lifeforms are carbon-based

• Have 4 valence electrons in outer shell, allowing for formation of strong covalent bonds

• Create large, stable structures that can only be broken through h

Structures of carbon

Chain, branched-chain, ring

Carbohydrates

• C, H, O, N

• Sugars, starches, and cellulose

Lipids

• C, H, O

• Insoluble in water

• Waxes, steroids, fatty acids, triglycerides

Proteins

• C, H, O, N, S

• Enzymes, muscles/skin

• One or more polypeptide chains of amino acids that folds into a 3D structure to become a protein

Nucleic acids

• C, H, O, N, P

• DNA/RNA

• Chains of nucleotides

• Sugar-phosphate backbone and nitrogenous base

Anabolic reaction

• Putting things together (adding)

• Net energy loss

• Energy + small molecules = larger molecule

• Protein synthesis: ribosomes creating proteins by assembling amino acids

• Storage of excess glucose: starch for plants, glycogen for animals

• Dehydration synthesis: condensation reactions

Catabolic reaction

• Breaking down molecules (cats break things)

• Net energy gain

• Large molecule = smaller molecules + energy

• Digestion of proteins, carbs, lipids in the digestive system

• Seed germination: starch breakdown for anaerobic respiration

• Glycogen breakdown in liver for energy

• Hydrolysis reactions (Ex. photosynthesis)

Monosaccharide

• Single sugar units

• Form ring structures in cells

• Hexoses: glucose, fructose, galactose

• Pentose: ribose

Polysaccharide

• Many monosaccharides linked together

• Starch, glycogen, cellulose

• Disaccharide: maltose, sucrose, lactose

Condensation reaction (aka dehydration synthesis)

• An anabolic chemical reaction - net energy loss

• Loss of an —OH group from one molecule and a —H from another

• Monosaccharides combine to form a polysaccharide and water molecules

Hydrolysis

• Water helping to break two monomers apart

• Restores the —OH and —H that were lost in the condensation reaction

• Catabolic reaction - net energy gain

Lactose intolerance

Low levels of enzyme lactase in the digestive system means that the hydrolysis of lactose doesn’t occur. Lactose enters the large intestine, where bacteria convert it into gas.

Amylose

• A straight chain of starch that will coil up into a helix

• About 20-25% of a plant’s starch

• Long-term and more efficient energy storage

• C1, C4 bonds; chains of alpha-glucose

Amylopectin

• Branched structure of starch

• Short-term energy storage

• C1, C6 bonds; glycosidic bonds

• 75-80% of the starch in a plant

Starch

• Amylose & Amylopectin

• Stores carbohydrates for plants in seeds, bulbs, and tubers

• Long-term storage

• Chains of alpha-glucose molecules

Glycogen

• Temporary storage of excess glucose for animals

• In liver or muscles

Cellulose

• Structural support for plant cell walls

• Beta-glucose molecules bond upside down

• Hydrogen bonds

Lipid function

• Energy source & long-term storage → release 2x more energy per gram than carbs when metabolized

• Insulation (lipids have a low thermal conductivity)

• Components of cell membranes (phospholipid bilayer)

Triglyceride

• Condensation reaction

• 3 fatty acids + 1 glycerol → 1 triglyceride + 3 H2O

• Simple lipid

Fat vs oil

Fat: solid at room temperature

Oil: liquid at room temp

Saturated fatty acid

• Long hydrocarbon chain capped by a carboxyl group (-COOH)

• Have a hydrogen at every possible position (straight)

• Usually in meats → unhealthy as they stack easier & can clog arteries

Unsaturated fatty acid

• Long hydrocarbon chain capped by a carboxyl group (-COOH)

• Double carbon bond means not complete saturation with hydrogen (bent)

• In seeds & plant products → healthier, less likely to stick in veins

• Monounsaturated: one double bond; Polyunsaturated: more than one

• Cis: same side H on the carbon that’s double bonding, healthiest

• Trans: H are on different sides

Polypeptide

• Chain of amino acids

• Amino acids are combined by condensation reactions into a polypeptide chain, linked with peptide bonds

Parts of an amino acid

• Double bond C=O

• Central carbon (alpha-carbon) C-H

• Carboxyl group (aka carboxylic acid) -COOH

• Amine group -NH2

• R group (varies)

Functions of protein

• Transport (e.g. hemoglobin)

• Storage

• Building & repairing tissues

• Catalyzing metabolic reactions (enzymes)

• Strength & structure (muscle contraction & movement)

• Protection (immune functions & antibodies)

• Cellular communication & coordination (hormones)

Essential vs non-essential amino acids

Essential: 9/20 amino acids, can’t be made by the human body so have to be gotten from diet

Non-essential: can be made by the human body, but made from essential amino acids

Combinations of amino acids

• 20 amino acids

• Almost infinite combinations (order, length of chain, etc)

Primary structure of protein

• Linear chain of amino acids held together by peptide bonds

• Aka simple protein or polypeptide chain

Secondary structure of protein

• Folding/coiling of the primary chain due to hydrogen bonds (carboxyl—amine) between polypeptide backbones

• Alpha-helix: a delicate coil (hair, wool, feathers)

• Beta-pleated sheet: 2 parts lie parallel, relatively insoluble in water (tend to be fibrous with structural function - muscle fibers)

• A and B can be found in the same chain

Tertiary structure of protein

• Folding of the chain caused by interactions between R groups

• Hydrophobic groups cluster together on the inside, hydrophilic groups on the outside (amphipathic)

• Hydrogen bonds: between polar R groups

• Ionic bonds: interactions between ions in R groups

• Disulfide bridges: 2 cysteine amino acids w/ sulfur in R groups will form H bonds

Quaternary structure of protein

• Multiple chains of amino acids linked together

• Held together by hydrogen & ionic bonds, disulfide bridges, and hydrophobic structures

• Not all proteins have a quaternary structure

• Non-conjugated: no prosthetic group

• Conjugated: incorporates other non-protein parts/prosthetic group (e.g. hemoglobin)

Hemoglobin

• Quaternary, globular, conjugated protein

• 4 chains - 2 alpha, 2 beta

• Each chain has a globular shape that is folded around the haem (prosthetic), which contains an iron atom that helps transport oxygen (a non-polar molecule)

Globular protein

• Round/spherical shape with irregular amino acid sequences

• Tend to be more specialized

• Generally soluble in water & sensitive to pH and temperature changes

• Ex. hemoglobin, enzymes, immunoglobulin, insulin

Fibrous protein

• Long and narrow, typically composed of repeating, regular structures

• Insoluble in water & stable in a large range of conditions

• Have a structural role - strength and support

• Ex. keratin, myosin, acting, fibrin, elastin, collagen

Insulin

• A small, globular, non-conjugated protein

• Shape allows it to bind to insulin receptors on the surface of liver, muscle, and fat cells, initiating a cellular response

• Secreted by beta cells in the pancreas

• A hormone - acts as a signal to cells in the body to absorb glucose and help reduce blood glucose concentration

Collagen

• Fibrous, non-conjugated quaternary protein

• 3 chains forming a triple helix, each strand composed of 3 repeating amino acids, 1200 amino acids in each chain

• Regular and geometric fibrous shape that allows it to form rope-like fibers with high tensile strength

• Makes up ~25% of all protein in the human body, structural support

• Helps prevent cracks in teeth and bones

• Forms a mesh of fibers in skin and blood vessels that resists tearing, also forms connective tissue

Amphipathic substances

• Have both hydrophilic and hydrophobic parts

• Ex. soap - can wash away both polar and non-polar substances

  • Phospholipid bilayer: hydrophilic heads & hydrophobic tails

Glucose

• The most important monosaccharide

• Used in photosynthesis & cellular respiration to store & release energy

• Polar molecule - soluble in water, can be transported in blood to all cells

• Ring form & 4 covalent bonds for each carbon make it a stable molecule

Enzyme

Denaturation

• The process in which a protein unravels to its primary structure, becoming inactive

• Renaturation can occur in some cases

• Enzymes are especially sensitive to denaturation

  • Human enzymes work best at 37 C (optimum temperature)

  • The optimum pH for human enzymes changes based on location (e.g. stomach vs intestines)

Reaction rate of enzymes

• Temp increase = kinetic energy increase; more chance of enzyme/substrate collision

• Substrate concentration increases, reaction rate increases

• The reaction rate levels off if:

  • The enzyme is saturated

  • All enzymes have their active site engaged

  • There are limiting factors

Metabolism

• Anabolism & catabolism

• A complex network of interacting and interdependent chemical reactions

• Nearly all metabolic reactions are enzyme-catalyzed in multi-step pathways and cycles

  • Ex. blood clotting, cellular respiration, photosynthesis, digestion

• Reactions/energy can be controlled & regulated by enzymes

Linear pathway

• A series of enzyme-catalyzed reactions which run in one direction from reactant'/substrate → product

• Ex. glycolysis in cellular respiration & light independent reactions of photosynthesis

Cyclical pathway

• Circular series of enzyme-catalyzed reactions where there is no end, as the initial substance is eventually reformed

• Ex. citric acid cycle aka Krebs cycle aka tricarboxylic acid cycle

Inhibition

• Controls enzymes to ensure that metabolism is regulated

• Negative feedback cycle, important for maintaining homeostasis

• Competitive & noncompetitive inhibitors, end-product & mechanism-based inhibition

Competitive inhibitors

• Molecules that bind to the active site of an enzyme

• Complete with the substrate - will still allow enzyme-substrate complexes to form, and if more substrate is added, it will be out-competed

• Ex. Statin: a medicine used to treat high blood cholesterol by competitively inhibiting the enzyme that forms cholesterol

Noncompetitive inhibitors

• Binds to the allosteric site of the enzyme

• Causes the enzyme to change shape, making the active site less effective

• Not affected by the amount of substrate, but can be overcome by the addition of more enzymes

• Ex. ACE inhibitor: medicine used to treat hypertension by preventing molecules from signaling constriction of the blood vessels

End-product inhibition

• The end of a metabolic pathway shuts down that pathway

• Prevents a cell from wasting chemical resources by synthesizing more product than is needed

• The end product can become a noncompetitive inhibitor and bind to the enzyme

Mechanism-based inhibition

• Aka suicide inhibitors

• Ex. heavy metals (mercury, lead): bind non-specifically and irreversibly to a wide range of enzymes through covalent bonding of the SH group in the active site

Penicillin

• A group of antibiotic chemicals obtained from molds

• Have a similar shape to the terminal ends of peptide chains, allowing them to bind in the active site

• As peptidoglycan synthesis is halted, its cell wall is compromised, leading to cell lysis & death as the cell is unable to maintain osmotic pressure