Biochemistry

The basics Element: substance that cannot be broken down into simpler chemical substances. Contains ONLY ONE TYPE OF ATOM Element: substance that cannot be broken down into simpler chemical substances. Contains ONLY ONE TYPE OF ATOM C, H, O, N --> make up >96% of human body C, H, O, N --> make up >96% of human body Trace elements --> Ca, Mg, Na, K … cannot live without them Trace elements --> Ca, Mg, Na, K … cannot live without them Atom: smallest particle of an element that maintains the characteristics of that element Atom: smallest particle of an element that maintains the characteristics of that element

The atom Atom: Atom: Nucleus Nucleus Has protons (+) and neutrons (no charge). Has protons (+) and neutrons (no charge). Heaviest part of atom Heaviest part of atom # of protons makes each atom unique # of protons makes each atom unique Electrons (e - ): Electrons (e - ): Floating in clouds around nucleus Floating in clouds around nucleus Different energy levels Different energy levels Outer shell is valence shell Outer shell is valence shell Atoms have neutral charge (equal number of protons and electrons) Atoms have neutral charge (equal number of protons and electrons) Atomic #: # of protons Atomic #: # of protons Atomic mass: # protons + # of neutrons Atomic mass: # protons + # of neutrons

1 Atomic Number H Symbol Mass Number 2 Atomic Number He Symbol Mass Number 3 Atomic Number Li Symbol Mass Number

Electron clouds Electrons reside in clouds around the nucleus. Electrons reside in clouds around the nucleus. These clouds are at different energy levels These clouds are at different energy levels First cloud can hold up to 2 e - First cloud can hold up to 2 e - Second cloud can hold up to 8 e - Second cloud can hold up to 8 e - Valence electrons: number of electrons in valence shell Valence electrons: number of electrons in valence shell They determine how many bonds that atom makes They determine how many bonds that atom makes

Bonds Atoms will bond with other atoms when this makes them more stable Atoms will bond with other atoms when this makes them more stable When it completes their valence electron cloud When it completes their valence electron cloud 2 types 2 types Ionic: one atom gains electrons and another loses them Ionic: one atom gains electrons and another loses them Covalent: atoms share electrons Covalent: atoms share electrons

Chemical Bonds Ionic Bonding Covalent Bonding

Isotopes htm htm htm htm rbon+dating&hl=en&emb=0&aq=f# rbon+dating&hl=en&emb=0&aq=f# rbon+dating&hl=en&emb=0&aq=f# rbon+dating&hl=en&emb=0&aq=f#

More vocabulary Compound: substance with atoms of 2 or more different elements that are chemically combined Compound: substance with atoms of 2 or more different elements that are chemically combined Properties change Properties change Compounds joined by covalent bonds are molecules Compounds joined by covalent bonds are molecules Mixture: uneven combination of substances in which elements preserve their properties Mixture: uneven combination of substances in which elements preserve their properties Solution: evenly distributed mixture in which one or more substances (solute) are evenly distributed in another substance (solvent) Solution: evenly distributed mixture in which one or more substances (solute) are evenly distributed in another substance (solvent)

Reactions REACTANTS  PRODUCTS REACTANTS  PRODUCTS 2 H 2 O  2 H 2 + O 2 2 H 2 O  2 H 2 + O 2 # of molecules# of atoms

Acids and bases Acidity is measured with the pH scale Acidity is measured with the pH scale Acid: substance that releases H + in water Acid: substance that releases H + in water Base: substance that releases OH¯ in water Base: substance that releases OH¯ in water neutral ACID BASIC

Properties of Water Properties of Water Polarity  unequal e- distribution Polarity  unequal e- distribution Ex) water: Ex) water: Oxygen  - Oxygen  - Hydrogen  + Hydrogen  + Hydrogen Bonds: weak attraction Hydrogen Bonds: weak attraction Properties Properties Cohesion: stick together Cohesion: stick together Adhesion: stick to another substance Adhesion: stick to another substance Capillary action Capillary action Universal solvent Universal solvent

Biomolecules Carbohydrates Carbohydrates Lipids Lipids Proteins Proteins Nucleic acids Nucleic acids

Structure All biomolecules have long carbon chains (some longer than others) All biomolecules have long carbon chains (some longer than others) All have MONOMERS (single molecules) that when bonded together make bigger biomolecules (POLYMERS) All have MONOMERS (single molecules) that when bonded together make bigger biomolecules (POLYMERS)

Carbon Can form 4 different bonds The foundation for the major molecules of life

Carbon can form long chains with itself A lot of energy can be stored in these chains

Carbon is green in this model

Macromolecules Carbon Chemistry Carbon Chemistry Carbon Chemistry Carbon Chemistry Form 4 covalent bonds Form 4 covalent bonds Bonds with itself forming straight chains, branched chains, or rings Bonds with itself forming straight chains, branched chains, or rings Can form single, double, or triple bonds Can form single, double, or triple bonds Definitions Definitions Polymer Polymer Monomer Monomer

Dehydration Synthesis= Polymerization Remove H 2 O 2 Monomers Bond= Polymer Anabolic reaction Anabolic reaction Produces polymer Produces polymer Monomer + Monomer  Polymer + Water Monomer + Monomer  Polymer + Water

Catabolic reaction Catabolic reaction Produces monomers Produces monomers Ex) Polysaccharides  monosaccharides Ex) Polysaccharides  monosaccharides Polymer + Water  Monomer + Monomer Polymer + Water  Monomer + Monomer Hydrolysis Add H 2 O Separate polymer into: 2 monomers

Carbohydrates Monomer: monosaccharide Monomer: monosaccharide Elements: C, H, O Elements: C, H, O Ratio: 2H : 1O Ratio: 2H : 1O Examples: Examples: Monosaccharide: glucose, fructose (C 6 H 12 O 6 ) Monosaccharide: glucose, fructose (C 6 H 12 O 6 ) Disaccharide: sucrose, galactose (C 12 H 22 O 11 ) Disaccharide: sucrose, galactose (C 12 H 22 O 11 ) Polysaccharide: starch (depends on number of C in chain) Polysaccharide: starch (depends on number of C in chain) Function: Function: Energy Energy Structure (in plants) Structure (in plants)

Monosaccharides: Isomers C 6 H 12 O 6 : Glucose, Fructose, GalactoseCarbohydrates Polysaccharide: Starch Monosaccharide: Glucose

Lipids Monomer: 1 glycerol and 3 fatty acids Monomer: 1 glycerol and 3 fatty acids Elements: C. H, O Elements: C. H, O Ratio: >2H : 1O Ratio: >2H : 1O Examples Examples Fats, waxes, steroids Fats, waxes, steroids Functions Functions Insulation (warmth) Insulation (warmth) Energy (more than carbs) Energy (more than carbs) Cushioning/protection Cushioning/protection Phospholipids in cell membrane Phospholipids in cell membrane

1Glycerol+3 Fatty Acids  1Trigyceride

Fats Saturated Saturated Solid at room temperature Solid at room temperature All bonds are SINGLE All bonds are SINGLE  risk for CAD  risk for CAD Unsaturated Unsaturated Liquid at room temperature Liquid at room temperature One or more bonds are double One or more bonds are double Monounsaturated, polyunsaturated Monounsaturated, polyunsaturated

One double bond > one double bond ALL SINGLE BONDS

Cholesterol Testosterone Carbons are Grey

Proteins Monomer: amino acids Monomer: amino acids All amino acids have CARBOXYL and AMINO groups All amino acids have CARBOXYL and AMINO groups

Proteins (cont) Elements: C, H, O, N Elements: C, H, O, N Examples and functions Examples and functions Enzymes: speed up reactions Enzymes: speed up reactions Antibodies: defense Antibodies: defense Structural: building and structure Structural: building and structure Hemoglobin: carry oxygen Hemoglobin: carry oxygen Membrane proteins: channels and pumps Membrane proteins: channels and pumps Proteins have very specific shapes. Their FUNCTION is dependant on their STRUCTURE. Proteins have very specific shapes. Their FUNCTION is dependant on their STRUCTURE.

Protein Structure

Protein Types Types Dipeptide: 2 aa Dipeptide: 2 aa Polypeptide: aa Polypeptide: aa Protein: aa Protein: aa Amino Acid (Glycine) Amino R Group Carboxyl Amino Acid (Alanine) Peptide Bond: Dipeptide

Protein  Amino Acid Relationship

Amino Acid Nitrogen added

Protein in muscle fiber One amino acid

Hemoglobin Each red blood cell contains hundreds

Enzymes ALL ENZYMES ARE PROTEINS ALL ENZYMES ARE PROTEINS Enzymes are CATALYSTS Enzymes are CATALYSTS They speed up reactions without being used up in those reactions They speed up reactions without being used up in those reactions They lower the ACTIVATION ENERGY needed for a reaction They lower the ACTIVATION ENERGY needed for a reaction EVERY REACTION IN THE BODY HAS A SPECIFIC ENZYME THAT HELPS IT HAPPEN EVERY REACTION IN THE BODY HAS A SPECIFIC ENZYME THAT HELPS IT HAPPEN

Enzymes (cont) Lock and key theory Lock and key theory Substrate (key) Substrate (key) Molecule enzyme works on Molecule enzyme works on Enzyme (lock) Enzyme (lock) Active site: part of enzyme that binds to substrate Active site: part of enzyme that binds to substrate

Activation Energy

Effect of enzymes

Nucleic acids Monomer: nucleotides Monomer: nucleotides Elements: C, H, O, N, P Elements: C, H, O, N, P Examples and functions Examples and functions DNA: has genes (information to make proteins) DNA: has genes (information to make proteins) RNA: carries information from DNA to where proteins are made RNA: carries information from DNA to where proteins are made

Nucleotide & DNA

Small Differences can make a Big Difference Vitamin C Aspirin

Small Differences can make a Big Difference Caffeine Nicotine