Copy of GRADE 12 BIOLOGY

UNIT 1: BIOCHEMISTRY CHEMISTRY BASICS

Atomic Theory

• All living things are made of matter.
• All matter is made of atoms.
• Therefore, all living things consist of atoms.
• Therefore, all living things are governed by the same laws of the physical universe that govern the interactions of atoms and molecules.

Rules of an Atom

• 96% of the atoms in the body are: N, O, C, H
• Every atom consists of P (+ve), ē (-ve), N (neutral)
• Rules of an atom:
  • Atomic weight: #P + #N
  • Atomic #: #P = #ē (in neutral atom → net charge = 0)
  • Neutral atoms: #P = #ē
• Bohr-Rutherford diagrams allow us to determine the valence or chemically active electrons of an element.
  • Valence number refers to the number of bonds an element is capable of forming.
• Notation: $A_ZX$
  • A - atomic mass
  • Z - # of P/ē (in neutral atoms)
  • X - element symbol

Ions (#P ≠ #Ē)

• Elements or compounds that have acquired an electric charge due to the gain or loss of electrons.
  • E.g. NaCl will dissociate in solution to form monatomic ions:
    • Na+ ions have lost one electron to the chlorine ions.
    • Cl- ions have gained one electron from sodium ions.

Isotopes

• Atoms of an element that contain the same number of protons but a different number of neutrons.
• Possess similar chemical properties but some different physical properties.
• E.g. 3 isotopes of carbon
  • C-12 (6 protons, 6 neutrons) – 99%
  • C-13 (6 protons, 7 neutrons) – stable form
  • C-14 (6 protons, 8 neutrons) – unstable (radioisotopes)

Radioisotopes

• The nuclei of some isotopes are unstable and break down or decay giving off particles of matter and energy that can be detected as radioactivity.
• The decay transforms the unstable, radioactive isotope – called a radioisotope – into an atom of another element.
• All have a characteristic half-life:
  • The time it takes for one half of the atoms in a sample to decay.
  • Constant for each isotope.

Applications of Radioisotopes

• Diagnosis – radioactive isotopes can “light up” organs and tissues of interest.
• Treatment – used to treat soft tissue disorders i.e., cancer.
• Research – can be used to track changes to biological molecules in metabolic pathways.
• Radiometric dating: provides the age of organic material, rocks, fossils, etc.
• Chart pg.26 (or 29)

Bonding

• Bonding allows atoms to form stable configurations as larger compounds.
• A sharing or distribution of valence electrons in order to stabilize outer electron orbitals.

Electronegativity

• Is the measure of an atom's attraction for the electrons it shares in a chemical bond with another atom.
• It is influenced by the atomic # and the distance between valence ē and the nucleus of an atom.
  • Therefore, EN will increase as the distance between the ē and the nucleus decreases.
• Scales ranges from 0 to 4.0
  • Cesium has the lowest value 0.7
  • Fluorine has the highest at 3.98
• ∆EN values determine the type of bond.

Types of Bonds

• Intramolecular – bonds within a molecule
  • Ionic
    • Gaining or losing electrons
    • Force of attraction between cations and anions
    • ∆EN > 1.7
    • Dissociate in water
    • Useful for biological reactions but not for creating biological structures
  • Covalent
    • Formed by the sharing of electrons
    • Can be single, double or triple
    • Most common form of bonding in biological molecules
    • Non-polar covalent
      • Molecule with evenly shared electrons
      • ∆EN=0-0.5
    • Polar covalent
      • 0.5 < ∆EN < 1.7
      • Similar to covalent, but the distribution of electrons is not equal resulting in a localized electric charge
      • Form H-bonds with each other
• Intermolecular – bonds between molecules
  • Hydrogen bonds
    • A force of attraction between the electropositive H of one polar molecule and an electronegative N, O, or F of a neighboring polar molecule.
    • Individual H-bonds are weak but significant if in large numbers
    • Ex. DNA, surface tension of water
  • Dipole-dipole forces
    • Holds polar molecules together
    • Partial positive side of one molecule with the partial negative side of another molecule
  • London dispersion forces
    • Weakest (holds nonpolar molecules to one another)
    • Is a temporary attractive force that results when the ē in two adjacent atoms occupy positions that make the atoms form temporary dipoles (unequal distribution of ē as they randomly move about the nuclei of atoms).
    • Weak bonds between small molecules results in gases at room temperature.
    • Weak bonds between large molecules results in liquids at room temperature.
    • Due to the cumulative effect

WATER

• Important biological molecule found in large percentages in all living things.
• Polar covalent molecule – causes intermolecular bonds.
• Universal solvent:
  • More substances dissolved in water than any other substance.
  • Each molecule has a partial positive and negative region, allowing it to readily penetrate or coat the surface of other charged molecules.
  • Surface coast of water (hydration shell)
    • Reduces the attraction between molecules/ions and promotes their separation into a solution (surrounded by water molecules).
    • Prevents molecules from re-association once in solution

“Like Dissolves Like”

• “Like dissolves like” – polar substances dissolve in other polar substances.
  • E.g. oil and water do not mix because oil is nonpolar and water is polar.
  • Fats and oils are hydrophobic since they cannot form H-bonds with water.

Amphipathic Molecules

• Amphipathic molecules: contain both hydrophilic and hydrophobic parts.
  • E.g. phospholipid
• Properties of Water

Cohesion

• The attraction between water molecules.
• Can form up to 4 H-bonds with other water molecules.
• Contributes to high surface tension of water.
  • I.e. a toothpick floats on water

Adhesion

• H-bonds form between water molecules and other polar or charged molecules.
• Capillary action of water depends on adhesion to “stick” water to ba surface.
  • I.e. xylem in plants (water to leaves)
  • Water sticks to sides (adhesion) but water molecules follow up the other water molecules which are lost at the leaves (cohesion).

High Specific Heat Capacity

• Hydrogen bonding causes water to take in large amounts of heat before this temperature is increased.
• Also causes water to lose large amounts of heat before its temperature is decreased.
  • Since the planet is mostly water, this acts as a heat sink or reservoir to moderate atmospheric effects.
  • Helps to maintain constant body temperature; ocean temperature.

High Specific Heat of Vaporization

• Hydrogen bonds cause liquid water to absorb large amounts of heat to become a vapour (gas) resulting in evaporative cooling.
• I.e. many organisms lose body by the evaporation of water from surfaces, such as the skin and tongue.

Highest Density at 4ºC

• As water molecules cool below 0ºC, they form a crystalline lattice with hydrogen bonds spreading the molecules apart.
• This reduces its density below that of liquid water leading to ice floating on water

BUFFERS Water

• Pure H2o contains, $H<em>2O$, $H</em>3O^+$, $OH^-$ (in equal amounts therefore, neutral)
• Autoionization of Water: when 2$H<em>2O$ molecules spontaneously react, 1$H</em>2O$ molecule transfers an $H^+$ ion to the other molecule, forming a $H_3O^+$ and $OH^-$
• $2H<em>2O \rightleftharpoons H</em>3O^+ + OH^-$

Acids

• Increase the [$H<em>3O^+$] when dissolved in $H</em>2O$
• They donate protons
• When more $H_3O^+$ exists = acidic
• Sour: conducts electricity; pH < 7; blue litmus = red

Bases

• Increase [$OH^-$] in a water solution
• They are proton acceptors that reduce the [$H^+$] of a solution
• When more $OH^-$ exists = basic
• Bitter; slippery; conducts electricity; pH> 7; red litmus = blue

Neutralization Reaction

• ACID + BASE → $H_2O$ + SALT

pH

• The [$H_3O^+$] compared to the [$OH^-$] ions determines the acidity.
• pH scale – logarithmic scale

Why are Some Acids/Bases Strong, and Some are Weak?

• Acids and bases may be classified as strong or weak according to the degree to which they ionize when dissolved in water.
• Strong acids/bases: ionize completely when dissolved in water.
• Weak acids/bases: ionize partially when dissolved in water.

Your Blood…

• Operates best at a pH of 7.4 (acceptable blood pH range: 7.35 to 7.45)
• When the pH of your blood drops:
  • $H_3O^+$ ions are able to do irregular things like bond to items (e.g. enzymes), impairing proper functioning.
• When the pH of your blood increases:
  • $OH^-$ ions are able to do irregular things like vasoconstriction.
• So how does your body maintain this optimal pH range? – buffers

Buf ers

• Buffers: a chemical that compensates for pH changes in a solution by accepting or donating $H^+$ ions
  • Many buffers are weak acids/bases or both because they will dissociate in a reversible reaction in water (therefore, absorbing or releasing $H^+$ or $OH^-$ as necessary)
  • An important buffer in the human body (both in and extracellular fluid) is the CARBONIC ACID – BICARBONATE BUFFER
    • Carbonic acid – ACID
    • Bicarbonate – BASE

Carbonic Acid – Bicarbonate Buf er

• The KEY here is that humans have the ability to control the amount of $CO_2$ in their body through breathing.
  • $H<em>2O + CO</em>2 \rightleftharpoons H<em>2CO</em>3 \rightleftharpoons HCO_3^- + H^+$
• Water + carbon dioxide ⇌ carbonic acid ⇌ bicarbonate ion + hydrogen ion

How it Works

• $H<em>2O + CO</em>2 \rightleftharpoons H<em>2CO</em>3 \rightleftharpoons HCO_3^- + H^+$
• Items in yellow – PART OF THE BUFFER

We ingest an acid, lowering the bodies’ pH

• More $H<em>2CO</em>3$ is made to maintain equilibrium: I.e. $H<em>2O + CO</em>2 \rightleftharpoons H<em>2CO</em>3 \rightleftharpoons HCO_3^- + H^+$

a) $H<em>2CO</em>3$ is a weak acid, raising the pH b) i) $H<em>2CO</em>3$ is converted to $H<em>2O + CO</em>2$ ii) this $CO<em>2$ is expelled from the body, so the body is forced to convert MORE $H</em>2CO<em>3$ to $H</em>2O + CO_2$ to maintain equilibrium; this raises the pH even More

Metabolic Acidosis

• Metabolic acidosis: occurs when the body produces too much acid, or when the kidneys and lungs are not removing enough acid from the body.
• pH< 7.35
  • Diabetic acidosis: develops when ketone bodies build up in the body.
  • Hyperchloremic acidosis: excess loss of $NaHCO_3$ from the body.
  • Lactic acidosis: build up of lactic acid

Metabolic Alkalosis

• Metabolic alkalosis: occurs when there is an increase in bicarbonate ($HCO_3$ -) concentration.
• pH > 4.5

ORGANIC COMPOUNDS

Organic vs. Inorganic

• With the exception of water, virtually all chemicals of life are carbon based
  • Organic compounds: compounds that contain primarily carbon and hydrogen (other than carbon dioxide and a few other exceptions)
  • Inorganic compounds: compounds that do not contain carbon and hydrogen together
• The unique position of carbon in the periodic table allows it to combine with as many as 4 other atoms, forming 4 stable covalent bonds. This is possible because carbon has 4 unpaired valence electrons

Carbon

• Valence of 4, so can form 4 covalent bonds
• Any particle (element or compound) attached to a carbon atom is called a functional group
• Will form single, double, or triple covalent bonds
• C-skeletons can be either linear, branches, or form a closed ring shape
• Molecules made up of only C and H atoms are called hydrocarbons

Examples of Hydrocarbons Carbon – Nomenclature

• Generally, hydrocarbons have a two-part name;
  • Prefixes are named for the number of carbons in the longest continuous chain
    • 1 meth 6 hex
    • 2 eth 7 hept
    • 3 prop 8 oct
    • 4 but 9 non
    • 5 pent 10 dec

Functional Groups

• Organic compounds fall into various organic families
  • An organic family is a group of organic compounds with common structural features that impart characteristic physical properties and reactivity
  • These structural feature are particle combinations of atoms called functional groups
• Functional group: a group of atoms that affects the function of a molecule by participating in chemical reactions
  • The usefulness of identifying functional groups on molecules is they have predictable chemical behaviours
• This is why the characteristics of large biological molecules are determined by their functional groups since the functional groups will determine how they interact with other molecules
• Unlike non-polar, hydrocarbon chains, they are usually ionic or strongly polar and therefore, very attracted to water
• Molecules must interact in order for a chemical reaction to take place so functional groups play an important role in living systems
• If a functional group is present a specific class of compound is formed…

Alcohols (family name)

• Contain hydroxyl (name of functional group) group
• General formula:
• If only one OH group, called monohydroxyl alcohol

Aldehydes

• Contain a carbonyl group (at the end of the molecules)
• General formula:

Ketones

• Contain a carbonyl group (not at the end of the molecule (within))
• General formula:

Carboxylic Acids (or Organic Acids)

• Contain a carboxyl group (-COOH)
• Gives organic molecules pacific properties because the -OH group readily releases its H as a proton in a water solution (proton donor)
• General formula:

Amines

• Contain an amino group (-$NH_2$)
• Readily acts as a base by accepting $H^+$ in a water solution
• General formula:

Amides (linkage)

• Produced from a carboxylic acid + amine
• General formula:

Amino Acids

• Contain both amino + carboxyl group
• 20 naturally occurring building blocks of protein
• General formula:

Nucleotides, Nucleic Acids & Other Cellular Molecules

• Contain a phosphate group (-$PO_4$ 2-)
• General formula:

Thiols

• Contain a sulfhydryl (-SH) group
• General formula:

(seen in proteins)

Ether

• (linkage)

Ester

• (linkage)

Biological Reactions

Metabolism

• A term used to refer to all the chemical reactions that take place in a living organism
• There are two main categories of metabolic reactions
  • Catabolic reactions: those that break large molecules into small ones; exergonic
    • E.g. digestion of proteins; respiration ($C<em>6H</em>{12}O<em>6$+ $O</em>2$ → $CO<em>2$ + $H</em>2O$ + energy)
  • Anabolic reactions: those that build larger molecules; endergonic
    • E.g. photosynthesis ($CO<em>2$ + $H</em>2O$ + sunlight → $C<em>6H</em>{12}O<em>6$ + $O</em>2$)

Dehydration Synthesis

• Also known as a condensation reaction
• Involved the removal of a hydrogen atom, -H, from a functional group of one subunit and the hydroxide group, -OH, from the functional group of a different subunit
• The -H and -Oh combine to form water
• This is an anabolic reaction

Hydrolysis

• Water is used to break the bond holding subunits together
• Water is broken down and the hydrogen atom, -H, is added to the functional group of one subunit and the hydroxide ion, -OH, is added to the functional group of the other and the bond holding the subunits together breaks
• This is a catabolic reaction
• Opposite of dehydration synthesis

Neutralization Reactions

• Acid + base → water + salt

Redox Reactions

• Reactions in which electrons are exchanged between atoms; one atom is oxidized (loses ē) and the other is reduced (gains ē)
• LEO says GER (OIL RIG)

BIOMOLECULES

Macromolecules

• Large biological molecules
  • Made up of C, H, O and sometimes N
  • Made up of a few basic subunits (monomers) that join in specific sequences (polymers)
    • Made by attaching more units to create long chains
    • Created through dehydration synthesis reactions; broken down by hydrolysis reactions
  • Include carbohydrates, lipids, proteins, and nucleic acids

Micromolecules

• Small biologically important molecules
  • Include vitamins and minerals

Carbohydrates

• Known as ‘sugars’
  • Primary source of energy for living things
  • Obtained from food
• Contain C, H, O in ratio 1:2:1
  • General formula – $(\text{CH}<em>2\text{O})</em>n$ (n= # of C-atoms)
• Basic subunits – called simple sugars or monosaccharides
  • Simple sugars contain a single chain of carbon atoms to which hydroxyl groups are attached
  • 3 main types: glucose ($C<em>6H</em>{12}O_6$), fructose, galactose
• 2 types:
  • Aldoses (are aldehydes) and ketoses (are ketones)

Aldehydes

• Carbonyl group – found at end of C chain
  • Sugar is called an aldose (general name)
  • E.g. glyceraldehyde

Ketones

• Carbonyl group – found within C chain
  • Sugar is called a ketose (general name)
  • E.g. dihydroxyacetone

Monosaccharides

• Simple sugars
• Distinguished by:
  • The carbonyl group they possess
  • The length of the C-backbone
  • The spatial arrangement of their atoms
• 2 main forms:
  • Open-chain forms
  • Ring forms

Open Chain Forms

• Are straight chain sugars
• Contain one carbonyl group with hydroxyl groups and other carbonds
• Pentoses and hexoses:
  • Exist as both straight chains (in a dry state) but readily form rings (more stable) when dissolved in water

Ring Forms

• Non-linear molecules
• Ring forms exist when dissolved in water
• Aldose: the functional groups on C1 and C5 react forming a covalent bond; called a 1,5 linkage
• Ketose: the functional groups on C2 and C5 react forming a covalent bond; called a 2,5 linkage

Ring Formation of Glucose

• When glucose (a 6-C sugar; primary source of energy for humans) dissolved in water, the hydroxyl group on C-5 reacts with the aldehyde group on C-1 to form a close ring structure
• If the OH group is below the plane of the ring an alpha bond forms → ⍺-glucose
• If the OH group is above the plane of the rings a beta bond forms → β-glucose
• Isomers
• Glucose, galactose, and fructose are isomers:
  • Same formula – $C<em>6H</em>{12}O_6$
  • Each has different shapes and physical and chemical properties

Disaccharides

• Formed through dehydration synthesis when two monosaccharides are bonded together
• Ether linkage in disaccharide = glycosidic linkage/bond
• Examples:
  • Glucose + galactose → lactose
  • Glucose + glucose (both alpha) → maltose
  • Glucose + fructose → sucrose

Polysaccharides

• They are large and insoluble
• Monomers are held together by glycosidic linkages
• Straight chained or branched (starch = straight, glycogen = branched)
• They function in 2 important ways:
  • Energy storage (starch and glycogen)
  • Structural support (cellulose and chitin)

Starch

• Glucose storage in plants
• Made of ⍺-glucose
• Is a mixture of amylose and amylopectin:
  • Amylose
    • Alpha 1,4 bonds – no branches; can be 1000s of molecules long
    • Straight chain with 1, 4 glycosidic linkages
  • Amylopectin
    • Similar to amylose, with 1, 4 linkages in the main chain
    • But has occasional 1, 6 linkages to create branches
• The angles at which the glycosidic linkages form cause the polymers to twist into coils that make them insoluble in water

Glycogen

• Glucose storage in animals
  • Stored in the liver and muscles
• Branched structure; have more branches than amylopectin

Cellulose

• Structural
• Straight-chain polymer (allows the hydroxyl groups of parallel molecules to form many H-bonds – producing tight bundles called microfibrils which can intertwine to form tough, insoluble
• Negative test: turns yellow/brown cellulose fibres used in the cell walls of plants) – also found in clothing and fabric
• Beta-acetal bonds
  • These bonds cannot be broken down by human enzymes

Chitin

• Made from a variant of glucose called N-acetylglucosamine
• Repeating units make up a tough outer skeleton for insects and crustaceans and the cell wall of many fungi

Are Sugars in Your Food?

Monosaccharide (simple sugars)

• Test: add Benedict's Reagent to the food sample
• Heat in boiling water for 5-10 minutes
• Positive test: turns a range of colours, depending on the concentration of monosaccharide
• Negative test: blue coloured solution

Polysaccharide (complex sugars)

• Test: add iodine to food sample
• Positive test: turns black
• Negative test: turns yellow/brown

Lipids

• Made up of C, H, and O
• They are hydrophobic
• Become more solid as the number of carbons increases
• Used primarily as long term storage of chemical energy
  • Store a greater amount of energy than carbohydrates

Function of Lipids

1. Energy source and storage molecule
2. Cushions internal organs
3. Key components of cell membranes
4. Act as raw materials for synthesis of hormones and other chemicals
5. Serve as insulation
6. Aid in the absorption of vitamins

Classes of Lipids

• There are four classes of lipids:
  • Neutral lipids
  • Phospholipids
  • Steroids
  • Waxes

Neutral Lipids

• Fats and oils
• Also called triglycerides
  • Most common type of lipid
• Consists of:
  • 1 glycerol
  • 3 fatty acids (can be the same or different)
• Synthesis of a triglyceride:
• Fatty Acids
• Long hydrocarbon chains with one carboxyl group at the terminal end
• 2 main types:
  • Saturated fatty acids
  • Unsaturated fatty acids
    • Mono-unsaturated
    • Poly-unsaturated

Saturated Fatty Acids

• Only single bonds between C-atoms
  • Each C has the max number of H-atoms stearic acid ←
• Found predominantly in animal fats
• Solid at room temperature
  • Chains are closer together (more Van der Waals attractions)
• Associated with heart disease
• Arteriosclerosis: the stiffening or hardening of the artery walls

Unsaturated Fatty Acids

• Contain at least one double bond between a pair of C-atoms in the chain
  • Fewer than the maximum number of H-atoms oleic acid ←
• Found predominantly in plant oils
• Liquid at room temperature
  • Double bonds cause kinks in the chain (Van der Waals attractions)

Mono- & Polyunsaturated Fatty Acids

• Monounsaturated fats – single double bond
• Polyunsaturated fats – many double bonds Linoleic acid ← (polyunsaturated)

Hydrogenated oils

• Unsaturated fats that have had H-atoms fused to carbons at the double bonds
  • Thereby making a very stable molecule (difficult to break down)
• Results in liquid fats becoming solid (e.g. margarine)

Phospholipids

• Major component in cell membranes
• Consists of a:
  • Glycerol molecule
  • 2 fatty acids
    • Water insoluble - nonpolar end
  • Phosphate group
    • Water soluble - polar end
• Cytoplasm above bilayer sheet, extracellular fluid under

Steroids

Common feature

• A multiple ring structure
  • Backbone of structure is 3 6C rings and 1 5C ring

Ex:

• Cholesterol, stronger, testosterone ( hormones)
• Cholesterol – one of the most important steroids
  • Precursor for many of the hormones
  • Will deposit itself on inner blood vessels
    • Results in increased blood pressure
    • May lead to heart attack and stroke
  • HDL – high density lipoprotein (good cholesterol)
  • LDL – low density lipoprotein (bad cholesterol)

Waxes

• E.g. beeswax, carnauba, paraffin
• Consists of alcohol or carbon rings with an ester linkage to a fatty acid
• They are hydrophobic
• Can be used by plants/some animals as waterproof coating

Formation

• Lipids are created through dehydration synthesis
• Lipids are broken down through hydrolysis

Are fats in your food?

Lipid (fats)

• Tests: rub sample of food on brown paper
• Positive test: the paper appears translucent (light can pass through)
• Negative test: the paper is NOT translucent

Proteins

• Largest percentage of body tissue is made up of protein
• Composed of C, H, O, N and sometimes S
• Coded for by DNA

Functions of Proteins

• Can have a structural or functional role
• Proteins are also components of membranes

Structural Proteins

• Form most of the solid material in the human body
  • E.g. keratin is the main component of hair and nails
  • E.g. collagen is the main component of cartilage, bones, and tendons

Functional Proteins

• Transport: hemoglobin – oxygen transport
• Movement: myosin – helps muscles contract
• Messengers: insulin – helps to regulate the storage of glucose in the body
• Defense: antibodies – help fight illness
• Cell markers: major histocompatibility complex (group of genes)
  • Help the immune system recognize foreign substance
• Subclass of functional proteins – enzymes – help carry out specific chemical reactions in the human body
  • Ex. amylase found in saliva and pancreatic digestive juices
    • Breaks down starch

Composition of Proteins

• Composed of amino acids
• 20 different amino acids
  • 9 are essential because the body does not have the ability to make them
• The number and arrangement of amino acids (the combinations) leads to formation of 1000s of different proteins in the body

Amino Acids

• R = a variable group or side chain
  • 20 different variable groups representing 20 different amino acids
  • Make the amino acid polar (hydrophilic), non-polar (hydrophobic), or charged (acidic/basic)
• When dissolved in water the ‘carboxyl’ donates an $H^+$ ion to the ‘amino’
• Amino acids are amphipathic → contain both acidic (carboxyl) and basic (amino) functional groups

Structure of Proteins

• Depends on the amino acids it contains, and the interaction between those amino acids
• There are four levels of complexity:
  • Primary
  • Secondary
  • Tertiary
  • Quaternary

Primary Structure

• The unique order of amino acids in a polypeptide chain
  • Determined by the DNA sequence
  • Determines the final conformation of the overall protein
  • E.g. pr-ala-val vs. ala-pro-val
    • Overall protein structure is going to be different

Secondary Structure

• Shape of polypeptide chain is created by the pattern of H-bonding between carboxyl and amino functional groups
  • ⍺-helix: twisting causes helical coils – every fourth amino hydrogen bonds with carboxyl
  • β-pleated sheets: parts of the polypeptide chain lie parallel to each other (non-helical) – hydrogen bonds form between different amino acids

Tertiary Structure

• Additional folding creates globular formation due to interaction between R groups
• There are 4 bonds responsible for folding:

1. Ionic bonds due to attraction of opposite charges on acidic (-) and basic (+) R groups
2. Disulfide bridges between 2 sulfhydryl groups (-SH) on cysteine R groups
3. H-bonds between opposite partial charges on R groups
4. Van der Waals (london dispersion) forces between neutral R groups

• Proteins at 3º and 4º level are functional; e.g. enzyme

Quaternary Structure

• Two or more globular or polypeptides come together forming a complex structure (functional protein)
  • E.g. hemoglobin
• 4º structure is determined by 1º
• H-bonds are responsible for keeping globes together

Conjugated Proteins

• Proteins that require non-protein parts called prosthetic groups to function
• Prosthetic groups are tightly bound non-protein components
  • These non-protein parts can be metal ions or organic molecules
  • Example: hemoglobin transports oxygen and is made up of 4 polypeptide subunits, but each subunit contains a structure called heme which includes a single iron ion and it is the heme that binds the oxygen so each hemoglobin protein binds 4 oxygen molecules

Af ecting Proteins

• The environment that the protein is in, has an effect on its tertiary structure
• Disruption in the folding of a protein
  • Leads to unfolding
    • Causes change in shape of the protein and a subsequent loss in functionality!
• This process is called DENATURATION
  • E.g. straightening/curling hair – exposing keratin proteins in hair to high heat

Factors That Af ect Protein Shape

• pH (acidic and basic) – $H^+$ and $OH^-$ attract charge R groups
• Temperature – faster movement of molecules break H-bonds
• Heavy metal ions – attract charged portions of R groups causing unfolding
• Ultraviolet light – is high energy and break bonds
• Solvents – such as organic solvents
  • Make proteins turn inside out

Formation

• Proteins are created through dehydration synthesis
• Proteins are broken down through hydrolysis
• Peptide bond – a covalent bond that holds amino acids together
• A group