Unit 1 - Biochem : Carbs, Lipids, Proteins, Nucleic Acid, Enzymes

Bonding

Depends on valence electrons (outside orbit of electrons)

2 types of intramolecular(inside) forces:

◼ Ionic bonds form between oppositely charged ions

◼ Covalent bonds form when atoms share one or more pairs of electrons

Covalent bonds form molecules – the focus of biochemistry

Electronegativity

• measure of an atom’s ability to attract electrons in a covalent bond – the higher the E = stronger the attraction

• determines strength of the bond; depends on the electronegativity of the atoms involved

• can lead to unequal sharing of electrons and therefore, partial charges (δ) on the atoms in a molecule

Polarity

greater the difference in electronegativities (ΔEn) , the greater the polarity of the molecule

• Covalent bonds can create polar + nonpolar

• Influences solubility (like dissolves like), the shape, and interactions of molecules

Polar vs Non-Polar Symmetry

Nonpolar- symmetrical, formed when electrons are shared equally, En is the same or molecules are symmetrical

Polar- asymmetrical, formed when Electronegativity is uneven, electrons pulled closer to 1 atom than the others

Intermolecular Forces/van der Waals forces

weaker than intramolecular forces

Influenced by size and shape of the molecules

◼ Linear molecules (eg. Cellulose) develop stronger intermolecular forces than globular (non linear) molecules (eg. Starch), resulting in more rigid solids

London dispersion forces (Inter)

• weakest forces between all atoms and molecules, and depend on where e- are at any given moment

• only forces that hold nonpolar molecules to one another

• Cumulative (eg: methane a gas at room temperature whereas octane is a liquid at room temperature)

Dipole-dipole forces

hold polar molecules to one another because Partial positive and negative charges are attracted to one another

Hydrogen Bonding

Strongest, most significant

Independently weak, collectively strong

• Form between H+ of one polar molecule and electronegative N, O, F of another polar molecule

  • Give water its unique characteristics

4 major reaction types

◼ Dehydration

◼ Hydrolysis

◼ Neutralization

◼ Redox

Dehydration/Condensation Reactions

Removal of a water molecule (H and OH) forms a bond joining reactant molecules making a bigger molecule+water

joining monomers

Hydrolysis Reactions

◼ Water molecules added to break apart a molecule to smaller molecules

hydration- separating into monomers

opposite of condensation

Neutralization Reactions

Acid + base salt & water

Redox Reactions

Transfer of electrons between two molecules

◼ Losing the e- is oxidation (molecule is oxidized)

◼ Gaining the e- is reduction (molecule is reduced)

◼ e- move from less electroneg. atoms to more electroneg. atoms

Water

Highly polar (asymmetrical and ΔEn = 1.4)

◼ Intermolecular hydrogen bonding

◼ Polar molecules / ions are attracted to water (hydrophilic) and therefore soluble

◼ Many non-polar molecules are not easily soluble in water (hydrophobic)

◼ Like dissolves like

Acids, Bases, Buffers

Acids- proton donors

Bases- proton acceptor

Buffer- resist pH changes

4 major chemicals in living cells (macromolecules)

1. carbohydrates

2. proteins

3. lipids

4. nucleic acids

All chemicals of life (except water) are carbon based- organic compounds

Carbon is backbone of these molecules, forms with H to form hydrocarbons

• forms 4 stable bonds.

Hydroxyl

Carbonyl

Carboxyl

Amino

Phosphate

Thiol/Sulfahydryl

Characteristics of Functional Groups

• Mostly ionic or strongly polar - makes them very reactive

• Important to help large macromolecules interact w/other molecules in the body

Polymers

• Many macro.m are made of polymers

• polymers - made up of repeating subunits; monomers (like a long train of cars)

  • linked by condensation/dehydration (water) reactions and broken by hydrolysis reactions enzyme assisted

• Organisms get all their macro.m + nutrients from diet

Carb structure (CH2O) 1:2:1 ratio

Monosaccharides- simple carbs

• Single molecule

• Building blocks for carbs

• May be straight chains or 6C ring structures found in aq sol. (ie.bodies)

• Have isomers; chem formula is C6H12O6 but arranged diff

• ie.Glucose

Disaccharide- simple carbs

• 2 mono.s together

• Oligosaccharide: 3-10 simple sugars

  • C12H22O11

• sucrose ; maltose ; lactose

Polysaccharides- complex carbs

• Polymers of monosaccharide (100s/1000s of mono.s joined)

• straight or branched (train like) linked very differently

• polar which makes them water loving but too large to dissolve

Functions of complex carbs

1. Energy storage

2. Support and protection

Energy storage - Complex Carbs

• animals-glycogen

• plants- starch

  • both polymers of glucose

Support and protection- Complex Carbs

provided by fibre (structural polysaccharides)

• animals- chitin ; ‘crunchy’ exoskeleton of insects

• plant - cellulose (polymer of glucose)

  • cellulose: plant cell wall for strength and structure

Fibre in humans

Fibre cannot be broken by human enzymes but starch, glucose are easily digested to glucose monomers

• Undigested fibre helps w/bowel movements

• helps reduce cholesterol, lower risk of colon cancer, weight loss ‘feeling full’

Glycosidic linkages

Simple sugars (carbs) covalently bonded

condensation reaction

Lipid solubility

made of C, have a higher ratio of H:O than carbs

• insoluble in water + solutions made w/water

• dont dissolve in blood

fats, oils, waxes, phospholipids, steroids (nonpolar)

Lipid function

• Imp. part of cell membrane

• make hormones

• source of energy (2x more than carbs)

• essential for brain development and growth

• fat storage (adipose tissue)

  • for insulation

  • cushion of organs

1. Fatty acid

the backbone of most lipids

• hydrocarbon chain (usually even-numbered, 14 -22) with a carboxylic acid at one end

• larger chain=less soluble in water

• (Chemical structure is unsat/sat fat)

Saturated fat - Fatty acid

single bonds between C-H

• solid at room temp (ie. veg oil)

• straight H-C chains fit close together (many van der waals attractions

Unsaturated Fat- Fatty acid

1 or more double bonds

• liquid at room temp (ie.animal fat)

• H-C chains bend at van der waals attractions

2. Fats

energy storing

• common form: triglycerides

Triglyceride chemical structure

• glycerol + 1-3 fatty acids (hydrocarbon + C=O)

monomers of glycerol= monomers + fatty acid

Trans fats; Hydrogenation

Unsaturated fats may become saturated by hydrogenation → adding H atoms to the hydrocarbon

• allows liquids to become solid at room temp; giving products long shelf life but dangerous to heart

ie. processed foods, margarine

3. Phospholipids function

Major component of cell membranes

Phospholipid chemical structure

glycerol + 2 fatty acids + PO4

Polar head

Non polar tail

4. Steroids

4 hydrocarbon rings

• chemical messengers (estrogen, cholesterol, testosterone)

• anabolic steroids are artificial

Waxes - structure and function

fatty acids + alcohols or C rings that are long

- hydrophobic, firm but pliable

- Waterproof feathers, conserves water in plants

- i.e. the waterproof coating of cherries or in honeycombs

Ester linkages

-lipids bond by condensation reactions forming ester linkages.

Proteins

• ‘Building Blocks of Life’ - control almost every biochemical reaction in the body

• Most diverse molecule (structural & functional)

• Amino acid (a.a.) polymers, twisted & coiled into 3-d shapes, directly related to function

Amino acid in body

40,000 proteins in the body are made from 20 amino acids

• 8 a.acid. are essential → must be obtained through our diet, cannot be synthesized by our bodies

• amino acids (a.a.) → central carbon, amino group, carboxyl group, ‘R’ side chain

  • subunit for protein

Protein Function

1. Protein Hormones (insulin)

2. Digestive enzymes (pepsin)

3. Structural proteins (cell membrane)

4. Storage proteins (egg white albumin)

5. Contractile proteins (in skeletal muscle)

6. Sensory proteins (retinol for eyesight)

7. Metabolic function (kidney proteins)

Polypeptide

amino.a polymer

• Constructed in the cytoplasm by ribosomes via protein synthesis

Peptide bonds

• A.a.’s are joined by peptide bonds between amino group & carboxyl group

• Structural proteins - linear (strands or sheets)

• Functional proteins - globular

primary structure- 4 levels of protein

unique sequence of a.a.’s – determined by nucleotide sequence in DNA – Determines final conformation & function

Secondary structure- protein

coils/spiral & folds as a.a.’s are added

• Folds into: – α-Helix → a coil held by groups of various a.a.’s

• β-Pleated sheet → when 2 parts of a polypeptide chain adjacent to each other (fold)

  • BOTH form H bonds between the CARBOXYL and AMINO groups

Folds into either not both

Tertiary Structure

supercoiling of polypeptide chain stabilized by side-chain interactions

Quaternary Structure

2 or more polypeptide chains coming together

Certain proteins do not work unless in proper quat. or tert. structure

Protein shape

• change of a single amino acid in a chain of thousands can make a protein non-functional

• change of shape can make a protein non-functional.

• Heat, salt concentration, and pH can all change a protein’s shape

Denaturation

change that makes the protein nonfunctional: unfolds permanently

• A high fever can cause proteins in the body to denature (40C in humans)

• Genetic causes of protein denaturation can result in disease such as sickle cell anemia - can cause clotting

• Pickling / curing of food denatures enzymes that would cause spoilage

• Heat allows temporary straightening / curling of hair

• Cooking denatures proteins in food, allowing them to be digested

Protein Prosthetic Groups

non protein molecules that help form proteins

• proteins are formed from polypeptide chains

Hemoglobin in our red blood cells bind and carry O2 .

The polypeptide chains making up hemoglobin attach to a heme group (Fe2+ ion) that binds the O2 .

Nucleic Acid

• Assembly instruction for all proteins

• DNA – stores heredity information

• RNA – involved in protein synthesis

• self-copying

Nucleotide

subunits: Nitrogenous base (A,T,G,C,U) + 5-C sugar + phosphate group

Phosphodiester bonds

condensation reactions that bind nucleic acids

at nucleotide+phosphate

DNA bonding

G - C →3 hydrogen bonds

A - T →2 hydrogen bonds

• Double-stranded, anti-parallel

sugar:deoxyribose

• ATP and GTP are the primary molecules involved in chemical energy transfer

• regulate and adjust cellular activity

RNA bonding

G - C →3 hydrogen bonds

A - U →2 hydrogen bonds

• Single-stranded

sugar: ribose

Enzyme

• protein catalysts (dont get used up)

• regulate cellular activity in all living organisms

What do enzymes do?

- Help regulate + speed up reactions

Characteristics of Enzymes:

• all enz. have a unique 3-d shape

• only affect rate of reaction nothing else

  • dont affect reaction energy (ΔG)

• not consumed

• dont change products - able to catalyze same reaction over again

◼ most enzymes end in ‘ase’

Enzymes and Substrates

◼ Enzy. bind reactants → substrates @ active site only

• form enzyme-substrate complex

  • specific to substrate they bind on on

Induced-Fit Hypothesis

• Induced fit model: Interactions change enz. + subs. shape slightly, creating a ‘snug’ fit.

• After a reaction, subs. shape changes, doesnt fit active site now + releases from the enzyme

  • free to catalyze again

How do enzymes work?

reduce activation energy (Ea)

by:

1. bending + stretching bonds that break

2. giving acidic / basic environment

3. bringing subst. into correct geometry

Cofactors and Coenzymes

- Cofactors – non-protein groups (metals) that bind to enz.

Many enzymes need cofactors to function properly

◼ Coenzymes – organic molecules that act as cofactors i.e e- carrier NAD+

What factors affect enzyme activity?

Enz. are effected by their environment.

• pH

• temperature

• Substrate concentration

• Enzyme concentration

Effect of pH - enzymes

Enzymes are sensitive to pH; temperature.

- functions within a narrow range, has optimal pH; temp

• decreases as it moves away from this value

optimal pH- reaction rate fastest

Enzyme temp reaction- molecules

↑ kinetic motion of molecules → more frequent, stronger collisions

- results in increased rate of reaction (up to a point)

Enzyme temp reaction- amino acid

results in ↑ kinetic motion of enz. amino acid chains

• Above certain temperatures, will denature the enzyme (40˚C-humans)

• denatured= loses 3-D shape due to stabilizing H-bonds being broken; now cant function

Enzyme Concentration

- Enz. work at a consistent rate if there is excess substrate present

- If every available enzyme is catalyzing a reaction the enzyme limits the reaction, it can only work so fast

Substrate Concentration

When substrate is limited, not every enzyme is working

increasing the substrate = increase reaction rate up to a point → saturation level (when every enzyme is busy catalyzing a reaction)

Inhibitors

slow down/prevent binding of substrates

• Enz. catalyzed reactions may be affected by inhibitors

• Substrate competition

general term

Competitive inhibitors

• similar to substrate

• Compete with substrate for active site

• ↑ concentration of inhibitors = ↓ rate of reaction

Noncompetitive inhibitors

change shape of enzyme by binding (not active site)

Reverse inhibition

weak binding, enzyme function returns when inhibitor is released

temporary

Irreversible inhibition

-strong bonding (covalent bonds), enzyme disabled

– i.e. drugs/pesticides

- antibiotics are toxic to bacteria (penicillin binds to enzyme that links 2 a.a. for peptidoglycan –cell wall)

- cyanide is toxic to cytochrome oxidase (cell resp.)

Allosteric Control of Enzyme Activity

Allosteric Regulation → receptors on enz. (not active site) are allosteric sites

• change shape of enzyme, affecting the active sites

• Used to regulate enzyme activity

• Behave like noncompetitive reversible inhibitors

• Activators → make active sites available

• Inhibitors → stabilize inactive form;make it less effective

Feedback Inhibition

Too much final product causes it to bind to an earlier enzyme

Prevents cell from making too much product; being efficient

• An allosteric inhibitor is usually an end product of the pathway

applications of enzymes?

various uses in many different industries/products;

• Dairy: production of cheese

• Starch: making sugar for foods, medicines, vitamins

• Brewing: beer making

• Detergents: stain removal, break down molecules

• Leather: removing hair, softening hides for clothing and furniture

Plant Cell

fill in structure+function

Animal Cell

Membrane functions

1. Gatekeeper

2. Regulates what enters and exits the cell

3. Brings in nutrients, removes wastes

4. Maintains protected environment for cellular processes

Cell membrane Structure - Lipid bilayer

• Lipid bilayer made of phospholipids (phosphate w/2 fatty acid tails)

  • polar phosphate head - hydrophilic

    • face cytoplasm + extra cellular liquid

  • nonpolar fatty acid tail - hydrophobic

    • orient together in middle

• Contains proteins, sterols, embedded in membrane

Fluid Mosaic Model

• Forms a semi-solid, oily ‘film’, not rigid

• Proteins + lipids ‘float’ freely

  • may move within the two layers

• contain a ‘mosaic’ of proteins

• lipids may vibrate, flex, spin or move within their bilayer

• Proteins move slowly / not at all (larger than lipids)

Glycolipids+glycoproteins

carbohydrates (sugars) attached to membrane

• gly.lip: lipid + carb

• gly.pro. : amino acid + sugar /carb

• act as markers on cell surface making unique identities for cells

  • (Identify blood types, foreign invader etc.)

• Face exterior of cell for recognition + cell-to-cell communication

Membrane asymmetry

– proteins facing outside of cell look diff inside the cell

Fluidity

• Depends on how tightly packed phospholipids are

  • tighter=more semi solid membrane

• influenced by fatty acid composition + temp

Fatty acid influence on fluidity

Sat. fatty acid chains → straight, pack tightly together

Unsat. fatty acids → bent at double bond, more loosely packed

Temp influence on fluidity

• lower temperature= less lipids move

• Cholesterol gives them stability+structure at high temps so they do not dissolve

Sterols/steroid

membrane stabilizers

• High temp: Restrain movement of lipids

• Low temp: Prevent fatty acids from forming solid gel

Membrane proteins

diff memb. protein make membrane unique+determine function

Attachment+recognition - membrane protein

large proteins on both side of membrane act as attachment points for the cytoskeleton, ECM and cell junctions.

Triggering signals - membrane protein

Membrane proteins may bind to specific chemicals

Binding changes on the inner surface of the membrane, starting a cascade of events within the cell.

Enzymatic activity-membrane protein

involved in biochemical pathways (cell respiration, photosynthesis)

act as enzymes

Transport- Membrane Protein

allows large or hydrophilic molecules to cross the membrane

Integral membrane proteins

Proteins embedded in bilayer

• Most are transmembrane proteins (right through the membrane)

• have at least one hydrophobic region

general term