SBI4U - Unit One - Biochemistry

Bonding

Ionic Bonds

• dissociate easily in water

• one or more electrons transferred between atoms with an electronegativity of greater than 1.7

• results in cation and anion

• soluble

Covalent Bonds

• share electrons between atoms

• three types:

  • polar

    • unequal sharing of e- pairs

    • EN between 0.41 and 1.7

    • eg. H2O

  • nonpolar

    • equal sharing of e-

    • electronegativity of less than 0.4

    • eg. H2, O2, N2, CO2, CH4

  • amphiphilic

    • some larger molecules have parts that are polar and parts that are nonpolar

    • eg. fatty acids

  • Note - like dissolves like, so polar dissolves polar, nonpolar dissolves nonpolar

Electronegativity

• determines the strength of the bond

  • F (fluorine) has the highest EN (highest “pull” of e-)

• has to do with the distance between valence e- and nucleus

• even though e- are being shared, one element may have a stronger “pull”

• can lead to the formation of polar molecules

• the shape of molecules is related to their polarity

Intermolecular Forces (aka van der Waals Forces)

• Hydrogen bonds

  • attractive force between a partially positively charged hydrogen atom and a partially negative charge in another molecule

  • eg. forces between water molecules

• Other van der Waals Forces

  • weak, momentary attractions of one molecule to the nuclei of another molecule

  • eg. London dispersion forces, dipole-dipole forces

Chemical Reactions

Dehydration Reaction (aka Condensation)

• Removal of an OH and H to join smaller molecules and make H2O

  • eg. occurs naturally in plants, including sugarcane and sugar beets, from which we refine the sugar into pure table sugar

Hydrolysis Reaction

• Adding water as OH and H splitting a larger molecule

  • eg. happens in digestion in your stomach under the influence of the enzyme lactase

Neutralization Reaction

• Between acids and bases to form water and salt

  • eg. digestion - pancreas releases sodium bicarbonate and it is added to the small intestine to increase pH

Redox Reaction

• Electrons are lost from one atom and gained by another

  • eg. Aerobic Cellular Respiration: burning of fuel/glucose to produce energy

• LEO - Lose Electrons Oxidation

• GER - Gains Electrons Reduction

Water

Polar Covalent Bonds

• Oxygen has a higher EN than hydrogen

Hydrogen Bonds

• Electrons spend more time near the O than the H

Cohesion

• Water molecules are attracted to other water molecules

Adhesion

• Water molecules attach to other polar molecules

Capillary Action

• Adhesion and Cohesion working together

• Climbs inside tubules up to 90m

Surface Tension

• Water molecules bond with their neighbours beside and below them

• BUT there are more bonds at the surface

Lower Density Solid

• Water expands when freezing and becomes less dense

• This is why ice floats

• Life persists when lakes freeze over because the ice stays on top

Spring/Autumn Turnover

• The turnover and shifting of water throughout a body of water

• Warm water stays on top, cold water sinks

• Oxygenates the deep water and releases sulfurous gases

High Heat of Vaporization

• Intenseheat and exercise may generate 1L of sweat per hour and 600 calories burned per litre of sweat evaporated

• When sweat evaporates, it pulls the heat with it, cooling us down

High Heat Capacity

• Large amounts of heat are required to raise the temperature of water

• This is one of many reasons why rising ocean temperatures are so dangerous and concerning

Universal Solvent

• Ionic and Polar substances dissolve in water

Properties Summary: (WILL BE ON THE TEST)

• Low density solid

• Universal solvent

• High heat capacity

• Heat of vaporization

• Adhesion/cohesion

• Capillarity

• Surface tension

The Carbon Chemistry of Life

Carbon Chains

• Carbon atoms are the backbone of biochemistry

• Carbon atoms form the basis of the most complex molecules due to their ability to make 4 bonds, allowing for single, double, and triple bonds (as well as combinations of these bonds)

Functional Groups

• Commonly found in large molecules

• React in predictable ways

• Include amino (NH2), carboxyl (COOH), carbonyl (CO), hydroxyl (OH), peptide (CHON), phosphate (PO4)

Macromolecules

• Carbohydrates

• Lipids

• Nucleic Acids

• Proteins

Carbohydrates

• CHO - made up of carbon, hydrogen, and oxygen

• Monosaccharide - Disaccharide - Polysaccharide

Monosaccharides

• CHO 1:2:1

• Soluble (polar alcohols - OH)

• eg. glucose (C6H12O6), fructose

• Energy is readily available and easily transported

Disaccharides

• Condensation (aka dehydration) reaction occurs when two monosaccharides combine, creating a disaccharide and H2O

• Hydrolysis uses H2O to break disaccharides back down into monosaccharides

• Glycosidic bond

• Transportable energy in plants and animals

• eg. sucrose, maltose, lactose

Polysaccharides

• Enzymes that digest α linkages can’t hydrolyze β linkages

• The cellulose passes through the digestive tract as “insoluble fibre”

• Many herbivores, from cows to termites, have symbiotic relationships with microbes that have enzymes to digest cellulose

Polysaccharides - structural

• β-linkages have alternating orientation of monosaccharides

• examples:

  • cellulose: long fibrous strings for structural support in plant cell walls

  • chitin, embedded in proteins, forms arthropod exoskeletons and is used to make strong and flexible surgial thread

Polysaccharides - storage

• α gycosidic linkages have uniform orientation of monosaccharides

  • glycogen - glucose

• eg. organelles called leukoplasts store energy in plant roots as starch (amylose, amylopectin)

Summary - Carbohydrates

• Functions: energy transport and storage, structural support

• Structure: monosaccharides - polysaccharides

• eg. glucose, lactose, starch, glycose, cellulose

• Functional groups: hydroxyl, carbonyls (aldehydes and ketones) (CARBONYLS ONLY SOMETIMES)

• Gycosidic bonds

Lipids

• CHO(P)

• No monomers and no polymerization

• Nonpolar (hydrophobic)

Monoglycerides - Diglycerides - Triglycerides

• Glycerol

• Fatty acid(s)

• Ester bond

• Essential unsaturated fatty acids are not synthesized in the human body and must be supplied in the diet

  • eg. Omega-3 fatty acids

    • Omega-3 fatty acids have one of their carbon-carbon double bonds at the 3rd carbon atom at the end of their carbon chain

Fat Functions

• Store energy

• Insulate

• Cushioning

• Nerve impulse transmission

Phospholipids

• Form cell membranes

• Amphiphilic

  • polar head (hydrophilic)

  • nonpolar tail (hydrophobic)

Other Fats

• Messengers (hormones)

  • blood pressure

  • sexual characteristics

  • growth

• Protection

  • waxy layer on leaves and fruit prevents invaders from entering tissue, dehydration

Summary - Lipids

• Functions - energy storage, membranes, messengers

• Structure - straight chains (fatty acids) and rings

• eg. testosterone, cholesterol, beeswax

• Functional groups - carboxyl, hydroxyl

• Ester bonds

Nucleic Acids

• CHONP

• DNA - deoxyribonucleic acid

• RNA - ribonucleic acid

Nucleodies - monomers

Bonding

• Covalent bonds

• Phosphodiester bonds

• H- bonds

Proteins

• CHON(S)

• Amino acids (monomers) - dipeptide - polypeptide

Amino Acids

• R group

  • 1-20

  • eg. glycine, alanine

  • Polar, nonpolar, electrically charged

Dipeptides

• Polymerization (anabolic)

• Condensation (catabolic)

• Breaking apart (hydrolysis)

Protein Functions

• Enzymes - catalyze reactions

  • eg. lactase

• Antibodies - fight invaders

  • eg. viruses

• Hormones - chemical messengers

  • eg. insulin

• Hemoglobin - transports O2 in RBC

• Movement - actin, myosin, etc.

  • muscles, cilia, flagella

• Support - collagen, elastin, keratin

  • tendons, ligaments, hair, horns, nails, feathers, quills

• Nutrient Storage - albumin, amandin

  • amino acids for developing plant/animal embryos

Protein Organization

• Primary

  • sequence of amino acids coded by DNA (peptide bonds)

• Secondary

  • α helix and β sheet (H- between polar R’s)

• Tertiary

  • 3D shape is globular or fibrous (various bonds)

• Quaternary

  • 2 or more polypeptides join (becomes a functional protein)

Proteins Denature

• Nonfunctional

• Bonding in the tertiary structure is disturbed

• Caused by:

  • Temperature

  • pH

  • Salt concentration

Summary - Proteins

• Functions - transport, movement, messengers

• Structure - 20 different amino acids - polypeptides

• eg. enzymes, hemoglobin, anitbodies, hormones

• Functional groups - amine, carboxyl

• Bonds - peptide

EVERYTHING ABOVE THIS POINT IS ON THE UNIT ONE QUIZ

Cell Membranes

Types of Cells

• can be prokaryotic

  • eg. bacteria cells

• can be eukaryotic

  • eg. plant and animal cells

Eukaryotic Cells

• organelles are the cell parts

• the amount of each type of organelle varies by cell type

  • eg. muscle cells contain many mitochondria

  • eg. white blood cells contain many lysosomes

  • eg. pancreatic cells that make insulin contain a lot of rough ER

The Cell Membrane

Functions

• maintain cell shape

• allows some things to enter/exit (semi-/selectively permeable)

• commication with other cells

• show cell identity

Fluid Mosaic Model

• flexible

• made of many different parts

• phospholipid bilayer with protein embedded throughout

• molecules are attracted to each other but float freely

Phospholipids

• form a bilayer spontaneously

• hydrophilic heads associate with water inside and outside of the cell

• nonpolar tails form hydrophobic inner layer

Carbohydrates (part 2!!!)

• markers that identify the cell

• glycoproteins

  • “person specific” so the immune system can recognize “invaders”

    • eg. sometimes transplants are rejected because of these markers

• glycolipids

  • “tissue specific” so cells stop multiplying and stay put

    • eg. metastasized tumors ignore these markers

Cholesterol

• contributes to the fluidity of the membrane

• reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification

Globular Proteins

• receptors for communication

• transport substances in and out

• speed up reactions

• anchors cells and their parts

• two types

  • integral

    • embedded in protein

  • peripheral

    • attached to surface

Fibrous Proteins

• form a cytoskeleton to maintain cell shape

• shape is closely tied to function

Passive Transport

• small particles diffuse across a membrane from high concentration to low concentration until an equilibrium is reached

Osmosis

• the diffusion of water across a membrane

Simple Diffusion

• movement of molecules from an area of [high] to [low] across a membrane

• small molecules (O2, CO2)

• nonpolar molecules only (steroids, amino acids)

Facilitated Diffusion

• requires a specific protein channel

• moves down concentration gradient

• requires no energy

• large, polar molecules (glucose, fatty acids, amino acids)

• ions require channel proteins (K+, Cl-, Na+, H+)

Solutions

• solvent - substance that dissolves the solute (eg. water)

• solute - substance that dissolves in the solvent

Hypotonic

• lower concentration of solute than inside the cell

• in animal cells, this is dangerous - the cell may burst

• in plant cells, the cell membrane pushes against the cell wall

  • Turgor pressure increases = turgid (firm, healthy)

Hypertonic

• higher concentration of solute than inside the cell

• in animal cells, the cell shrinks and becomes flaccid

• in plant cells, the cell membrane tears away from the cell wall

  • Plasmolysis - rupture of the membrane occurs, killing the cell

Isotonic

• equal concentration of solute inside and outside of the cell

  • EQUILIBRIUM

Active Transport

• the movement of particles from an area of low concentration to an area of high concentration (against the concentration gradient)

• uses ATP (cell energy)

  • eg. a toxic substance outside of the cell will actively be pumped out

  • eg. micronutrients need to be brought into the cell no matter how low the concentration is

Carrier Proteins

• certain membrane proteins use ATP (cell energy) to change their shape, allowing particles to be taken in or out against natural diffusion

Endocytosis

• the cell membrane folds around a substance, bringing it into the cell

• this folded membrane becomes a vacuole

• two types

  • phagocytosis

    • cell “eating” - taking in solids

  • pinocytosis

    • cell “drinking” - taking in liquids

• receptor-mediated endocytosis

  • substances attach to membrane receptors

  • this causes the membrane to fold inward creating a coated vessicle

    • eg. LDL (cholesterol) uptake, glucagon, prolactin, insulin, GH, LH

      • these are all hormones

Exocytosis

• vacuoles containing wastes, to be removed or cell products (eg. proteins) for export

• the vacuole approaches the cell membrane, fuses with it, expelling the contents

Enzymes and Energy

Enzyme

• biological catalyst that speeds up a chemical reaction without being consumed in the reaction

Active Site

• a pocket or groove in an enzyme that binds to a substrate

Substrate

• a substance that is recognized by and binds to an enzyme

Anabolic Enzyme

• pulls molecules together

Catabolic Enzyme

• pulls molecules apart

Induced-Fit Hypothesis

Enzymes

• are somewhat flexible, changing shape to better accommodate a substrate

• bind to one or more substrates (enzyme - substrate complex)

• convert the substrate(s) into one or more products

• ready to be reused as soon as products leave the active site

• break down between 100 and 40 million molecules per second

Activation energy is lower when enzymes are present

• (the energy needed to start the reaction)

Cofactors and Coenzymes

• cofactors must bind to an enzyme for it to work

• cofactors include magnesium, manganese, iron, copper, zinc, calcium, cobalt

• coenzymes (NAD+, NADP+, and FAD derived from vitamins) act as electron carriers

Factors Affecting Enzyme Activity

Temperature

• enzymes @ low temperatures - inactive

• enzymes @ high temperatures - denatured

pH

• different enzymes have different levels of ideal pH

• too basic or too acidic for any given enzyme results in inactivity and denaturation

Concentration

• enzymes have a certain amount of “work” that they can do (some can break down 100 substrates per second, others can do 40 million)

Allosteric Regulation

• Competitive Inhibitors

  • interference by a molecule (inhibitor) binding to the active site and blocking the substrates

• Non-Competitive Inhibitors

  • a molecule bonds to another place on the enzyme causing a change in the shape of the active site