Biology - Unit 1: Biochemistry

Biological Macromolecules

• a large molecule produced/needed by a living organism

• made of carbon, can form 4 bonds

Monomer

• small molecules that form a polymer

Polymer

• many monomers linked together

Hydrolysis

• reaction to break down compounds using water

• releases energy that the body can use

• e.g. digestion of macromolecules

Condensation (Dehydration Synthesis)

• reaction to make polymers

• releases water, uses energy

• e.g. synthesis of macromolecules

Carbohydrates

• energy source, structural support

• has a ring structure in aqueous solutions

Monosaccharides

• monomer

• classified by number of carbons

• major source of fuel

• glucose, fructose, galactose

Disaccharides

• 2 monosaccharides with a glycosidic linkage

• formed by a condensation reaction

• sucrose, lactose, maltose

Polysaccharides

• several 100s to 1000s of monosaccharides linked together

• 2 categories - storage & structural polysaccharides

Glycogen

• short term energy storage in animals

• depleted in one day without food

• α-1,4 & α-1,6 glycosidic linkages

• highly branched → easy to digest

Starch

• short term energy storage in plants

• 2 types - amylose & amylopectin

Amylose

• unbranched starch, 20-30% of starch

• α-1,4 linkages only, hard to digest, insoluble

• cannot digest - lacking enzyme

Amylopectin

• branched starch, 70% of starch

• α-1,4 & α-1,6 linkages, easier to digest, soluble

Chitin

• insect/crustacean exoskeletons

• cell wall of fungi

• β-glucose + N-acetyl groups

Cellulose

• plant cell walls

• unbranched, β-1,4 linkages with every other β-glucose flipped

• cannot digest - lack enzyme

Lipids

• hydrophobic due to many hydrocarbons

• no true monomers

Triglycerides

• energy storage, insulate vital organs, absorb vitamins

• important for cell membranes

• rich in C-H bonds → rich in energy

• 1g has 2x the energy stored in 1g of a polysaccharide

• in adipose cells

Adipose Cells

• specialized cells that store triglycerides

• forms adipose tissue which provides energy storage, insulation, and cushioning for vital organs

Triglyceride Structure

• glycerol + 3 fatty acid chains

• formed by condensation - releases 3 waters

• ester linkage

Fatty Acids

• hydrocarbons with a carboxyl group at one end

• ~16-18 carbons

Saturated Fats

• all C-C (single bonds)

• solid at room temp → rigid cell membrane → prevents sending of messages between cell membranes

• increases LDL → increases heart disease

Unsaturated Fats

• 1+ carbon-carbon double bond

Monounsaturated Fats

• one double bond

• lowers LDL and raises HDL → decreases heart disease

• olives, canola oil, nuts

Polyunsaturated Fats

• 2+ double bonds

• sunflower oil, fatty fish, seeds, nuts

Essential Fats

• omega 3 & 6, needed but cannot be produced by our own bodies

Cis Fats

• side groups on same side (natural)

Trans Fats

• made through hydrogenation

• side groups on different sides

• more solid

• increases LDL → transports cholesterol throughout entire body and clogs arteries

Phospholipids

• cell membrane (phospholipid bilayer)

• 2 fatty acid chains attached

• hydrophilic heads, hydrophobic tails

Phospholipid Bilayer

• semi-permeable

• has proteins and channels embedded within

Steroids

• 4 fused carbon rings

• functional groups attached will vary

Cholesterol

• steroid with hydroxyl functional group

• in animal cell membranes

• produces hormones and controls membrane fluidity

• as T increases, membrane becomes fluid, cholesterol increases to increase rigidity (and vice versa, cholesterol decreases to increase fluidity)

Waxes

• diverse, long carbon chains

• solid at room temp

• plants - prevent water loss (e.g. waxy cuticle)

• animals - prevent entering of water (waterproofing)

Proteins

• stores iron in safe form, transport molecules, receptors, antibody proteins

• makes up more than 50% of dry weight in most cells

Collagen

• 40% of all proteins in body

• 3 helical polypeptides coiled together

• strengthens connective tissue in skin, bones, ligaments, tendons

Amino Acids

• has a central carbon atom bonded to a hydrogen

• amino group, carboxyl group, side chain

• side chain (R-group) determines properties of polypeptide

Polypeptides

• chain of amino acids linked by peptide bonds

• formed through condensation reactions

Backbone

• chain of N’s and C’s in the middle of a polypeptide

N-terminus

• amino terminus, end of polypeptide with amino group

C-terminus

• carboxyl terminus, end of polypeptide with carboxyl group

Primary Structure

• polypeptide, linear amino acid chain

Secondary Structure

• some folds due to hydrogen bonding

Alpha-Helix

• helical structure formed by H-bonds in every 4 amino acids (carboxyl to amino)

Beta-Pleated Sheet

• polypeptide(s) bonded by H-bonds to form fan-like shape

Tertiary Structure

• weak interactions between R-groups

• disulfide bonds (two cysteines)

• H bonds

• electrostatic attraction

• hydrophobic/hydrophilic

Keratin

• protein in hair

• many disulfide bonds → curly

• few disulfide bonds → straight

Quaternary Structure

• 2 or more polypeptides bond together to form a functional protein

• optional, depends on protein

Sickle Cell Anemia

• mutation in 6th amino acid from Glu to Val

• sickle-shaped RBCs

Denaturation

• protein unravels from bonds breaking → lack of structure → non-functional protein

• unfavourable conditions - temperature, pH, salinity

• increased heat → increased collisions → more bonds broken

DNA

• encodes instructions to make proteins

• monomer: nucleotide

RNA

• intermediate messenger for protein synthesis

• monomer: ribonucleotide

Nucleotide

• 1’C from deoxyribose to nitrogenous base, 5’C to oxygen on phosphate

Phosphodiester Bonds

• links two nucleotides from 5’ to 3’

Deoxyribose

• pentose sugar in DNA, missing a oxygen atom on 2’C

Ribose

• pentose sugar in RNA

Genes to Proteins

• enzymes copy genes and make mRNA

• mRNA travels to ribosomes

• ribosomes read RNA and make proteins

Enzymes

• catalyses reaction, lowers activation energy

• enzymes are proteins

• have an optimum temperature and pH

• increasing concentration of substrate/enzyme until saturation point increases reaction rate

Activation Energy

• the amount of energy needed in the reactants for a reaction to proceed

Substrate-Enzyme Complex

• enzyme bonded to substrate

Active Site

• where substrates bind to for the reaction to occur

Competitive Inhibitor Molecule

• competes against substrate to bind to active site

Allosteric Inhibitor Molecule

• binds to allosteric site, changes shape of active site → no reaction

Allosteric Site

• site on an enzyme where certain molecules can bind to to regulate an enzyme’s activity

Cell Membrane

• transports raw material and manufactured products into membrane

• transports waste out of membrane

• prevents unwanted material from entering (e.g. viruses)

• facilitates cell communication through receptor proteins

Fluid Mosaic Model

• the current model of the phospholipid bilayer

• fluid - proteins and cholesterol can move freely, phospholipids can drift sideways

• mosaic - random positioning of macromolecules (proteins, etc.)

Peripheral Proteins

• on the “outside”, no contact with hydrophobic core

• anchors membrane to cytoskeleton

Integral Proteins

• embedded in bilayer, has contact with hydrophobic core

• receptor or transport proteins

Glycoprotein

• type of receptor protein

• has a carbohydrate chain attached to it

• allows signal molecules (e.g. hormones) to bind

• cell recognition (acts as ID tag) & immune responses

Glycolipid

• carbohydrate chain on a phospholipid

• stabilize membrane

• cell recognition and immune response

Adenine Vs. Guanine

• Guanine - 1 carbonyl

• Adenine - no carbonyls

Cytosine vs. Thymine vs. Uracil

• cytosine - 1 carbonyl

• thymine - methyl group

• uracil - 2 carbonyls & no methyl

Prokaryotes

• no nucleus

• unicellular

• circular DNA

Eukaryotes

• has a nucleus

• unicellular/multicellular

• linear DNA

Nucleus

• holds DNA

• nuclear pores - allows mRNA to exit and travel to ribosomes

Nucleolus

• produces ribosomes

• small, spherical structure in the nucleus

Cytosol

• jelly-like material that fills space between organelles

Cytoplasm

• cytosol + organelles (but excluding nucleus)

Mitochondria

• produces ATP using glucose through cellular respiration

• many folds → increase surface area

• more active → more mitochondria in a cell

Rough Endoplasmic Reticulum

• produces and transports proteins

• has ribosomes (gives rough appearance)

Smooth Endoplasmic Reticulum

• produces and transports lipids

Golgi Apparatus

• processes and packages lipids and proteins from ER into vesicles

• vesicles are to be transported out of the cell

Vacuoles

• small bubble filled with liquid

• stores food and water, expels waste, maintains pressure in the cell

Ribosomes

• makes proteins

Centrosome

• 2 centrioles, for cell division

Cell Wall

• rigid structure made of cellulose

• provides structure and protection

Central Vacuole

• stores food and water, expels waste, maintains pressure

Chloroplasts

• has chlorophyll, performs photosynthesis

Passive Transport

• transport without ATP

Simple Diffusion

• flow of solute from high to low concentration to achieve equilibrium

• short distances

• gases (e.g. O₂, CO₂), hydrophobic molecules, and small polar molecules (e.g. water)

• moving along a concentration gradient

Factors Affecting Simple Diffusion

• Temperature

• Size

• Distance

• Concentration Gradient

• Surface Area : Volume

• Polarity/Charge

Facilitated Diffusion

• uses specialized integral proteins to transport specific substances across

• moves along concentration gradient (high to low)

• for large, polar molecules and ions

Channel Proteins

• transports ions, typically are ion channels

• does not change shape

• opens/closes in response to hormones, electric charge, or pressure

Carrier Proteins

• transports large, polar molecules (e.g. glucose, amino acids)

• changes shape

• takes more time than channel proteins (needs time to reset)

Ligand-Binding Domains (LBD)

• site for a ligand to bind to open/close a transport protein

Ligand

• a molecule/atom/ion that binds to the LBD, causes the transport protein to open/close

Osmosis

• flow of solvent (usually water) from high to low concentration

• “water follows salt”

Isotonic Conditions

• solution and cell have equal solute and water concentration

• dynamic equilibrium

• animal cell - normal

• plant cell - flaccid/wilted (not enough turgor pressure)

Hypotonic Conditions

• solution has lower solute concentration than cell

• water flows into cell → dynamic equilibrium

• animal cell - lysed

• plant cell - turgor/normal

Hypertonic Conditions

• solution has higher solute concentration than cell

• water flows out of cell → dynamic equilibrium

• animal cell - shrivel/crenation 

• plant cell - plasmolysed (cell membrane shrinks away from cell wall due to water loss in cytosol and central vacuole)

Dynamic Equilibrium

• equal amounts of water moving in and out (particles are always moving)

Active Transport

• use of ATP to transport molecules against a concentration gradient

• 2 types - protein pumps, membrane assisted transport