Chapter 2: Molecular Biology

Molecular Biology: explains living processes in terms of chem substances involved

- Relationship bw genes + proteins →
Nucleic acids: comprise DNA + RNA
- Chemicals used to make genes
Proteins: varied in structure, carry out many tasks within cell
- Ctrl chem reactions of cells, act as enzymes

Synthesis of Urea
UREA: organic compound, discovered in human urine in 18th century, structure →
- Nitrogen-containing compound - produced when excess of amino acids in body as means of excreting nitrogen from
amino acids
- Produced in liver, transported by blood stream to kidneys where it is filtered out and passes out of body in urine
- According to the theory of vitalism it was predicted that urea could only be made in living organisms because it was an
organic compound, so a vital force was needed

Vitalism: theory, origin + phenomena of life due to vital principle, which is diff from purely chemical/physical forces
- 1828: Ger chemist artificially synthesized urea (compound in urine) - 1st organic compound to be synthesized artificially
- using silver isocyanate and ammonium chloride
- No vital principle been involved in synthesis
- Deduction: if urea had been synthesized w/o vital principle, other organic compounds could be too → evidence
against theory of vitalism
- Still cant make hemoglobin - need ribosomes, etc

Carbon Compounds
Carbon atoms: can form 4 bonds allowing diversity of compounds to exist
- Used to make many diff molecules
- Given living organisms limitless possibilities for chem composition + activities of cells

Properties
- Form covalent bonds w other atoms: formed when 2 adjacent atoms share pair of electrons, one electron contributed by
ea atom
- Strongest type of bond bw atoms so stable molecules based on carbon can be produced
- Can form up to 4 covalent bonds → more than most other atoms → molecules containing carbon can have complex
structures
- Bonds can be w other carbon atoms to make rings/chains of any length
- Bonds can also be w other elements (hydrogen, oxygen, nitrogen, phosphorus)
- Can bond w 1 other element OR can bond to 1+ element
- 4 bonds can all be single covalent bonds OR can be 2 single + 1 double covalent bond

Classifying Carbon Compounds - Biochemical Macromolecules

Living organisms use 4 main classes of carbon compound w diff properties + diff purposes:

1.Carbohydrates Composed of CARBON + HYDROGEN + OXYGEN

- 2 hydrogen atoms to 1 oxygen

2. Lipids Broad class of molecules, insoluble in water

 - Ex, steroids, waxes, fatty acids, triglycerides (fats if solid @ room temp, oils if liquid @ room
temp)

3. Proteins Composed of 1+ chains of amino acids

- All amino acids in these chains contain elements of CARBON + HYDROGEN + OXYGEN +
NITROGEN (also sulphur)

4. Nucleic Acids Chains of subunits called nucleotides - contain CARBON + HYDROGEN + OXYGEN + NITROGEN +
PHOSPHORUS
- 2 types of nucleic acid:
- Ribonucleic acid (RNA)
- Deoxyribonucleic acid (DNA)

Organic: contains CARBON + HYDROGEN atoms TOGETHER

Metabolism
Metabolism: web of all enzyme catalysed reactions in cell/organism, sum of all reactions that occur in organism
- All living organisms carry out lrg # of diff chem reactions which are catalysed by ENZYMES
- Most happen in cytoplasm of cells but some are extracellular (reactions used to digest food in small intestine)
- Consists of pathways by which one type of molecule is transformed into another, in series of small steps
- Chains of reactions, cycles
- Divided into two parts: ANABOLISM + CATABOLISM
Intracellular - inside cell
Extracellular - outside cell

Polymer: large units made up of smaller subunits

Monomer: subunits linked together to form polymers by DEHYDRATION SYNTHESIS / CONDENSATION
REACTIONS

Anabolism
Condensation: join 2 molecules by removal of water molecule
MONOMER + MONOMER → POLYMER + WATER
Define: SYNTHESIS of complex molecules from simpler molecules incl formation of MACROMOLECULES from
MONOMERS by condensation reactions
- Reactions that build up larger molecules from smaller ones
- REQUIRE ENERGY, supplied in form of ATP

Examples:
- Protein synthesis w ribosomes
- DNA synthesis during replication
- Photosynthesis (production of glucose from CO2 + H2O
- Synthesis of complex carbs (Starch, cellulose, glycogen)

Catabolism
Hydrolysis: uses water molecule to break apart molecules
POLYMER + WATER → MONOMER + MONOMER
Define: breakdown of complex molecules into simpler molecules incl hydrolysis of MACROMOLECULES into MONOMERS
- Part of metabolism where larger molecules broken down into smaller ones
- RELEASE ENERGY, energy captured in form of ATP which is used in cell

Examples:
 - Digestion of food
- Cell respiration → glucose/lipids oxidized to CO2 + H2O
- Digestion of complex carbon compounds in dead organic matter by decomposers

Functional Groups ⇒where reactions occur, reactive

1. Hydroxyl OH - found in alcohols
2. Carboxyl COOH/COO- - found in acids
3. Amine NH/NH2/NH3+
4. Sulfhydryl group SH
5. Phosphate PO4-3
6. Carbonyl C=O or C=OH

Bonding Capacity: oxidation number (or number of bonds that an atom can form with
neighbouring atoms or the ionic charge)
C-4 O-2 N – 3 or 5
H-1 S – 2 or 6 P – 5 (in phosphate)

2.2 Water
Hydrogen Bonding in Water
Water molecules are polar covalent, hydrogen bonds form bw them
- Water molecule formed by covalent bonds bw oxygen atom + 2 hydrogen atoms
- Bond bw hydrogen + oxygen involves unequal sharing of electrons → POLAR COVALENT BOND
- Nucleus of oxygen atom more attractive to electrons than nuclei of hydrogen atoms
- Bc of unequal sharing of electrons in water molecules, hydrogen atoms have partial positive charge + oxygen has
partial negative charge
- Bc water molecules BENT → 2 hydrogen atoms are on same side of molecule + form on pole and oxygen forms
opposite pole - DIPOLAR
- Oxygen has high electronegativity
- Strong pull on electrons
- Hydrogen had low electronegativity
- Weak pull on electrons
- Positively charged particles (positive ions) + negatively charged particles (negative ions) attract each other and form
ionic bond
- Water molecules have only PARTIAL CHARGES so attraction is less but still enough to have significant effects
- Attraction bw water molecules is HYDROGEN BOND → intermolecular force, force that forms when
hydrogen atom in one polar molecule is attracted to slightly negative atom of another polar covalent
molecule
- Hydrogen bond weak force → water molecules small, so many of them per unit volume of water + large
number of hydrogen bonds

Properties of Water
- Odourless, Colourless, Liquid @ rm temp, Polar covalent
- Function: transport of nutrients + waste / lubricants + cushions joints
Hydrogen bonding + polarity explain properties of water
Cohesive Cohesion: binding together of 2 molecules of same type (2 water molecules)
Properties
Water molecules COHESIVE: They cohere→ stick to ea other, due to hydrogen bonding
Property useful 4 water transport in plants
- Water sucked through XYLEM VESSELS at low pressure
- Method only work if water molecules not separated by suction forces
- Due to HB, this rarely happens + water can be pulled up to top of trees

Surface Many hydrogen bonds of water molecules together allow it to have higher stronger surface tension
Tension

Adhesive Adhesion: HB form bw water + other polar molecules, causing water to stick to them
Properties
Property useful in leaves, water adheres to cellulose molecules in cell walls
- If water evaporates from cells walls + is lost from leaf via network of air spaces, adhesive forces cause
water to be drawn out of nearest xylem vessel
- Keeps walls moist so they can absorb CO2 needed 4 photosynthesis

Opposite: HYDROPHOBIC - minimizes contact w non-polar substances

Thermal High specific heat capacity: hydrogen bonds restrict motion of water molecules + increases in temp of water
Properties require HB to be broken
- Energy needed to do this
- Result: amount of energy needed to raise temp of water is large
- To cool down: water must lose large amounts of energy
- Water’s temp remains stable in comparison to air/land → thermally stable habitat 4 aquatic
organisms

High latent heat of vaporization: when molecule evaporates, it separates from other molecules in liquid and
becomes VAPOUR MOLECULE. Heat needed to do this is LATENT HEAT OF VAPORIZATION
- Evaporation has cooling effect: Lot of heat needed to evaporate water → HB have to be broken →
make it good evaporative coolant → sweating , use of water as coolant

High boiling point: boiling point - highest temp can reach in liquid state
- Water boiling point high
- Water liquid over broad range of temp (0-100) → temp range found in most earth habitats

Solvent POLAR NATURE of water → forms shells around charged + polar molecules
Properties - Prevent them from clumping together + keeping in solution

- Polar substances that dissolve in water: HYDROPHILIC

- Interactions bw opposite charges
- Non-polar substances that don’t dissolve are: HYDROPHOBIC
- Hydrophobic interactions result from cohesion

Water forms hydrogen bonds w POLAR MOLECULES

- Partially negative oxygen pole attract to positively charged ions + partially positive hydrogen pole
attract to negatively charged ions → both dissolve

Example: cytoplasm, complex mixture of dissolved substances in which metabolism occurs

Density - Solid form less dense than liquid

 - Molecules spread apart in CRYSTAL LATTICE
- Increases space bw molecules + reduces density

Hydrophilic + Hydrophobic
Hydrophilic: substances that are chemically attracted to water, all substances that dissolve in water incl polar molecules
(glucose) + particles w positive/negative charge (sodium, chloride ions), also substances that water adheres to (cellulose)

Hydrophobic: substances insoluble in water although they dissolved in other solvents such as propanone (acetone)
- Molecules hydrophobic if they don’t have negative/positive charged + are nonpolar
- All lipids + fats/oils

If nonpolar molecule surrounded by water molecules, HB form bw water molecules but not bw nonpolar molecule + water
molecules
- If 2 nonpolar molecules surrounded by water molecules + random movement bring them together → behave as
though they are attracted to ea other
- Slight attraction bw nonpolar molecules, but if they’re in contact w ea other, more HB bonds can form bw water
molecules
- Water molecules more attracted to ea other than to nonpolar → nonpolar molecules tend to join together in water
to form larger groups

Hydrophobic interactions: forces that cause nonpolar molecules to join together into groups in water

2.3: Carbohydrates + Lipids

Carbs
- Most important/abundant energy storage molecules (end w -ose)
- Uses:
- Main source of energy - SHORT TERM
- Building material (exoskeleton)
- Cell surface recognition molecules (glycocalyx)

Structure
- Contain C:H:O in 1:2:1 ratio
- Isomers common
- Galactose, glucose, fructose all C6H12O6 but have diff atom arrangements, physical and chem properties
- Functional groups (site of chem rxns)
- CARBONYL
- HYDROXYL

Monosaccharides
MONOSACCHARIDE (glucose, fructose, ribose) monomers linked together by condensation reactions to form
DISACCHARIDES + POLYSACCHARIDE POLYMERS
- Monosaccharides - single simple sugar units/monomers
- Disaccharides: 2 monosaccharides linked together
- Maltose: 2 glucose molecules linked together
- Sucrose: glucose + fructose link
- Polysaccharides: many monosaccharides linked together
- Ex. starch, glycogen, cellulose
- Differentiated by
 - # of carbons in chain
- 3C - triose
- 5C - pentose
- 6C - hexose
- Carbonyl group (aldose/ketose)

Combine through CONDENSATION: loss of -OH from one molecule + -H from another, which form H2O. involves
combination of subunits and yields water
- Linking together monosaccharides to form disaccharides/polysaccharides is ANABOLIC PROCESS
- Energy had to be used
- ATP supplies energy to monosaccharides and this energy used when condensation reaction occurs

Alpha-Glucose vs Beta-Glucose

TWO POSSIBILITIES: → STEREOISOMERS (diff rotation of C1

atoms)
1. Alpha: OH @ C1 below C
2. Beta: OH @ C1 above C

L-Glucose vs D-Glucose

- Living organisms only use D-glucose molecules

Glucose vs Galactose
Position of OH group on C4 diff → glucose OH is
down, galactose OH is up

Glucose vs Fructose
Glucose: Forms 6-SIDED RING
Fructose: Forms 5-SIDED RING

Condensation Reaction
GENERAL FORMULA ⇒MONO + MONO → DISACCH + WATER
Examples
1. Glucose + glucose → maltose + water
2. Glucose + fructose → sucrose + water
3. Glucose + galactose → lactose + water
 Monomer 1 Monomer 2 Disaccharide Linkage Found in

α Glucose α Glucose MALTOSE α 1-4 Starch

Glucose Fructose SUCROSE α 1-2 Cane, Maple,

Beet, Table
Sugars

Glucose Galactose LACTOSE α 1-4 Milk

β Glucose β Glucose CELLOBIOSE β 1-4 Cellulose

Polysaccharides
All composed of glucose, but diff structures/functions → diff type of glucose + type of linkage bw glucose molecules
- Thousands of sugar monomers joined by glycosidic linkages
- Chains: straight/branched - easily modified

Storage

I. STARCH
- Polymer of alpha-D-glucose, w all glucose subunits in same orientation, giving
polymer helical shape
- In CHLOROPLASTS
- Two forms:
- Amylase: only 1,4 linkages, STRAIGHT CHAIN, unbranched
- Amylopectin: some 1,6 linkages so BRANCHED molecule
- Used by plants to STORE GLUCOSE in INSOLUBLE FORM that doesn’t cause
osmotic problems
- By making molecule branched it is possible to load or unload glucose more rapidly as
there are more points on starch molecules to which glucose can be added or detached.

III. GLYCOGEN
- Branched polymer of alpha-D-glucose
- In CYTOPLASM
- Replenished daily 4 energy
- More 1,6 linkages - more branched than amylopectin, compact energy
- Used by mammals to STORE GLUCOSE IN LIVER + MUSCLE CELLS
- INSOLUBLE → large amounts stored whereas if glucose was stored, it would
cause water to enter cells by osmosis and there would be bursting danger

Structural

I. CELLULOSE
- Unbranched polymer of beta-D-glucose - alternating orientation, inverted 180*
 - Most abundant organic substance
- Orientation of glucose units alternates (up-down-up) → polymer STRAIGHT CHAIN rather than curved,
allows for H-bonding within + bw molecules
- Structures called cellulose microfibrils
- A lot of tensile strength withstands osmotic pressure + basis of plant cell walls
- Requires special enzymes to digest
- Humans: dietary roughage

IV. CHITIN
- 2nd most abundant organic molecule
- Similar to cellulose
- Contains N
- Hard exoskeleton of crustaceans
- Contact lenses, stitches

Lipids
Lipids: diverse group of carbon compounds
- Organic C-H
- Non-polar (C-H nonpolar bonds)
- Insoluble in water

I. Fats
- Long-term energy storage in plants + animals
- Cushions organs, can absorb shock
- Provides insulation (poor heat conductor)
- 1g fat = 9 cal
- 1g carb = 4 cal
- Contains:
- Fatty acids (Func group: COOH) → carboxyl group (COOH) + carbon chain
- Glycerol (Func group: OH) → 3 carbons + 3 hydroxyl groups (OH)
- Ester linkage

Vary in # of carbon atoms in hydrocarbon chain + in bonding of carbon atoms to ea other and to hydrogens
TRIGLYCERIDE (TAG) - one of principal groups of lipids → Triglyceride formed by condensation from 3 fatty acids +
1 glycerol
- Fats liquid @ body temp (37*C) but solid @ room temp (20*C)
- Oils liquid @ both body temp + room temp
- Each fatty acid linked to glycerol by CONDENSATION REACTION -- 3 water molecules produced
- Linkage formed bw each fatty acid + glycerol → ESTER BOND
- Bond formed when acid reacts w -OH group in alcohol -- reaction bw -COOH group on fatty acid + -OH on
glycerol
- Used as ENERGY STORES -- energy from them can be released by AEROBIC CELL RESPIRATION
- Don’t conduct heat well, used as heat insulators (blubber)
- Stored in adipose tissue (adipocytes/fat cells) *cyt-cell*
- Too many TAGs → atherosclerosis, heart disease, stroke

FATTY ACIDS
A. SATURATED: all of carbon atoms in chain connected by SINGLE COVALENT BONDS - # of hydrogen atoms bonded to
carbons can’t be increased
- Saturated w max HB
- Linear structure allows for Van Der Waals
- SOLIDS - butter

B. UNSATURATED: 1+ DOUBLE BONDS bw carbon atoms in chain, so more hydrogen could be bonded to carbons if double
bond replaced by single bond
- Causes bend in molecule
MONOUNSATURATED: only ONE DOUBLE BOND
POLYUNSATURATED: 2+ DOUBLE BONDS

TWO TYPES
CIS-FATTY ACIDS: Bend in hydrocarbon chain at double bond
- Hs on same side → causes molecule to bond
- Creates bend/kink in structure
- Prevents backing
- Makes triglycerides containing cis-unsaturated fatty acids less good @ packing together in regular arrays than saturated
fatty acids - LOWER MELTING POINT
- Triglycerides w cis usually LIQUID @ RM TEMP - OILS

TRANS-FATTY ACIDS: don’t have bend in hydrocarbon chain @ double bond - have HIGHER MELTING POINT - SOLID
@ RM TEMP
- Hs on opposite side
- Produced artificially by partial hydrogenation of veg/fish oils - done to produce SOLID FATS

Position of double bond

- Omega 3: 3rd bond from CH3
- Omega 6: 6th bond from CH3

Others
- EPA: heart health
- DHA: brain health
- Found only in cold water fish
- Many double bonds
II: PHOSPHOLIPIDS
- Cell membranes - BILAYER
- Hydrophilic head (polar)
- Func group: phosphate, charged
- Hydrophobic tails (non-polar)
- 2 uncharged fatty acids
- MICELLES: tiny spheres of phospholipids where tails are orientated towards
centre
- Form naturally if placed in water

III: STEROIDS
- structure : 4 linked carbon rings
- Cholesterol
- Essential but hazardous in large amounts
- Ex. making Vit D, bile salts (too much = gallstones), embedded in plasma membrane
- Sex hormones
- Estrogen, progesterone, testosterone
- gametes , sex traits, puberty, pregnancy
- When plaques clob blood vessels:
- Brain → stroke
- Heart → heart attack
- Other body parts → numbness, tissue dies

IV: WAXES
- Long-chain FA + alcohol/carbon-rings
- Firm, pliable
- Hydrophobic nature → waterproof
- Cuticle plants - cutin
- Bird feathers
- Honeycombs
2.4 Proteins
Amino Acids + Polypeptides
POLYPEPTIDES: Chains of amino acids that are made by linking together amino acids by condensation reactions.
- Happens on ribosomes thru TRANSLATION
- Main component of proteins, only component in many proteins (some have one, some have 2+)
- Diverse macromolecules
- Essential amino acids: body cannot synthesize de novo, must be consumed (12 for children, 8 for adults)

Condensation: involves amine group (-NH2) of one amino acid + carboxyl group (-COOH) of another
- Water eliminated
- New bond formed - PEPTIDE BOND

Dipeptide: molecule of 2 amino acids linked by peptide bond

Polypeptide: molecule of many amino acids linked by peptide bond
- Oligopeptides: chains of <20 amino acids
- Titin: largest polypeptide

Diversity of Amino Acids

- Amino acids linked together by ribosomes
- Structure: CARBON ATOM in centre bonded by AMINE GROUP, CARBOXYL GROUP, HYDROGEN ATOM +
carbon bonded to R group (diff in ea amino acid)
- 20 diff amino acids used by ribosomes to make polypeptides
- R groups give polypeptide character - allows living organisms to make/use wide range of proteins, chemically diverse
- Some proteins contain amino acids that are not part of 20
- Due to one of 20 being modified after polypeptide has been synthesized
- Ex. modification of collagen - structural protein used to provide tensile strength in tendons, ligaments, skin,
blood vessel walls
- Collagen polypeptides made by ribosomes contain proline at many positions, but at some o these
positions it is converted to hydroxyproline, which makes the collagen more stable

Polypeptide Diversity
- Ribosome can make peptide bonds bw any pair of amino acids, so any sequence of amino acids possible
- # of possible amino acid sequence calculated starting w dipeptides
- For polypeptide of n amino acids, there are 20^n possible sequences
- If add all possible sequence for amino acids, # is infinite

Classification of Amino Acids

Dependent of R group
1. Polar: OH, SH, NH2+, //O
2. Non-polar: CH2, CH3 -only CH bonds
3. Charged: -/+
Note: cysteine is only one that contains sulfhydryl fg

Hydrophilic: polar, charged

- Lysine, arginine, serine

Proline: r group bonds w amine group

Structures
PRIMARY
- Basic polypeptide sequence, linear
- Sulfhydryl in cysteine bonded w each other, bend linear polypeptide
SECONDARY
1. Alpha-helix
- Coil head together by H-bonds
- 3.6 aa per turn
2. Beta-sheet
- Strands lie adjacent to one another
- Held together by H-bonds
TERTIARY
- Helices + beta-sheets supercoil
- Interactions:
- Ionic bonds
- H-bonds
- Hydrophobic interactions
- Disulfide bridges (cys-cys), strongest stabilizers, covalent
QUATERNARY
- Polypeptide interacting w 1+ polypeptides
- Hemoglobin molecule

Denaturation
- Change in shape of protein, may unravel/breakdown
- high/low pH
- Heat
- Radiation
- Example: egg white, transparent → white

Genes + Polypeptides
- Living organisms only produce small fraction of amino acid sequences
- Typical cell produces polypeptides w 1000s of diff sequences, must store info needed to do this
- amino acid sequence of each polypeptide is stored in a coded form in the base sequence of a gene
- Use genetic code
- 3 bases of gene needed to code for ea amino acid in polypeptide
- Genes always longer, w extra base sequences at both ends + sometimes in middle
- OPEN READING FRAME: base sequence that codes for polypeptide
- Only occupy small proportion of total DNA of species

Proteins and Polypeptides

Proteins: single polypeptides, others composed of 2+ polypeptides linked together

Example Background

Lysozyme - Enzymes in nasal mucus/tears

- Kills some bacteria by digesting peptidoglycan in cell walls
- 1 pp

Integrin - Membrane protein

- Hydrophobic portion embedded in membrane
 - 2 polypeptides either adjacent or unfold/move apart when working
- Used to make connections bw structures inside + outside cell
- 2pp

Collagen - Structural protein in tendons, ligaments, skin, blood vessel walls

- High tensile strength w limited stretching
- 3pp

Hemoglobin - Associated w non-polypeptide structures

- 4 parts interacts to transport oxygen more effectively to tissues that need it than if they were
separate
- Binds oxygen in lungs + releases it in tissues w reduced oxygen concentration
- 4 pp

Rubisco - Enzyme w active site, catalyses photosynthesis reaction that fixes CO2 from atmosphere,
providing all carbon needed by living organisms to make sugars/other carbon compounds

Insulin - Hormone - carried dissolved in blood, binds to insulin receptors in membranes of body cells
- Cause cells to absorb glucose + lower blood glucose concentration

Immunoglobulins - Antibodies - bind to antigens on pathogens

- Immune sys produce many, allow specific immunity against many diff diseases

Rhodopsin - Pigment - makes rod cells on retina light sensitive

- Non-amino acid retinal absorbs photon of light - rod cell sends nerve impulse to brain

Spider silk - Structural protein - used to make webs to catch prey

- Lifelines, spiders suspend
- High tensile strength, becomes stronger when stretched, resist breakage

Protein Conformations
3-DIMENSIONAL STRUCTURE
- Conformation determined by AMINO ACID SEQUENCE of protein + constituent polypeptides
Fibrous proteins: (collagen) elongated, w repeating structure
Globular: intricate shape, includes parts helical/sheet-like

Amino acids added one by one, to form polypeptide

- Always added in same sequence to make particular polypeptide
- Globular: polypeptides fold up as they are made, to develop final conformation
- Stabilized by bonds bw R groups of AA that have been brought together by folding

Globular that are soluble in water, there are HYDROPHOBIC R GROUPS on outside of molecule + hydrophobic groups on
inside
- Globular membrane proteins: regions w hydrophobic R groups on outside of molecule, which are attracted to
hydrophobic centre of membrane
Fibrous proteins: AA sequence prevents folding up, ensures chaino of AA remains in elongated form

Protein Functions
Catalysis Thousands of dif enzymes to catalyse specific chem reactions within cell or outside

Muscle Actin + myosin together cause muscle contractions used in locomotion + transport around body
contraction
 Cytoskeletons Tubulin is subunit of microtubules that give animal cells their shape + pull on chromosomes during
mitosis

Tensile Fibrous proteins give tensile strength needed in skin, tendons, ligaments, blood vessel walls
strengthening

Blood clotting Plasma proteins act as clotting factors that cause blood to turn from liquid to gel in wounds

Transport of Proteins in blood help transport oxygen, carbon dioxide, iron, lipids
nutrients + gases

Cell adhesion Membrane proteins cause adjacent animal cells to stick to ea other within tissues

Membrane Membrane proteins used for facilitate diffusion + active transport + for electron transport during cell
transport respiration + photosynthesis

Hormones Insulin, FSH, LH proteins, chem diverse

Receptors Binding sites in membranes + cytoplasm for hormones, neurotransmitters, tastes + smells + for light in
eye, plants

Packing of DNA Histones associated w DNA in eukaryotes + help chromosomes to condense during mitosis

Immunity Most diverse, cells can make huge #s of diff antibodies

- Make up 50% body’s dry weight
- Last source of energy

Proteomes
Proteomes: all proteins produced by cell, tissue, organism
Genome: all genes of cell, tissue, organism

To find out how many different proteins are being produced, mixtures of proteins are extracted from a sample and are then
separated by gel electrophoresis. To identify whether or not a particular protein is present, antibodies to the protein that have
been linked to a fluorescent marker can be used. In the cell fluoresces, the protein is present.

Genome fixed, proteome variable → diff cells in organism make diff proteins
- Vary over time depending on cell’s activities
- Proteome reveals what is acc happening in organism, not what could happen
- Each individual has unique proteome
2.5 Enzymes
Function
- Bio catalysts - Lowering activation energy (Ea) needed to break
- Speed up rate of rxn w/o being consumed/altered bonds bw reactant molecules
- Reusable - add/remove protons
- Involved in every biochem process in body - twist/bend molecules
- Increase efficiency - Increase probability of molecules coming in close
- Rxns occur 10Bx faster proximity and reacting

-
Enz
yme
No
me
ncla
ture
- M
olec
ule
acted upon + suffix “ase” (hydrolytic)
- Examples:
- Amylase: breaks down starch
- Lactase: catalyzes lactose
- Dextrase: converts dextrose into lactic acid
- Peptidase: breaks peptide bonds
- Class: proteases: catalyze proteins
- Class: lipases: catalyze lipids
- Also end w in - trypsin, pepsin

How Enzymes Work

- Substrate: reactant
- Active site: where enzyme-catalyzed reaction occurs, has unique crevices, usually hydrophilic - has polarity/charge
- Due to molecular motion, substrates collide w + bind to active site of enzyme creating enzyme-substrate complex for
reaction to occur
- Products released

Collisions
- Dissolved particles can collide
- Smaller particles collide faster
- Effective collisions result in reactions

Lock and key model

- Enzymes specialized for particular type of reaction
- Substrate + active site much posses complementary shapes for binding to
occur

Induced-fit model
- Enzyme capable of changing shape slightly to lock in substrate (securely)
FACTORS THAT AFFECT ENZYME ACTIVITY
I. Temperature
- Kinetic energy → collisions
II. pH
- High concentration of Hydrogen
ions interfere with bonds,
structure of enzyme, change in
shape
III. Substrate concentration
- More collisions
- Reaches saturation point

Enzyme immobilization
- Attachment to surface such as glass
- Entrapment by membrane or gel
- Aggregation by bonding enzymes together
Use
- Medicine
- Agriculture
- Food industry

Competitive inhibitor
- Molecule w shape similar to substrate
may bind to active site
- Prevents enzyme action
- Reduces amount of product
- Poisons: cyanide, arsenic
- Drugs: kind that intoxicate you and king
that make you better, incl antiretrovirals
against HIV, anti-epileptic drugs and
insecticides
Non-competitive inhibitor
- Changes shape of enzyme so it can’t bind to substrate - binds to
ALLOSTERIC SITE, changes shape to fit enzyme
- Occupy diff site
 - Induced enzyme to change shape
- Prevents it from bonding w normal substrate but may/may not change affinity for substrate
- Enzyme can no longer catalyze rxns
- No competition bw substrate and inhibitor for active site

Allosteric regulation
- Enzyme regulated by effector molecule
- Effector binds to allosteric site to induce change in shape
- Allosteric activator: shape increase activity
- Allosteric inhibitors: shape decreases activity

Feedback Inhibition
- How body communicates w itself
- Method of controlling enzyme activity i.e. amount of product formed
- Product formed later in series used to bind allosteric site of enzyme early in series
- Used to maintain HOMEOSTASIS

Mutation of enzyme
- Phenylalanine hydroxylase - catalyzes phenylalanine to tyrosine
- Accumulation of Phe results in PKU, mental retardation, seizures
2.6 Structure of DNA + RNA
Nucleic Acids + Nucleotides
Nucleic acids DNA + RNA = polymers of nucleotides
Nucleic Acids: v large molecules, constructed by linking together
nucleotides to form polymer. Two types of nucleic acid: DNA + RNA.
Have 3 parts:
1. Sugar: five carbon atoms, PENTOSE SUGAR
2. Phosphate group: acidic, negatively-charged part of nucleic acids
3. Base: contains nitrogen, has either one/two rings of atoms in
structure

Base + phosphate linked by covalent bonds to pentose sugar

To link nucleotides together into chain/polymer, COVALENT BONDS formed bw phosphate of one nucleotide + pentose sugar
of next nucleotide
- Creates strong backbone for molecule of alternating sugar + phosphate group w base linked to ea sugar
4 diff bases in both DNA + RNA ⇒4 diff nucleotides
- 4 diff nucleotides linked together in any sequence, bc phosphate + sugar used to link them are same in every nucleotide
- Any base sequence is possible along DNA/RNA molecule → key to nucleic acids acting as store of genetic info →
base sequence is store of info and sugar phosphate backbone ensures that store is stable/secure

Differences bw DNA + RNA

DNA RNA

Sugar (names based on sugars) Deoxyribose - fewer oxygen atoms than Ribose
ribose - ONE LESS

# of Polymers 2 polymers of nucleotides 1 polymer of nucleotide

- Aka ‘strands’ - DOUBLE STRANDED - SINGLE STRANDED

# of Bases (4) 1. Adenine 1. Adenine

Purine: large → ADENINE + 2. Cytosine 2. Cystonine
GUANINE 3. Guanine 3. Guanine
4. Thymine 4. Uracil
Pyrimidines: small → CYTOSINE +
THYMINE
- Purines always pair with
pyrimidines

DNA Functions
- Direct growth + development of every living thing by means of chem code
- Controls production of proteins and other chem messengers
 - located inside nucleus, cannot leave - necessitates RNA
- DNA → RNA → Protein (Central Dogma)
- Hereditary molecule and basis of genetics
Proteins crucial to everything in body
- DNA controls everything in body thru production of proteins - thats it
- Proteins do all the work (mitosis, mood, pregnancy, puberty, appetite, vision, hemoglobin, addiction, hair/nails)

Structure of DNA
DNA is double helix made of 2 antiparallel strands of nucleotides linked by hydrogen bonding bw complementary base
pairs
- Ea strand consists of chain of nucleotides linked by COVALENT BONDS
- 2 strands parallel but run in opposite directions so they are ANTIPARALLEL
- 1 strand orientated in direction 5’ to 3’, other orientated in direction 3’ to 5’
- 2 strands wound together to form DOUBLE HELIX
- Strands held together by HYDROGEN BONDS bw nitrogenous bases
- ADENINE always paired w THYMINE
- GUANINE w CYSTONINE
- Complementary base pairing ⇒A+T complement ea other by forming base pairs, G+C complement ea other
by forming base pairs
Strands formed by Phosphodiester bonds
- 5’ carbon and 3’ carbon, 2 ester bonds
- Purines always pair w pyrimidines
- Purines: adenine + guanine
- Pyrimidines: thymine + cytosine
Hydrogen bonds
- A pairs w T (2 HB)
- C pairs w G (3 HB)

RNA FUNCTIONS
- Single-stranded
- Integral part of protein synthesis
- Transfers DNA msg outside of nuc
- Usually in cytoplasm
- DNA sequence - TTAACCGG
- RNA complementary sequence: AAUUGGCC

2.8 Cell Respiration

Release of energy by cell respiration
Cell respiration: controlled release of energy from organic compounds to produce ATP
- Organic compounds broken down to release energy - which used in cell
- Ex. energy released in muscle fibres by breaking down glucose into CO2 + H2O → energy used for muscle
contraction
- Humans: food is source of organic compounds broken down in cell respiration
- Carbs + lipids used, but amino acids from proteins used if eat more protein than needed
- Plants: use carbs/lipids made by photosynthesis
 - CR carried out using enzymes carefully/controlled so as much as possible of energy released retained in usable form
- Form: chem substance called ADENOSINE TRIPHOSPHATE (ATP)
- To make STP, phosphate group linked to ADESONINE DIPHOSPHATE (ADP)
- Energy required to carry out reaction → energy comes from breakdown of organic compounds
- ATP not transferred from cell to cell an all cells require continuous supply → reason for CR being essential
function of cell life

ATP Source of Energy

ATP from CR immediately avail as source of energy in cell
Cells require energy for 3 types of activity:
1. Synthesizing large molecules (DNA/RNA/proteins)
2. Pumping molecules/ions across membranes by active transport
3. Moving things around inside cell (chromosomes/vesicles) or in muscle cells the protein fibres that cause muscle
contraction
Energy for ^ supplied by ATP
- Advantage: energy immediately avail → released simply by splitting ATP into ADP + PHOSPHATE → ADP +
PHOSPHATE converted to ATP by CR

When energy from ATP used in cells, all converted to HEAT

- Heat energy useful to keep organism warm, but can’t be reused for cell activities and eventually lost to environment
- Reason for cells requiring continual source of ATP for cell activities

Anaerobic Respiration
Anaerobic cell respiration gives small yield of ATP from glucose
- Glucose broken down in ANAEROBIC CR w/o using any oxygen
- Yield of ATP small, but ATP produced quickly
Anaerobic useful for:
1. When short but rapid burst of ATP production needed
2. When oxygen supplies run out in respiring cells
3. In environments that are deficient in oxygen (ex, waterlogged soils)

Products: not the same in all organism

- Humans: glucose converted to LACTIC ACID (usually in dissolved form known as lactate
- yeast/plants: glucose converted to ETHANOL + CO2
Both LACTATE + ETHANOL toxic in excess → must be removed from cells that produce them, or produced in limited
quantities

Anaerobic Respiration in Humans

Lactate production in humans when anaerobic respiration used to maximize power of muscle contractions
 - Lungs + blood supply oxygen to most organs of body rapidly enough for aerobic respiration to be used, but sometimes
use anaerobic CR in muscles
- Reason: anaerobic respiration can supply ATP v rapidly for short period of time → used to max power of muscle
contractions
- Used during training/sport:
- Weight lifters
- Short-distance runners
- Long distance runners. Cyclists, rowers during sprint finish
- Involves production of lactate, so when being used to supply ATP, concentration of lactate in muscle increases
- Limit to concentration that body can tolerate - limits how much anaerobic respiration can be done
- Reason for short timescale over which power of muscle contractions can be maximized
- Only sprint for short distances
- After vigorous muscle contractions, lactate must be broken down → involves use of oxygen
- Can take several minutes for enough oxygen to be absorbed for all lactate to be broken down
- Demand for oxygen that builds up during period of anaerobic respiration = OXYGEN DEBT

Aerobic Respiration
Aerobic cell respiration requires oxygen + gives large yield of ATP from glucose
- If oxygen avail to cell, glucose can be more fully broken down to release greater quantity of energy than anaerobic cell
respiration
- Whereas yield of ATP only 2 molecules per glucose w anaerobic cell respiration, it’s more than thirty per glucose per
aerobic CR
Aerobic CR: involves series of chem reactions
- CO2 + H2O produced
- Most organisms - CO2 is waste product that has to be excreted, but water is often useful
- Humans: half a litre produced everyday
In EUKARYOTIC CELLS: most of reactions of aerobic cell respiration happen inside MITOCHONDRIA
2.9 Photosynthesis
What is Photosynthesis
Photosynthesis: production of carbon compounds in cells using light energy and simple inorganic substances (CO2 + H2O)
- Need complex carbon compounds to build structure of cells + carry out life processes
- Example of energy conversion → light energy converted into chem energy in carbon compounds
- Carbon compounds produced incl CARBS + PROTEINS + LIPIDS

Wavelengths of Light
Light made up of all wavelengths of electromagnetic radiation that eyes can detect → visible to us, other wavelengths are
invisible
- Spectrum of electromagnetic radiation from v short to v long wavelengths
- SHORTER WAVELENGTHS: x-rays/ultraviolet radiation have HIGH ENERGY
- LONGER WAVELENGTHS: infrared radiation/radio waves have LOWER ENERGY
- Visible light has wavelengths longer than ultraviolet + shorter than infrared
- Range of wavelengths of visible light: 400 - 700 nanometers

Sunlight mixture of diff wavelengths (see as diff colours, incl violet/blue/green/red)

- violet/blue shorter wavelengths
- Red longest

Wavelengths of light detected by eye are those used by plants in photosynthesis

- Reason: emitted by sun + penetrate Earth’s atmosphere in larger quantities than other wavelengths - abundant

Light Absorption by Chlorophyll

Chlorophyll absorbs red + blue light most effectively + reflects green light more than other colours
First stage in photosynthesis: ABSORPTION OF SUNLIGHT
- Involved chem substances PIGMENTS
- white/transparent subst doesn’t absorb visible light
- Pigments absorb light, appear coloured
- Pigments that absorb all the colours appear black, because they emit no light

Pigments that absorb some wavelengths of visible light but not others
- Ex. pigment in gentian flow absorbs all colours except blue → appears blue bc this part of sunlight reflected and can
pass into eye to be detected by cells in retina

Photosynthesizing organisms use range of pigments, but main photosynthetic pigment = chlorophyll
- Various forms of chlorophyll but all appear green
- Bc they absorb red + blue light effectively but intermediate green light less effectively
- Wavelengths of green light reflected
- Reason for main colour in plant ecosystems being green

Oxygen Production in Photosynthesis

Oxygen produced in photosynthesis from photolysis of water
Essential step of photosynthesis: splitting on molecules of water to release electrons needed in other stages

⇒PHOTOLYSIS
- Only happens in light
 - All of oxygen generated in photosynthesis comes from photolysis of water
- Oxygen is waste product + diffuses away

Effects of Photosynthesis on Earth

PROKARYOTES first to perform photosynthesis - 3 500 mya
- Joined later by algae + plants

Consequences:
- Rise in oxygen concentration of atmosphere → GREAT OXIDATION EVENT 2 400 mya
- 2% volume by 2 200 mya
- 2 200 mya: earth experience first glaciation, due to reduction in greenhouse effect
- Due to rise in oxygenation causing decrease in concentration of methane in atmosphere + photosynthesis
causing decrease in CO2 concentration
- Both methane + CO2 potent in greenhouse gases
- Increase in oxygen concentrations in oceans bw 2 400 and 2 220 mya caused oxidation of dissolved iron in water,
causing it to precipitate onto sea bed
- Distinctive rock formation produced called BANDED IRON FORMATION w layers of iron oxide alternating w
other minerals
- Oxygen concentration of atmosphere remained at 2% from 2 200 mya until 750-635 mya
- Significant rise to 20%
- Corresponds w period when many groups of multicellular organisms were evolving

Production of Carbs
Energy needed to produce carbs + other carbon compounds from CO2
- Plants convert CO2 + H2O into carbs by photosynthesis
𝑐𝑎𝑟𝑏𝑜𝑛 𝑑𝑖𝑜𝑥𝑖𝑑𝑒 + 𝑤𝑎𝑡𝑒𝑟 − −> 𝑐𝑎𝑟𝑏𝑜ℎ𝑦𝑑𝑟𝑎𝑡𝑒 + 𝑜𝑥𝑦𝑔𝑒𝑛
Energy REQUIRED → ENDOTHERMIC
- Reactions involving production of oxygen endothermic
- Reactions combining smaller molecules to make larger ones endothermic, molecules of carbs (glucose) much larger than
CO2 or H2O

Energy for conversion obtained by absorbing LIGHT

- Reason photosynthesis only occurring in light
- Energy absorbed from light doesn’t disappear -- converted to chem energy in carbs

Limiting Factors
Rate of photosynthesis affects by:
1. Temp
2. Light intensity
3. CO2 concentration
Limit rate if below optimal level
- Under any combination of light intensity, temp, CO2, only one limiting rate of photosynthesis → factor that’s
furthest from its optimum
- If factor changed to make closer to optimum, rate of photosynthesis increases, but changing other factors will
have no effect, not the limiting factor
- As limiting factor moved closer to optimum, point reached where this factor no longer the one that is furthest from its
optimum and another factor becomes limiting factor
- Ex. at night - light intensity limiting factor - when sun rises, light intensity increases - temp take over as limiting factor
- As temp increases during morning, CO2 concentration might be limiting factor