Molecular Biology

• study of molecular basis of biological activity in cells

• explain living processes in terms of involved chemical reactions

• gives better understanding of many processes

• ex. relationship between genes and proteins

Carbon

• builds life

• in all organic molecules (lots of compounds)

• 15th most common element

• nonpolar covalent bonds

• very strong and stable, more than other elements

• diverse

Organic Compounds

• has carbon

• found in living things

• 4 classes:

  • lipids

  • carbohydrates

  • proteins

  • nucleic acids

  • exceptions are carbon oxides, carbonates, and cyanide

Carbohydrates

• has carbon, hydrogen, and oxygen (C,H,O)

• ratio CH2O

• most sugars end in -ose

• monomer is monosaccharide

• 5C and 6C sugars form rings in solution

Lipids

• nonpolar

• mostly C, H in 1:2 ratio

• diverse in structure

• don't form polymers

• triglycerides, phospholipids, and steroids

• no particular monomer

• fats, waxes, oils

• energy storage, cushion, thermal insulation, hormones, cell membrane

• triglycerides, steroids, phospholipids

Proteins

• most functions

• large organic compounds made of amino acids

• many shapes and sizes

• have CHONS

• 50% of dry mass

• structure in enzymes

• polypeptides formed with bonds between amino acids

Nucleic Acids

• monomer: nucleotide

• contain CHONP

• DNA & RNA

• have nitrogenous base

Molecule bonds

• Carbon-4

• Nitrogen-3

• Oxygen-2

• Hydrogen-1

Steps to draw molecular structure

1. Draw carbon.

2. O or OH or N in amino acid.

3. Fill in H with correct number of bonds.

Alpha Glucose Drawing steps

1. 5 Carbons and 1 Oxygen in a hexagon

2. 6th carbon above 5th carbon

3. Draw OH starting from 1st carbon-down, down, up, down and one to right of 6th carbon

4. Fill in other hydrogen atoms

Beta Glucose drawing steps

1. 5 carbons and 1 oxygen in a hexagon

2. 6th carbon above 5th carbon

3. Draw OH starting from 1st carbon-up, down, up, down and one to right of 6th carbon

4. Fill in other hydrogen atoms

Ribose drawing steps

1. 4 Carbons and 1 Oxygen in a pentagon

2. Add carbon 5 pointing up on carbon 5

3. Add H2OH to carbon 5

4. Add OH to carbons 1, 2, and 3 pointing down

Saturated Fatty Acid drawing steps

1. draw 8 C in a chain

2. add carboxyl group to 1st C

3. add Hs to make 4 bonds per carbon

4. for unsaturated FA, make a bend between carbons 5 and 6 with double bonds

Amino Acid drawing steps

1. central C

2. carboxyl group

3. amino group on the left

4. R group below carbon

5. H above central carbon

Vitalism

• theory saying life (emergent property) is due to non-physical vital force that is different from chemical and physical forces

• organisms have an inner force or "psyche" (Aristotle)

• organic compounds in plants and animals made only with help of "vital principle"

Urea & Vitalism

• urea does not have a lot of potential and does not break down easily

• produced in liver with excess of amino acids

• in 1828, Wohler artificially synthesized urea, questioning need for vital force

• deduced that other compounds can also be synthesized

• today, urea is an artificial fertilizer

Metabolism

• sum of chemical reactions in an organism

• series of pathways catalyzed by enzymes where one molecule is transformed into another

Anabolism

• synthesis of complex molecules from simpler ones

• monomer → polymer

• dehydration (condensation) reaction

• ex. protein synthesis, photosynthesis, synthesis of complex carbs like starch

Catabolism

• breakdown of complex molecules into simpler molecules

• polymer → monomer

• hydrolysis reaction

• ex. digestion, cell respiration

Condensation Reaction (dehydration synthesis)

• a chemical reaction where two molecules combine

• water is released

Hydrolysis Reaction

• water is used to break down a polymer into monomers

Water Structure

• 2 H + 1 O

• polar covalent bond

• most electronegative

• 2 polar bonds in each molecule

Hydrogen Bond

• weak attraction between H atom of 1 molecule and slightly negative atom of a different molecule

• in water, O is negative and H is positive

• O end of one molecule is attracted to H end of another molecule, forming H bond

Thermal Property of Water

• high specific heat

• high heat of vaporization

• temperature stabilizer

• easier to melt than evaporate

• cooling mechanism

Specific Heat

• the amount of energy required to raise the temperature of 1 gram of a substance by 1 degree celsius

Heat of Vaporization

• the amount of energy required for the liquid at its boiling point to become a gas

Adhesion

• H bond between water and other polar molecules

• how water moves up plant

Cohesion

• H bonds between water molecules

Universal Solvent

• bond polarity lets water surround ions

• polar molecule solvent

• medium for cell reactions

• excellent medium for substance transport

Transport in Blood Plasma

• mostly water

• lets polar and semi-polar substances be dissolved and transported

• ex. salts, amino acids, glucose

• nonpolar substances need a different method

• ex. O needs hemoglobin, lipids need lipoproteins, and cholesterol use the monolayer

Other Properties of Water

• only substance naturally in all 3 states of matter

• liquid necessary for life

• transparent and colorless → underwater photosynthesis

• less dense in solid form

Methane

• byproduct of anaerobic respiration from prokaryotes

• CH4

• nonpolar

• very different from water

Sweat

• vaporization as thermoregulation

• high temperatures denature proteins

• hypothalamus controls sweating

• plants transpire more when they overheat

• dogs pant when they overheat

Watery Environment

• dissolves substances so organisms can digest them

• cytoplasm watery so it can dissolve stuff

• blood plasma is 95% water and 5% solute Glucose

• water soluble

• transport in blood plasma

Amino Acid

• have charges

  • • and - charges

• solubility based on R group

• all 20 are water soluble

• transport by blood

Fats

• large, nonpolar, not water soluble

• in lipoprotein complexes in water

Cholesterol

• hydrophobic

• inside lipoproteins with fats

Oxygen

• nonpolar, small, water soluble

• saturates water at low concentrations

• as temperature increases, solubility decreases

• blood needs hemoglobin to adhere to and transport oxygen

Sodium Chloride

• ionic compound easily dissolved in water

• Na+ and Cl- separate and transport in water

Monosaccharides Examples

• glucose

• fructose

• galactose

Disaccharides Examples

• sucrose

• lactose

• maltose

Polysaccharide Examples

• starch

• cellulose

• glycogen

Building Sugars

• uses dehydration synthesis

• makes glycosidic bond

Polysaccharide

• cost little energy to build

• easy to reverse (release energy)

Function

• energy storage

• starch (plants)

• glycogen (animals)

• structure

• cellulose (plants)

Starch

• energy storage in plants

• humans can digest

• alpha glucose monomers

• 2 types: amylose and amylopectin

Amylose

• straight chain

• water insoluble

• iodine stains it blue-black

• more difficult to digest

Amylopectin

• branched chain

• slightly soluble in water

• swells into gel in hot water

• iodine stains it red-brown

• easy to digest

Glycogen

• energy storage in animals

• stored in granules in liver and muscle cells

• easily converted into glucose if needed

• alpha glucose monomers

• more branched than amylopectin

Cellulose

• plant structure in cell wall

• beta glucose

• animals can't digest it because of the orientation of glucose bonds

• fiber

Differences in Fatty Acids

• 14-20 carbon atoms

• single bonds & 2 H atoms on C atoms or

• double bonds & less room for H atoms Triglycerides

• store energy

• adipose tissue or sunflower seed tissue

• capital E shape

• glycerol backbone & 3 fatty acids

• ester bonds between each fatty acid and glycerol

• nonpolar hydrocarbon chains

Saturated Fatty Acid

• no double bond

• animal fat

• solid at room temperature

• contributes to heart disease?

Unsaturated Fatty Acid

• double bonds

• plant, vegetable, and fish fats

• oil at room temperature

Monounsaturated Fatty Acid

• 1 double bond

Polyunsaturated Fatty Acid

• -2+ double bonds

Cis- fats

• common in nature

• H atoms missing from one side

• bend in molecule

• can't pack tightly

• liquid at room temperature

Trans Fats

• artificially produced

• H atoms missing from opposite sides

• linear molecule

• can pack tightly

• solid at room temperature

Phospholipid

• cell membranes

• glycerol backbone, 1 phosphate, 2 fatty acids

Steroids

• hormones

• typically 4 rings

Lipids and Energy Storage

• long-term energy storage in animal adipose tissue

• 2x as much energy in 1g of lipid than carb for cell respiration since lipids do not have oxygen

• less lipid mass to store energy

• 6x more efficient 1g glycogen and 2g water for osmotic balance

• poor heat conductor-shock absorber

Body Mass Index (BMI)

• nondiagnostic screening tool for weight issues

• mass (kg)/(height in m)^2

• does not account for other impacting factors such as whether the weight is fat or muscle

• charts and monograms are alternatives

BMI Ranges

• <18.5 = underweight

• 18.5-24.9 = normal

• 25.0-29.9 = overweight

• 30.0+ = obese

Amino Acid structure

• amino acid subunit bond to make polypeptides

• 20 different amino acids distinguished by R group

• same generalized structure

Types of amino acids

• polar

• nonpolar

• ionic

• cysteine

Proteins and Polypeptides

• various proteins arrange into different kinds of polypeptides

• many possible sequences

• instructions in DNA

• 3 base pairs for 1 amino acid

• base pair sequence controls polypeptide building during translation

Polypeptides

• some are single polypeptides ex. lysozyme in mucus and tears to break down bacteria cell walls

• some have 2+ linked strands ex integrin

• collagen has 3 structural proteins and 3 polypeptides

• hemoglobin has 4 polypeptides with heme group

• n amino acids → 20^n possible sequences

• not every protein

Fibrous Proteins

• long, narrow shape

• secondary structure, some quaternary structure

• insoluble in water

• many polypeptide chains

• ex. collagen and actin (muscle contractions)

Globular Proteins

• rounded 3D shape

• tertiary structure

• ex. hemoglobin and insulin

Proteome

• all proteins produced by cell, tissue, or organism

• process of gel electrophoresis to extract proteins from samples to see how they are made

• antibodies with fluorescent markers identify proteins

• vary between cells because of different functions and activities

• similarity within species, different within individuals due to different amino acid sequences

Denaturation

• 3D protein structure maintained by weak bonds between R groups of amino acids

• change protein conformation

• temporary or permanent

• factors are heat, pH, environmental change, radiation

Heat

• causes vibrations that temporarily or permanently break bonds

• proteins vary in heat tolerance

Extreme pH changes

• charges of R groups changes

• breaks or forms new bonds, altering protein structure

• exceptions like stomach enzyme pepsin

Central Dogma of Genetics

• DNA → transcription → RNA → translation → protein

• 3 bases code for 1 amino acid

Primary Structure

• amino acid order

• determine rest of structure

Secondary Structure

• made with hydrogen bonds between one amino acid's carboxyl group and another's amino group

• alpha helix and beta pleated sheet

Tertiary Structure

• polypeptide chains bend and fold because of R group interactions

• 3D Shape

4 rules:

• hydrophobic inside

• hydrophilic outside

• cysteines line up and form disulfide bond

• acidic and basic side chains pair up to form salt bridges

Quaternary Structure

• multiple polypeptide chains

• single protein

• not in all proteins

• non-protein substances in some

• ex. hemoglobin with heme group

Enzymes

• organic catalysts lowering activation energy

• let reactions happen at normal cell temperature

• just speeds them up

• proteins

• specific chape

• not used up

Substrate

• specific molecule acted on

Active site

• enzyme region where enzyme fits

Enzyme Action

• molecular motion and substrate collision in active site

• random movement

• when substrate binds to active site, enzyme changes shape because of R-group interactions

• enzymes can be denatured

Induced-fit model

• current model of enzyme action

Mechanism of Action

1. substrate surface contact active site

2. enzyme changes shape to accommodate substance

3. temporary enzyme-substrate complex

4. Ea lowers and substrate altered

5. new substrate product released

6. unchanged enzyme can react with other substances

Measuring reactions

• Ea can be determined through measuring reactants consumed or products produced

• use experimental design

Factors affecting enzyme activity

• heat and pH

• optimum range for each, then denaturation

Substrate Concentration

• with constant amount of enzyme, an increase would increase reaction rate

• plateau when all enzymes are working

Inhibition

• pH, substrate concentration, temperature affect Ea

• inhibitors slow it down

• competitive and noncompetitive

Competitive Inhibition

• competes for enzyme's active site

• similar structure to substrate

• fewer interactions, fewer reaction rate

• increased substrate concentration increases reaction rate

Competitive Inhibition in Action

• alcohol dehydrogenase-enzyme group breaking ethanol into acetate

• antabuse CI to ALDH

• ALDH buildup leads to hangover symptoms

• drinking deterrent

Non-Competitive Inhibition

• binds to allosteric site

• distorts enzyme's tertiary structure

• active site shape distorted and substrate can't bond

• increasing substrate concentration does NOT affect rate

Enzymes and Metabolism

• metabolism catalyzed by enzymes

• chemical changes are sequence of small changes

• chain or cycle of reactions

End-Product Inhibition

• type of allosteric inhibition

• prevents cell from wasting resources by making to much

• high quantities of end product slow enzyme

• assembly line reactions

• negative feedback

Immobilized Enzymes

• enzymes attached to another material to restrict movement

• widely used in industry

Advantages of Immobilized Enzymes

• easily separate product and enzyme

• easy recycle

• increase enzyme stability to temperature and pH changes

• substrates exposed to higher enzyme concentration, increasing reaction rate

Lactose-free Milk

• about 1/2 of the human population is lactose intolerant

• they don't make enough lactase

• can't digest lactose

• symptoms vary in severity

How are lactose-free products made?

• lactase converts lactose to glucose and galactose

• enzyme from yeast, purified and sold to manufacturing companies

• sold as an additive or make lactose-free products

• via immobilized enzymes

Benefits of lactose-free dairy

• lactose-intolerant people can consume dairy

• galactose and glucose are sweeter so less sugar is needed

• glucose and galactose are more soluble in ice cream than lactose which crystallizes → smoother ice cream

• bacteria ferment glucose and galactose more quickly so yogurt and cheese production is faster