Molecular Biology

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

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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

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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

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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

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Central Dogma of Genetics

• DNA → transcription → RNA → translation → protein
• 3 bases code for 1 amino acid

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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

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