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

Draw carbon.
O or OH or N in amino acid.
Fill in H with correct number of bonds.

Alpha Glucose Drawing steps

5 Carbons and 1 Oxygen in a hexagon
6th carbon above 5th carbon
Draw OH starting from 1st carbon-down, down, up, down and one to right of 6th carbon
Fill in other hydrogen atoms

Beta Glucose drawing steps

5 carbons and 1 oxygen in a hexagon
6th carbon above 5th carbon
Draw OH starting from 1st carbon-up, down, up, down and one to right of 6th carbon
Fill in other hydrogen atoms

Ribose drawing steps

4 Carbons and 1 Oxygen in a pentagon
Add carbon 5 pointing up on carbon 5
Add H2OH to carbon 5
Add OH to carbons 1, 2, and 3 pointing down

Saturated Fatty Acid drawing steps

draw 8 C in a chain
add carboxyl group to 1st C
add Hs to make 4 bonds per carbon
for unsaturated FA, make a bend between carbons 5 and 6 with double bonds

Amino Acid drawing steps

central C
carboxyl group
amino group on the left
R group below carbon
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

substrate surface contact active site
enzyme changes shape to accommodate substance
temporary enzyme-substrate complex
Ea lowers and substrate altered
new substrate product released
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