Download Biochemistry Review

Biochemistry
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CHEMISTRY AND WATER
CHON (carbon, hydrogen, oxygen, nitrogen) make up 96% of living matter.
Trace elements are required by organisms in very small amounts. Ex: Fe in hemoglobin and I in thyroid gland.
Two covalent bonds hold a water molecule together.
Hydrogen bonds hold water molecules together.
Acid rain (Ph < 5.6) caused mostly by sulfur oxides, but also by nitrogen oxides that react with water in the air and form strong
acids.
The source of these oxides is from the burning of fossil fuels in factories and cars.
Acid rain hits fish and eggs when they are most vulnerable.
On land, acid rain washes away ions from the soil that are essential for plants.
Limestone maintains the pH of lakes.
Oceans don’t become acidic due to the salt soil and will not become acidic if salt ions are present to act as a buffer.
H-bonding: cohesion (water sticks itself), adhesion (water sticks to other stuff), capillary action (water travels
narrow tubes). Plants need water to flow from roots up the xylem.
High surface tension: “invisible film” due to hydrogen bonds. Ex: Jesus Christ lizard, water strider walks on water.
High Specific Heat: takes a lot of heat input or withdraw to change water’s temp. Ex: large bodies of water help
moderate land temperature.
Density (ICE): water expands at OoC and forms a crystal lattice. Insulates bodies of water from low temp. outside
Density (4o): at 4o holds most water/ most dense and allows for fall and spring turnover. Mix nutrients and oxygen in
lakes.
High Heat of Vaporization (evaporative cooling): takes a lot of heat to cause water to go from a liquid to a gas.
Sweating dissipates heat and cools you off. The hottest molecules leave as a gas and thus cool you down.
MEMORIZE THE FUNCTIONAL GROUP OF ORGANIC COMPOUNDS AT THE BINDER!!
CARBON
 Cells are between 70% to 95% water.
 The rest is mostly carbon.
 Miller and Urey recreated the conditions of the primordial earth. They put
water, CH4, NH3, and H2, But NO O2!! Then use an electrical discharge as
lighting. Miller and Urey recombined the molecules into a variety of organic
monomers. These monomers were the building blocks of the 4
macromolecules. This is the setting of the stage for the origin of life on earth.
 Adipose tissue: storage area for lipids/fats, lots of hydrocarbons.
 Structural isomers vary in terms of their covalent partners.
 Geometric isomers have the same covalent partners but a different spatial
arrangement around a double bond.
 Enantiomers are mirror images, can’t be superimposed on each other.
 Thalidomide: women used this as a sedative, but caused birth defects,
babies born without limbs.
MACROMOLECULES
 4 major classes of macromolecules/ biomolecules: (* polymer)
1.
Carbohydrates *
2.
Lipids
3.
Proteins *
4.
Nucleic acids *
 Polymer: long molecules with many repeating units, made up by monomers, linked together by covalent bonds, form
covalent bonds by dehydration/ dehydration reactions, water must be lost. Broken apart by hydrolysis reactions,
must use a water molecule.
 Large molecules can’t enter the cell.
 Hydrolysis is needed to break down these large molecules into smaller ones.
 These monomers then enter into the bloodstream, then finally into cells. Once inside the cells, the monomers get rebuilt into
new and different polymers needed for the cell to function.
 Carbohydrates form the major source of food for people around the world.
 They are cheapest, most easily obtainable, and most readily digested form of fuel.
 They serve to spare the burning of proteins.
 Sugars differ from one another 1) by the # of C,H,O (size) and 2) their spatial arrangement (hydroxyl groups) and carbonyl
groups (aldehydes and ketones).
 Glucose and most other sugars form rings in aqueous solutions.
 Glycosidic linkage: a covalent bond formed between 2 monosaccharides by a condensation/ dehydration reaction.
 Plants generally transport carbohydrates from their leaves to their roots in the form of sucrose (glucose+ fructose).
 Polysaccharides serve 2 roles: 1) storage and 2) structural.
 Starch: helical shape, little or no branching, store in plants’ roots, hydrolysis breaks it down to yield glucose
monomers/ energy. Glucose monomers are in the α linkage (down) position.
 Glycogen: helical shape, extensive branching, store in liver and muscle, hydrolysis breaks it down to yield glucose
monomers/ energy.
 Cellulose: most abundant organic compound on earth, found in the cell wall of plants. β linkage up position.
 Chitin: carbohydrate found in the exoskeleton of arthropods and used as surgical thread that decomposes after the
incision heals.
 Roles of carbohydrates
Ex of molecules
Storage
Starch and glycogen
Provide structure
Chitin and cellulose
Energy
Glucose
Transport
Glucose (animal) and sucrose (plant)
 Lipids are not polymer, they are smaller than the other macromolecules, they are hydrophobic, and they contain mostly
hydrocarbons.
 They are formed by dehydration reactions linking a glycerol backbone to 3 fatty acids chains (16-18 carbons).
 The head region near the glycerol contains a carboxyl.
 The tail region contains nonpolar C-H bonds.
 Saturated fats: single bonds, solid at room temperature, animal fats, converted into cholesterol and may develop
atherosclerosis.
 Unsaturated fats: one or more double bonds, mostly from plants, fish, and are liquid at room temperature, like olive
oil, hydrocarbon tails not allowing the molecules to pack closely together.
 Lipids and fossil fuels yield lots of energy when they are broken down/ burned.
 Get vegetable oils from the seeds of plants.
 Mammals store fats in adipose tissue that can shrink and swell as fat is deposited and withdrawn from storage.
 Mammals also store fat around vital organs to cushion the organs and beneath the skin to insulate the body.
 Phospholipids: similar to fats but only have 2 fatty acids, not 3. The head region contains phosphate and is negative
charged.
 The head is hydrophilic and the tail is hydrophobic.
 Micelle: when you place phospholipids into water they assemble into a cluster, helps to shield the hydrophobic tails.
 At the surface of a cell phospholipids are arranged into a bilayer providing a boundary between the cell and its external
environment.
 Steroids: lipids that have carbon skeletons with 4 fused ring. Ex: cholesterol
 Cholesterol: comes from animal cell membranes, it is necessary in the body in small amounts to build other steroids
such as the sex hormones like testosterone and progesterone.
 Types of Proteins
Function
Ex:
Structural
Support
Collage-tendons and ligaments
Keratin- hair, horns, feathers
Storage
Amino acid
Albumin- egg white
Transport protein
Transport other substances
Hemoglobin transports oxygen
Hormonal (not all hormones are proteins) coordinate of other substances
insulin to regulate blood sugar
Contractile
movements
Actin & myosin- move muscles
Cilia & flagella propel cells
Defense
protects against disease
antibodies
Enzymes
accelerate chemical reaction
digestive enzymes
Receptor
chemical stimuli
nerve cell detects chemical
Signals from other nerve cells
 Each protein/ polypeptide has a unique 3-D shape or Conformation
and is constructed from 20 different amino acids.
 Amino acids are grouped according to their side chains called R-group
(nonpolar, polar, acidic, basic)
 Amino acids contain an amine group and a carboxyl group.
 Covalent peptide bonds hold amino acids together.
 Peptide bonds form when an enzyme joins 2 amino acids by a
condensation/ dehydration reaction, linking a carboxyl to an amino
group.
 10 structures: linking of amino acids in a chain by covalent peptide
bonds.
 20 structures: 1) α-helix is formed when weak H- bonds from many times between the oxygen on the carboxyl group
and H on the amino group. Ex: keratin in hair. 2) β-pleated sheets form when 2 regions of a polypeptide chain lie
parallel to each other and form H- bonds. Ex: silk.
 30 structures: when all the R groups of the amino acids come into play causing several bonds to occur: hydrophobic/
nonplar side chains cluster at the core away from water, Vander Waals reinforce the hydrophobic interactions, Hbonds form between eh polar side chains to due to polar molecules having partial charges, ionic bonds from between
the + and – charged side chains, and disulfide bridges form where 2 cysteine amino acids that have a –SH side chain
are brought together.
 40 structures: 2 or more polypeptides (tertiary) come together to form a functional protein. The folding occurs with
the aid of chaperone proteins, help to fold the proteins into their correct 3-D conformation.
ENZYMES
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Metabolism: sum of all chemical reactions in the body.
Catabolic: pathways release energy by breaking down molecules.
Anabolic: pathways require energy to build complex molecules.
Kinetic energy: energy of motion. Ex: contracting leg muscles push a bike forward.
Potential energy: stored energy. Ex: chemical energy within food molecules not yet eaten.
Spontaneous reaction= -∆G, low ∆H, and high ∆S or both.
Enzyme + substrate  ES complex product + enzyme.
Cofactors: inorganic molecules that bind to the active site of an enzyme and are needed for that particular enzyme to
function. Ex: Cu, Fe,
 Coenzyme: organic molecules that bind to the active site of an enzyme. Ex: vitamins.
 Competitive inhibitors: molecules that resemble the substrate and compete for admission to the active site of the
enzyme, it is reversible.
 Non-competitive inhibitors/ allosteric inhibitors: do not bind to an enzyme’s active site, but another part of the
enzyme by altering the shape of the enzyme.