Fundamentals-1: Intro to Biochem

Oxygen, Hydrogen, Carbon, Nitrogen

• carboxyl
• amine
• hydroxyl
• thioester
• amido
• phosphoryl

Many medications are made to be copies with only a single change so that the shape of the molecule is the same as an organic molecule found in our bodies.

This is so that the natural barriers our body uses to reject non-self molecules do not reject the medication

Micromolecules turn into or are the precursors of macromolecules

• Nucleotide--> nucleic acids
• Amino Acid--> protein
• Carbohydrate--> Polysacchride
• Lipid--> membranes

In a condensation reaction the product of 2 molecules --> 1 big molecule and water.

condensation reactions form water as a product

• Ether +water
• amide+ water
• ester+ water

A reaction in which something needs water to break down into two small molecules.

The opposite of condensation reactions

hydrogen bonds are not a true bond becasue they are reversible.

• They are significant i secondary protein structure. The alpha and beta pleated sheets are stabalized by hydrogen bonds
• The strongest is the dipole- dipole bond. It is like when a water molecule binds to another water molecule + end to - charged ends. usually H-N, H-O or H-F
• Both molecules act as an H donor and an H acceptor allowing clusters to form

The more bounded together the more stable the structure/molecule.

The water is cohesive because of the hydrogen bonding

water by binding with hydrogen bonds

irreversible bonds consisting of a single bond, double bonds, and resonance structures.

Triple bonds do not occur in vivo

covalent bonds make up organic/carbon compounds

Electrostatic interactions--the +amino acid and (-)amino acid for a bridge

Hydrophobic interaction--occur in the core of a folded protein

Hydrogen bonds--water cohesivness, alpha and beta secondary structures of proteins

Reversible bonds maintain structure of large macromolecules

Adenosine triphosphate

it is the energy carrier for most biological reactions

it sheds energy by hydrolysis of the phosphate groups (losing a phosphate group).

product of glycolysis and oxcidative phosphorylation

high energy molecule

• Acytl-CoA
• critical molecule that enters the TCA cycle
• fatty acids and amino acids are broken down and metabolized into acytl-coA
• Pyruvate-->acytl-coA

An isomer is a compound that has the same molecular formula but differ in function

• The two groups of isomers are the
• 1. constitutional group-- these vary in the functional groups, the physical properties, the names, and the cemical properties
• 2. Sterioisomers--only differ in the way that they are oriented in space/their configuration. The naming, and functional groups are the same

• Diasteriomers--which include the cis-trans isomers
• Enantiomers- steroisomers whose molecules are nonsuperimposable mirror images of one another.
• Enantiomers also have identical chemical and physical properties of one another, but they have different polerimeter.
• Polerimeter means that they rotate plane polerized light in the oppostie direction of one another.

• Cellulose vs Starch
• Cellulose is trans
• Starch is Cis

The celulose is a beta linkage- rigid and have folds, it is the most abundant polysacchride and its very strong

Starch is an alpha linkage which is more flexable

they have minor conformational differences but they have very different reactivity

Cis--when the R group is on the same side of the double bond

Trans- when the R group is on the opposite side of the double bond

• Chiral- when the mirror image of the structure is not superimposable
• If the compound has 4 substituents that are not the same they are not superimposable--they are chiral. The carbons that have the elements/R groups attached are said to be the Chiral center

• Achiral- the mirror image is superimposable
• If a carbon has two molecules attached that are the same it will be achiral or superimposable

means that when two enantiomers mix there are 50% of L and 50% of D. They are optically active which means there is no net rotation of plane polerized light.

• When a drug molecule is chiral you do not need to give the racemic mixture because you do not know if the enantiomer is inactive or dangerous
• ex: thalidimide

stereoisomers that are not mirror images of each other

They have different physical and chemical properties of one another unlike the enantiomers

Have atleast 2 chiral centers

Binding sites on receptors are very specific.

because the sterioisomers are similar but differ in the formation and configuration in space if the molecule is chiral it is even more specific and will bind one of the sterioisomers but not the other.

The receptor sites in the nose are chiral.

Sterioisomers R-Carvone and S-Carvone each smell very different.

• R-carvone is spearmint
• S-carvone is carway seed odor

Taxol is a biologically active molecule that contains stereogenic centers on the ring carbons.

Taxol is an anti cancer agen used to treat ovarian cancer and breast cancer

High H+ => low pH or acidosis this can be very dangerous because it can denature proteins, damage cells and tissues, and interferes with normal physiological functions

Low H+=> high pH or alkylosis which rarely causes problems

A solution of a weak acid/base and a salt that can resist canges in pH in the presence of small amounts of acids or bases

Ex: bicarbonate in blood