Lecture 1 Flashcards
Chemical Bonds in Biological Systems
what organic molecules primarily make up the body?
oxygen (63%)
hydrogen (25.2%)
carbon (9.5%)
nitrogen (1.4%)
what is the information storage for life?
DNA
What compounds do all amino acids contain?
O,H,C,N
which amino acids contain sulphur?
cysteine and methionine
which amino acid contains selenium?
selenocysteine
how many bonds do each of the primary organic molecules contain?
Oxygen - 2 bonds Hydrogen - 1 bond Carbon - 4 bonds Nitrogen - 3 bonds also Sulfur - 2, but up to 6 Phosphorus - up to 5 bonds
what is a covalent bond?
a chemical bond that shares electron pairs between atoms with similar electronegative and the ability to fill their octet to become more stable
what is a non polar covalent bond?
a chemical bond formed between same atoms or atoms with similar electronegativity. The difference is usually less than 0.5
what is a polar covalent bond?
a chemical bond formed when the atoms of slightly different electronegativity share electrons usually between 0.5 and 1.9.
what is the driving force for chemical bonding between atoms
achieving the octet configuration
if a c containing molecule gains H atoms or loses O atoms what does it become, oxidized or reduced?
reduced
if a c containing molecule loses H atoms or gains O atoms what does it become, oxidized or reduced?
oxidized
in terms of considering the pKa value for a functional group, if the pH is lower than the pKa of the group, is the group protonated or deprotonated?
protonated, and deprotonated if the pH value is higher than pKa
what kind of molecule is water?
dipolar molecule
how can molecules be soluble in water?
they must have charged or polar groups that can interact with the partial positive and negative charges of water
what are polar groups called?
hydrophilic water soluble
what are non polar groups called?
hydrophobic non soluble
acid and alcohol form?
ester
acid and sulfhydryl form?
thioester
acid and amine form?
amide
phosphoric acid and alcohol form?
phosphoester
acid and acid form?
anhydride
what are the 5 common biochemistry reactions?
group transfer, cleavage, condensation, rearrangement, oxidation-reduction
what is a group transfer?
part of one molecule is transferred to another, glycolysis (phosphorylation of glucose)
what is cleavage?
a molecule is split into pieces, gluconeogenesis (hydrolysis of glucose-6-phosphate)
what is condensation?
molecules are joined and water is produced, protein synthesis (the formation of a peptide bond)
what is rearrangement?
bond structure changed forming a new molecule, gluconeogensis (conversion of glyceraldehyde 3-phosphate to dihroxyacetone phosphate)
oxidation-reduction?
electrons lost or gained, TCA cycle (oxidation of succinate to fumigate and of ethanol to acetaldehyde)
what type of biochemistry reaction do you have when you have the phosphorylation of glucose?
group transfer
what type of biochemistry reaction do you have when you have the hydrolysis of glucose-6-phosphate?
cleavage
what type of biochemistry reaction do you have when you have the formation of a peptide bond ?
condensation
what type of biochemistry reaction do you have when you have the conversion of glyceraldehyde 3-phosphate to dihroxyacetone phosphate?
rearrangement
what type of biochemistry reaction do you have when you have the oxidation of succinate to fumigate and of ethanol to acetaldehyde
oxidation-reduction
isomers that have the same molecular formula and connectivity but differ in the position of the atoms in space. They cannot be interconverted by rotation around a single bond?
stereoisomers
in terms of stereochemistry, a counterclockwise direction is?
S rotation
in terms of stereochemistry, a clockwise direction is?
R rotation
Stereoisomers that are mirror images of each other are?
enantiomers
Pairs of isomers that have opposite configurations at one or more chiral centers but are NOT mirror images are?
diastereomers
Two sugars that differ in configuration at only one chiral center are?
epimers
isomers that have the same formula and connectivity but differ in the position of the atoms in space (3-D orientation)
Stereoisomer
a molecule with the same molecular formula as another molecule, but with a different chemical structure (constitutional isomerism)
Isomer
Carboxyl’s have pKa values around 2-3. So, for physiological pH values of 7.2-7.3, the pH is greater than the pKa, so the carboxyl group will be deprotonated or protonated?
deprotonated
Amines have pKa values around 9-10. So for physiological pH values of 7.2-7.3, the pH is less than the pKa, so the amine group will be deprotonated or protonated?
protonated
