Biochem 250 lecture 3 and 4

what is water?

inorganic, transparent, tasteless, odorless, and colorless chemical substance

importance of water

1. macromolecular components assume shapes in response to water

2. most metabolic machinery operates in an aqueous environment

whats the structure of water

V-sha

properties of water

1. polarity

2. hydrogen bonding

3. water is a universal solvent

Polarity

covalent bond between oxygen and hydrogen atoms with bond angle of 104.5

what are the bonds in water

permanent dipole and hydrogen bond

what changes happen to water due to the hydrogen bond

1. a high melting point

2. a high specific heat

3. a high heat of vaporization

specific heat

amount of heat needed to raise the temperature of 1 gm of substance 1C

why is the heat of vaporization high

because the hydrogen bonds must be broken to change water from liquid to gas

water as a solvent for polar compounds

water can dissolve Polar compounds that ionize

water as a solvent for organic compounds

depends on their polarity and their ability to form hydrogen bonds with water.

water and hydrophobic molecules

non polar molecules are hydrophobic and non soluble in water

hydrophobic effect

the tendency of nonpolar molecules to aggregate in aqueous solution and exclude water molecules

example of hydrophobic molecules

oil, fats, and greasy substances

amphipathic effect

molecules that have both polar and nonpolar regions

example of amphiphilic molecules

phospholipid and surfactants

surfactants

commercial cleaning agents

four major noncovalent forces

1. hydrogen bond

2. hydrophobic interaction

3. ionic bonds

4. van der waals forces

what elements are valid for a hydrogen bond

oxygen, flour or nitrogen

what are hydrophobic interactions important for

protein shape and membrane structure

ionic bonds

are the strongest non covalent bond but can be weakened by water molecules

van der waals forces

occurs between neutral atoms

acids

proton donor ( donate hydrogen ions)

base

proton acceptor ( accept H+ )

strong acids and base

ionize into cations and anions almost completely and conducts electricity well

example of strong acids

HNO3, HCl, H2SO4

example of weak acids

Acetic acid and H2CO3

example of weak base

NH3, HCO3-

example of strong base

KOH, NaOH

water can act like

both acid ( OH-) and base (H3O+)

Henderson-Hasselbalch equation

pH= pKa+log(A-)/(HA)

whats the pKa

Acid dissociation constant

pH

the measure of the acidity or basicity of an aqueous solution

pH equation

pH= -log (H+)

acids on the pH scale

pH less than 7

Bses on the pH scale

pH greater than 7

buffers

solution that prevent or resist changes in pH when a small amount of bases or acids are added.

buffers consists of

a weak acid and its conjugated base

what are the 2 main biological buffers

1. Bicarbonate buffer system

2. phosphate buffer system

Bicarbonate buffer system

acts in blood plasma keeping the pH between 7.35 and 7.45

phosphate buffer system

acts in the cell cytosol between 7.0 and 7.4

function of proteins

1. biochemical catalysts

2. control cell functions

3. mode of transport

4. first line of defense against microbial invasion

5. mechanical support

6. movement

what are the elements in amino acids

carbon, hydrogen, oxygen and nitrogen

amino acid are made up of groups

amino group, carboxylic group and a side-chain (R)

NH2

gain a proton

COOH

lose a proton

zwitterion

a molecule containing a positively charged ion at one end and a negatively charged ion at the other

in acidic conditions (amino acid)

amino acid acts as a base and accepts a proton at the amino group

in alkaline conditions (amino acids)

amino acid acts as an acids and donates a proton from its carboxyl group

when is amino acid act as a zwitterion

at it neutral pH ( around 7)

chiral atom

an atom in a molecule that is bonded to four different chemical atoms or groups

essential amino acids

cannot be made by the body and must be supplied by food

semi-essential amino acids

the synthesis of histidine tends to run low during infancy

nonessential amino acids

are made by the body

peptide Bond

a covalent chemical bond formed between two amino acids molecules when the carboxyl group of one molecule reacts with the amino group of the process is a dehydration synthesis reaction

polypeptide

a single linear chain of amino acids bonded together by peptide bonds

primary structure

1. linear structure

2. one dimensional

3. in the ribosome

4. made during the process of protien biosynthesis

5. are not functional

6. peptide bond

secondary structure

1. two dimensional

2. a-helices and b-pleated sheets

3. in the ribosome

4. hydrogen bonds

5. non functional

tertiary structure

1. globuler structure

2. three dimensional

3. in the golgi apparatuse

4. non-covalent hydrophobic interactions and disulfide bonds

5. functional

Quaternary structure

1. Four-dimensional

2. 2or more subunits

3. golgi apparatus

4. functional

5. non-covalent hydrophobic interactionand disulfide bonds

simple proteins

made of amino acids units only, joined by peptide bond

conjugated proteins

simple protiens combined with prothetic group

example of conjugated proteins

glycoproteins, phosphoproteins and hemoglobins

derived proteins

obtained from simple proteins by the partial hydrolysis action of enzymes or chemical agentss

example of derived protein

gelatine, protease, peptones, and peptides

denaturation of protein

an irreversible change and unfolding of secondary, tertiary and quaternary structure of a protein , caused by breaking bonds that stabilize these three level structures into functional unfolded random coil of primary structure

denaturation factors

1. high temprature

2. agitation by stirring

3. extreme pH

4. ultraviolet and x-rays

5. heavy metal ions

6. oxidizing or reducing agents

protein digestion enzyme

1. pepsin

2. trypsin

3. chymotrypsin

4. exopeptidases

5. dipeptidases

6. enterokinase

pepsin

in the stomach wall cells. it breaks proteins into smaller polypeptide

trypsin

in the pancreas. breaks down proteins into smaller polypeptide chains

chymotrypsin

in the pancreas. breaks down proteins into smaller polypeptide chains

exopeptidases

in the small intestine. breaks down peptides into oligopeptides dipeptides and amino acids

dipeptidases

in the small intestine. breaks down dipeptides into amino acids

enterokinase

in the small intestine. breaks down trypsinogen into trypsin