Biochemistry

water, acids, bases & buffers

100

What is the percent of body water inside the intracellular and extracellular? 

intracellular- 60%

extracellular- 40%

200

list the 4 properties of water 

• The polarity of water allows polar molecules to dissolve
• Hydrogen bonds are formed with polar compounds and “hydration shells” surround ions
• Hydrogen bonds are weak, constantly breaking and reforming, so that solutes can move in solution and water can move through pores in cell membranes
• Water can surround a polar molecule to allow to dissolve

300

What is osmolality? 

Osmolality is the concentration of all dissolved solutes in the blood (electrolytes, proteins, etc)

400

pH=pKa=6.30 ok in the body? 

it not because it is not 1 below or above 7.35-7.45

500

What does hemoglobin have for a buffer and what does it do 

Hemoglobin has an amino acid side chain that can accept H+

Structures of the major compounds of the body

100

When do you use "ane", "ene", "iso" "yl"? 

ane-single bonds 

ene-double bonds 

iso- a prefix when 2 carbons are bonded to another carbon,  forming a branch which is an isomer of the straight chain compound

yl- implies that it is a group attached to a compound

200

What doe LEO the Lion says GER mean? 

Loss of electrons (loss of H or gain of O) is oxidation; gain of electrons (gain of H or loss of O) is reduction

300

Name properties of amines 

compounds with nitrogen are usually basic 

can have positive charge 

400

What are D- and L- Sugars? 

• They are non-superimposable mirror images of each other, named for whether the OH farthest from the carbonyl group is the same as D- or L- glyceraldehyde

500

What are are anomer of cyclic glucose and what angle is the beta and alpha in?

• These exist in equilibrium with the straight-chain form in solution
• The OH group on the anomeric carbon can react with an –OH or an –NH group on another molecule
• These are glycosidic bonds and can be α or β
• Beta is on a up angle
• Alpha is on the down angle

Amino Acids

100

proteins cant maintain their structure if? 

pH or temperature is far out of optimal range

200

List the nonpolar, aliphatic amino acids and what are their properties  

properties-no charge, hydrophobic 

list: glycine, alanine, proline, valine, leucine, isoleucine 

300

Name the polar, uncharged amino acids and list of properties 

Polar, Uncharged- Asparagine, Glutamine, Serine, Threonine 

List of Properties- electronegative O and N atoms, negative and polar, hydrophilicity

 

400

For charged amino acids name the acid, name the charge, if acid or base 

Negative Charge (acidic)-aspartate, glutamate 

Positive Charge (basic)- Arginine, Lysine, Histidine 

 

500

What are side-chain interactions considered? 

electrostatic interactions or bond 

Structure & Function in Proteins

100

Name the Protein Structure Rules 

• The three-dimensional structure must be flexible enough to function properly but stable enough that it will not convert to another conformation
• It must have amino acids with side groups that are compatible with the environment or environments (such as a transmembrane protein) the protein will function in
• So, polar groups on the outer surface if it will function in aqueous environments, hydrophobic groups in membrane insertion areas if it is a transmembrane protein
• The peptide bond that forms the backbone of proteins is that between an amino group and a carboxyl group
• Because of its partial double-bond characteristics the peptide bond it is fairly rigid
• The R-groups are usually on opposite sides of the bond

200

What is Tertiary Structure? 

• The α-helices and β-sheets, combined with irregular elements such as loops and turns, make up the tertiary structure of a protein
• This is coded for in the DNA and every molecule of this protein should assume the same conformation if folded correctly

300

When can denaturation occur? 

• Proteins can be denatured, by changes in temperature as shown in the photo
• Changes in pH also cause structural changes, due to disruption of the hydrogen and ionic bonds
• Change in conformation usually inhibits the function, which is why it is important to maintain proper temperature and pH

400

Loss or gain of a proton could cause what? 

the breaking of the hydrogen bonds that hold the protein in its proper conformation

500

What is the structure of immunoglobulins and what do they do? 

• immunoglobulins perform important defense functions in our bodies
• The immunoglobulins all have this structure with 2 light and 2 heavy chains held together by disulphide bonds 

Enzyme

100

What is an enzymes? 

Enzymes are proteins that make chemical reactions go faster – they “catalyze” the reaction

200

Name the steps of enzyme-catalyzed reaction 

1. binding of the substrate 

2. conversion of substrate to product 

3. release of product 

300

What does cofactors do? 

cofactor helps lower the energy required to cause the reaction

400

What is the Lock & Key Model and Induced-Fit Model? 

Lock & Key 

• The lock and key mechanism, looks at an enzymes as a rigid lock
• The substrate fits into this lock like a key
• This model explains the specificity of an enzyme but NOT the ability of the enzyme to stabilize the transition state

Induced- Fit

• This model allows for flexibility of the enzyme in binding to the substrate, and so is thought to be the most accurate
• Binding of the substrate induces changes in the shape or “conformation” of the enzyme
• This allows for changes such as closing of the actin fold of hexokinase once glucose is bound

500

What is Enzyme inhibition? 

• A competitive inhibitor is a molecule with a similar shape to one of the substrates