Biochem - Aa's, Peptides, Enzymes

Front 1

What are the 4 general features of standard amino acids?

Back 1

1. All alpha
2. Zwitterionic form
3. Cross cell membranes via transport proteins
4. Exist in L-configuration

Front 2

The amine group on standard amino acids is attached to which carbon?

Back 2

Attached to the alpha carbon, the first carbon away from the COOH group that is attached to the amine and R group

Front 3

Zwitterionic form means that

Back 3

There is one formal + and one formal -charge on the molecule at the same time

Front 4

What are the classifications of aa's by side chain?

Back 4

Charged --> negative, positive

Neutral --> polar, aromatic, non-polar/aliphatic

Front 5

What aa's are in the negatively charged classification?

Back 5

Aspartic acid
Glutamic acid

Front 6

What aa's are in the non-polar, aliphatic aa classification?

Back 6

Glycine
Alanine
Valine
Leucine
Methionine
Isoleucine
Proline

Front 7

Phenylalanine, tyrosine, and tryptophan are what aa classification?

Back 7

Neutral aromatic

Front 8

What aa's are in the neutral polar aa classification?

Back 8

Serine
Cysteine
Threonine
Asparagine
Glutamine

Front 9

Classification & draw: Proline

Back 9

Neutral
Non-polar, aliphatic

Front 10

Classification & draw: Isoleucine

Back 10

Neutral
Non-polar, aliphatic

Front 11

Classification & draw: Methionine

Back 11

Neutral
Non-polar, aliphatic

Front 12

Classification & draw: Leucine

Back 12

Neutral
Non-polar, aliphatic

Front 13

Classification & draw: Valine

Back 13

Neutral
Non-polar, aliphatic

Front 14

Classification & draw: Alanine

Back 14

Neutral
Non-polar, aliphatic

Front 15

Classification & draw: Glycine

Back 15

Neutral
Non-polar, aliphatic

Front 16

Classification & draw: Tryptophan

Back 16

Neutral
Aromatic

Front 17

Classification & draw: Tyrosine

Back 17

Neutral
Aromatic

Front 18

Classification & draw: Phenylalanine

Back 18

Neutral
Aromatic

Front 19

Classification & draw: Serine

Back 19

Neutral
Polar

Front 20

Classification & draw: Cysteine

Back 20

Neutral
Polar

Front 21

Classification & draw: Threonine

Back 21

Neutral
Polar

Front 22

Classification & draw: Asparagine

Back 22

Neutral
Polar

Front 23

Classification & draw: Glutamine

Back 23

Neutral
Polar

Front 24

Classification & draw: Lysine

Back 24

Positively charged

Front 25

Classification & draw: Histidine

Back 25

Positively charged

Front 26

Classification & draw: Arginine

Back 26

Positively charged

Front 27

Classification & draw: Aspartic acid

Back 27

Negatively charged

Front 28

Classification & draw: Glutamic acid

Back 28

Negatively charged

Front 29

What three aa's are classified as 'branched-chain aa's?"

Back 29

Valine
Leucine
Isoleucine

Front 30

What 4 aa's have abbreviations that do not follow normal rules?

Back 30

Asparagine: Asn
Glutamine: Gln
Isoleucine: Ile
Tryptophan: Trp

Front 31

Disulfide linkages only occur between:

Back 31

2 cysteines

Front 32

Peptide or amide bonds are formed via what mechanism? Sulfide bonds?

Back 32

Dehydration and hydrolysis

Oxidation and reduction

Front 33

Draw formation of a peptide bond

Back 33

Go ahead, draw it.....

Front 34

T/F: peptide bonds are covalent

Back 34

T

Front 35

Draw a sulfide bond

Back 35

Get artsy....

Front 36

Why can't peptide and protein drugs be taken orally?

Back 36

Broken down by GI tract (i.e. insulin) via bond cleavage

Front 37

What is the pI?

Back 37

pH at which a solution of amphoteric molecules have a NET charge of zero (+/- charges balance)

Front 38

How does the net charge in soln change with the pH increases or decreases from the pI?

Back 38

Increase in pH above pI leads to negative charge and more basic (travels roward anode), decrease in pH below pI leads to positive charge and more acidic (travels toward cathode)

Front 39

How does pH changes in relation to pI affect solubility

Back 39

aa's are least soluble in water at their pH. Increase or decrease in pH will increase solubility.

Front 40

Define: enzyme

Back 40

Proteins that catalyze reaction. Do not affect end point ratio, only speed via lowering the energy of activation

Front 41

Enzymes increase reaction rate by lowering

Back 41

The energy of activation

Front 42

Denaturing is....

Back 42

Complete or partial unfolding of a protein, causing loss of three-dimensional and biological activity

Front 43

The three mechanisms that will denature a protein are:

Back 43

Heat
pH extremes
Detergents, solvents

Front 44

Compare denaturing with digestion

Back 44

Digestion is the breakage of peptide bonds whereas denaturing is the change in folding of the protein

Front 45

Small molecules required for enzyme activity are:

Back 45

Cofactors

Front 46

Which cofactors must be organic?

Back 46

Coenzymes

Prosthetic groups CAN be, but can also be inorganic

Front 47

Loosely bound cofactors are

Back 47

Coenzymes

Front 48

Tightly/permanent cofactors are

Back 48

Prosthetic groups

Front 49

The 6 mechanisms of enzyme regulation are:

Back 49

Product inhibition
Allosteric regulation
Covalent modification
Protein-protein regulation
Zymogen cleavage
Enzyme synthesis and degredation

Front 50

Summarize the enzyme regulation: product inhibition

Back 50

Reversible
Enzyme inhibition via product competing with substrate for active site.

Product builds up and competes with substrate, therefore inhibiting more product catalysis

Front 51

Summarize the enzyme regulation: allosteric regulation

Back 51

Reversible
Inhibition (negative) OR activation (positive)
Molecule binds and causes conformational change in enzyme by binding somewhere OTHER than the active site

Front 52

Summarize the enzyme regulation: covalent modification

Back 52

Reversible
Inhibition OR activation
Modification via covalent bonding (phosphorylation)

Front 53

Summarize the enzyme regulation: protein-protein interaction

Back 53

Reversible
Inhibition OR activation
Enzyme is bound to protein to form a complex

Front 54

Summarize the enzyme regulation: zymogens

Back 54

Irreversible
Activation
Inactive enzyme precursor (zymogen) is cut via proteolytic cleavage to expose active site (digestive enzymes)

Front 55

Summarize the enzyme regulation: enzyme synthesis/degradation

Back 55

More enzyme causes increased rate
Less enzyme with no change in regular degradation leads to less [E]

Front 56

Define: Vmax

Back 56

Rate approached when [S] is high and product is being formed at the quickest rate

Front 57

What are the two definitions of Km?

Back 57

1. Km is the substrate concentration at which half of the enzyme pool is bound or saturated

2. Km is the substrate concentration at which the rate is 1/2 the max V

Front 58

Changes in Vm are beneficial if they

Back 58

Increased Vm leads to faster reaction

Front 59

Changes in Km are beneficial if they

Back 59

Get lower. Means a greater affinity for the [S] to be utilized by enzymes

Front 60

The 3 types of enzyme inhibition are:

Back 60

Competitive
Noncompetitive
Irreversible

Front 61

Define: competitive inhibition

Back 61

An inhibitor that competes with substrate for active site

Do not affect Vm- can supersaturate soln with [s] and still reach Vmax

Increases Km- more substrate must be added to maintain affinity levels

Front 62

An example of drugs that follow the 3 inhibition types are:

Back 62

Competitive: ibuprofen
Noncompetitive: caspofungen
Irreversible: aspirin

Front 63

How does ibuprofen block pain?

Back 63

Competitive inhibitor for enzyme that creates prostoglandins and pain

Front 64

Define: noncompetitive inhibition

Back 64

Binds enzyme somewhere OTHER than the active site and can bind [s] alone, or [es] complex

Lower vmax since they inhibit enzyme even if more substrate is added

No change in Km since it will bind both the [e] and [es]

Front 65

Caspofungin works as

Back 65

Blocks synthesis of fungal cell wall via noncompetitive inhibition

Front 66

Define: irreversible inhibition

Back 66

Inhibitor poisons enzyme by binding to enzyme, renders it useless

Vmax is lowered since enzyme # decreases

Km is no change since a non-existant enzyme doesn't affect affinity

Front 67

Aspirin works as what type of inhibitor?

Back 67

Irreversible - binds COX and causes them to be inhibited

Front 68

Define: allosteric regulated enzymes

Back 68

Do not follow MM eqn, sigmoidal curves

Allosteric activators decrease Km, inhibitors increase Km. Vmax is unpredictable