Biochem Fundamentals

Front 1

Draw a basic amino acid structure

Front 2

At physiological pH, what is the charge of the amino group of the aa?

Back 2

NH3+, it has a 1+ charge at physiological pH

Front 3

At physiological pH, what is the charge of the carboxylic acid group of the aa?

Back 3

COO-, it has a -1 charge at physiological pH

Front 4

How does the charge of the R group affect the charge of the amino acid?

Back 4

As the amino group and the carboxylic acid group cancel each other out, the charge of the R group determines the charge of the amnio acid overall.

Front 5

How does the R group affect the hydrophobicity/hydrophilicity of the amnio acid?

Back 5

The R group determines all functional characteristics of a specific amino acid, including the hydrophobicity or hydrophilicity of the amino acid.

Front 6

More than 99% of our amino acids are in which stereoisomeric form: L or D?

Back 6

L. That is, if you drew the aa with the carboxylic acid at the top, if the H is on the right and the amino group is on the left, you have an L isomer. The opposite is a D isomer.

Front 7

Why is glycine unique in terms of its stereoisomeric forms?

Back 7

Unlike all other aa, glycine is achiral, and cannot have D or L isomers.

Front 8

Name the 5 varieties of amino acids

Back 8

1. Nonpolar Aliphatic

2. Aromatic

3. Uncharged polar

4. Negative Polar

5. Positive Polar

Front 9

What are the common characteristics of nonpolar aliphatic amino acids?

Back 9

1. Hydrocarbon chains

2. Nonpolar

3. Hydrophobic

4. Tend to cluster in a protein via hydrophobic interactions (stay away from aqueous environment)

Ala, Gly, Pro, Val, Leu, Ile, Met

A, G, P, V, L, I, M

Front 10

What are the common characteristics of aromatic amino acids?

Back 10

1. Aromatic R groups

2. Relatively nonpolar

3. Relatively hydrophobic

The hydroxyl group of tyrosine is able to form limited H bonds, and is important in phosphorylation events, and is the least hydrophobic

Phe, Tyr, Trp

F, Y, W

Front 11

What are the common characteristics of uncharged polar R groups?

Back 11

1. Uncharged polar R group

2. Hydrophilic

3. Capable of forming H bonds via R group

4. Serine and threonine, with their hydroxyl groups, can participate in phosphorylation as well

Ser, Thr, Cys, Asn, Gln

S, T, C, A, Q

Front 12

How is cystine formed?

Back 12

The uncharged polar amino acid, cysteine, can form a disulfide bond with another cysteine via oxidation, which forms a cystine.

This is reversible under reducing conditions.

This is also very important in the stability of protein structures.

Front 13

What are the common characteristics of negatively charged polar R groups?

Back 13

1. Very Hydrophilic

2. Net -1 charge

Asp and Glu

D, E

(E= glutamate, Q= glutamine)

Front 14

What are the common characteristics of positively charged polar R groups?

Back 14

1. Very Hydrophilic

2. Net +1 charge

Lys, His, Arg

K, H, R

Front 15

How do you determine if a group is charged, using the pKa?

Back 15

If the pKa of the R group is greater than the pH (physiological is 7.2-7.4), then it accepts a +1 charge H

If the pKa of the R group is less than the pH, then it donates a H+, giving it a negative charge

Front 16

At physiological pH, what is the charge of the carboxylic acid group? The amino group?

Back 16

As the pKa of the carboxylic acid group is 2, the physiological pH is always greater, so it donates a H+ giving it a net -1 charge.

As the pKa of the amino group is 9, it is always greater than the physiological pH, and therefore accepts a +1 H, and has a net +1 charge.

At physiological pH, the charges of the amino group and the carboxylic acid group cancel.

Front 17

When pH= pKa, _____% of the group in questions are ions.

Back 17

50%

As the pH gets higher for the carboxylic acid group, more base is around, so the carboxylic acid acts more acidically, and is ionized to have a negative charge.

As the pH gets lower for the amino group, more acid is around, so the amino group acts basically, and is ionized to have a positive charge.

Front 18

Which three amino acids can be phosphorylated? Why?

Back 18

Serine, Threonine, and Tyrosine

Each has a hydroxyl group in its R

Front 19

Which type of enzyme is responsible for phosphorylation? What are the two types of kinases?

Back 19

Kinase

Serine/Threonine Kinase, Tyrosine Kinase

Front 20

What type of enzyme reverses phosphorylation?

Back 20

A phosphatase removes the phosphate from a phosphorylated amino acid

Front 21

T/F Phosphorylation can inactivate OR activate a protein, depending on its structure and function

Back 21

TRUE

If phosphorylation activates a protein, dephosphorylation will deactivate it, and vice-versa

Front 22

Peptide bonds are which types of bonds?

Back 22

Covalent

Front 23

Peptide bond formation is a ___________ reaction

Back 23

Condensation

Front 24

The peptide bond has what type of structure (geometrically)?

Back 24

Planar

Front 25

Between what is the peptide bond formed?

Back 25

The peptide bond is formed between the COO- carboxylic acid group of the preceding amino acid and the NH3+ group of the next amino acid.

Front 26

In terms of both ordering and synthesis, what is the directionality of amino acids?

Back 26

From the NH3+ to the COO- end, R1 to R2

For example, if a peptide bond were between a R1 Gly and an R2 Ala, it would be Gly-Ala, or Glycyclalanine

Front 27

Which molecule must be input in order to break a peptide bond?

Back 27

H2O, a water molecule

Front 28

Define Primary structure

Back 28

The amino acid sequence, from NH3+ to COO- (alpha amino terminal end to the alpha carboxyl terminal end)

Front 29

Define Secondary structure

Back 29

The basic structural units formed by immediate folding of the amino acids, such as alpha helices and beta sheets, or other stable regional structures

Front 30

Define Tertiary Structure

Back 30

All of the secondary structures in a polypeptide chain or peptide

Front 31

Define Quaternary Structure

Back 31

The conformation of 2 or more polypeptide chains in the protein (with multiple polypeptide subunits)

Front 32

Define and describe Cystinuria

Back 32

Autosomal defect in resorption of cystine in the kidneys, producing calculi (stones) in the kidneys, bladder and urine, called urolitiasis .

Both cysteine and cystine are fairly insoluble, and can precipitate to form the calculi.

Drugs can elevate the pH, rendering cysteine more soluble, and can help flush it out.

Front 33

Define and describe PKU

Back 33

PKU, or phenylketonuria, is the inability to break down phenylalanine.

This is one of a number of "Inborn Errors of Metabolism". PAH, or phenylalanine hydroxylase, is unable to break down the Phe, leading to its buildup in the body.

It is an autosomal recessive disorder. Phe is important in neurotransmitter creation, and PKU can lead to mental retardation.

Front 34

WHich is the smallest amino acid?

Back 34

Glycine

Front 35

Which amino acid forms a good physiologic buffer?

Back 35

Histidine

Front 36

Which amino acids are branched chain, and build up in maple-syrup urine disease?

Back 36

Val, Leu, Ile

Front 37

Which amino acid is an alpha-helix breaker?

Back 37

Proline

Front 38

Which amino acid is the only one with its side chain cyclized to its alpha amino group?

Back 38

Proline

Front 39

Which amino acids have aromatic side chains?

Back 39

Phenylalaine, Tryptophan, Tyrosine

Front 40

Which amino acid forms disulfide bonds?

Back 40

Cysteine

Front 41

Which amino acids are phosphorylated by kinases?

Back 41

Serine, Threonine, Tyrosine

Front 42

What must be supplied in PKU?

Back 42

Tyrosine, as it is metabolized from Phe

Front 43

Which amino acids are basic and positive at pH=7?

Back 43

Lys, Arg, His

Front 44

Which amino acids are acidic and negative at pH=7?

Back 44

Asp and Glu