Biochem-Exam 1

Question 1

Name the non-polar amino acids:

Answer 1

Glycine Alanine Tryptophan Valine Leucine Cysteine Tyrosine Phenylalanine Isoleucine Methionine Proline —-Grab At That Very Large Crusty The PIMP

Question 2

Name the uncharged polar amino acids:

Answer 2

Threonine Asparagine Glutamine Serine —-Remember “Uncharged T.A.G.S.”

Question 3

Name the charged polar amino acids:

Answer 3

Glutamate Aspartate Lysine Arginine Histidine —-Remember “Charged G.A.L.A.H.”

Question 4

What is the acronym for the non-polar amino acids

Answer 4

Grab At That Very Large Crusty The PIMP

Question 5

Quick way to tell the buffering zone of most amino acids?

Answer 5

+/- 1 from neutral pH (aka, zwitterion pH)

Question 6

What is the MOST charged form of an amino acid?

Answer 6

Zwitterion

Question 7

At what pH is an amino acid likely in its zwitterion form?

Answer 7

pH=6 to pH=8

Question 8

What is a tell-tale sign of a polar-covalent bond?

Answer 8

Anything bonded to Oxygen or Nitrogen

Question 9

What is the main reason that proteins assume a 3-d shape?

Answer 9

Hydrophobic effect

Question 10

What are the four main components of an amino acid?

Answer 10

Carboxyl group, Amino group, H, and R group

Question 11

Which bond is called the “Phi” bond in an amino acid?

Answer 11

The N-C(alpha) bond

Question 12

What do INTRA-polymer bonds form in a polypeptide?

Answer 12

Alpha helices

Question 13

What do INTER-polymer bonds form in a polypeptide?

Answer 13

Beta-pleated sheets

Question 14

What three things can denture a protein?

Answer 14

pH Thermal energy Detergent

Question 15

In what direction is DNA read?

Answer 15

3’ to 5’

Question 16

In what direction is DNA synthesized?

Answer 16

5’ to 3’

Question 17

In what direction does the DNA template strand run

Answer 17

3’ to 5’

Question 18

What DNA base pairs are Purines?

Answer 18

Adanine and Guanine “Pure As Gold”

Question 19

What DNA base pairs are Pyrimidines?

Answer 19

Cytosine and Thymine “Cut The Pie”

Question 20

What two types of Tertiary structures are there?

Answer 20

1. Fibrous 2. Globular

Question 21

What is the difference between a nucleoside and a nucleotide?

Answer 21

There is a phosphate group on a nucleotide

Question 22

What makes rRNA?

Answer 22

RNA Pol 1

Question 23

What makes mRNA?

Answer 23

RNA Pol 2

Question 24

What makes tRNA?

Answer 24

RNA Pol 3

Question 25

What is the acronym used to remember which RNA is made by which RNA polymerase?

Answer 25

"Run Mr. T" o rRNA via RNA Pol 1 o mRNA via RNA Pol 2 o tRNA via RNA Pol 3

Question 26

How many H-bonds aqueous Cl- have around it?

Answer 26

6

Question 27

What is the relationship that can be used to express pH, pKa, base, and acid

Answer 27

If pH \> pKa, then b \> a If pH

Question 28

What are the pKa's of the charged polar amino acid Glutamate and Aspartate?

Answer 28

pKa=4-5

Question 29

What are the pKa's of the charged polar amino acid Histidine?

Answer 29

pKa=6-7

Question 30

What are the pKa's of the charged polar amino acid Lysine?

Answer 30

pKa=9-10

Question 31

What are the pKa's of the charged polar amino acid Arginine?

Answer 31

pKa=12

Question 32

Which non-polar amino acids are amphiphilic?

Answer 32

Tyrosine and Tryptophan

Question 33

What is the pKa of the carboxylic acid part of glycine?

Answer 33

2.34

Question 34

What is the pKa of the ammonium part of glycine?

Answer 34

9.6

Question 35

What is the isoelectric point of glycine?

Answer 35

5.97

Question 36

What is the REACTIVE part of the Glutamate and Aspartate side chains?

Answer 36

---COO-

Question 37

What is the reactive part of Glycine?

Answer 37

H

Question 38

What is the REACTIVE part of Serine?

Answer 38

---OH

Question 39

What is the REACTIVE part of Arginine and Lysine?

Answer 39

It can have positively charged ammonium groups

Question 40

What is the structure of Histidine?

Answer 40

Question 41

What is the structure of Proline?

Answer 41

Question 43

Which bond is called the "Psi" bond in an amino acid?

Answer 43

The C(alpha)-C=O bond. I.e, the one further from N.

Question 44

What is a Ramachandran diagram and how is it read?

Answer 44

It shows

Question 45

What is the general orientation of the amnio acid backbone and associated side chains of an alpha helix?

Answer 45

The backbone spiral in the the clockwise direction. The side chains come out of the spiral 3-4 residues apart.

Question 46

How is an alpha helix formed (what bonds to what and where)?

Answer 46

C=O is H-bonded to an amide 4 residues down the chain.

Question 47

What percentage of actual proteins have alpha helices?

Answer 47

0-90%

Question 48

How are beta-pleated sheets formed?

Answer 48

Formed when polypeptides line up in a parallel or anti-parallel arrangment, and there is H-bonding between the donor of one strand and the acceptor of another.

Question 49

How are the R-groups arranged in a beta-pleated sheet along a given strand?

Answer 49

Each is oriented opposite to the adjacent R-group (above and below the sheet)

Question 50

How are beta-turns (aka, hairpin loops, hairpin turns/bends) formed?

Answer 50

When R-groups that are 3 residues from each other H-bond. For example, when #1 NH h-bonds to #4 C=O

Question 51

What are Loops in a polypeptide chain?

Answer 51

When segments longer than beta turns ( \> 4 residues apart) reverse the direction of the chain

Question 52

Where are loops frequenty found in a protein?

Question 53

What is one protein mentioned in lecture that shows examples of alpha helices, beta sheets (parallel and antiparallel), beta turns, and loops?

Answer 53

Thioredoxin

Question 54

Which side chain destabilizes alpha helices and beta sheets?

Answer 54

Proline

Question 55

Why does Proline destabilize alpha helices and beta sheets?

Answer 55

The proline side chain is basically jammed into the space that should be occupied by the backbone of the alpha helix

Question 56

What is the usual structure and function of fibrous proteins (tertiary structure)? Give an example of a fibrous protein

Answer 56

Long, thin chains. Interchain H-bonds cause side chains to point away from fiber axis (no INTRAchain sidechain interactions). Mechanical support Collagen (triple helix fibrous protein)

Question 57

What are the two main regions of globular proteins and how do they form?

Answer 57

Surface--Forms when there is H-bonding with surrounding environment Interior (core): forms when there is little to no interaction with surrounding environment (ex. no h-bonding with water)

Question 58

What are proteopathies?

Answer 58

A classification of the many disorders resulting from misfolded proteins

Question 59

What is the general term for what binds to a proteins active site?

Answer 59

Ligand

Question 60

What complimentary interactions (non-covalent interactions) cause tertiary structure to form?

Answer 60

Complementary shape, size, and polarity

Question 61

Where are polar UN-charged side chains found in a globular protein (surface or interior)?

Answer 61

BOTH | (ha ha trick question)

Question 62

Which amino acid can form di-sulfide bonds (covalent)?

Answer 62

Cysteine

Question 63

What is the beta-alpha-beta motif and how does it form?

Answer 63

Its a supersecondary structure formed by: 2 parallel beta strands 4 or more can form an alpha-beta barrel

Question 64

What types of supersecondary structures are considered DNA binding motif?

Answer 64

helix-turn-helix zinc finger

Question 65

What causes quaternary structure to form?

Answer 65

Complimentarity of shape, size, and polarity

Question 66

What are structural domains?

Answer 66

Independently folded sections within one polypeptide chain of larger proteins

Question 68

What is most generally true about the location of a reverse (beta) turn in a globular protein?

Answer 68

It is partially exposed to the surface, and partial interior exposure. Remember, beta sheets and alpha helices have amphipathic traits.

Question 69

How many H-bonds can the backbone of each amino acid form with an opposing strand in a beta-pleated sheet conformation (same for parallel and anti-parallel)?

Answer 69

2 h-bonds per amino acid backbone residue

Question 70

What CANNOT form if a protein has mostly, if not all, polar side chains?

Answer 70

Tertiary structure

Answer 71