1st Unit / Ch 1 Amino Acids and Protein Structure

Question 1

What is the alpha carbon?

Answer 1

The central carbon closest to the carboxylic acid

Question 2

What does every amino acid have?

Answer 2

an amino group and carboxylic acid

Question 3

How are polar amino acids named by?

Answer 3

The character of their side chain

Question 4

What is the simplist amino acid?

Answer 4

Glycine due to its side chain being “H”

Question 5

All amino acids have D and L conformations except….

Answer 5

Glycine

Question 6

Where do side chains attach?

Answer 6

the alpha carbon

Question 7

Is Glycine optically active?

Answer 7

No

Question 8

Which 8 amino acids are hydrophobic?

Answer 8

Hydrophobic (normally buried inside the protein core):
• Alanine - Ala - A
• Isoleucine - Ile - I
• Leucine - Leu - L
• Methionine - Met - M
• Phenylalanine - Phe - F
• Valine - Val - V
• Proline - Pro - P
• Glycine - Gly - G

Question 9

Which 8 amino acids are polar?

Answer 9

Glutamine - Gln - Q
• Asparagine - Asn - N
• Histidine - His - H
• Serine - Ser - S
• Threonine - Thr - T
• Tyrosine - Tyr - Y
• Cysteine - Cys - C
• Tryptophan - Trp - W

Question 10

Which 4 amino acids are charged and can make salt bridges?

Answer 10

Arginine - Arg - R
• Lysine - Lys - K
• Aspartic acid - Asp - D
• Glutamic acid - Glu - E

Question 11

What does glycine help synthesize?

Answer 11

Collagen, the most abundant protein in the body.

Question 12

Why is Proline Unique? Can proline be in hydrogen bonding?

Answer 12

It has a secondary amine, in that the alpha-amino group is attached directly to the side chain, making the α carbon a direct substituent of the side chain. becuz of this it cannot be involved in hydrogen binding.

Able to creat kinks in structures to form a helix and beta sheets

Question 13

What type of charge does acidic amino acids have?

Answer 13

Negative becuz they have 2nd carboxylic group ( 2 x COO)

Question 14

What type of charge does Basic amino acids have?

Answer 14

Posittive and becuz they have 2nd amine group at bottom of chain. ( 2 x NH2)

Question 15

What makes Cysteine Unique?

Answer 15

It has covalent bonds becuz of S-S di sulfide bridges. These bonds stay when protein denatures and allow primary structure to stay in tact. So it can renature itself.

Question 16

Purpose of Methylation?

Answer 16

adding methly groups to control protein synthesizing.

Question 17

How are Di peptides synthasized? How are these new formed proteins broken?

Answer 17

Synthesized by carboynl end connecting to an amino end of another acid.

protein can only be broken by enzymes

Question 18

What are some charateristics of peptide bonds?

Answer 18

They are planr, partial double bonds, and are rigid on main chain of amid linkage, done by covalent bond. Their is rotation about side changes.

Question 19

List additional bonding charateristics of Peptide bonds?

Answer 19

They assume trans configuration and the carbonal “O” and amine groups “H”are polar to form hydrogen bonds.

Question 20

How does the primary structure remain stable?

Answer 20

due to its covalent backbone (amide linkage)

Question 21

What is the secondary structure?

How does it form?

What is the best example?

Answer 21

The primary backbone in 3 dimensional space. Like alpha helixs, where the negative end of carbonal end binds with hydrogen.

By the hydrogen bond between the 1st and the 4th in a right handed pattern (clockwise, introchain bonding)

The best example is “fibrous structure”

Question 22

Do R groups participate in secondary structure?

Answer 22

No, they point away, but can stabilize or destabilize.

Question 23

How does secondary structures arise?

What determines what kind types secondary structures can occur.

What are the 2 types?

Answer 23

from interactions between neighboring amino acids residues.

The rigity of the peptide backbone determines the type of secondary structures can occur.

Alpha helixs and Beta pleated sheets.

Question 24

How are Beta pleated sheets made?

Can they form intra bonds?

Answer 24

Peptide bond planes are arranged like a folded sheet of paper with 2 or more seperate chains side by side with H—-O bonds happening.

They are more extended than alpha helixs.

Cannot form intra bonds becuz those “H” are used to bond with other chain forming the beta sheet by inter’ chain

Question 25

What is a Antiparallel Beta strands?

Answer 25

2 or more seperate chains with alternating ends.

C===================N

H o H o

o H o H

N==================C

Question 26

What is a Parallel beta sheet?

Answer 26

It is a single polypeptide chain folding back on itself.

Question 27

What is a Beta-turn?

What do they often connect?

Answer 27

A tight turn, resulting in a 180 degree. 4 amino residues form a B-turn called Reverse or B Bend. This turn allows the reversal of the polypeptide chain helping it form a compact globular shape.

They often connect anti-parrellel Beta strands hence their name.

Question 28

What is a Tertiary Structure?

What are they consisted of?

Answer 28

It is the overall 3 dimensional conformation of a protein. The arrangement of various secondary structures into the compact shape of a globular protein.

They consits of a helixs and B strands in a 3d form.

In conclusion…..they are 3d shape of folding chain

Question 29

How does Tertiary structure arise and what is it depended on?

What does their folding depend on?

What kind of bond stabilizes Tertiary structures?

Answer 29

Arises from interactions between side chains, R groups that are at far distances but due to folding, they are close now. It is determined by its primary structure.

The folding patterns depend on the side chains and R groups which in turn stabilize the structures. Like H, disulfide bonds which are covalent bonds. Also non covalent bonds and hydrophobic interactions.

Question 30

What is a Quarternary structure?

Answer 30

It is the spatial association (relationship) of 2 or more polypeptide chains or sub units in a multisubunit protein. Where each have their own tertiary structure in the protein.

Question 31

What is Denaturation?

What is Renaturing?

Answer 31

It is the loss of native conformation and unfolding into random foldings due to disruption of non covalent bonds.

Renaturing is the return to form, can be done if u have primary structure still, like S-S bonds.