Lecture 6: Amino Acids Building Blocks of Proteins

Question 1

Only __\_ Dimer found in cells

Answer 1

Only L Dimer found in cells

Question 2

Hydrophobic Amino Acids? (7)

Answer 2

Glycine

Alanine

Proline: only R group that R group bonds w/ amino group

Valine

Leucine

Isolucine

Methionine (Sulfur containing)

Question 3

Aromative R Groups (3)

Answer 3

Phenylalanine

Tyrosine (Hydroxyl group can be phosphorylated)

Tryptophan

Question 4

Polar Uncharged R groups (5)

Answer 4

Serine

Threonine

Cysteine (Sulfur containing)

Asparagine

Glutamine

Question 5

Positive R-Groups

Answer 5

Lysine

Arginine

Histidine

Question 6

Negative R-Groups (2)

Answer 6

Aspartate

Glutamate

Question 7

______pH=high concentration of H+

Every protonated group has hydrogen on it

AA Takes on ____ charge

Answer 7

Low pH=High concentration of H+

Every protonated group has hydrogen on it

Takes on a positive charge

Question 8

For Glutamate as pH increases:

Proton first drops from _______\_

Then proton from ________\_

Finally ________\_ is deprotonated

Answer 8

For Glutamate as pH increases:

Proton first drops from core carboxyl

Then proton from R group carboxyl

Finally, amino group is deprotonated

Question 9

_______\_ is the Amino Acid w/ pK has pK closest physiological pH

Answer 9

Histidine is the Amino Acid w/ pK has pK closest physiological pH

Question 10

______\_ ________is when AA has no charge

Answer 10

Isoelectric Point is when AA has no charge

Question 11

Peptide bonds form with the removal of _____\_

Answer 11

Peptide bonds form with the removal of Water

Question 12

Proteins grow from the ______\_ terminus

Answer 12

Proteins grow from the N to C terminus

Question 13

Between C and N partial double bond ____\_, no free rotation of R groups so maintained in particular geometry

Answer 13

Between C and N partial double bond rigid, no free rotation of R groups so maintained in particular geometry

Question 14

A Peptide bond is a ________________\_ of two structures

_____\_ reactive than esters

Rigid and _____

Large dipole moment in favored trans config.

Answer 14

A Peptide bond is a resonance hybrid of two structures

Less reactive than esters

Rigid and planar

Large dipole moment in favored trans config.

Question 15

Di-sulfide bridge formed between strands by sulfur-containing the Amino Acid ______\_

Answer 15

Di-sulfide bridge formed between strands by sulfur-containing the Amino Acid Cystine

Question 16

Bonds between Polypeptides: 1y to 2y

________\_: between positive and negative

_________: between oxygen and hydrogen

_\________: Short range interaction between atoms in AA

_________: are Covalent

Answer 16

Bonds between Polypeptides: 1y to 2y

I__onic bonds: between positive and negative

Hydrogen Bond: between oxygen and hydrogen

Vander walls attraction/ repulsion: Short range interaction between atoms in AA

None are Covalent

Question 17

_______\_ regions of polypeptide seek to be within protein,

________\_ regions face out: Helps drive folding of protein

Answer 17

Hydrophobic regions of polypeptide seek being within protein,

Hydrophillic regions face out: Helps drive folding of protein

Question 18

Van der Waals Interactions two components:

____________\_ - Depends on the polarizability

-Dominates at longer distances (0.4-0. 7 nm)

______________ -Depends on the size of atoms

• Dominates at short distances
• Minimum contact distanced

Answer 18

Van der Waals Interactions two components:

Attractive force - Depends on the polarizability

-Dominates at longer distances (0.4-0. 7 nm)

Repulsive force -Depends on the size of atoms

• Dominates at short distances
• Minimum contact distanced

Question 19

Alpha Helixes:

– stabilized by ____________\_ between nearby residues

– within the R groups of a single chain

–________-_Handed helix

–Side Chains _________\_ w/ helical acess

Answer 19

The Alpha helix

– stabilized by hydrogen bonds between nearby residues

– within the R groups of a single chain

–_Right-_Handed helix

–Side Chains Perpendicular w/ helical access

Question 20

Small ______\_residues such as ___\_ and ___\_ are strong Alpha helix formers

Answer 20

Small hydrophobic residues such as Ala and Leu are strong Alpha helix formers

Question 21

__\_ acts as an alpha helix breaker because the rotation around the N-Ca bond is impossible

Answer 21

Proline acts as an alpha helix breaker because the rotation around the N-Ca bond is impossible

Question 22

___\_ acts as a helix breaker because the small R-group (H) supports other conformations

Answer 22

Gly acts as a helix breaker because the small R-group (H) supports other conformations

Question 23

• stabilized by hydrogen bonds between adjacent segments that may not be nearby
• R groups protrude in alternating up and down direction
• The planarity of the peptide bond and tetrahedral geometry of the a-carbon create a pleated sheet structure

Answer 23

The Beta Sheet

Question 24

____\_in position 2 or ____\_ in position 3 are common in beta-turns

Answer 24

Proline in position 2 or glycine in position 3 are common in beta-turns

Question 25

Beta turns are stabilized by a hydrogen bond from a __________to amide proton three residues down the sequence

Answer 25

Beta turns are stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence

Question 26

Protein Tertiatry Structures two major classes:

• ____________ proteins
  
  • typically insoluble; made from a single secondary structure
• ___________\_ proteins
  • _​_water-soluble proteins
  • lipid-soluble membraneous proteins

Answer 26

Protein Tertiatry Structures two major classes:

• Fibrous Proteins
  
  • typically insoluble; made from a single secondary structure
• Globular Proteins
  • _​_water-soluble proteins
  • lipid-soluble membraneous proteins

Question 27

______\_: Phosphorylates by removing phosphate from ATP

Answer 27

Kinase: Phosphorylates by removing phosphate from ATP

Question 28

________\_:

• Transports Oxygen in Blood
• Tetramer composed of

2 _______\_

2 _______\_

Answer 28

Hemoglobin:

• Transports Oxygen in Blood
• Tetramer composed of

2 Alpa chains

2 Beta chains

Each subunit binds a porphyrin which picks up oxygen in the lungs and transports it to where needed