Lecture 6: Amino Acids Building Blocks of Proteins Flashcards
Only __\_ Dimer found in cells
Only L Dimer found in cells
Hydrophobic Amino Acids? (7)
Glycine
Alanine
Proline: only R group that R group bonds w/ amino group
Valine
Leucine
Isolucine
Methionine (Sulfur containing)
Aromative R Groups (3)
Phenylalanine
Tyrosine (Hydroxyl group can be phosphorylated)
Tryptophan
Polar Uncharged R groups (5)
Serine
Threonine
Cysteine (Sulfur containing)
Asparagine
Glutamine
Positive R-Groups
Lysine
Arginine
Histidine
Negative R-Groups (2)
Aspartate
Glutamate
______pH=high concentration of H+
Every protonated group has hydrogen on it
AA Takes on ____ charge
Low pH=High concentration of H+
Every protonated group has hydrogen on it
Takes on a positive charge
For Glutamate as pH increases:
Proton first drops from _______\_
Then proton from ________\_
Finally ________\_ is deprotonated
For Glutamate as pH increases:
Proton first drops from core carboxyl
Then proton from R group carboxyl
Finally, amino group is deprotonated
_______\_ is the Amino Acid w/ pK has pK closest physiological pH
Histidine is the Amino Acid w/ pK has pK closest physiological pH
______\_ ________is when AA has no charge
Isoelectric Point is when AA has no charge
Peptide bonds form with the removal of _____\_
Peptide bonds form with the removal of Water
Proteins grow from the ______\_ terminus
Proteins grow from the N to C terminus
Between C and N partial double bond ____\_, no free rotation of R groups so maintained in particular geometry
Between C and N partial double bond rigid, no free rotation of R groups so maintained in particular geometry
A Peptide bond is a ________________\_ of two structures
_____\_ reactive than esters
Rigid and _____
Large dipole moment in favored trans config.
A Peptide bond is a resonance hybrid of two structures
Less reactive than esters
Rigid and planar
Large dipole moment in favored trans config.
Di-sulfide bridge formed between strands by sulfur-containing the Amino Acid ______\_
Di-sulfide bridge formed between strands by sulfur-containing the Amino Acid Cystine
Bonds between Polypeptides: 1y to 2y
________\_: between positive and negative
_________: between oxygen and hydrogen
_\________: Short range interaction between atoms in AA
_________: are Covalent
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
_______\_ regions of polypeptide seek to be within protein,
________\_ regions face out: Helps drive folding of protein
Hydrophobic regions of polypeptide seek being within protein,
Hydrophillic regions face out: Helps drive folding of protein
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
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
Alpha Helixes:
– stabilized by ____________\_ between nearby residues
– within the R groups of a single chain
–________-_Handed helix
–Side Chains _________\_ w/ helical acess
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
Small ______\_residues such as ___\_ and ___\_ are strong Alpha helix formers
Small hydrophobic residues such as Ala and Leu are strong Alpha helix formers
__\_ acts as an alpha helix breaker because the rotation around the N-Ca bond is impossible
Proline acts as an alpha helix breaker because the rotation around the N-Ca bond is impossible
___\_ acts as a helix breaker because the small R-group (H) supports other conformations
Gly acts as a helix breaker because the small R-group (H) supports other conformations
- 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
The Beta Sheet
____\_in position 2 or ____\_ in position 3 are common in beta-turns
Proline in position 2 or glycine in position 3 are common in beta-turns
