BIOCHEM Chp.1 Amino Acids Flashcards
Amino acids, peptides and proteins
Amino function group
NH2
Carboxylic Acid Functional Group
C=O-OH
Alakane Functional Group
C-C
Alkene Functional Group
C=C
Alkynes Functional Group
triple bond
Alcohol Functional Group
C-OH
Ketone Functional Group
C=O
Ether Functional Group
R-O-R
Thiol Functional Group
R-S-H
Aldehyde Functional Group
R-C=OH
Ester Functional Group
R-C=O-O-R
Alanine 1 and 3 letter code
A, Ala
Arginine 1 and 3-letter code
R, Arg
Aspargine 1 and 3-letter code
N, Asn
Aspartic acid 1 and 3-letter code
D, Asp
Cysteine 1 and 3-letter code
C, Cys
Glutamic Acid 1 and 3-letter code
E, Glu
Hisitine 1 and 3-letter code
H, His
Isoleucine 1 and 3-letter code
I, Ile
Glutamine 1 and 3-letter code
Q, Gln
Leucine 1 and 3-letter code
L, Leu
Lysine 1 and 3-letter code
K, Lys
Methionine 1 and 3-letter code
M, met
Phenylalanine 1 and 3-letter code
F, Phe
Proline 1 and 3-letter code
P, Pro
Valine 1 and 3-letter code
V, Val
Tyrosine 1 and 3-letter code
Y, Tyr
Tryptophan 1 and 3-letter code
W, Trp
Threonine 1 and 3-letter code
T, Thr
Serine 1 and 3-letter code
S, Ser
Which AA are achiral
All AA are chiral except glycine, threonine and isoleucine
Which AA has an R-absolute configuration?
cysteine because the CH2SH has priority over the carboxylic group
Which AA has nonpolar, nonaromatic sidechains?
glycine, alanine, valine, leucine, isoleucine, methionine, proline
Which AA has aromatic side chains?
Tryptophan, phenylalanine, tyrosine
Which AA has polar side chains?
serine, threonine, asparagine, glutamine, and cysteine
Which AA has acidic side chains?
aspartic acid, glutamic acid, and aspartate, glutamate
Which AA has basic side chains?
arginine, lysine, and hisditine
Which functional group is weaker, thiol or hydroxyl?
thiol is weaker than hydroxyl because it is prone to being oxidized
Which AA is hydrophobic?
alanine, isoleucine, leucine, valine, and phenylalanine are strongly hydrophobic
Which AA is hydrophilic?
histidine, arginine, lysine, aspartate, glutamate, asparagine, glutamine
Where is hydrophobic AA found in the protein?
hydrophobic AA are more likely to be found in the interior of the protein, away from the water on the surface of the protein
What happens to AA at high vs low pH?
At very acidic or low pH, ionizable groups are protonated or positively charged, and deprotonated or negatively charged at very basic or high pH
What happens to AA at pH greater vs less than pKa?
When pH > pKa, the species is deprotonated and protonated when pH < pKa
What is the isoelectric point of acidic and basic AA?
AA with acidic side chains have relatively low isoelectric points (pI below 6), while those with basic side chains have relatively high ones (pI above 6)
How are peptide (amide) bonds formed?
the electrophilic carbonyl-carbon on the first amino acid is attacked by the nucleophilic amino acid on the second amino acid, then the hydrogel group of the carboxylic acid functional group is kicked off forming an amide bond.
Why Can peptide bonds form resonance?
amide groups have delocalized pi electrons in the carbonyl and in the lone pair of the amino nitrogen, thus the C-N bond in the amide has a partial double bond character
What are the 2 hydrolytic enzymes in peptide bond hydrolysis?
Trypsin cleaves at the carboxyl end of arginine and lysine, while Chymotrypsin cleaves at the carboxyl end of phenylalanine, tyrosine, and tryptophan, breaking apart the amide bond by adding a H-atom to the amide nitrogen ad OH to the carbonyl carbon
What is hydrolysis?
the breaking of an amide bond by adding an H atom to the amide nitrogen and an OH to the carbonyl carbon through the use of a hydrolytic enzyme
What is the primary structure of a protein?
the order of the proteins aa which can be determined via lavatory sequencing
What is the secondary structure of a protein?
alpha-helix and beta-sheets, both of which result from hydrogen bonding
What is the tertiary structure of a protein?
its 3D shape, which is determined by the hydrophilic and hydrophobic interactions between R-groups of aa
What is the quaternary structure of a protein?
an aggregate of smaller globular proteins, or subunits, and represents the functional form of the protein
Describe the structure of a-helix.
peptide chain coils clockwise around the central axis, stabilized by H-bonds b/w the carbonyl atom and hydrogen atom 4 residues down with the side chains pointing away from the core
Describe the structure of b-sheet
peptide chains lie alongside each other in parallel or anti-parallel rows held together by H-bonds b/w the carbonyl oxygen atom and the amide hydrogen atom of an adjacent chain with the side chains pointing above and below the sheet
What structural proteins are a-helix an important component of?
Keratin, a fibrous structural protein found in human skin, hair, and fingernails.
What structural proteins are b-sheets an important component of?
Fibronin, the primary component of silk fibers
Where is proline often found in secondary protein structures?
in the turns b/w the chains of b-pleated sheets, and as residues at the start of an a-helix
What role does proline serve in secondary structures?
it creates kinks in the a-helices and turns in b-sheets of the peptide chain
What is an important component of tertiary structures?
disulfide bonds are formed when 2 cysteine molecules are oxidized to cystine, creating loops in the protein chain.
What happens if a protein loses its tertiary structures?
if a protein loses its tertiary structure, a process commonly called denaturation, it loses its function
What is the result of a negative entropy (change in S)
a negative entropy represents increasing order (decreasing disorder/entropy) to a system and, thus is unfavorable b/c it makes the overall process nonspontaneous (change in G > 0)
Which grouping of aa makes a protein’s tertiary structure most stable?
by moving hydrophobic residues away from water molecules and hydrophilic residues toward water molecules, a protein achieves maximum stability
What are the roles of the formation of the quaternary structures?
- More stable by further reducing the surface area of the protein complex
- reduce the amount of DNA needed to encode the protein complex
- Can bring catalytic sites together
- induce cooperativity or allosteric effects
What are examples of quaternary structures?
hemoglobin, immunoglobulin
How do conjugated proteins function?
they derived part of their function from covalently attached molecules called prosthetic groups, which can be organic molecules such as vitamins or metal ions such as iron.
What are proteins with lipids, carbohydrates, and nucleic acid prosthetic groups referred to?
Lipoproteins, glycoproteins, and nucleoproteins
What is the role of prosthetic groups in proteins?
they play a major role in determining the function of their respective proteins, and can also direct the protein to be delivered to certain locations such as the cell membrane, nucleus, lysosomes, or ER
What are the 3 main causes of protein denaturation?
- heat - increasing the temperature of a protein increases its average kinetic energy causing the protein to unfold
- high solutes (urea) - directly interfere with the forces that hold the protein together, disrupting tertiary and secondary structures by breaking disulfide and hydrogen bonds
- detergents (SDS) - solubilize proteins, disrupting noncovalent bonds
How are tertiary and quaternary structures stabilized?
van der Waals forces, H-bonds, ionic and covalent bonds
