Amino Acids, Peptides, Proteins Flashcards
Amino Acids
molecules that contain two functional groups: amino (NH2) and carboxyl (COOH)
also has one Hydrogen and side chain R-Group
Proteinogenic Amino Acids
the 20 alpha amino acids
Alpha-Carbon
4 different groups attached to it so its chiral
most amino acids are optically active/chiral except Glycine (2 Hs)
All chiral amino acids in Eukaryotes are ______. This is an ____ absolute configuration.
This does not apply to ____ as it is ________ amino acid but as _______ configuration
L-amino acids
S
cysteine
L
R
Non-Polar, Non Aromatic Side Chains
glycine alanine valine leucine isoleucine methionine proline
Aromatic Side Chains
uncharged aromatic side chains
Tryptophan
Phenyalanine
Tyrosine (phen with OH)
Polar Side Chains
Serine and THreionine (OH)
Aspargine and Glutamine (Coo- with NH2 terminal)
Cysteine (thiol)
Negatively Charged (Acidic) Side Chains
aspartate/aspartic acid
glutamate/glutamic acid
end with a carboxyl group (acid has a full carboxyl, the anion hs the charge)
Positively Charged (Basic) Side Chains
Arginine (3 N groups)
Lysine (ends with NH2)
Histidine (aromatic pentane with an NH with addable H)
Amino acids with long alkyl chains are strongly ______ and found in the ___ parts of protein
All chains with charged side chains are ______.
hydrophobic
interior
hydrophillic
Amino Acid Abbreviations: Alanine
Ala, A
Amino Acid Abbreviations: Arginine
Arg, R
Amino Acid Abbreviations: Asparagine
Asn, N
Amino Acid Abbreviations: Aspartic Acid
Asp, D
Amino Acid Abbreviations: Cysteine
Cys, C
Amino Acid Abbreviations: Glutamic Acid
Glu, E
Amino Acid Abbreviations: Glutamine
Gln, Q
Amino Acid Abbreviations: Glycine
Gly, G
Amino Acid Abbreviations: Histidine
His, H
Amino Acid Abbreviations: Isoleucine
Ile, I
Amino Acid Abbreviations: Leucine
Leu, L
Amino Acid Abbreviations: Lysine
Lys, K
Amino Acid Abbreviations: Methionine
Met, M
Amino Acid Abbreviations: Phenylaline
Phe, F
Amino Acid Abbreviations: Proline
Pro, P
Amino Acid Abbreviations: Serine
Ser, S
Amino Acid Abbreviations: Threonine
Thr, T
Amino Acid Abbreviations: Tryptophan
Trp, W
Amino Acid Abbreviations: Tyrosine
Tyr, Y
Amino Acid Abbreviations: Valine
Val, V
Amphoteric Apecies
able to accept a proton or donate a proton depending on the pH of the environment
Ionizable groups tend to ___ protons under acidic conditions and ____ them under basic conditions.
gain
lose
If pH < pKA, a species will be ______
If pH > pkA species will be ____
protonated
deprotonated
Zwitterions
multicharged, dipolar ions whose charges cancel out
When pKas are met, the amount of _____ and protonated/deprotonated amino acid are the same. The titration curve is ____and the solution is acting as a _____
zwitterion
flat
buffer
Isoelectric Point
every molecule is a neutral zwutteruib. pH- pImeans neutral solution
pI = pKaNH3 + pKaCOOH / 2
When molecule is neutral, it is very sensitve to ______, hence titration curve is _____
pH change
vertical
pI For Acidic Amino Group (fully protonated charge +1)
pI = pKa R + pKaCOOH /2
so its low
pI For Basic Amino Group (fully protonated state charge +2)
pI = pKa R + pKaNH /2
so its high
Peptides
consist of amino acid subunits/residues
Oligo vs Polypeptides
small peptides upto 20 residues
longer chains of residues
Peptide Bonds
join peptide bonds together between the COO- and NH3+ of 2 amino acids
formed via dehydration/condensation
partial double bond characteristic due to carbonyl and lone pair on amino nitrogen, thus resonance occurs
Condensation Reaction of Peptide Bonds
electrophillic carbonyl carbon is attacked by nucleophillic amino group of another amino acid and hydroxyl of carboxy is kicked off
No rotation aroun the ______ bond
Carboxy-Amino
Hydrolysis of proteins is carried out by _____ or ______. They cleave at ______ of the peptide chain by adding a ______ to the _____ and a _____ to the _______.
trypsin
chymotrypsin
specific parts
H
amino
OH
carbonyl
Proteins
polypeptides that range from a few amino acids to thousands and act as:
enzymes, hormones, membrane pores and receptors
Primary Structure
linear sequence from N amino end to C carboxy end
stabilized by: covalent peptide bonds
allows for encoding for high folding structures
can be sequenced
Secondary Structure Alpha Sheets
hydrogen bonding between amino acids
coils around a central axis
intramolecular hydrogen bonds between carbonyl oxygen and adjacent amino hydrogen, side chains point away from coil
Secondary Structure Beta Sheets
parallel or antiparallel
peptide chains lie alongside one another by intramolecular hydrogen bonds between carbonyl oxygen and amide hydrogen in adjacent chain
rippled/pleated to accomodate for most H bonds
R groups are above or below the plane of the sheet
Due to itsrigid, cyclic nature, ____ will cause kinks in peptide chains in a ______ structure, hence theya re rarely found in them.
They are rarely found in middle of _____ but are in the ___ between chains of B pleated sheets and at the start of a alpha helix.
proline
alpha helix
pleated sheets
turns
Tertiary Structure
determined by hydorphobic and hydorphillic interactions between R groups of amino acids
stabilized further by electrostatic and hydrogen bonds between hydrophillic residues that get pulled within. Also have disulfide bonds from two cysteine molecules oxidizing to make structure more stable
amino acids have charged/polar R groups on the outside
Molten Globules
intermediate states between secondary structure, hydrophobic interactions/H bonding and three dimensional shape
Denaturation
protein losing its tertiary structure, thereby losing its function
Solvation layer
when solute dissolves in a solvnt, the solvent molecules form a layer around the solute
when hydrophobic residues in contact with water, difficulty in making h-bonds so water rearranges itself (cages) to create a negative change in entropy making it unfavorable (delta G gets more positive so nonspontaneous)
opposite occurs for hydrophillic residues
Quaternary Structure
not all proteins have Quaternary structure
aggregate of smaller globular peptides/subunits that represent function
Pros
- more stable by reducing SA of protein complex
- reduce DNA needed to code complex
- Bring catalytic sites together
- Induces Cooperativity/allosteric effects
Hemoglobin
4 distinct subunits which can each bind to one oxygen, so it can carry a total of 4
Conjugated Proteins
derive function from covalently attached molecules known as prosthetic groups
Prosthetic Groups
can be organic molecules or metals
lipoproteins (lipid)
glycogrpoteins (carbohydrate)
nucleoproteins (nucleic acid)
Two main causes of denaturation are
temperature and solutes
When temperature gets to high, it can overcome the _____ which hold the proteion together and cause it to unfold.
hydrophobic interactions
Solutes can denature proteins by breaking ______, overcoming ______ and other side chain interactions and non-covalent bonds.
disulfide bonds (cysteine goes to 2 cysteines)
hydrogen bonds
