Amino Acids Flashcards
What are the 2 functional groups of amino acids?
Amino group (NH2) and carboxyl group (COOH)
What is a alpha-carbon
carbon that bonds the amino and the carboxyl is the same carbon
What are the 4 components of amino acids?
Amino group, carboxyl group, hydrogen and a side chain (R-group)
What does the side chain do?
Determines the proprieties and the functions of the amino acid
What are called the 20 alpha-amino acids encoded by the human genetic code?
Proteinogenic amino acids
What do you call the carbon when the alpha-carbon is in the center?
Chiral (stereogenic)
How is the amino acid when the alpha-carbon is chiral?
Optically active
What is the only amino acid non optically active?
Glycine
How come Glycine isn’t optically active?
It has an hydrogen as the side chain, so it’s achiral
What type of amino acids are all chiral amino acids used in eukaryotes?
L-Amino acids
How do you draw an L-amino acid in the Fisher projection?
The amino group is drawn on the left
What type of configuration has almost all of amino acids in Cahn-ingold-Prelog System
(S) absolute configuration
Which amino acid is the exception of the Cahn-Ingold-Prelog System?
Cysteine has an (R) absolute configuration
Why cysteine has a (R) absolute configuration?
The CH2SH group has priority over the COOH group
What are the amino acids with non-polar, nonaromatic side chains?
Glycine, Alamine, Valine, Leucine, Isoleucine, Methionine, Proline
What are the 3 letter and the 1 letter name for Glycine?
Gly and G
What are the 3 letter and the 1 letter name for Alamine?
Ala, A
What are the 3 letter and the 1 letter name for Valine?
Val, V
What are the 3 letter and the 1 letter name for Leucine?
Leu, L
What are the 3 letter and the 1 letter name for isoleucine?
Ile, I
What are the 3 letter and the 1 letter name for Methionine?
Met, M
What are the 3 letter and the 1 letter name for Proline?
Pro, P
What are the 3 letter and the 1 letter name for Tryptophan
Trp, W
What are the 3 letter and the 1 letter name for Phenylalanine?
Phe, F
What are the 3 letter and the 1 letter name for Tyrosine
Tyr, Y
What are the 3 letter and the 1 letter name for Serine
Ser, S
What are the 3 letter and the 1 letter name for Threonine
Thr, T
What are the 3 letter and the 1 letter name for Arginine
Arg, R
What are the 3 letter and the 1 letter name for Asparagine
Asn, N
What are the 3 letter and the 1 letter name for Aspartic acid
Asp, D
What are the 3 letter and the 1 letter name for Glutamic acid
Glu, E
What are the 3 letter and the 1 letter name for Cysteine
Cys, C
What are the 3 letter and the 1 letter name for Glutamine
Gln, Q
What are the 3 letter and the 1 letter name for Histidine
His, H
What are the 3 letter and the 1 letter name for Lysine
Lys, K
Which amino acid is the smallest?
Glycine
Which amino acid is achiral?
Glycine
What is the side chain of Glycine?
A single H
What are the 2 amino acids with a sulfur atom in their side chain?
Methionine and cysteine
Why is methionine relatively non polar?
The sulfur atom is attached to a methyl group
What causes the 5 membered chain in Proline?
Limit its flexibility and has an effect on its role in secondary structure
What makes Proline unique?
The amino nitrogen’s becomes part of the side chain
What are the amino acid with aromatic side chains?
Tryptophan, Phenylalanine and Tyrosine
What is the only double ring amino acid?
Tryptophan
What is the side chain of Phenylalanine?
Benzyl (benzene ring + CH2 group)
How can we compare the Phenylalanine and the Tyrosine polarity?
Phenylalanine is less polar (relatively non-polar) and Tyrosine is more polar (relatively polar)
What the difference between Phenylalanine and Tyrosine?
Phenylalanine with an OH added
What are the amino acids with polar side chains?
Serine, Threonine, Cysteine, Asparagine and Glutamine
What are the two amino acids with polar side chains that has an OH group in their side chain?
Serine and Threonine
What the effect of having a OH group making Serine and Threonine highly polar amino acids?
They are able to participate in hydrogen bonding
What Asparagine and Glutamine have in common?
Both have amide side chains
What is Cysteine side chain?
Thiol side chain
What is a thiol side chain?
-SH group
Why is the thiol group prone to oxydation?
It’s thiol side chain (S-H bond if longer and weaker than O-H bond + the sulfur is more electronegative than the O)
What is the main difference between Asparagine/Glutamine and Aspartate/Glutamate?
Aspartate and Glutamate have a carboxylate group (-COO-)
What are the amino acids with a side chain negatively charged (acidic)?
Aspartic acid (aspartate) and Glutamic acid (glutamate)
What is aspartate compared to aspartic acid and glutamate compared to glutamic acid?
They are the anion (deprotonated aspartic acid or glutamic acid)
What are the amino acids with positively charged (basic) side chains?
Arginine, Lysine and Histidine
How many nitrogens are there in Arginine side chain?
3
What is Imidazole?
The aromatic ring with 2 nitrogens in Histidine
Where are amino acids with long alkyl side chains?
In the interior of the protein because it is HYDROPHOBIC
How are amino acids with charged side chains?
Hydrophilic
What are the amino acids with long alkyl side chains?
Alanine, Isoleucine, Valine, Phenylalanine
What are the amino acids with charged side chains?
Positively charged Histidine ,Arginine, Lysine, Negatively charged glutamate and aspartate and amides asparagine and glutamine
What are the amino acids more in the middle of the protein?
Cysteine, Glycine, Leucine, Methionine, Proline, Serine, Threonine, Tryptophan, Tyrosine
What is the acid group in the amino acid?
Carboxylic group (COOH)
What is the basic group in the amino acid?
Amino group (NH2)
What are amphoteric species?
Can either accept or donate a proton depending on the environment pH
What does ionizable group do in acidic conditions?
Tends to gain protons (protonated)
What does ionizable group do in basic conditions?
Tends to lose protons (deprotonated)
What means the pKa
pH where on average half of the molecules are protonated and half are deprotonated
Why does amino acids have 2 or more pKa
Because at least 2 groups can be protonated/deprotonated
What is the average pKa for carboxyl group?
2
What is the average pKa for amide group?
9-10
At pH 1, what would be the charge an amino acid?
Positively charged (amino group and carboxylic acid group are both protonated. Amino = positively charged. Carboxylic acid = neutral charge)
At pH 7.4, what would be the charge of an amino acid?
Electrically neutral. Amino protonated (positively charged) and carboxylic deprotonated (negatively charged).
How do you call an electrically neutral amino acid?
Zwitterions or dipolarions
At pH 10.5, what would be the charge of an amino acid?
Negatively charged. Amino acid deprotonated (negatively charged) and carboxyl deprotonated (negatively charged).
Why would the titration of an amino acid would look like 2 or 3 monoprotic titration curves?
If the side chain is charged it will be 3 curves
What happens to the titration curve when the pH is close to the pKa
The curve flattens
What is the pI
Isoelectric point (when every molecule is now electrically neutral
How do you calculate the pI of an neutral amino acid?
(pKa amino group + pKa carboxyl group)/2
How do you calculate the pI of an acid amino acid?
(pKa R group + pKa carboxyl group)/2
How do you calculate the pI of an acid amino acid?
(pKa amino group + pKa R group)/2
What are peptide made from?
Residue (amino acid subunits)
How many residue are in a dipeptide?
2
How many residue are in a oligopeptide?
20 or less
How many residue are in a polypeptide?
More than 20
What are peptide bonds?
Bonds between an COO- group of aa1 and NH3+ group of aa2
Peptide bond formation is made with what reaction?
Condensation or déshydratation (results in the removal of a water molecule (H2O)
How else can a peptide bond formation be viewed as?
Acyl substitution reaction
How is a peptide bond formed?
The electrophilic carbonyl carbon of aa1 is attacked by the nucleophilic amino group of aa2. The hydroxyl group of the carboxylic group is kicked off
What does resonance causes?
Rotation of the protein backbone around C-N amide bonds is restricted (not around other bonds that are single bonds) = protein more rigid
What is resonance?
C-N bond in the amide gets a partial double bond character
How do you read a peptide bond?
From N-Terminus (amino-terminus) to C-Terminus (carboxy-terminus)
What is hydrolysis?
Breaking down peptides into amino acids by adding an hydrogen atom to the amide group and a OH group to the carboxyl group
What are hydrolytic enzymes?
Enzymes that does hydrolysis
Hame 2 hydrolytic enzymes
Trypsin and Chymotrypsin
Where does trypsin acts?
At the carboxyl end of arginine and lysine
Where does Chymotrypsin acts&
At the carboxyl end of phenylalanine, tryptophan and tyrosine
What are examples of what a protein can be?
Enzymes, hormones, membrane pores and receptors, elements of cell structure
What is the primary structure of a protein?
Linear arrangement of aa coded in DNA, from N-terminus to C-terminus
How are primary structure stabilized?
By covalent peptides bonds between adjacent aa
How can you find the primary structure of a protein?
In a lab while doing sequencing (from the DNA or the protein itself)
True or False, the primary structure encodes all the information needed for higher structural levels?
True
What is the secondary structure?
Neighbouring aa (either in alpha-helix or beta-pleated sheet)
Secondary structure is created by what?
Hydrogen bonding between nearby aa
How are secondary structure stabilized?
Intramolecular hydrogen bonds between residues
What direction goes the alpha-helix formation?
Clock-wise around a central axis
How are intramolecular hydrogen bonds are matched in alpha-helix?
From carbonyl oxygen atom to the amide hydrogen 4 residue down
How are the side chains placed in alpha-helices&
Pointing away of the helix core
What is an example of alpha-helix protein?
Keratin
What are beta-pleated sheets like?
Parallel or antiparallel, chains along side another. Pleated or rippled shape
How are the intramolecular hydrogen bonds are matched in beta-pleated sheets?
From atoms from adjacent chains
How are the side chains orientated in beta-pleated sheets?
Above and below the plane of the sheet
What is an protein example of beta-pleated sheet?
Fibroin
What happens if a proline is in a alpha-helix formation?
It’s rigid cyclic structure would cause a kink in the peptide chain in the middle of the alpha-helix
When could you see a proline in an alpha-helix formation?
If it’s in protein that crosses the cell membrane
Where would a proline be placed in an alpha-helix formation?
At the start
Where would you rarely see a proline in a beta-pleated sheet?
In the middle
Where would you find a proline in a beta-pleated sheet?
In the turns between the chains
What are the 2 types of proteins?
Fibrous and globular
What is the shape of a fibrous protein?
Sheets or long strands
Name an example of fibrous protein
Collagen
Name an example of globular protein
Myoglobin
How are tertiary and quaternary structure made?
Protein folding
What determines the tertiary structure?
Hydrophilic and hydrophobic interactions between R-groups of aa.
Hydrogen bonding
Acid-base interactions
Disulfide bonds
What is the mechanism of hydrophilic and hydrophobic interactions that causes the protein to fold?
The hydrophobic residue wants to be inside of the protein. The hydrophobic residues inside the protein pull hydrophilic bonds such as N-H and C=O inside so they can form electrostatic interactions and hydrogen bonds that’ll stabilize the protein from the inside.
Phenylalanine is a highly hydrophobic group, where will it will almost always be in the protein?
It will mostly be inside, not on the surface of the protein
What are residues at the surface of the protein usually like?
Hydrophilic and polar or charged
What are salt bridges?
Acid-base interactions between aa with charged groups
What are disulfide bonds?
When 2 cysteine oxidized into 1 cystine
What does disulfide bonds do to the protein?
Create loops
What determines how wavy or curly our hair is?
Disulfide bonds
What is required to do a disulfide bond?
The loss of 2 protons and 2 electrons
What is called the intermediate state while the protein in folding?
Molten globules
What is denaturation?
When a protein loses its 3D structure
What is a salvation layer?
The layer formed around a solute with the solvant
What are quaternary structure made from?
Protein that contains more than 1 polypeptides chain.
What is a quaternary structure?
Aggregate of smaller globular particules or subunits
What does the quaternary structure represents?
The functional form of a protein
Does every protein has a quaternary structure?
No
What are examples of quaternary structure?
Hémoglobine and immunoglobulin G
What are the similarity between hémoglobine and immunoglobuline G
They both have 4 subunits
Why would one be in quaternary structure?
More stable,
Limits the amount of DNA needed to encode protein complex
Bring catalytic sites closer together
Induce cooperatively or allosteric effets
What is the point of bringing catalytic sites closer together?
Intermediates from one reaction are directly shuttled to a second reaction
What are conjugated proteins?
Proteins that gives part of their function ro a covalently attached molecule
What are called the group giving the conjugated protein their function
Prosthetic group
Lipoprotein, glycoprotein, nucleoproteins, what are they?
Prosthetic groups made from either lipid, carbohydrate or nucleic acid respectfully
Other than giving functionality to a protein, what can a prosthetic group do?
Direct protein to be delivered to a certain location
Is denaturation reversible?
It can be. It is usually irreversible tho
What can’t an unfolded protein do?
Catalyse reactions
What are the 2 main causes of denaturation?
Heat and solute
How does heat can desaturate a protein?
While the Temp is rising, the kinetic energy level is too. Once it’s high enough, it can overcome the hydrophobic-hydrophilic reaction holding the protein together
How can solute denaturate a protein?
Break disulfide bridges
Overcome hydrogen bonds and other side chains interactions holding alpha-helix and beta-pleated sheets
Solubilize protein
What does solubilizing a protein does?
Disrupt the non covalent bonds and promote denaturation
