What are the four different roles of proteins?
1) Catalysis
2) Transport
3) Structure
4) Motion
Does each cell make a similar or different repertoire of proteins?
Different
Define genome.
Refers to all the genes encoded in a cell’s DNA.
Define transcriptome.
Refers to complete RNA profile.
Define proteome. How do proteomes vary by tissue?
Refers to protein complement expressed by a cell.
ex: proteome of liver not the same as heart.
Subsets of proteins depend on what?
They are tissue dependant
How many genes do we have? And proteins?
30 000 genes
50 000-100 000 proteins
Define peptide.
Small protein containing 2-50 amino acids
Define polypeptide.
More than 50 amino acids
How many naturally occurring amino acids are there?
20
Name the three classes of protein.
1) Soluble Proteins
2) Membrane Proteins
3) Fibrous/Structural Proteins
What is the chemical composition of an amino acid?
Amino Group + Side Chain (R) + Carboxyl Group
Name two properties of amino acids.
- Can function as buffers
- Capacity to polymerize
Define a chiral molecule.
Non-superimposable on its mirror image; possesses an asymmetric carbon center.
How do you achieve chirality?
If you attach 4 different groups to an alpha carbon
Which amino acid is the only non-chiral one?
Glycine (2 hydrogens)
Define enantiomers. Give an example of an enantiomer.
Non-superimposable mirror image.
Amino acids are enantiomers
Define racemization.
Conversion of an enantiomerically pure mixture into a mixture with more enantiomers.
Define a racemic mixture.
D and L configurations present in equal quantities.
How does racemization between L and D isomers occur? Is it fast?
Spontaneously
Reaching equilibrium is a VERY slow process
What is the most abundant configuration of amino acids?
CORN configuration (L configuration)
What biological compound can back convert?
Enzymes but ONLY in living cells (D to L)
How many essential amino acids are there?
8
Which two amino acids are considered essential for infants?
Arginine and HIstidine
Name the 5 classes of amino acids.
1) Non-polar, aliphatic
2) Aromatic
3) Polar, uncharged
4) Positively charged
5) Negatively charged
Which classes of amino acids are hydrophobic?
1) Non-polar, aliphatic
2) Aromatic
Which classes of amino acids are hydrophilic?
1) Polar, uncharged
2) Positively charged
3) Negatively charged
Which amino acid is referred to as a secondary amine? Why?
Proline, since it cycles back and reacts with the alpha amino group
Which group of amino acid has a strong ultraviolet light absorption properties?
Aromatic group
Which amino acid in the aromatic group does not have strong ultraviolet light properties? Why?
Phenylalanine, since it does not have conjugation
Which amino acid can be involved with covalent disulfide bonds?
Cysteine
What are cysteine bonds (disulfide bonds) critical for?
Controlling the structure of proteins when they are released outside the cell
Where do cysteine bonds occur?
In an oxidizing environment
Which amino acids are always positively charged under biological systems? Why?
Arginine and Lysine
Since they have high pKas
Which amino acid is not always positively charged under biological systems, but can be?
Histidine, pKa=6
Neutral at pKa>6, Positively charged at pKa
If you add a proton to Histidine, what becomes positively charged?
the N will undergo protonation
At neutral pH, the carboxyl group is ______ but the amino group is ______. The net charge is ___.
deprotonated, protonated, 0
At acidic pH, the carboxyl group is ______ but the amino acid is in its ______ form. The net charge is ___.
protonated, cationic, +1
At alkaline pH, the amino group is ______ but the amino acid is in its ______ form. The net charge is ___.
neutral, anionic, -1
Define Zwitterions.
Positive and negative ions that can act as either an acid or a base
Define isoelectric point.
pH where the net charge on the molecule is 0.
Occurs at 1 equivalence, no net charge
What is the equation to define the isoelectric point?
pI = (pK1 + pK2)/2
If it is an acidic amino acid, which range will the pI be in?
Acidic range
If it is a basic amino acid, which range will the pI be in?
Alkaline range
How do amino acids undergo polymerization?
In a head to tail fashion.
How are peptides formed? What does it result in?
By condensation, results in the loss of water
What is the primary structure of a protein?
The linear sequence of amino acids.
Where does the primary structure being? End?
Begin: free amino end (or N-terminal)
End: free carboxyl end (C-terminal)
What does the primary structure contain?
Information that allows 2nd and 3rd structure.
What character do peptide bonds display? Why?
Partial double bond character due to electron delocalization
What does the partial double bond character cause?
Restricts rotation around the peptide bond.
How do single, double, and peptide bond lengths differ?
Peptide bond lengths are right in between the two
Which type of peptide rotations are permitted? Which aren’t?
Permitted: rotation around bonds connected to the alpha carbon
Not permitted: rotation around the peptide bond
The phi angle refers to which bond?
Amide nitrogen bond (N-C)
The psi angle refers to which bond?
Carbonyl carbon bond (C-C)
Which configuration is conformationally favorable? Why?
Trans since atoms can’t occupy the same space
What angles can psi and phi angles never be? Why?
0 or 180 since atoms can’t occupy the same space
Why is Proline conformationally unique? Why?
Since it switches between cis and trans configurations (second amine)
What gives rise to secondary structure?
Phi and psi angles
Name the three secondary structures.
- a-helix
- B-sheets
- B-turn
What defines and stabilizes the secondary structure?
- Hydrogen bonds between the main chain peptide groups
- R-chain helps stabilize as well
What stabilizes the a-helix?
Intra-hellical hydrogen bonds
What is the pitch of the a-helix per turn?
3.6
What atoms are hydrogen bonded in an a-helix?
H-bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom
Which amino acid likes to form helices? Which don’t?
Like: Alanine
Don’t like: Proline and Glycine
How can R-groups affect the structure of a helix.
They will either stabilize (attraction) or destabilize (repulsion)
How does pH influence the structure of a helix?
For ex, putting a protein into an acid will disrupt the hydrogen bonds (protonation) and cause the protein to unravel
What is the driving force for proteins to fold?
Hydrophobic interactions
Which hand is the most common helix
Right hand
Name a biological molecule that has a left-handed helix.
Collagen
Where is the - end on a helix? And _?
Carboxyl (-)
Amino (+)
What’s the difference between parallel and antiparallel B-sheets?
Parallel: amino groups point in the same direction
Antiparallel: amino groups point in opposite directions
What’s critical for antiparallel B-sheets?
To have a tight-turn to allow the protein strand to do an 180o turn
Which type of B-sheet cannot be contiguous?
Parallel
What does the Ramachandran plot dictate?
Protein structure is dictated by the phi and psi angles
How many amino acids do B-Turns involve?
4 amino acids
Where are proline and glycine situated on a B-turn?
Proline (2) Glycine (3)
What is the function of the B-turn?
Allows the proteins to do an 180o turn
What are the characteristics of spider silk?
Stronger than steel, stretches
What is spider silk stabilized by?
Hydrogen bonds & Van der Waals interactions
What amino acids are in high abundance in spider silk?
Glycine and Alanine
What is the MAIN driving force of tertiary structure?
Bury hydrophobic interactions
Are B-sheets flat? Why/Why not?
B-sheets are flat, but not completely planar because of angles (tend to have a twist)
Name some favorable interactions in proteins.
- Hydrophobic Effect
- Hydrogen Bonds
- Van der Waals Interactions
- Electrostatic Interactions
- Disulfide Bonds
How is the tertiary structure of proteins held together?
Electrostatic interactions
How does protein structure evolve?
To accommodate the environment
Define homomeric.
Same subunits
Define heteromeric.
Different subunits
Define oligomeric.
More than one subunit (could be homo or hetero)
Provide examples of how quaternary structures bind together.
- Hydrophobic interactions
- Hydrogen bonds
- Disulfide bonds
Describe the function of the Allosteric effect.
- Easier to load and unload oxygen
- Allows to more tightly regulate the activity of an enzyme
If there is a change in amino acid, which protein structure would it affect the most?
Quaternary
Describe briefly the 4 levels of protein structure.
Primary: amino acid residues (important order of polymerization)
Secondary: a-Helix
Tertiary: polypeptide chains
Quaternary: assembled subunits
For a generic amino acid, NH2CRHCOOH (uncharged), what would be the predominant form at:
a) pH=1
b) pH=7
c) pH=11
a) +NH2CRHCOOH
b) +NH2CRHCOOH-
c) NH2CRHCOOH-
What determines how curly a human’s hair is?
Disulfide bonds
What do disulfide bonds create?
Loops in the protein chain
Do all proteins have quaternary structure? In what case?
No, exist for proteins that contain more than one polypeptide chain
In a neutral solution, most amino acids exist as ____?
Zwitterions
At pH 7, what is the charge on a glutamic acid molecule?
2x negative because of 2x carboxyl
1x positive because of amino
so -1
What holds up tertiary structure?
Disulfide bridges and hydrophobic effects
Which amino acids would be likely to be found in a transmembrane portion of the a-helix?
Amino acids with a hydrophobic side chain
Which amino acid is likely to be found in high concentration in collagen?
Glycine, reduce steric hindrance
Why can amino acids ionize?
Since both the carboxyl and amino groups (sometimes side chains as well) can ionize
Why is glycine not optically active?
It does not have a D and L isomer, not chiral
Which amino acid allows the most structural flexibility (least amount of steric hindrance)? Which the least?
Most: Glycine
Least: Proline
What happens to an R-group when pH < pka? When pH pka?
pH smaller than pka: protonation
pH higher than pka: deprotonation
Name the amino acids that are positively charged at physiological pH.
Lysine and arginine
Histidine (possibly, but low pKa)
Name the amino acids that are part of the aromatic R group, hydrophobic and neutral at any pH
Phenylalanine and tryptophan
not tyrosine since it has an OH
Name the amino acids that have saturated hydrocarbon R groups.
Alanine, valine, leucine, isoleucine
Name the only amino acid having an R group with a pKa near 7.
Histidine
Name the only amino acid with a substituted a-amino group.
Proline
Why are all individual amino acids soluble in water but not all peptides are soluble?
Individual amino acids are zwitterions at physiological pHs
What do the amino acids threonine and tyrosine have in common?
Both have an OH group (contributes to polarity and hydrogen bonding)
What makes amino acid cysteine so important? Can methionine perform the same function?
Cysteine can form disulfide bridges to stabilize the structures of proteins, methionine cannot
Are protein structures static?
No, they undergo changes in conformation
Where do phi and psi angles occur?
In the peptide backbone
How many residues per turn does an alpha helix have?
3.6 residues/turn
The rise along the helical axis for each amino acid residue is ____?
Rise: 5.4/3.6 residues per turn = 1.5
Where are the amino acid sidechains on an a-helix?
The amino-acid side-chains are on the outside of the helix, and point roughly “downward”
Where are the R groups located in a B-sheet?
Opposite directions, either below or above the peptide chain (alternating)
What noncovalent forces stabilize B-sheet structures?
Hydrogen bonds
What is unusual about peptide bonds involving the nitrogen of proline in B turns?
It readily assumes the cis configuration, a form that is particularly amenable to a tight turn.
How can we permanently wave someones hair?
1) Reduce disulfide bonds to seperate cysteines
2) Curl the hair with heat
3) Oxidize the hair to form new disulfide bonds with the curled formation
What are the roles of soluble proteins (globular)?
Antibodies, enzymes, structural
What are the roles of membrane proteins?
Hydrophobic proteins, transporters, receptors
What are the roles of fibrous/structural proteins?
Keratin, muscles (myosin), spider webs (silk)
How many pKa values does glycine have? It can act as a buffer in how many regions?
- Two pKa values (carboxyl and amino group)
- Buffer in two regions
What is the most likely charge of tyrosine at pH 7?
Neutral
What is the probability of histidine to have a positive charge at ph=7? ph=6?
pH7: 10%
pH6: 50%
Very sensitive to pH change in the physiological range
What is the phi angle between? Psi? Peptide bond?
Phi: N-Ca
Psi: Ca-C
Peptide bond: C-N