Biochem Protein Lecture 3 Flashcards
What is the maximum number of H2O molecules that one H2O molecule can hydrogen bond with?
4
What are some of the amino acid side chains that can participate in H bonding because of their functional groups?
Serine, NH groups,
Do H atoms that are covalently bonded to C atoms participate in H-bonding? Explain.
No. C is only slightly more electronegative than H
This means fear of water
Hydrophobic
Nonpolar sidechains of amino acids are hydrophobic or hydrophilic?
Do they form H bonds?
Hydrophobic
No.
What structure do water molecules form around nonpolar groups in aqueous solution?
Ordered cage structures (clathrates)
Water molecules in cage structures limits the random motion and number of possible H-bonding arrangements, how does this effect entropy?
How does this effect solubility?
It decreases entropy
It limits solubility
ΔG = ΔH‐TΔS
MEMORIZE
A negative ΔG is more or less stable?
So removing a nonpolar group from an aqueous environment lowers or increases the free energy of the system
If the entropy change is negative, it makes a positive or negative contribution to ΔG? Is this favorable?
More
Lowers the free energy
Positive, not favorable
The combined behavior of an amino acid toward water is referred to as the
What two behaviors does it examine?
What describes it for the 20 common AAs? (Don’t memorize values but remember trends - highest/lowest values, in between, and why?)
A more positive number means….
Hydropathy
Hydrophobicity, hydrophilicity
Hydropathy Index
More hydrophobic AA. More negative number means more hydrophilic AA
Which AAs have the highest hydropathy values?
Which have the lowest (most negative) values?
What falls in the middle?
Non polar (isoleucine, valine, leucine, phenylalanine)
Polar (arginine, lysine, asparagine)
OH groups like serine
Why is isoleucine higher in hydropathy index than alanine?
It has a more branched chain
Note: the two hydropathy scales give same order, but table 4-1 tells you hydrophobic/less hydrophobic, etc
!
The more negative hydropathy means more hydrophilic or hydrophobic molecule?
What about more positive numbers?
Hydrophilic
Hydrophobic
These values are used to predict which portions
of a polypeptide chain are inside a protein and
not exposed to water, and which portions are
outside exposed to the aqueous environment
Hydropathy index
Amino acids can form these bonds, which refer to electrostatic interaction between positively nd negatively charged groups
Salt bonds
In the neutral pH region, carboxyl groups are a source of positive/negative charge?
Negative charge
in neutral pH, where can positive charge come from?
AA groups of side chain lysine
N-terminal AAs,
guanidno groups of arginine,
imidazolium ions of histidine side chains
The force of attraction between groups forming salt bridges is calculated using the formula…
F=q1q2/Dr^2
What is D in the force of attraction formula?
r?
The Dielectric constant
The distance between charges
These values are used to predict which portions
of a polypeptide chain are inside a protein and
not exposed to water, and which portions are
outside exposed to the aqueous environment
Dielectric constant
Insulators have high/low dielectric constants
Conductors?
Low
High
How do different solvent affect the strength of salt bonds?
They have different Ds
The attractive force in an aqueous environment is larger or smaller than in a nonpolar environment (for salts)
Much smaller, they dissociate easily
Salt bonds are impt to protein structure where ionic groups have more or less polar environments
Salts generally dissociate in
Salt bonds are important to protein structure where ionic groups have a less polar environment
Water
Metal can be bound reversibly with AAs, they associate with _____ and _____ligands
Anionic and neutral
Electrostatic interactions and nonbonded ligand
electron pairs donated to vacant metal orbitals are
important for bond formation
Basic forms of ionizable groups of amino acids as well as the sulfur of methionine can bind metal ions
What are the metal ions that are associated with AAs in proteins
Ca2+ Mg2+ Mn2+ Fe2+/Fe3+, Cu2+ Zn2+
Which AAs have absorption bands in the UV region
Which one has the greatest absorbance?
Where do proteins occur around in absorbance
Why?
What can UV absorption be used to estimate about proteins in a solution?
Trp, Tyr, Phe
Trp
280nm
The aromatic groups are responsible
Concentration
Two molecules of cysteine can oxidize and form a ____ bond
The oxidation product is called
Disulfide bonds are important to protein structural ____
disulfide
cystine
Stability
Show the side chain portion of the oxidation reaction of cysteine to cystine
~CH-CH2-SH + SH-CH2-CH~ –>
~CH-CH2-S-S-CH2-CH~ + 2H(+) + 2e(-)
Two amino acids can link together to form a covalent bond called _____, also defined as a substituted amide linkage
Peptide Bond
When a peptide bond forms, water is formed. What is the name of this reaction?
Where does the OH come from?
Where does the H come from?
Condensation Recation
The α‐COOH
The α‐NH2 of another AA
Are hydroxyls good leaving groups?
So the condensation reaction that forms a peptide bond favors AAs or dipeptide formation?
No they are poor leaving groups
It favors AAs over dipeptide formation
This term means few amino acids
This term means man amino acids, and is used it the molecular weight is less than 10,000
What term is used it mw>10,000
Oligopeptide
Polypeptide
Protein
Note that polypeptide and protein are used interchangeable
Peptide bonds are stable/unstable.
Their half life is
Stable
7 years
AAs are named starting from which terminus?
Their amino terminus, left to right
Are the constants of the newly formed free alpha amino and alpha carboxyl groups the same as before a peptide bond linkage? Why or why not?
No. They are no longer linked to the same alpha carbon, and are further away.
True or false: the pKa of an ionizable R-group can change when an AA becomes a residue of a peptide
True!
Name the two ways that can determine the pIs of peptides
Paper electrophoresis
Estimating the pI of a molecule by considering the contribution each ionizable group makes to the charge on the molecule at a given pH
Another method of determining pIs of polypeptides that is an electrophoretic method that establishes a pH gradient in a gel.
Isoelectric Focusing
The pH gradient in isoelectric focusing is formed by a mixture of low molecular weight molecules that contain both _____ and ______ groups
What are molecules that contain these groups called?
Carboxylic acid and amine groups
Ampholytes
How do the ampholytes distribute across the electric field generated across the gel tube during isoelectric focusing?
According to their pI values
If there is an equal number of molecules in each pI range on an isoelectric focusing gradient, what is the pH of the mixture?
Molecules with a pI less than 6.0 will be positively or negatively charged and move towards the cathode/anode?
Molecules with a pI greater than 6.0 will be positively or negatively charged and move toward the cathode/anode?
6.0
Negatively, Anode
Positively, cathode
When a protein molecule is added to the gel in isoelectric focusing, it migrates to the pH region corresponding to its ___ and then stops because it has _____
pI, zero charge
Naturally occurring peptides range from 2 amino acid residues to 1000s of residues
Can the smallest peptide have biologically important effects?
What is an example?
Yes
Aspartamate, a dipeptide known as nutrasweet
Can small peptides exert their effects at low concentrations?
What are examples?
Yes
Oxytocin, 9 aa residues
Antibiotics
Proteins can have a single polypeptide chain or multiple subunits, which are 2 or more polypeptides associated noncovalently, called
Do the chains have to be the same for these?
Multisubunit proteins
No. Same or different
If at least 2 individual polypeptide chains in a multisubunit protein are identical, the protein is
The identical units are called
What is an example?
oligomeric
Protomers
Hemoglobin, a tetramer or a dimer of αβ protomers
These proteins contain only amino acids
These proteins contain permanently associated chemical components in addition to amino acids
The non-AA part is called
Does it have to be organic?
Simple proteins
Conjugated proteins
Prosthetic Group
No, the prosthetic group can be organic or inorganic
Conjugated proteins are classified by the ____ because it is important to the biological function of the protein
Prosthetic group
Prosthetic groups can be composed of..
Nucleoproteins (contain nucleic acids)
Lipoproteins (contain lipids)
metalloproteins (contain metal ions)
To calculate the approximate number of AA residues in simple proteins, divide the mw of the protein by
How do they get this value?
110
Avg mw is 138
Smaller aa are most common, reduces it to ~ 128
A water molecule is removed (mw18)
=110
