BIO CHEM CH.4 PART 1 Flashcards
What is the unique feature of all twenty amino acids?
Side chain which gives it its physical and chemical properties that distinguish it from the other nineteen
What are the two acidic amino acids?
- Aspartic acid
2. Glutamic acid
What is the side chain of the two acidic amino acids?
Carboxylic acid functional group with a pKa of 4
What is the difference between glutamate and glutamic acid?
Refer to the anionic form (deprotonated)
Which amino acids are considered basic?
Lysine, arginine and histidine
What is the pKa value of the 3 basic amino acids?
Lysine: 10 Arginine: 12 and Histidine: 6.5
What is the three letter code fo glutamic acid and aspartic acid?
Glu and Asp
What is the one letter code for glutamic acid and aspartic acid?
E and D
What is unique about histidine?
Unique in having a side chain with a pKa close to physiological pH and can be protonated or deprotonated at pH 7.4
Amino acids containing -COOH side chains are always…
Anionic
Amino acids containing -NH2 side chains are always….
Cationic
What is the three letter code for histidine, lysine and arginine?
His, Lys and Arg
What is the one letter code for histidine, lysine and arginine?
H, L, and R
What do the hydrophobic amino acids contain for their side chains?
aliphatic (alkyl) or aromatic side chains
What are the amino acids with an aromatic side chain?
Phenylalanine, tryptophan and tyrosine
What are the amino acids with an aliphatic side chain?
Glycine, alanine, valine, leucine and isoleucine
Why are hydrophobic side chains found on the interior of folded globular proteins?
Hydrophobic residues tend to associate with each other rather than with water
The large the hydrophobic group of the amino acid…..
The greater the hydrophobic force repelling it from water
What is the three letter code for glycine, alanine, valine, leucine?
Gly, Ala, Val and Leu
What is the three letter code for isoleucine, phenylalanine, tryptophan?
Ile, Phe and Trp
What is the one letter code for glycine, alanine, valine, leucine?
G, A, V and L
What is the one letter code for isoleucine, phenylalanine, tryptophan?
I, F and W
How are the polar amino acids characterized?
R-group polar enough to form H bonds with water but does not act as an acid or base
What do the side chains of polar amino acids usually have?
Hydroxyl or single double bonded O
Which amino acids have a hydroxyl group on their side chains?
Serine, threonine and tyrosine
What happens to the hydroxyl group of serine, threonine and tyrosine?
Often modified by a kinase to attach a phosphate
What are the five amino acids corresponding to the polar amino acid groups?
Serine, threonine, tyrosine, asparagine and glutamine
What is the three letter code for serine, threonine, tyrosine, asparagine and glutamine?
Ser, Thr, Tyr, Aan and Gln
What is the one letter code for serine, threonine, tyrosine, asparagine and glutamine?
S, T, Y, N and Q
What are the two amino acids that have sulfur-containing side chains?
Cysteine and methionine
What type of side chain does cysteine include?
Contains a thiol
What type of side chain does methionine include?
Thioether
What type of amino acid polarity does cysteine have? What about methionine?
Polar; nonpolar
Why is proline unique?
Its amino group is covalently bound to its non polar side chain, creating a secondary alpha-amino group and distinctive ring structure
What type of polarity does proline have?
Nonpolar
What is the one letter code for cysteine, methionine and proline?
C, M and P
What is the three letter code for cysteine, methionine and proline?
Cys, Met and Pro
What are the nine essential amino acids that cannot be synthesized by humans?
- Lysine 2. Histidine 3. Threionine 4. Valine 5. Leucine 6. Isoleucine 7. Phenyalanine 8. Tryptophan 9. Methionine
Are amino acids amphoteric?
Yes
What is the pKa of carboxyl groups on amino acids?
2
What is the pKa of ammonium groups on amino acids?
9 or 10
What does the Henderson-Hasselbach explain?
Mathematical formula that describes the relationship between pH, pKa and the position of equilibrium in an acid-base reaction
What is the Henderson-Hasselbach equation?
pH = pKa + log [A-]/[HA] = pKa + log([base form]/[acid form])
What happens to the acidic group when the solution is less than the pKa of the acidic group?
Protonated form
What happens to the acidic group when the solution is more than the pKa of the acidic group?
Deprotonated form
Acids with low pKa tend to _______ more easily….
Deprotonated
Alll amino acids contain what two groups? What do they act as based on acids and bases?
Amino and carboxyl group; amino as a base and carboxyl as an acid
What is the protonated or acidic form of the amino group?
Ammonium group
What’s the pKa of the ammonium group?
Between 9-10
A molecule with a positive and negative charges that balance is referred to as a ….
Dipolar ion or zwitterionic
What is the name of the pH at which a molecule is uncharged (zwitterionic)?
Isoelectric point (pI)
How to determine the pI of an amino acid?
Figure out the pH value at which the positive and negative charges balances
If the p is higher than the pKa, the group is mostly….?
Deprotonated
If the p is higher than the pKa, the group is mostly….?
Protonated
What are the two common bond between amino acids in proteins?
- Peptide bonds linking amino acids together into polypeptide chains
- Disulfide bridges between cysteine R-groups
How are polypeptides formed?
Formed by linking amino acids
Where is a peptide bond formed based on two amino acids forming it?
Between the carboxyl group and alpha-amino group of amino acids
What is lost during peptide formation?
Water
Based on the polypeptide chain, what’s always first and what’s always last?
Amino terminus is first and carboxyl terminus is last
What is the term to explain hydrolysis of a protein?
Proteolysis or proteolytic cleavage
What is protease?
Protein that complete proteolysis
What is the reactive group on the cysteine?
Thiol (sulhydryl SH) in its side chain
What is the importance of a disulfide bridge?
Stabilizing tertiary protein structure
What does denaturation refer to?
Disruption of a protein’s shape without breaking peptide bonds
What can cause a protein denaturation?
- Urea 2. Extreme pH 3. Extreme temperature or 4. Changes in salt concentration
What is the primary structure in protein folding?
The order of amino acids bonded to each other in the polypeptide chain
What is the secondary structure in protein folding?
Initial folding of a polypeptide chain into shapes
What is the secondary structure stabilized by?
Stabilized by hydrogen bonds between backbone
The hydrogen bonds are stabilized between what, based on secondary structure?
Between backbone NH and CO groups
What are the two common motifs of the secondary structure in protein folding?
Alpha-helix and beta pleated sheets
The alpha helixes of proteins are always…..?
Right-handed, 5 angstroms in width with each subsequent amino acid rising 1.5 angstroms
How many amino acids are present per turn in an alpha helix shape?
3.6 amino acid residues per turn
Which amino acid has a problem in the polypeptide chains during secondary structure of protein folding?
Proline
Why does proline disrupt the backbone hydrogen bonding in the polypeptide chain?
Because the formation of peptide bond with proline eliminates the only H atom on the nitrogen atom of proline
What does the structure of proline force the polypeptide chain to do?
Kink
Prolines can be present in alpha and beta pleated sheets. T/F
False: proline residues never appear within the alpha-helix
Hormone receptors and ion channels are often found where, based on secondary structure?
With α-helical transmembrane regions integrated into the hydrophobic membranes of cells
Why is the α-helic a favorable structure for a hydrophobic transmembrane region?
Because all polar NH and CO groups in the backbone are hydrogen-bonded to each other on the inside of the helix
What do α-helical regions have that allow them interact with the hydrophobic interior of the membrane?
Hydrophobic R-groups
Where do the NH and CO groups bonding happen in the beta-pleated sheets?
Bonding occurs between residues distant from each other in the chain or even on separate polypeptide chains
What are the two types of beta pleated sheets?
Parallel and antiparallel
What is a parallel beta pleated sheet?
Adjacent polypeptide strands running in the same direction
What is an anti-parallel beta pleated sheet?
Adjacent polypeptide strands running in opposite directions
What is the tertiary protein folding?
Interactions between amino acid residues located more distantly rom each other in the polypeptide chain
In which protein folding is there electrostatic interactions between acidic and basic side chains?
Tertiary folding
What is the tertiary structure folding driven by?
Interactions between R groups and with the solvent (water)
What is the hydrophobic effect?
During tertiary structure, hydrophobic R-groups tend to fold inwards while hydrophilic fold outwards
What is quaternary structure in protein folding?
Describes interaction between polypeptides
What bond cannot be involved in quaternary structure and why?
Peptide bond because this bond defines sequence; primary structure
As catalysts, enzymes have a _____ role and not a ____ one.
Kinetic role, not thermodynamic
Enzymes can control the direction, therefore can go forward or backwards when demanded. T/F
False: Enzymes cannot control the direction in which a reaction proceeds
What are hydrolases?
Hydrolyzes chemical bonds
What are isomerases?
Rearranges bonds within a molecule to form an isomer
What are ligase?
Forms a chemical bond
What are lyases?
Breaks chemical bonds by means other than oxidation or hydrolysis
What are kinases?
Transfers a phosphate group to a molecule from a high energy carrier
What are oxidoreductases?
Runs redox reactions
What are polymerases?
Polymerization
What are phosphatase?
Removes a phosphate group from a molecule
What are phosphorylase?
Transfers a phosphate group to a molecule from inorganic phosphate
What are proteases?
Hydrolyzes peptide bonds
What is a reaction coupling?
One very favorable reaction is used to drive an unfavorable one
Why is reaction coupling possible?
Because free energy changes are additive
What is a favorable reaction the cell can us to drive unfavorable reactions?
ATP hydrolysis
What are the two ways ATP hydrolysis can drive an unfavorable reaction?
- Causing a conformational change in a protein
2. Transfer of a phosphate group from ATP to a substrate
What is the active site model theory?
The substrate and the active site are perfectly complementary
What is the induced fit model?
The substrate and active site differ slightly in structure and binding of substrate induces a conformational change of the enzyme
How does enzymes accelerate the rate of given reaction?
Helping stabilize the transition state
Which configuration of amino acids are found in animals?
L amino acids
Many proteases have an actives site with…?
Serine residue whose OH group can act as a nucleophile,
How does the serine residue’s OH group act as a nucleophile?
Attacks the carbonyl carbon of an amino acid residue in a polypeptide
What are examples of the proteases with a OH serine group nucleophile ?
Trypsin, chymotrypsin and elastase
Why is pH important for enzymes to function?
Several amino acids possess ionizable R groups that change charge depending on pH
What is a cofactor?
An associative additional molecule for an enzyme to run
What is a coenzyme?
When the cofactor is an organic molecule
How are enzyme regulated by proteolytic cleavage?
Enzymes synthesized in inactive forms at are then activated by protease cleavage
How are enzymes regulated by covalent modification?
Different groups covalently attached them which can regulate their activity
What is the most common example of covalent modification
Phosphoryl group from ATP by a protein kinase to the hydroxyl of serine, threonine or tyrosine
How does protein phophorylases does its work?
Uses free-floating inorganic phosphate in the cell
How can protein phosphorylation be reversed?
By a protein phosphatase
How are enzymes regulated by association with other polypeptides?
Some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit
