AA, Peptides, Proteins Flashcards
Amphoteric Species
Functional group that can act as e- donor or e- acceptor
Under these conditions, ionizable group will become protonated.
Acidic Conditions (low pH)
Under these conditions, ionizable group will become deprotonated.
Basic (High pH)
pKa
pH at which half of the molecules of a species ar deprotonated ([protonated species] = [Deprotonated])
OR
[HA] = [H+]
pH < pKa
Majority of species will be protonated
pH > pKa
Majority of species will be deprotonated
Each _______ proton will have its own pKa.
ionizable proton (important for polyprotic species)
pKa for cabroxylic group
~2
pKa for amino group
~9-10
Molecule with a positive and negative charge, but is electrically neutral.
Zwitterion
AA with non-ionizable side chains will be _______ charged under acidic conditions and _______ charged under basic conditions. Also under normal physiological conditions, these types of AA will exist as _________.
- Positively
- Negatively
- Zwitter Ions
What is the isoelectric point?
Point at which AA is electrically neutral
When pH is close to pKa, solution will act as a _______.
Buffer
The titration curve is nearly ______ flat at pKa values and _______ flat at pI value of an AA.
- horizontally
- Vertically
How do you calculate pI point of an AA with no ionizable R-group/side chain.
Average the pKa values of the values of the amino and carboxyl group.
(pI = (pKa1 + pKa2)/2)
How do you find the pI point for acidic AA?
Average pKA values between R-group and Carboxyl Group
(add them then divide by 2)
How do you find pI point for basic AA?
Average pKA values between R-group and Amino Group
(add them then divide by 2)
AA with acidic side chains have a pI point ______ 6, while AA with a basic side chain has a pI point ______ 6.
- Below
- Above
How are peptide bonds formed? broken?
- Dehydration/Condensation (loss of H2O)
- Nucleophilic attach of amine Nitrogen on carboxyl alpha carbon (where OH leaves thens comes back to steal a H+ from amine group)
- Hydrolysis (addition of H2O)
- Catalyzed by hydrolytic enzymes (Trypsin or Chymotrypsin)
Describe the Primary Structure of AA.
Linear sequence of AA, held stabilized by covalent peptide bonds between adjacent AA.
Also important to note that the primary structure alone encodes for all info needed for folding at higher structural levels.
Describe te seconday structure of AA. List the two types.
- Hydrogen bonding between backbone structures of AA
- Types
- Alpha Helices
- Beta sheets
Describe the structure of alpha helices.
- Right handed spiral conformation
- Hydrogen bonds between amine hydrogen and carboxyl oxygen located 4 residues away
(alpha helices are important component of keratin)
Describe the Structure of Beta Pleated Sheets.
- Rippled Strands that lie alongside one another
- Antiparallel
- Parallel
- Connected via H-Bonds
- carboxyl oxygen on one strand with joins with amine hydrogen on on adjacent strand
<em>(Think Fibrinin)</em>
Describe tertiary structure of an AA.
Three dimensional shape of a single polypeptide chain
What are the five ways in which tertiary structures are stabilized?
- H-bonds
- Salt-Bridges
- Disulfide Bridges
- Acid-Base interactions
- Hydrophobic/Hydrophillic Interactions of side chains (Most tertiary structures are determined by these types of interactions with hydrophobic residues on the interior and hydrophillic residues on the exterior)
Bonds that form when two cysteine moleclues become oxidized to form cystine.
Disulfide bridges
Associated with a protein losing its tertiary structure, and therefore its function.
Denaturation
Descriibe the Quaternary structure of an AA.
- Creation of multiple subunits based on polypeptide chain interactions with the protein (ONLY exists in proteins with more than one polypeptide chain)
Proteins with covalently attached molecules. What is the name of the molecule?
- Conjugate Proteins
- Prosthetic Group
- Non-polypeptide (contains no AAA) required for biological functioning of some proteins
Increasing what two things can lead to denaturation of a protein? Is denaturation reversible?
- Heat and Solutes
- It can be reversible, but is usually irrerversible
What are the reasons for conjugating a protein?
- Necessary for proper functioning of the protein
- Direct their delivery to cell membrane
- Direct delivery to a particular organelle
What is a buffer?
solution that resists changes to pH (buffering capacity comes from the presence of a weak acid and its conjugate base (or weak base and its conjugate acid) in roughly equal amounts)
Hydrolysis ocf a protein by another protein.
proteolytic cleavage (protease/proteolytic enzyme does the cleaving)
Enzyme that transfers a phosphate fron a high energy carrier (i.e. ATP) to another molecule.
Kinase
Enzyme that removes a phosphate group from a molecule.
phosphatase
Transfers a phosphate to an iorganic molecule.
Phosphorylase
How are thermodynamically unfavorable reactions able to be carried out?
Reaction Coupling
Definition: when one thermodynamically reaction is used to drive another thermodynamically unfavorable reaction.
(an example can be the hydrolysis of ATP to drive another unfavorable reaction)
What is another way in which enzyme activity can be regulation (other than inhibition)?
- covalent modifcation (i.e. addition/removal of a phosphate group)
- proteolytic cleavage
- Association with other polypeptides
- i.e.: constitutive activity
- continuous rapid catalysis if a regulatory subunit is not bound
- Some enzymes need to bind to a specific polypeptide in order to function
- i.e.: constitutive activity
