Amino Acids, Peptides & Proteins: Theory + Calcs Flashcards
At what point is the pH of an amino acid solution equal to the pK of one of its functional groups?
when half of that functional group has been deprotonated
ex: glycine’s carboxyl pK = 2.3 so…
With 20 ml of 0.1 N glycine solution, addition of 10 ml 0.1 NaOH will cause deprotonation of half the carboxyls and thus give the solution a pH of 2.3
How does an ⍺-ketoacid’s structure differ from the amino acid it is derived from?
The H and amino groups of the alpha carbon are replaced by a double-bonded oxygen.
Thus they have a ketone on the alpha carbon…
What are the non-polar amino acids?
aliphatic - Met, Gly, Ala, Val, Leu, Ile, Pro,
aromatic - Phe, Trp
Many Gleeful Alligators Try Phor Vaping Leisurely In Ponds
Which amino acids are polar?
aliphatic - Ser, Thr, Cys, Gln, Asn
aromatic - Tyr
Several Throbbing Cysts Glow As Turqouise
What amino acids have aliphatic side chains?
this is most easily remembered by just knowing the aromatic side chain amino acids and knowing that ALL others are aliphatic
What amino acids have aromatic side chains?
Phe, Trp, Tyr, His
Tyrannosauruses Trying to Hi-five are Phunny
How does one indicate the number of carbons in an amino acid?
The number of carbons plus the letter C in parentheses
EX: Ala (3C), Gly (2C)
What is transamination?
Transamination (AKA aminotransfer)
- an exchange between two molecules (an amino acid and a keto acid) of the amino group -NH2 and the keto group =O
What are the branched chain amino acids?
How can their structures be remembered?
Valine, Leucine and Isoleucine
- Valine is the simplest and contains a “V” of methyls branching off a carbon
- Leucine is just valine with an extra carbon
- Isoleucine is just leucine with its branching from the first carbon instead
How can buffers be formed from fully protonated amino acid solutions?
By **partially neutralizing **the solution with NaOH so that the acidic and conjugate base forms of the amino acid exist in equal amounts.
EX: 10 ml of a 1 M fully protonated AA solution can be made into a buffer with the addition of 5 ml 1M NaOH
What is a peptide bond?
What groups make it up?
Via what kind of reaction?
What conformation does it have?
How does it move and why?
a bond formed between two amino acids
- between the alpha amino and alpha carboxyl groups
- occurs via condensation reactions (AKA dehydration)
- has a trans configuration
- has limited rotation because it is a partial double bond between the C and N
Which amino acids have a net positive charge at neutral pH?
Arg, Lys, His
Which amino acids have a net negative charge at neutral pH?
Asp, Glu
Which amino acids have basic side chains?
same as those with positive charge
His, Lys, Arg
- all also have N in their side chains
Which amino acids have acidic side chains?
Glu, Asp
- same as those with ‘negative’ side chains
- both have COOH groups
What are the free amino and carboxyl ends of the amino acids called?
N terminus and C terminus, respectively
Describe the electromagnetic forces that influence peptide bonding.
- highly electronegative =O draws e-s from lone pair on N
- this creates a semi-double bond between carboxyl C and amino N (allows no rotation)
(amino H becomes H bridge donor and =O becomes H bridge acceptor)
In what direction are polypeptides formed?
N terminus to C terminus
What determines the net charge of a polypeptide chain?
Why only this?
the ratio of the acidic and basic amino acid residues
the charges of the amines and carboxyls involved in peptide bonding are lost in the bonding process
What is the primary structure of a protein and what bonds are responsible for it?
the amino acid sequence
covalent bonds between amino and carboxyl groups forming peptide bonds
What is the secondary structure of a protein and what kind of bonds are responsible for it?
- general three-dimensional form of local segments of a protein (⍺ helix, β sheet etc.)
- formed by H bonds between carboxyl and amino groups of the peptide bonds
How are ⍺ helices formed?
How many AAs in one turn of the helix?
Where are the side chains in relation the helix?
- every backbone N-H group donates a hydrogen bond to the C=O group 4 amino acids earlier in the sequence
ex: 4 to 1… 5 to 2… 6 to 3… etc. - 3.6 AAs per turn
- side chains stick out from the sides of the helix like bristles from a pipe cleaner
What is a disulfide bridge?
What AA forms them?
Where do proteins with them often go and why?
- side chain bonds between the thiols of two cysteine residues
- usually in proteins meant for extracellular purposes because disulfide bonds are unstable in the reducing environment of the cytosole
What decreases the stability of an alpha helix?
- electrostatic **repulsion **of charged side chains
- bulkiness of side chains
- **ionic interaction **of side chains spaced 4 residues apar
- terminus charges (+ amino at C terminus, - at N terminus)
- proline
R B I T P
Describe the general structure of a beta sheet.
- At least two beta strands (usually 3-10 AAs long with extended conformation backbone)
- at least 2-3 hydrogen bonds between the backbones
- pleatedness of the sheet forms ‘peaks’ and ‘troughs’ and side chains stick ‘up’ from the peaks and ‘down’ from the troughs
What is the name for the curved area between two anti-parallel strands of a beta sheet?
How many amino acids make it up and which are common in it?
What bond holds it together?
Where is it found in the protein?
Beta turn
- made up of 4 AAs … often with **Gly **and Pro
- **H bonds **between AA 1 and 4 peptide groups
- found near surface of protein
What is the tertiary structure of a protein?
Examples of common tertiary structures?
What affects tertiary structure?
- its 3 dimensional structure
- **globular **and **fibular **structures are common
- affected by side chain interactions and long-range** aspects** of the AA sequence
What types of interactions are important in tertiary structure formation?
- **noncovalent **interactions
- **hydrophobic **interactions
- polar interactions
- H bonds
- **salt bridges **(ionic interactions)
N H P H S
No Phuss
What is a protein’s quaternary structure?
What bonds hold it together?
- a structure made up of multiple protein sub-units
i. e. hemoglobin - bonds between side chains of different polypeptides
What is a protein’s domain?
In an enzyme, what might two examples of domains be?
a section of the protein structure meant for a certain task
- enyzmes can have substrate-binding domains and coenzyme-binding domains
How can quaternary structures be categorized based on…
… their number of sub units?
… the similarness/differentness of the sub units?
1 subunit = monomer, 2 = dimer… 4 = tetramer etc.
two of the same subunit = homodimer
two different subunits = heterodimer
What are chaperones?
- proteins which assist in protein folding during synthesis
- help move hydrophobic regions of proteins to their interior
What molecule helps in disulfide bridge formation?
Protein Disulfide Isomerase
What molecule can aid in creating beta turns by altering conformation of a peptide bond?
Proline-cis, trans-isomerase
- can alter a proline’s peptide bond to give optimize it for a turn
What 3 auxiliary molecules aid in protein folding?
- chaperones
- protein disulfide isomerase
- proline cis trans isomerase
