Chapter 3 Flashcards
What makes a molecule polar?
Carries a charge
Hydrogen binding capabilities
How many different ways can a peptide of three amino acids be formed? How about 100 amino acids?
3- 8000 ways
100- 1.3x10^130 ways
Do all amino acids have a chiral carbon and stereoisomers?
All of them except glycine
What is the basic common structure of all amino acids?
COO-
|
H3N+-C- H
|
R
They all have a carboxyl group, amino group (H3N+), an alpha carbon (chiral center), and a R group which is where amino acids differHow can you determine which amino acids weigh more than others?
The complexity and size of their side chains
What is post translational modification?
Where certain amino acids can be covalently modified after their incorporation into a protein
Can change the properties of the residue to influence activity of the protein
Example is phosphorylation
What are the five groups of amino acids?
Non-polar aliphatic Aromatic Polar, uncharged Polar, positively charged Polar, negatively charged
What are the 5 polar, uncharged amino acids?
Serine, threonine, cysteine, asparagine and glutamine
Have hydrogen bond capabilities but no charge
Serine and threonine can undergo kinase-meditated phosphorylation of their hydroxyl Group
How does cysteine help stabilize structures of proteins?
It can form disulfide bonds when the two sulfur hydrogen compounds on the amino acid lines up
What are the 3 positively charged amino acids?
THEY HAVE THE POTENTIAL TO CARRY CHARGES, they won’t always carry them
Lysine, arginine, histidine
Lys and arg always carry a +1 net charge and physiological pH
Histidines imidazole (circle group) has pKa near physiological pH so fraction of them will have +1 charge while most will have 0
What are the 2 negatively charged amino acids?
Aspartate and glutamate carry net charge of -1 at physiological pH
Both have carboxyl groups in side chains
Flavour enhancers
What are the 7 non polar, aliphatic amino acids?
Which one is found at the turns of polypeptides?
Glycine, alanine, proline, valine, leucine, isoleucine, and methionine
Proline in combination with glycine turns amino acids
What are the 3 aromatic amino acids?
What could be considered the fourth?
All these have circle groups on side chains
Phenylalanine, tyrosine, tryptophan
Histidine also has a circle
What does amphoteric mean?
Can act as both weak acids and bases
Amino acids ionize in aqueous solution and are amphoteric
What is a zwitterion?
The diplomat ion of an amino acid
When it carries a negative and positive charge in one molecule
What are the two groups that accept and donate protons that ever amino acid has and what are their relative pKa?
(There is also a third)
The carboxyl group pKa~ 2.0
The amino group pKa ~ 10.0
There is also the side chains of triprotic amino acids that can donate and accept protons
pKa is in between 10 and 2
What are the 7 triprotic amino acids?
Lysine, Arginine, histidine, asparangine, glutamine, cysteine, tyrosine
What is the isoelectric point (pI) of an amino acid?
The pH at which the net charge on the molecule is equal to zero
You take the max pH that has zero and minimum pH that has zero and add them then divide by two
When the pH is above the pKa is the protonated or unprotonated form dominating?
The unprotonated form dominates
(NH2, COO-)
More negative
How do you draw titration curves for diprotic amino acids?
With the given pKa values for the carboxyl and amino group, you can draw the titration line on a graph and flatten the line out at that point,
Then with the given pH you draw a line to the graph to determine which protonated or unprotonated compounds you use
All diprotic aminos will have similar titration curves
See chapter 3 titration curve examples
How do you find the net charge of an amino acid from a titration chart?
You use the titration chart to draw the amino acid then add up the charges and then the charges go down by 1/2 per section
I II III IV
+1 +1/2 0 -1/2
How do you draw the titration curve for triprotic amino acids?
Same as diprotic just with an extra side chain buffering region inbetween the carboxyl and amino group buffering regions
See examples on chapter 3 titration curves
How do you know which element gets the hydrogen when protonating the side chain of a triprotic amino acid?
There should be only one element that can accept a hydrogen due to not having full bonds
How can you compare the pKa’s of side chains of triprotic acids from smallest to largest?
The bigger the side chain, the bigger the pKa
What are petite bonds?
Are formed by condensation reactions (loss of water molecule, or dehydration synthesis)
Between the carboxyl of one amino acid and the amino group of the other
(Take the O from carboxyl group and 2 H’s from H3N)
Do the amino acid flash cards
IN BACKPACK
When connecting amino acids by a peptide bond what double bond shows resonance?
The oxygen double bonded to the carbon has resonance with the nitrogen now bonded to the same carbon
What are the three advantages of creating biomolecules as polymers of smaller, simpler building blocks?
- Simplicity of chemistry- one reaction for polymerization, one for degradation
- Recycling- biomolecules can be digested back into component building blocks (reusable)
- Diversity- cast number of molecules of varying lengths and sequences
What compose peptide chains? How do you write out peptide chains?
Amino acid residues
You use the one letter code of amino acids in a sequence
Ex: Tyr-Gly-Gly-Phe-Leu
YGGFL
What are host defence peptides and retro-inverso peptides?
Host defence- used to help kill off germs and protect against future bacteria
Retro inverso- isomers in which the sequence in reversed and D-amino acids are employed
