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Flashcards in Chapter 3 Deck (30)
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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?

H3N+-C- H
They all have a carboxyl group, amino group (H3N+), an alpha carbon (chiral center), and a R group which is where amino acids differ


How 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
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
+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



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?

1. Simplicity of chemistry- one reaction for polymerization, one for degradation
2. Recycling- biomolecules can be digested back into component building blocks (reusable)
3. 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


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