Unit 1 Flashcards
Write generalized structures for the functional groups
Draw all of them out
Formation of an amide from an acid and ammonia
Reactants: NH3, acetic acid
Lone pair on oxygen grabs H on ammonia and nucleophillic N attacks carbon on carboxylic acid
Formation of an acid anhydride from two molecules of acetic acid
Reactants: acetic acid
Hydroxyl oxygen will grab hydrogen off of the other acetic acid to deprotonate it. Then, the oxygen will attack the carbon to form the anhydride
Hydrolysis of an ester
Reactants: esther and water
Oxygen on water molecule will attack the carbon kicking off the single bonded oxygen and R group. Then the oxygen and r group that was just kicked off will deprotonate the ester
What is a hydrogen bond?
a type of non-covalent bond that forms between a hydrogen atom covalently bonded to an electronegative atom (such as nitrogen, oxygen, or fluorine) and another electronegative atom nearby. Due to partial charges on molecules.
What is required for a functional group to behave as a hydrogen bond donor?
To be a hydrogen bond donor, you must be an electronegative atom with a hydrogen
What is required for a functional group to behave as a hydrogen bond acceptor?
Has to be electronegative like oxygen or nitrogen
Hydrophobic
Nonpolar solvents that dissolve easily in nonpolar molecules but can’t in polar molecules like water
Hydrophillic
Compounds that dissolve easily in water (polar)
Amphipathic
Compounds that contain regions that are polar (or charged) and regions that are nonpolar
- To be amphipathic you have to have a good mix of both
What are some ways you can classify if a molecule is hydrophillic?
If it has polar groups such as OH, COO-, or NH3+
What are some ways you can classify if a molecule is hydrophobic?
If they have long carbon chains
Describe a micelle
A micelle is an aggregate of AMPHIPATHIC molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface exposed to water to form a sphere
What interactions stabilize micelles?
The hydrophobic effect
Why do micelles form?
A lipid by itself in water is nonpolar and it would cause a cage-like structure around it which makes the water more ordered and decreases entropy. To minimize teh water that is ordered, the lipid molecules cluster together to decrease the amount of ordered water
4 types of non-covalent interactions that stabilize biomolecules
- Hydrogen bonds:
hydrogens bound to electronegative atoms interacting with another electronegative atom - Ionic interactions:
Charged ions either being attracted or repulsed - Van der Waals:
weak forces that exist between two atoms in close proximity - Hydrophobic effect:
nonpolar molecules interacting with each other to minimize exposure to polar solvents
A “strong” acid is one that ionizes (losing the H and transferring it to water) almost 100% in aqueous solution. If the Keq for acid X is 10-8 and for acid Y is 10-2, which is the stronger acid?
The higher the Keq, the higher the Ka, the higher the dissociation of acid, and the strong eer the acid is.
When looking at the Keq equation, H+ is in teh numerator. Since we want a solution that has more H+ at equilibrium, that would mean the Keq is also high. !!!
Therefore, acid Y is the stronger acid because it is the bigger number.
Define pH
pH = log (1/[H+]) = -log[H+]
Given an H+ concentration in molar (M) or millimolar (mM) terms, calculate the pH. For example, what is the pH of a solution in which [H+] is 3 mM?
2.52
*remember if you are going from a smaller number to a bigger one, multiply by a smaller number. if you are going from a bigger number to a smaller number, multiply by a bigger one
nano
10-9
micro
10-6
milli
10-3
What is an ester made of?
An OH and acid
When finding the H+ concentration for the pH formula, do you divide by -1 first ?
Yes
Define pK
pka = -log (Ka) = log (1/[Ka])
Which is the stronger acid, acetic acid (pK=4.7) or lactic acid (pK=3.1)?
The lower the pK, the stronger the acid because the higher the Ka. SO the answer is lactic acid
What is the Henderson-Hasselbalch equation?
pH = pKa + log ([A-]/[HA])
Referring to the Henderson-Hasslebalch equation, at what pH does the concentration of acid equal that of conjugate base?
When the pH is equal to the pka. This is because when you subtract pKa from pH, you will get 0. The only way you can take the log of something and get 0 is if it is the log(1). That means that [A-]/[HA] is 1 so they’re the same
Spell out a rule of thumb about the relative amount of two species when the pH is one unit below the pK, one unit above the pK, and two units below and two units above the pK
One unit down is /10
two units down is /100
Define buffer and circle the buffering region on your titration curve
Buffers are aqueous systems that tend to resist changes in pH when small amounts of acid or base are added. A buffer system consist of a weak acid adn its conjugate base
*able to resist change because if other molecules are occupied neutralizing there are now the acid and base buffer thtat can neutralize it well. (apart of the solvent system)
The pH value at which the compound has maximum buffering capacity
When the pH=pKa, this is because the amount of proton donors exactly equals that of proton acceptors. Once you add more base, it’ll sway towards one side, but at that point, it is difficult to notice drastic change in pH.
The pH range over which the compound is useful as a buffer
Take the pK for that compound and do one minus it and one plus to figure out the buffer region.
Ex. pKa is 4.7, the buffer region would be 3.7-5.7
Write a generalized structure for an amino acid
*NH3
Why do all amino acids except glycine have optical activity?
All amino acids except glycine have optical activity because they are all chiral centers (which means they are bonded to four different groups) but glycine has two H atoms
Do the amino acids of proteins have the D- or L- isomeric forms
The L isomeric forms
Nonpolar, aliphatic R groups
GAPVLIM
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
Glycine
*Draw
- Gly
- G
Alanine
*Draw
- Ala
- A
Proline
*Draw
- Pro
- P
Valine
*Draw
- Val
- V
Leucine
*Draw
- Leu
- L
Isoleucine
*Draw
- Ile
- I
Methionine
*Draw
- Met
- M
Aromatic R Groups
- Phenylalanine
- Tyrosine
- Tryptophan
Phenylalanine
*Draw
- Phe
- F
Tyrosine
*Draw
- Tyr
- Y
Tryptophan
*Draw
- Trp
- W
Polar, uncharged groups
- Serine
- Threonine
- Cysteine
- Asparagine
- Glutamine
Serine
*Draw
- Ser
- S
Threonine
*Draw
- Thr
- T
Cysteine
*Draw
- Cys
- C
Asparagine
*Draw
- Asn
- N
Glutamine
*Draw
- Gln
- Q
Positively charged R groups
- Lysine
- Arginine
- Histidine
Lysine
- Draw (4 CH2)
- Lys
- K
Arginine
- Draw (3 CH2 instead of 4 and alternating NH)
- Arg
- R
Histidine
- Draw
- His
- H
Negatively charged R groups
- Aspartate
- Glutamate
Aspartate
- Draw
- Asp
- D
Glutamate
- Draw
- Glu
- E
Identify the functional group on each of the amino acids with polar side chains
- Serine has a hydroxyl group
- Threonine has a methyl and hydroxyl group
- Cysteine has a Sulfhydryl
- Asparagine has a Amido
- Glutamine has an Amido
What is the hydropathy index?
- Quantifies how hydrophobic the R groups are. It is tested through the changes in energy between the hydrophobic and water environments
- Negative hydropathy –> polar or charged side groups
- Positive hydropathy –? nonpolar or hydrophobic side chains
Which side chains are hydrophobic?
All the nonpolar, aliphatic side groups and the aromatic R groups
Which amino acids can hydrogen bond?
Technically all of them can, but certain side chains cannot
- Tyrosine (donor and acceptor)
- Tryptophan (donor and acceptor)
- Serine (donor and acceptor)
- Threonine (donor and acceptor)
- Cysteine * donor and acceptor although there are strong bonds that can be formed
- Asparagine ( donor and Acceptor)
- Glutamine ( donor and Acceptor)
- Lysine (Donor and Acceptor )
- Arginine (Donor and Acceptor)
-Histidine (Donor and Acceptor) - Aspartate (Acceptor)
- Glutamate (Acceptor)
What is an ionic interaction, which amino acid R groups can interact ionically?
An ionic interaction is either an attraction or repulsion between two charged ions.
The positively charged and negatively charged R groups are the only ones that can interact ionically
Given the acid RNH3+ with pK=9, draw the form which predominates at pH 7 and pH 11
If the pK is 9, any pH lower than that is protonated (NH3+) and any pH higher is deprotonated.
Given the acid RNH3+ with pK of 9, use the Henderson-Hasselbalch equation to calculate the ratio of unprotonated to protonated form at pH 7 and pH 11
This question is asking for you to plug into the Henderson-Hasselbalch equation to determine what ([A-][HA]) is. THIS HERE IS THE RATIO. For every __ [A-], you have one HA
Define the isoelectric point
The characteristic pH at which the net electric charge is 0 is called the isoelectric point
Isoelectric point formula
pI = 1/2(pk1 +pk2)
- To do this, draw out your flow chart and identify your Zwitterion. The pK values that your Zwitterion is sandwiched in between is your pk1 and pk2 values)
Draw a peptide bond
*Draw
Draw the structure of a tripeptide using R for side chains. Circle the peptide bonds, Point out the N-terminal and C-terminal ends of the peptide
*Draw
Write the abbreviated name for the peptide glutaminylasparaginylisoleucyltryptophan using the 1 letter and 3-letter abbreaviation for each amino acid residue
3 letter:
Gln - Asn - Ile - Trp
Q - N - I - W
Procedure for answering questions that ask you to draw the two forms of an amino acid at a certain pH:
- Start by identifying your amino acid, and drawing it in its fully protonated state
- Then using the relative pKas, determine which groups would be the first, second, or last to lose the Hydrogen. Draw those species
- Place the pKas between the different groups that lost their hydrogen.
- When given a pH, determine which pK it is closest to. Take that pK and write down the species that comes directly before and directly after the pK, those are the dominant species
- To find the ratio of [A-]/[HA], use the Henderson-Hasselbalch equation. The pK you’re using is the pK that was most similar to your pH value
How to calculate pI when given a peptide chain?
- Draw in your amino and carboxyl groups - fully protonated
- Cross out any amino acid residues that are not contributing to the charge
- List out all of the pKas in order including the ones for the amino and carboxyl group)
- Determine what the charge of the whole molecule would be before and after each pKa switch (adding together the charges of all the groups) JUST REMEMBER WHICH ONES ARE POSITIVELY CHARGED AND NEGATIVELY CHARGED AND WHAT ADDING A PROTON WOULD DO
- Determine where the Zwitterion is and the pKa’s that it is sandwiched in between are your pk1 and pk2 values
- Plug it into the pI formula
How to calculate pI of a single amino acid?
- You want to go back to perform a titration so draw all the forms of your single amino acid, starting with the most protonated form
- Determine which groups will have an effect (the relative pkas at the front)
- Determine the Zwitterion and calculate the pI by looking at the drawing that is the Zwitterion and using the pK that comes right before and the pK that comes right after
