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Biochemisty > 2. Amino Acids > Flashcards

2. Amino Acids Flashcards

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1
Q

True/False: Proteins are workhorse of the cell and are involved in almost all cellular processes.

A

True; they fulfill their myriad array of function, proteins come with different shapes and sizes.

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2
Q

What are the common parts of an Amino acid?

A

An amino group (-NH3+), a carboxylate (-COO-), and an R group.

There are 20 amino acid commonly found in proteins and they differ in the chemical characteristics in their R group.

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3
Q

True/False: Amino acids are Zwitterions at neutral pH

A

True

Zwitterions: a molecule or ion having separate positively and negatively charged groups.

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4
Q

What happens to the carboxyl group and the amine group at high pH levels?

A

Both groups are deprotonated. The pH > pKa for both groups.

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5
Q

What happens to the carboxyl and amine groups when the pH is neutral (6 - 9)?

A

The “zero ionic” zone

Carboxyl group: pH > pKa
Amine group: pH < pKa

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6
Q

What happens to the carboxyl and amine group at low pH levels?

A

Both groups are protonated.

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7
Q

True/False: All amino acids found in mammalian proteins are not L - conformers.

A

False; All amino acids found in mammalian proteins ARE L - conformers. All L - amino acids EXCEPT CYSTEINE are S configuration.

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8
Q

True/False: Glycine is chiral

A

False; Glycine is ACHIRAL

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9
Q

Why is Cysteine an exception to the S configuration rule?

A

Cysteine has an —SH attached to the CH2 group that changes the priority.

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10
Q

What are the four groups of amino acids?

A
  • Hydrophobic amino acids
  • Polar amino acids
  • Positively charged amino acids
  • Negatively charged amino acids
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11
Q

What makes Hydrophobic/nonpolar amino acids hydrophobic?

A

Hydrophobic amino acids have mainly hydrocarbon side chains that do not interact or interact weakly with water, thus they are hydrophobic/nonpolar.

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12
Q

What are the Hydrophobic/nonpolar Amino acids?

A 
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M)
Proline (Pro, P)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
***Glycine (Gly, G)***
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13
Q

What makes Polar amino acids polar?

A

Polar AA have polar residues that have side chains that can form hydrogen bonds with water, they are not charged

Their side chains contain an electronegative atom

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14
Q

What is important about polar side chains that carry an aromatic group or multiple —CH2- groups?

A

Polar side chains that carry an aromatic group or have multiple —CH2- groups can also participate in hydrophobic interactions.

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15
Q

What are the Polar amino acids?

A 
Serine (Ser, S)
Threonine (Thr, T)
Tyrosine (Tyr, Y)
***Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)

“Snort Coke Throught Your Nose (for the) Queen”

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16
Q

What side chains do positively charged amino acids have?

A

Positively charged amino acids have basic side chains

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17
Q

Which “positively” charged amino acid is special?

A

Histidine (His, H) - this amino acid is context dependent it can be neutral or positive depending on its surrounding environment.

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18
Q

What are the negatively charged amino acids? What do they share?

A

Asparatate (Asp, D)
Glutamate (Glu, E)

They share having another carboxyl group.

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19
Q

What kind of side chains do negatively charged amino acids have?

A

Acidic side chains

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20
Q

What is a notable property of Thiol groups? What is an example?

A

They can be oxidized and can form disulfide bonds. When 2 Cysteine groups are near each other, their oxidation potential is greater, thus the chance of creating a disulfide bond is higher.

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21
Q

What is unique about Proline?

A

It’s alpha carbon is covalently bonded to its amino group, this feature makes it conformationally more restricted than the other amino acids.

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22
Q

What are the aromatic amino acids?

A

Phenylalanine, tyrosine, and tryptophan

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23
Q

What is unique about Phe?

A

It is the only purely hydrophobic amino acid

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24
Q

What is UV absorption used for?

A

It is often used for protein concentration determination.

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25
What is a peptide bond or an amide bond?
A bond formed between C’ and N of two amino acids
26
What do amino acids contain?
Amino acids contain an amino group, carboxylate group, and a side chain
27
True/false: amino acids have ionization states
True; protatinated group is dominated at a neutral pH and become zwitterions at neutral pH
28
True/False: Amino acids are chiral except for cysteine.
False; amino acids are chiral except for GLYCINE! - GLYCINE IS ACHIRAL
29
True/ False: All amino acids except cysteine are R configurations
False; All amino acids are S configurations except for cysteine
30
What does the R - group or side chains determine in amino acids?
Determines whether an amino acids is polar, nonpolar, or charged. The differ in shape, size, charge, H - bonding capacity, chemical reactivity, hydrophobicity.
31
Alanine has:
Ala, A | One carbon chain, 1 methyl group
32
Valine:
Val, V 3 carbon chain 2 methyl groups
33
Leucine;
Leu, L 3 carbon chain 3rd carbon has an Isopropyl
34
Isoleucine ;
Ile, I 4 carbon chain With a methyl from the back
35
Methionine
Met, M 3 carbons 1 sulfur and methyl group
36
Proline
Pro, P Five - membered ring Cyclic aliphatic hydrophobic amino acid in which the R group is bonded to the alpha carbon and the amino group **The carbon makes a covalent bond with an amine group which leave it restricted
37
Phenylalaine
Phe, F | Benzene ring
38
Trytophan
Trp, W | 1 benzene and 1 pentene
39
Glyciene
Gly, G | ** is non polar but is an exception and special because it has H as a side group
40
What do polar amino acids include:
- includes an OH or an electronegative group - have side residues that can form hydrogen bonds with water but are not charged - side chains contain an electronegative atom - polar side chains that carry an aromatic group or has multiple hydrocarbon chains can participate in hydrophobic interactions
41
Serine:
Includes an OH group
42
Threonine:
Thr, T | Includes methanol and a methyl group
43
Tyrosine;
Tyr, Y | Phenol group
44
Cysteine
Cys, C | Exception! Not really polar just slightly lol
45
Asparagine
Asn, N Carboxyl and amine group on the same carbon 1 carbon chain
46
Glutamine
Gln, Q 2 carbon chain Carboxyl with amine group on the same carbon (the same as asparagine but with extra ch2)
47
Positvely charged amino acids:
Have basic side chains | High pka
48
Lysine
Lys, K 4 carbon groups Amine group Positive charge results in higher pka
49
Arginine
``` Arg, R Higher pka than lysine because of resonance, positve charge is carried. 3 carbon groups 2 NH2 groups 1 NH group ```
50
Histidine
Context dependent 5 membered ring with 2 N inserted ** can be charged if protinated but is a special case because His has a pKa of 6, and a basic side chain so it can be positvely charged or neutral depending on the local environment. **residues are found in the active side of enzymes where the imidazole groups can bind or release a proton during enzymatic reactions.
51
Negatively charged amino acids:
Have acidic side chains | Low pKa
52
Aspartate
Asp, D | Has a carbon, carboxylic acid (carboxylate group when deprotinated)
53
Glutamate
Glu, E | Has 2 carbons, carboxylic group (carboxylate when deprotinated)
54
What is unique about trypotophan and tyrosine?
These aromatic groups can absorb UV light at 280nm and are used for protein concentration determination. **unique because most proteins absorbs 260 nm
55
How do peptide bonds link amino acids in proteins?
Through condensation reactions that create peptide bonds/aminde bonds. The reaction is unfavorable but kinetically stable.
56
What are the components of a polypeptide chain?
Consists of a backbone/main chain. - alpha carbon, hydrogen, amine group, amide bond, carbonyl group Variable side chains; R chains is what define a protein **When it comes to nucleic acids, the nucleic acid determine the identity of a sequence in a chain the same way the R groups defines the sequence of amino acids. **
57
True/False: Protein amino acid sequences are read from the N terminus to the C terminus
True; amino terminal (N terminus) residue holds an amine group at the end of a chain
58
True/False: every protein has a unique amino acid sequence
True
59
True/False: pKa values in a protein can be different because they are influenced by the microenvironment by neighboring residues
True; if a negatively charged protein comes near to a negatively charged residue or side chain (same charged residues), it would be harder for an electrostatic interaction to occur because of repelling charges - Results in a higher pka and is less likely to pull off a proton —-> shifts the equilibrium to the left (reactants) **It would be easier for an electrostatic interactinon to occur because of opposing charges it results in a lower pka and more likely to pull of a proton - this will shift equilibrium to the right
60
How will Lys residues affect the pka of an Asp residue?
- Asparatic acid is a negatively charged protein - Lysine is a postively charged protein This will decrease the pka which is favorable and pushes the equilibrium to the right because the opposing charges interact with one another
61
True/False: peptide bonds have double bond nature
Typical peptide bond: 1.32A - shorter than a single bond (1.49A) but longer than a double bond (1.27A) - This is due to resonance where it shortens bond length - It gives rise to partial double bond features
62
What is unique about the double bond feature of amide bonds?
The amide bond cannot be rotated because of its double bond nature through resonance. The peptide bond is defined through a peptide plane or amide plane The coplanar nature of the peptide bond affects the orientation of where the groups lie TRANS is the general configuration and is most favored unlike cis configurations where there is steric clashing with one another *** exception is Proline because with other residues - The energies between the trans an cis structures are not as significant because both groups are clasing with one another in both configurations (trans and cis exists in both structures) It is not as significant and undergoes trans and cis configurations to accomadate to do a function but needs an enzyme for it to switch from configuration to configuration.
63
What part of the poly peptide chain is the phi/psi bond in a polypeptide?
N - C (alpha) bond is phi C’ - C (alpha) bond is psi Both are dihedral angles or torsion angles and both can be identified by whatever the alpha carbon is attached to. Can be rotated because they don’t have double bond resonance properties.
64
What is the purpose of the phi/psi angles?
CAN be rotated because they do not have the double bond property that amide bonds do. By changing the orientation, it determines how the 2 plances will orient from each other. These angles describe the geometry of the protein because the local structure of the phi and psi bonds determine that proteins can be different depending on the phi and psi angles.
65
True/False: All psi and phi angles are allowed
False: not all psi and phi angles are allowed! Certain angles can result in steric clashes and atoms will interpenetrate with one another in their van der waal radii. Not stable because they will repulse with one another. Thus, the sterically available combinations are the basis for preferred secondary structures. Some proteins are completely incompatible because of the sterics of the local interactions depending on the angle of psi and phi bonds.
66
What is the ramachandran Diagram?
Shows allowed conformations of a peptide chain. Shows the combinations of different angles. The residues in protein chains limit secondary structure space in secondary structures because of steric clashes

Biochemisty (3 decks)

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