Chapter 1: Amino Acids

Question 1

What is an Amino Acid?

Answer 1

Have four groups attached to a central alpha carbon.
An Amino group, R group, Carboxyltic Acid group, and hygrogen

Question 2

What group of the Amino Acid determines chemistry and function?

Answer 2

The R group

Question 3

All Amino Acids have an (S) configuration except?

Answer 3

Cysteine

Question 4

Which stereoisomer configuration of Amino Acids is present in all Prokaryotes?

Answer 4

(D) Amino Acids

Question 5

All Amino Acids are chiral Except

Answer 5

Glycine, cuz it has a hydrogen atom as the R group

Question 6

Name the Nonpolar Nonaromatic Amino Acids (Aliphatic)

Answer 6

Nmumonic:
GAVLIMP or LIMPVAG 😏

Question 7

Name Acidic Acids
D/E
ASP/GLU

Answer 7

They’re hydrophilic with a Negative charge
Nemonic: DE

Question 8

What does Aliphatic mean?

Answer 8

In the context of the MCAT, aliphatic amino acids are amino acids that have an aliphatic side chain functional group, which is a non-aromatic hydrocarbon chain. Aliphatic amino acids are non-polar and hydrophobic, and their hydrophobicity increases as the number of carbon atoms in their hydrocarbon chain increases. Because of their non-polar side groups, aliphatic amino acids tend to interact with other non-polar molecules.

Question 9

Name the Aromatics AA

Answer 9

Nemonic:
FYW?
Fuck You Want?😡

Question 10

Name the Polar AA
SQTNC

Answer 10

NMnumoic:
SQNTC
Selling Qualudes To Naive Children

Question 11

Name Basic Animo Acids
Lys/k
Arg/R
His/H

Answer 11

They’re hydrophilic with a Positive charge.
Nemonic:
RHK
Right Handed King

Question 12

Why Are Serine (S) Tyrosine (Y) and Threonine (T) able to be phosphorylated?

Answer 12

Because it binds to the OH on the R group

Question 13

What is phosphorylation?

Answer 13

Phosphorylation is like giving a toy a power boost, but on a more detailed level, it’s a chemical process where a phosphate group is added to a protein or molecule. This addition acts like pressing a special button on a toy car that makes it go faster or changes how it works. In your body, phosphorylation can change the shape or activity of proteins, turning them on or off, or altering how they interact with other molecules. This is crucial for many cellular processes, like metabolism, cell signaling, and how cells respond to different signals. Essentially, phosphorylation is a way to “power up” or regulate various functions inside your cells, helping them perform their necessary tasks.

Question 14

Show how ATP gets phosphorylated

Answer 14

Goes from ATP to ADP and Phosphorylase.

Question 15

Why can’t the Carboxyl group get protonated?

Answer 15

Due to Resonance

Question 16

Acid Base Reactions:
Show the Charges and PKA of an Amino Acid

Answer 16

+1 → PKA 2.2→ 0→ PKA 9 → -1

Question 17

Where do Hydrophobic AA reside in a protein?
Where do Hydrophilic AA reside?

Answer 17

Hydrophobic AA reside in the interior away from water.
Hydrophilic AA remain on the surface.

Question 18

Why are Amino Acids called Polyampholytes?

Answer 18

Titrate at more than 1 position (PKA)

Question 19

What is Isoelectric Point (PI)?

Answer 19

Calculate by averaging the two PKA v values.

Question 20

What is the zwitterion?

Answer 20

At pH near the pI of the amino acid, the amino acid is a neutral
zwitterion.

Question 21

What do Amphoteric Species do?

Answer 21

Can either accept OR donate a protein

Question 22

What do ionizable groups do?

Answer 22

Ionizable groups GAIN PROTONS in acidic conditions and LOSE PROTONS in basic conditions.

High pH = Deprotonated
Low pH = Protonated

Question 23

What would the predominant side chain be?
A. At pH 1
B. At pH 7
C. At pH 11

Answer 23

A. NH3+ CRH COOH
B. NH3+ CRH COO-
C. NH2 CRH COO-

Question 24

What is the PI of the following AA?
Aspartic Acid
PKA 1 = 1.88
PKA 2 = 3.65
PKA 3 = 9.6

Answer 24

For an Acid we choose PKA 1 & 2

PI= (1.88 + 3.65)/2 = 2.77

Question 25

What is the PI of the following AA?
Arginine
PKA 1 = 2.17
PKA 2 = 9.04
PKA 3 = 12.48

Answer 25

For Basic AA we choose 2 & 3

PI = (9.04 + 12.48)/2 = 10.76

Question 26

What is the PI of the following AA?
Valine
PKA 1 = 2.32
PKA 2 = 6.62
PKA 3 = 9.62

Answer 26

For Neutral gotta take PKA 1 and PKA 3
PI = (2.32 + 9.62)/2 = 5.97

Question 27

PI chart; How does something act as a buffer

Answer 27

When the pH equals the PKA it acts as a buffer.

Question 28

What are peptides? Dipeptides? Tripeptides? Oligopeptides? Polypeptides?

Answer 28

Peptides are composed of Amino Acids subunits called Residues.
Dipeptides contain 2.
Tripeptides contain 3
Oligopeptides contain up to 20
Polypeptides contain more than 20

Question 29

How are peptides bonded together?

Answer 29

They’re joined with PEPTIDE BONDS which connect the COO- group with NH3+ of another AA.

It’s an example of condesation or dehydration as a water molecules gets removed for acyl substitution to occur.

Question 30

Where does Trypsin cleave?

Answer 30

Trypsin cleave at the Carboxylic end of Arginine and Lysine.

Question 31

Where does Chymotrypsin cleave?

Answer 31

Chymotrypsin cleaves at carboxyl end of phenylalanine, tryptophan, and tyrosine

Question 32

How many oligopeptides would be formed in enzymatic cleavage of chymotrypsin.

Val - Phe - Glu - Lys - Tyr _ Phe - Trp - Ile - Met - Tyr - Gly - Ala

Answer 32

Val - phe;
Glu - Lys - Tyr;
Ile - Met - Tyr;
Gly - Ala

Question 33

What is the primary (1°) structure of a protein?

Answer 33

Primary (1°) structure is the linear sequence of amino acids and is stabilized by peptides bonds.

Question 34

What is the secondary structure of a protein?

Answer 34

Formed by Hydrogen Bond interactions within a protein chain.

Alpha Helix: are clockwise coils around a central axis

Beta Pleated Sheets: are rippled strands that can be parallel or antiparallel (mostly antiparallel)

Question 35

What Amino Acid can interrupt secondary structure?

Answer 35

Proline can interrupt secondary structure because of it’s Rigid cyclic nature.

Question 36

What is the Tertiary structure of a protein?

Answer 36

3D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions (salt bridges), Hydrogen bonding, and disulfide bonds.

Basically, regulated by R group interactions with their environments.

Question 36

Describe Hydrophobic interactions within Tertiary Structure:

Answer 36

push hydrophobic R groups to the interior of the protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs Free Energy.

Question 36

Describe Disulfide Bonds within Tertiary Structure:

Answer 36

Occurs when two Cysteine molecules are oxidized and create a covalent bond to form Cystine.

Question 37

What is protein folding relation to Delta S?

Answer 37

Delta S driven process, Entropicallaly favorable

ΔG=ΔH ↓ −TΔS ↑

When a protein folds, it’s like going from a messy room (lots of disorder) to a clean room (more order). This means the protein itself becomes more organized, which lowers its entropy (less disorder).

However, folding pushes water-fearing parts of the protein inside, freeing up water molecules that were tightly packed around those parts. This lets the water molecules move around more freely, which increases their entropy (more disorder).

So, even though the protein gets more ordered, the surrounding water becomes more disordered, and this overall increase in entropy helps make protein folding happen naturally and easily.

Question 37

What is the Quatrenary structure of a protein?

Answer 37

It’s the interactions between peptides in proteins that contain multiple subunits.

3° + 3° + 3° = 4°
Globin + globin + Globin = Hemoglobin

Question 37

What is a Conjugated Protein?

Answer 37

Is the interaction between peptides in proteins that contain multiple subunits, usually including Prostethic Groups

Question 38

What is a prosthetic group?

Answer 38

A prosthetic group is a helper molecule that’s permanently attached to a protein and is crucial for the protein to work properly. Unlike other molecules that can come and go, a prosthetic group stays stuck to the protein and helps it do its specific job.

For example, in hemoglobin (the protein that carries oxygen in your blood), there’s a helper group called heme, which contains iron and binds the oxygen. Without this heme group, hemoglobin wouldn’t work.

Prosthetic groups can be things like metal ions, vitamins, lipids, carbohydrates, or nucleic acids.

Question 39

What is denaturation and what casues it?

Answer 39

It’s the loss of the tertiary structure.

It’s caused by increasing heat and solute concentration.

Question 40

[…] is when a protein (or nucleic acid) loses its 4°, 3°, and 2° structures due to breaking non-covalent interactions

Answer 40

Denaturation is when a protein (or nucleic acid) loses its 4°, 3°, and 2° structures due to breaking non-covalent interactions

Question 41

[.. proteins] compose the cytoskeleton, anchoring proteins, and much of the extracellular matrix

Answer 41

Structural proteins compose the cytoskeleton, anchoring proteins, and much of the extracellular matrix

The most common structural proteins are:

Collagen
Elastin
Keratin
Actin
Tubulin

Question 42

L and D indicate […] configuration

S and R indicate […] configuration

Answer 42

L and D indicate relative configuration

S and R indicate absolute configuration

Question 43

[…] are complex proteins, such as hemoglobin, consisting of amino acids combined with other substances

Answer 43

Conjugated proteins are complex proteins, such as hemoglobin, consisting of amino acids combined with other substances

Question 44

The 3° structure of proteins is stabilized primarily by […]

Answer 44

The 3° structure of proteins is stabilized primarily by hydrophobic interactions

Question 45

The stereochemistry of the α-carbon in all eukaryotic amino acids (except glycine) is ________

Answer 45

The stereochemistry of the α-carbon in all eukaryotic amino acids (except glycine) is L

Question 46

The isoelectric point formula when there is a neutral side chain is:

Answer 46

pI Neutral = 1/2 (pKa1 + pKa2)

Question 47

[Type of proteins] are calcium dependent glycoproteins that hold similar cells together

Answer 47

Cadherins are calcium dependent glycoproteins that hold similar cells together

Question 48

All chiral amino acids except cysteine have _____ configuration.

Answer 48

All chiral amino acids except cysteine have (S) configuration

Question 49

A/an […] is the attached molecule in a conjugated protein and can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Answer 49

A prosthetic group is the attached molecule in a conjugated protein and can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Question 50

In a neutral solution, most amino acids exist as:
A. positively charged compounds.
B. zwitterions.
C. negatively charged compounds.
D. hydrophobic molecules.

Answer 50

B
Most amino acids (except the acidic and basic amino acids) have two sites for protonation: the carboxylic acid and the amine. At neutral pH, the carboxylic acid will be deprotonated (−COO−) and the amine will remain protonated (−NH+3). This dipolar ion is a zwitterion, so (B) is the correct answer.

Question 51

At pH 7, the charge on a glutamic acid molecule is:
A. −2.
B. −1.
C. 0.
D. +1.

Answer 51

B
Glutamic acid is an acidic amino acid because it has an extra carboxyl group.
At neutral pH, both carboxyl groups are deprotonated and thus negatively charged. The amino group has a positive charge because it remains
protonated at pH 7. Overall, therefore, glutamic acid has a net charge of −1, and (B) is correct. Notice that you do not even need to know the pI values to solve this question; as an acidic amino acid, glutamic acid must have a pI
below 7.

Question 52

Which of the following statements is most likely to be true of nonpolar R groups in aqueous solution?
A. They are hydrophilic and found buried within proteins.
B. They are hydrophilic and found on protein surfaces.
C. They are hydrophobic and found buried within proteins.
D. They are hydrophobic and found on protein surfaces

Answer 52

C
Nonpolar groups are not capable of forming dipoles or hydrogen bonds; this
makes them hydrophobic. Burying hydrophobic R groups inside proteins
means they don’t have to interact with water, which is polar. This makes (C)
correct. (A) and (B) are incorrect because nonpolar molecules are hydrophobic, not hydrophilic; (D) is incorrect because they are not generally found on protein surfaces.

Question 53

Scientists discover a cDNA sequence for an uncharacterized protein. In their initial studies, they use a computer program designed to predict protein structure. Which of the following levels of protein structure can be most accurately predicted?
A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure

Answer 53

A
The cDNA sequence is a DNA copy of the mRNA used to generate a protein. A computer program can quickly identify the amino acid that corresponds
to each codon and generate a list of these amino acids. This amino acid sequence is the primary structure of the protein. These observations support (A) as the correct answer. By contrast, the secondary, tertiary, and
quaternary structures involve higher level interactions between the backbone and R groups and are increasingly difficult to predict.

Question 54

How many distinct tripeptides can be formed from one valine
molecule, one alanine molecule, and one leucine molecule?
A. 1
B. 3
C. 6
D. 27

Answer 54

C
There are three choices for the first amino acid, leaving two choices for the
second, and one choice for the third. Multiplying those numbers gives us a
total of 3 × 2 × 1 = 6 distinct tripeptides. (Using the one-letter codes for
valine (V), alanine (A), and leucine (L), those six tripeptides are VAL, VLA,
ALV, AVL, LVA, and LAV.)

Question 55

Which of the following best describes the change in entropy that occurs during protein folding?
A. Entropy of both the water and the protein increase.
B. Entropy of the water increases; entropy of the protein decreases.
C. Entropy of the water decreases; entropy of the protein increases.
D. Entropy of both the water and the protein decrease.

Answer 55

B
As the protein folds, it takes on an organized structure and thus its entropy
decreases. However, the opposite trend is true for the water surrounding the
protein. Prior to protein folding, hydrophobic amino acid residues are
exposed and the water molecules must form structured hydration shells
around these hydrophobic residues. During folding, these hydrophobic
residues are generally buried in the interior of the protein so that the
surrounding water molecules gain more latitude in their interactions. us,
the entropy of the surrounding water increases, making the correct answer
(B).

Question 56

An α-helix is most likely to be held together by:
A. disulfide bonds.
B. hydrophobic effects.
C. hydrogen bonds.
D. ionic attractions between side chains

Answer 56

C
The α-helix is held together primarily by hydrogen bonds between the carboxyl groups and amino groups of amino acids. Disulfide bridges, (A),
and hydrophobic effects, (B), are primarily involved in tertiary structures, not secondary. Even if they were charged, the side chains of amino acids are too far apart to participate in strong interactions in secondary structure.

Question 57

Which of the following is least likely to cause denaturation of
proteins?
A. Heating the protein to 100°C
B. Adding 8 M urea
C. Moving it to a more hypotonic environment
D. Adding a detergent such as sodium dodecyl sulfate

Answer 57

C
High salt concentrations and detergents can denature a protein, as can high
temperatures. But moving a protein to a hypotonic environment—that is, a
lower solute concentration—should not lead to denaturation

Question 58

A particular α-helix is known to cross the cell membrane. Which of these amino acids is most likely to be found in the transmembrane portion of the helix?
A. Glutamate
B. Lysine
C. Phenylalanine
D. Aspartate

Answer 58

C
An amino acid likely to be found in a transmembrane portion of an α-helix
will be exposed to a hydrophobic environment, so we need an amino acid
with a hydrophobic side chain. The only choice that has a hydrophobic side
chain is (C), phenylalanine. e other choices are all polar or charged.

Question 59

Which of these amino acids has a chiral carbon in its side chain?
I. Serine
II. Threonine
III. Isoleucine
A. I only
B. II only
C. II and III only
D. I, II, and III

Answer 59

C
Every amino acid except glycine has a chiral α-carbon, but only two of the
20 amino acids—threonine and isoleucine—also have a chiral carbon in
their side chains as well. us, the correct answer is (C). Just as only one
configuration is normally seen at the α carbon, only one configuration is
seen in the side chain chiral carbon.

Question 60

Following translation and folding, many receptor tyrosine kinases exist as monomers in their inactive state on the cell membrane.
Upon the binding of a ligand, these proteins dimerize and initiate a signaling cascade. During this process, their highest element of protein structure changes from:
A. secondary to tertiary.
B. tertiary to quaternary.
C. primary to secondary.
D. secondary to quaternary.

Answer 60

B
In their inactive state, the receptor tyrosine kinases are fully folded single
polypeptide chains and thus have tertiary structure. When these monomers
dimerize, they become a protein complex and thus have elements of
quaternary structure. is change from tertiary to quaternary structure
justifies (B).

Question 61

Which of these amino acids has a side chain that can become
ionized in cells?
A. Histidine
B. Leucine
C. Proline
D. Threonine

Answer 61

A
Histidine has an ionizable side chain: its imidazole ring has a nitrogen atom
that can be protonated. None of the remaining answers have ionizable atoms
in their side chains.

Question 62

In lysine, the pKa
of the side chain is about 10.5. Assuming that
the pKa
of the carboxyl and amino groups are 2 and 9,
respectively, the pI of lysine is closest to:
A. 5.5.
B. 6.2.
C. 7.4.
D. 9.8.

Answer 62

D
Because lysine has a basic side chain, we ignore the pKa of the carboxyl
group, and average the pKa of the side chain and the amino group; the
average of 9 and 10.5 is 9.75, which is closest to (D).

Question 63

Which of the following is a reason for conjugating proteins?

I. To direct their delivery to a particular organelle
II. To direct their delivery to the cell membrane
III. To add a cofactor needed for their activity

A. I only
B. II only
C. II and III only
D. I, II, and III

Answer 63

D
Conjugated proteins can have lipid or carbohydrate “tags” added to them.
ese tags can indicate that these proteins should be directed to the cell membrane (especially lipid tags) or to specific organelles (such as the lysosome). ey can also provide the activity of the protein; for example, the heme group in hemoglobin is needed for it to bind oxygen. us, (D) is the
correct answer.

Question 64

Collagen consists of three helices with carbon backbones that are
tightly wrapped around one another in a “triple helix.”

Which of these amino acids is most likely to be found in the highest concentration in collagen?

A. Proline
B. Glycine
C. Threonine
D. Cysteine

Answer 64

B
Because collagen has a triple helix, the carbon backbones are very close
together. Thus, steric hindrance is a potential problem. To reduce that
hindrance, we need small side chains; glycine has the smallest side chain of
all: a hydrogen atom.