Major Amino Acids + MCAT Biochem: Amino Acids + Proteins

Histidine: structure, pK_a

Abbreviation: His, H

pK_a of R group: 6.0

will exist as either protonated or deprotonated at physiological pH given how close it is (pH = 7.4)

Lysine: stucture, pK_a

Abbreviation: Lys, K

pK_a of R group: 10.5

Aspartic Acid/ Aspartate: Structure, pK_a

Abbreviation: Asp, D

pK_a of R group: 3.9

Glutamic Acid/ Glutamate

Abbreviation: Glu, E

polar (hydrophilic) amino acid

pK_a of R group: 4.1

Serine

Abbreviations: Ser, S

Threonine

Abbreviation: Thr, T

Cysteine

pK_a of R group: 8.4

Abbreviation: Cys, C

only amino acid in R configuration (others in S-configuration)

• Extracellular space is oxidizing, favoring formation of disulfide bridges

• Intracellular space is reducing, favoring cysteines

Asparagine

Abbreviation: Asn, N

Glutamine

Abbreviation: Gln, Q

Glycine

Abbreviations: Gly, G

One of the alpha helix breakers since it has two Hs, making it not optically active

Alanine

Abbreviation: Ala, A

Proline

Abbreviations: Pro, P

One of two amino acid to be “alpha helix breakers“ due to flexible structure, inhibiting bond formation

Valine

Abbreviation: Val, V

Leucine

Abbreviation: Leu, L

Hydrophobic (Nonpolar)

Isoleucine

Abbreviation: Ile, I

Methionine

Abbreviation: Met, M

Phenylalanine

Abbreviation: Phe, F

Nonpolar, aromatic

Tyrosine

Abbreviation: Tyr, Y

pK_a of R group: 10.5

Tryptophan

Abbreviation: Trp, W

Arginine: structure, pK_a

Abbreviation: Arg, R

pK_a of R group: 12.5

N-terminus vs C terminus

The N-terminus includes the first amino acid of a protein, which has a free amino group at this end of the polypeptide chain. This is made first.

The C-terminus includes the final amino acid of a protein, and is therefore where synthesis of a polypeptide ends. There is a free carboxyl group at this end of the polypeptide chain.

Gabriel Synthesis

The gabriel synthesis starts with N-pthalamidomalonic ester "Thad", which protects both the amine group and carboxylic acid. The alpha-carbon will be alkylated, hydrolyzed, and then heated for a decarboxylation.

Strecker Synthesis

The strecker synthesis is much more simple and efficient. It starts with ammonia, KCN, and an aldehyde/ketone. The aldehyde/ketone and ammonia will react to form an imine, which in acid with KCN will form a nitrile, and hydrolysis in acid will yield the alpha-amino-acid.

What is most likely to occur if a patient with HIV is administered a medicinal drug that deactivates the enzyme reverse transcriptase?

Rate of survival would increase.

Would increase because HIV spreads using reverse transcriptase, so blocking it would prevent the spread.

How to calculate the pI of a Neutral R group

the pI is the average of the carboxylic acid group and amino group pKa values.

How to calculate the pI of an Acidic R group

the pI is the average of the carboxylic acid group and side chain pKa values.

How to calculate the pI of a Basic R group

the pI is the average of the amino group and side chain pKa values.

Peptide bonds are broken via

hydrolysis reactions

Peptide bonds are formed via

condensation reactions

Acidic polar amino acids have what group

Carboxyl group

Residue

Single amino acid in a polypeptide chain because some of the molecules of the amino acid are lost in the condensation reaction to form peptide bonds, leaving a "residue" behind.

Conformational protein

active and properly folded protein

When will the amino acid be fully protonated?

At a low pH, the amino acid will be fully protonated with a positive net charge.

When will the amino acid be fully deprotonated?

At a high pH, the amino acid will be fully deprotonated with a negative net charge.

Benefit of linear polymer structure

The linear polymer structure of DNA, RNA, and protein helps to transfer and preserve the encoding of information during transcription and translation.

Which of the following terms best describes the amino acids that are coded for in the human genetic code?

Proteinogenic Amino Acids

Zwitterions

When a compound has two ions of opposite charges

2 < pH < 9

Peptide bond

A bond formed between two amino acids through a condensation reaction.

Reverse transcriptase

converts RNA to DNA

RNA viruses

• viruses that have genetic information encoded as RNA, not DNA

  • Can be used directly by host cell machinery like it was mRNA

  • Or can be converted into a complementary strand

  • Like COVID-19

ncRNA

• can directly be used to perform tasks for the cell

  • rRNA and tRNA are both examples, and they help contribute to translation of messenger RNA into proteins

Examples of DNA modification

DNA methylation and histone modification

alpha carbon

carbon adjacent to a carbonyl group (not the carbon actually bonded to the oxygen)

Proteolytic cleavage:

cleavage of amino acids and normally has high specificity

Chirality

refers to optical activity (if active, it would result in the carbon rotating towards any present light)

Isoelectric point

 pH where the acid will be neutral (no charge)

pK_a

: when the amino acid is equally protonated and deprotonated

Alkyl amino acids

Glycine

Alanine

Valine

Leucine

Isoleucine

Proline

Methionine

Aromatic, nonpolar amino acids

Tryptophan

Phenylalanine

Neutral, polar amino acid

Serine

Threonine

Cysteine

Glutamine

Asparagine

Tyrosine

Basic amino acid

Lysine

Arginine

Histadine

Acidic amino acid

Glutamate

Aspartate

Hydrophobic effect

hydrophobic compounds pack together to form circles in polar compounds

Also means that water molecules try to maximize hydrogen bonding surrouding the hydrophobic cells (THEY DON’T FORM SOLVATION LAYERS)

Hydrophobic side chain

more CHs means that the compound is more hydrophobic and electronegative

Ionizable amino acids

Glutamate

Aspartate

Histidine

Cysteine

Lysine, Tyrosine, Arginine

Primary structure of proteins

sequence of amino acid chain linked by peptide bonds

Secondary structure of proteins

• close (backbone) interactions between the different parts of the amino acid chain 

  • Based on hydrogen bonds

  • Uses alpha helices and beta-pleated sheet

Tertiary Structure of proteins

•  higher order protein folding (overall 3D structure)

  • Based on distant interactions in the polypeptide

    • Hydrophobic interactions

    • Disulfide bridge interactions

    • Van der Waals interactions

  • hydrophobic effect driving the structure through long distance interactions on distant amino acids

Quaternary structure of proteins

•  based on interactions between polypeptides

  • using bonds

    • Hydrophobic interactions

    • Disulfide bridge interactions

    • Van der Waals interactions

Hydrogen bond donor and acceptor on the peptide bond

• Hydrogen bond donor: N-H

• Hydrogen bond acceptor: C=O

London dispersion forces

• (Van der Waals interactions): interactions between instantaneous dipole interactions

Disulfide bridges

intramolecular reaction of covalent bonds between two adjacent cysteine groups on separate parts of the chain

• Fibrous protein:

• structural protein containing long fibers

  • Like collagen, keratin

• Globular protein:

• forms circular structure through polypeptides

  • DNA polymerase is an example

How to break a protein’s structure

• Temperature change

• pH change

• Addition of chemicals

• enzyme

Heat change on different types of protein structure

• you destroy all layers except the primary structure

pH change on different types of protein tructure

: destroy tertiary and quaternary structure since they are based on H+ ions

Addition of chemicals on types of protein structure

 denature secondary, tertiary, and quaternary structure

Addition of enzymes on types of protein structure

break down individual primary structure to make proteins we need

Gabriel Synthesis

pH is lower than 7.4. What amino acids wouldn’t be protonated?

The amino acids were pIs that are substantially lower than 7.4, like Glutamic Acid (pI=3.0)

At a pH roughly equal to 7, an amino acid will have

a carboxylate (deprotonated carbyoxlyic acid) along with a positively charged amino group

Beta turns

found on the surface of proteins and consist of amino acids

Hydrogen bond

intermolecular bond that forms between compound with carbonyls and groups like -NH,-SH, or -OH

Alpha helix

hydrogen bond every 4 carbons that result in a twisting helix shape that helps to form the secondary structure

Beta pleated sheets

portions of the amino acid strand that are attracted to each other do to hydrogen bonding, which allows them to stack together and aggregate

formed at least 4 carbons away