biochem mod 2 (unfinished)

In every living organism, proteins are constructed from a common set of

20 amino acids

Each amino acid has a side chain with

distinctive chemical properties

In proteins, amino acids are joined in linear sequences through a common amide

linkage called a

peptide bond

The amino acid sequence of a protein constitutes its - structure

primary

For study, individual proteins can be separated from the thousands of other proteins present in a cell, based on

differences in their chemical and functional properties arising from their distinct amino acid sequences

Amino acid sequences (structure) are a key resource for understanding

the function of individual proteins and for tracing broader functional and evolutionary relationships.

Amino Acids Share Common Structural Features:

• α carbon and four substituents

• α carbon is the chiral center

• tetrahedral

The central alpha-carbon in every amino acid is bound to four different chemical groups:

An amino group (—NH2)

A carboxyl group (—COO)

A hydrogen atom (—H)

A unique side chain (—R)

*except glycine, has 2 H’s

Glycine is special in that

glycine has a second hydrogen atom instead of an R group

Because the alpha-carbon is bound to four distinct groups, it serves as a chiral center.

L Stereoisomers

Which amino acid residue in proteins is optically inactive and lacks a chiral center?

Glycine. Its alpha-carbon is bound to two hydrogen atoms, making it achiral (has no enantiomers).

What type of isomers are D- and L-amino acids to each other?

Enantiomers

Which stereoisomer form of amino acids is exclusively found in ribosome-synthesized proteins? / The Amino Acid Residues in

Proteins are

L-stereoisomers (L-amino acids).

Where can D-amino acids be found naturally in biology, even though they are absent from ribosome-made proteins?

In bacterial cell walls (e.g., D-alanine and D-glutamate in peptidoglycan) and certain peptide antibiotics (e.g., valinomycin, gramicidin), synthesized non-ribosomally by specialized enzymes.

Amino Acids Can Be Classified by R Group. There are 5 main classes:

nonpolar, aliphatic (7)

– aromatic (3)

– polar, uncharged (5)

– positively charged (3)

– negatively charged (2)

Name the 7 amino acids with nonpolar, aliphatic R groups.

Glycine (Gly, G)

Isoleucine (Ile, I)

Alanine (Ala, A)

Valine (Val, V)

Leucine (Leu, L)

Proline (Pro, P)

{ Methionine (Met, M) }

What makes Glycine unique among all 20 standard amino acids?

ts R group is a single hydrogen atom.

It is the smallest amino acid, the only achiral/optically inactive one, and provides unique conformational flexibility to polypeptide chains.

What is the primary thermodynamic force that drives nonpolar, aliphatic amino acids to cluster inside a folded protein?

the hydrophobic

effect, stabilizes

protein structure

Glycine

Alanine

Proline

Valine

Leucine

Methionine

Isoleucine

Which three amino acids have aromatic R side chains?

Phenylalanine (Phe, F)

Tyrosine (Tyr, Y)

Tryptophan (Trp, W)

At what wavelength range do aromatic amino acids absorb UV light?

270–280 nm

How do aromatic R groups contribute to protein folding and stability?

Their nonpolar ring structures contribute significantly to the hydrophobic effect, causing them to pack inside the interior core of folded proteins.

Phenylalanine

Tyrosine

tryptophan

Name the 5 polar, uncharged amino acids found in proteins.

Serine (Ser, S)

Threonine (Thr, T)

Cysteine (Cys, C)

Asparagine (Asn, N)

Glutamine (Gln, Q)

Polar unchrged R groups can form

hydrogen bonds

Cysteine can form

Disulfide bonds

Positively Charged R Groups have

significant positive charge at pH 7.0

Name the 3 positively charged (basic) amino acids.

Lysine (Lys, K)

Arginine (Arg, R)

Histidine (His, H)

Lysine

Arginine

Histidine

Negatively Charged R Groups have a

net negative charge at pH 7.0

Name the 2 negatively charged (acidic) amino acids.

Aspartate (Asp, D)

Glutamate (Glu, E)

What are the 4 main ways uncommon amino acids originate or function in cells?

Modified after protein synthesis (post-translational).

Modified during protein synthesis (specialized incorporation).

Modified transiently (regulatory switches).

Free metabolites (intermediates in metabolic pathways, not in proteins).

Give an example of an amino acid modified after protein synthesis and state its function.

4-hydroxyproline (modified from proline), which provides structural stability to collagen

Give an example of an amino acid modified during protein synthesis and state its function.

Pyrrolysine, which is incorporated during translation in certain organisms to assist in methane biosynthesis.

What is the main purpose of transiently modifying amino acid side chains (e.g., via phosphorylation)?

To reversibly alter a protein’s structure, activity, or interactions as a regulatory switch (turning enzyme activity on or off).

What is a free metabolite amino acid? Give an example.

An amino acid that is not incorporated into proteins but serves as an intermediate in metabolic pathways.

Example: Ornithine (an intermediate in arginine biosynthesis and the urea cycle).

Amino acids can act as both an acid (proton donor) and a base (proton acceptor). This is because they contain both

an acidic functional group (COOH) and a basic functional group (NH2) {amphoteric}

What term describes a molecule that can act as both an acid and a base?

Amphoteric (or an ampholyte)

Which 3 functional parts of an amino acid can participate in acid-base (proton transfer) reactions?

The alpha-carboxyl group ($-\text{COOH}$)

The $\alpha$-amino group ($-\text{NH}_3^+$)

Ionizable R groups (e.g., Asp, Glu, His, Cys, Tyr, Lys, Arg)

How does a zwitterion behave when placed in a strongly acidic (low pH) solution? Basic?

It acts as a base, accepts a proton, + cation

It acts like an acid, donates a proton, -

What is a zwitterion?

A dipolar ion containing both positive ($-\text{NH}_3^+$) and negative ($-\text{COO}^-$) functional groups, resulting in a net electric charge of zero at neutral pH.

What sequence of ionic forms does a simple amino acid transition through as pH increases from 1 to 14?

cation (+1) ⇌ zwitterion (0) ⇌ anion (-1)

Which group deprotonates first during the titration of a non-ionizable amino acid? Why?

The alpha-carboxyl group (COOH), because it has an acidic pka of ~2.34

Which group deprotonates second during the titration of a non-ionizable amino acid?

The alpha-amino group (NH3), because it has a basic pka ~ 9.6

Define the isoelectric point (pI) of an amino acid.

The specific pH at which the molecule carries no net electric charge (100% zwitterion form).

What is the net charge of an amino acid when pH < pI?

Net positive charge (predominantly in the cationic form).

What is the net charge of an amino acid when pH > pI?

Net negative charge (predominantly in the anionic form).

How many buffer regions does a simple amino acid (like Glycine) have on its titration curve?

Two buffer regions

Effect of the Chemical Environment on pKa:

α-carboxyl group is - - than reg carboxyl in carboxylic acids

α-amino group is - - than reg amino in amines

more acidic

less basic

What three major pieces of biochemical information can be determined from an amino acid's titration curve?

pka values of each ionizing group (at inflection/midpoints).

Regions of buffering power ($\text{pH} = \text{p}K_a \pm 1$).

Net electric charge at any given $\text{pH}$, including the isoelectric point ($\text{pI}$).

Buffers prevent changes

in pH close to the pKa

Glycine has two buffer regions:

centered around the pKa of the α-carboxyl group (pK1 = 2.34)

centered around the pKa of the α-amino group (pK2 = 9.6)

For amino acids without ionizable side chains, the isoelectric point (pI) is:

pH = pI = net charge is zero (amino acid least

soluble in water, does not migrate in electric field)

pH > pI =

net negative change

pH < pI =

net positive charge

Amino Acids Differ in Their Acid-Base Properties

• ionizable side chains:

• have a pKa value

• act as buffers

• influence the pI of the amino acid

• can be titrated (titration curve has 3 ionization steps)

peptide bonds are

covalent

Peptide bonds are formed through - and broken through -

condensation, hydrolysis

dipeptide

= 2 amino acids, 1 peptide bond

tripeptide =

3 amino acids, 2 peptide bonds

oligopeptide

= a few amino acids

polypeptide

= many amino acids, molecular weight < 10 kDa

Protein

= thousands of amino acids, molecular weight > 10 kDa

Peptide Terminals:

Numbering (and naming) starts from the

amino-terminal residue (N-terminal)

In what direction are peptide sequences always read, named, and written?

From the $\text{N}$-terminus to the $\text{C}$-terminus (left to right).

When writing the full amino acid name of a peptide, how are all non-terminal amino acid residues modified?

The "-ine" or "-ate" suffix of each non-terminal amino acid is replaced with "-yl", with only the final $\text{C}$-terminal amino acid retaining its full name (e.g., serylglycyltyrosylalanylleucine).

Which amino acid residue in the peptide Ser–Gly–Tyr–Ala–Leu occupies the $\text{N}$-terminus, and which occupies the $\text{C}$-terminus?

{N}$-terminus: Serine (Ser / S)$\text{C}$-terminus: Leucine (Leu / L)

Naming Peptides

• full amino acid names:

serylglycyltyrosylalanylleucine

• three-letter code abbreviations:

Ser–Gly–Tyr–Ala–Leu

• one-letter code abbreviation:

SGYAL

Peptides Can Be Distinguished by Their Ionization Behavior

• ionizable groups in peptides:

one free α-amino group

– one free α- carboxyl group

– some R groups

Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes and Compositions

• length of naturally occurring peptides =

2 to many thousands of amino acid residues

multisubunit protein =

2+ polypeptides associated noncovalently

oligomeric protein

= at least 2 identical subunits

^ identical units =

protomers

amino acid composition is

highly variable

number of amino acid residues =

molecular weight/110

average molecular weight of amino acid =

~128

molecule of water removed to form peptide bond =

18

If a protein has a molecular weight of $55\text{,}000\ \text{Da}$, approximately how many amino acid residues does it contain?

55,000 / 110 = 500 residues

Some Proteins Contain Chemical

Groups Other Than

amino acids

conjugated proteins =

contain permanently associated chemical components

non–amino acid part of conjugated proteins =

prosthetic group

lipoproteins contain -

glycoproteins contain -

metalloproteins contain -

lipids

sugars

specific metals

Proteins Can Be Separated and Purified based on

size

– charge

– binding properties

– protein solubility

Methods for Purifying Proteins

• first step =

break open tissue or microbial cells

crude extract

= releases proteins in solution

Methods for Purifying Proteins

• second step =

fractionation

fractionation

separate proteins into fractions based on size or charge

“salting out” =

lower solubility of proteins in salt to

selectively precipitate proteins