Peptides

General structure of amino acids

α‑carbon, amino group, carboxyl group, H, and an R‑group that “differs in each amino acid” .

Are amino acids amphoteric

yes

Amphoteric meaning

can accept or donate protons

How are amino acids amphoteric

ability to donate protons from the carboxyl group and accept protons at the amino group

What pH groups are both functional groups charged?

pH 6.5-7.5

What are zwitterions?

Zwitterions are molecules that contain both positive and negative charges, resulting in no net charge overall.

When are amino acids zwitterions in the pH

physiological pH,

Classes of side chains

• non-polar

• polar uncharged

• charged

non-polar side chains

• no charge or electronegative atoms

• therefore do not form hydrogen bond

• not soluble in water

• are typically found in the interior of proteins to help stabilize their structure.

Polar or uncharged/neutral amino acids

• have partial charges that can form hydrogen bonds

• are soluble in water

Charged amino acids

• charged side chains which form hydrogen and ionic bonds

• very soluble in water

What is chiral in AA

alpha-carbon

What amino acid is not chiral

• glycine is not chiral

What amino acids do proteins only contain

L-amino acids

What configuration to L AA have

• L-amino acids have an S configuration except for cysteine, which has an R configuration.

Isoelectric point

the pH at which a molecule carries no net electrical charge,

How are peptides formed

amino acids join via the peptide bond, which is “resonance stabilised” and has partial double‑bond character

how many AA do peptides have

<50

How many AA do proteins have

Typically over 50

How amino acids are separated

Electrophoresis (separation by pI)

• Amino acids migrate in an electric field depending on charge.

Chromatography separation by polarity

Ion‑exchange chromatography separates amino acids by charge/polarity.

How is isoelectric point calculated

x

How are peptides bonds resonace stabilised

• electrons are shared unequally

• therefore, greater electron density on the oxygen

• with orbital overlap imparting partial double bond character to the amide bond

Primary Proteins

• linear sequences of amino acids linked by peptide bonds, forming the basic structure of proteins.

secondary protein

• the folding and twisting of a single polypeptide chain into alpha helices and beta sheets, stabilized by hydrogen bonds between backbone atoms.

α‑helix

right‑handed coil; H‑bonds between C=O of residue i and NH of i+4

β‑sheets

parallel or antiparallel strands; R‑groups alternate above/below the sheet.

Tertiary structure

the overall 3D shape of a polypeptide, formed by interactions between including hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bridges.

Quaternary protein

When 2 or more polypeptide chains interact via the same forces as tertiary proteins

what are the 2 categories of proteins

Fibrous and globular proteins.

What is a common quaternary protein

Haemoglobin