Water and Aqueous Solutions, Amino Acids, Peptides, and Proteins

These flashcards cover key concepts related to the structure of water, amino acids, peptides, proteins, and related biochemical principles.

Water Structure

Water has 4 electron pairs in sp3 orbitals, leading to a net dipole moment and hydrogen bonding.

Hydrogen Bonding

The ability of water to form hydrogen bonds allows substances that can form H-bonds to be more soluble in water.

Rank the imfs

Ionic > hbond > dipole dipole > van Der waals

What substances or molecules are soluble in water?

Polar, OH group

Hydrophobic Effect

Lowers system entropy and favors ligand binding, as binding sites are often hydrophobic.

pH and Buffers

pH is defined as -log[H+], and buffers consist of a weak acid and its conjugate base.

Strong acid, small or large pka?

Small pka, large Ka

Buffer capacity

Midpoint ± 1 pH unit

Isoelectric Point

The pH at which the net charge of a molecule is zero.

Chirality

Chiral molecules cannot be superimposed on their mirror images; achiral molecules can.

Peptides

Small condensation products of amino acids, usually under 10 kDa.

Chromatography

A technique to separate compounds; larger molecules elute first in size-based chromatography.

Peptide Hormones

Biologically active molecules like insulin and oxytocin that play crucial roles in physiology.

Cofactors

Non-amino acid components that assist enzyme functions, including coenzymes and prosthetic groups.

Affinity chromatography

Protein of interest elute last

examples of hormones

Insulin, oxytocin, sex-peptides

Net charge chromatography

Negative beads = negative particles elute last

Example Neuropeptides

Substance P

Antibiotics example (peptides)

Polymyxin B (gram -), Bacitracin (gram +)

Toxin peptides

Amanitin (mushrooms), conotoxin (cone snails), chlorotoxin (scorpion)

Electrophoresis, who stays at the top of the field?

Negative and más pesadas

What’s is Sanger protein sequencing for?

• determine amino acid terminus ( gly at amino side)

• Determine amino acid content by hydrolysis

• Cleavage into smaller polypeptide

Cleveage points of trypsin

Lysin and arginine

What does sequence define?

Structure

What does structure define?

Function

What’s this aminoacid?

glycine

What’s this aminoacid?

alanine

What’s this aminoacid?

valine

What’s this aminoacid?

leucine

What’s this aminoacid?

Methionine

What’s this aminoacid?

Isoleucine

What’s this aminoacid?

phenylalanine

What’s this aminoacid?

Ty

What’s this aminoacid?

Tryptophan is an essential amino acid used in protein synthesis and a precursor for serotonin.

What’s this aminoacid?

serine

What’s this aminoacid?

threonine

What’s this aminoacid?

cysteine

What’s this aminoacid?

proline

What’s this aminoacid?

asparagine

What’s this aminoacid?

glutamine

What’s this aminoacid?

lysine

What’s this aminoacid?

arginine

What’s this aminoacid?

histidine

What’s this aminoacid?

aspartate

What’s this aminoacid?

glutamate

which one is the smallest aminoacid?

glycine

Only amino acid that can form disulfide bonds?

cysteine

CO is toxic to humans because

It binds to the Fe atom in hemoglobin and prevents the binding of O2

what is post-translational modiication?

The chemical alteration of a protein after its translation, adding functional groups like phosphates or sugars, or undergoing cleavage, changes its activity and structure.

example of post-translational modification

phosporylation, glycosylation, ubiquitination and acetylation.

Model of ligand binding to proteins, conformational may occur upon ligand binding

Induced fit

Model of ligand binding to proteins, it is assumed that complementary surfaces are preformed

lock and key

condition to unfold a protein

high temperature

loss of 3D structure and loss of activity

denaturation

method to determine the 3D structure of a protein

x-ray crystallography

experiment that demonstrated the sequence alone determines the native fold of a protein

ribonuclease refolding

The interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha helixes

h-bond

In a globular protein, the amino acids Asparate, Lysine, Glutamate, and Histidine would be found more often in where?

external surface of the protein

Rate at which proteins fold into their native structures.

Leevinthal’s paradox