BIOCHEM Week 2

Water interacts _______ with other water molecules via ______ bonds.

noncovalently; hydrogen bonds

Each water molecule can form ____ short-lived hydrogen bonds.

4

Van der Waals interactions

are weak, short-lived interactions between dipoles of close proximity neutral molecules and depend highly on molecules being close to each other

Hydrophobic effects

occurs between nonpolar molecules that do NOT form hydrogen bonds with water because they are attracted to each other; play a role in protein folding reactions

Amphoteric

can act as an acid or base (i.e. water)

pH < 6.5 =
pH > 7.5 =
6.5 < pH < 7.5 =

acidic; basic; neutral

What does it means if a pH is neutral?

The concentration of H+ and OH- are relatively the same.

Titration curve

plot of pH (y-axis) and equvalent of base added (x-axis)

Buffers contain

roughly equal concentration of acid and conjugate base which are about 1 pKa unit above and below the equivalence point

Polyprotic acid

an acid with more than one dissociable H+

Polypeptides

long amino acid polymers

Peptides

shorter polypeptides (< 40 amino acids in length)

Residues

amino acids within a polypeptide chains (interchangeable terms)

Chiral Center (and its relation to amino acids)

an atom in molecule that is bonded to four different and unique groups which causes creates a non-imposable mirror image; all amino acids except for glycine have an alpha-C that is a chiral center

Almost all proteins found in nature have which configuration?

L

Which two amino acids are most commonly have a phosphate group added?

Serine and Threonine

Cysteine acts as a ____ and can form stable ______ bonds by donating it’s ______ from the _____ group.

weak acid; disulfide bonds; H; sulfhydryl

Which two amino acids are acted upon by kinases?

Serine and Threonine

What are phosphatases?

Enzymes that remove phosphate groups from a molecule

What are the six amino acids with ionizable side chains?

Lysine, Arginine, Tyrosine, Cysteine, Histidine, Aspartic Acid, Glutamic Acid

Isoelectric point

the pH at which the amino acid carries no charge, calculated using two pKa values

The formation of a peptide bonds is what type of reaction and what is the product?

Condensation reaction where water in the product

The breaking of a peptide bond is what type of reaction and what is the reactant?

Hydrolysis reaction where water is a reactant

Wild-type sequence

original protein sequence

Silent mutation

a single nucleotide change that allows the intended protein to remain unchanged

Missense mutation

a single nucleotide change that ends up in a single protein being changed.

Nonsense mutation

a stop codon interrupts the protein sequence (stops early)

Frameshift

the addition or deletion of a nucleotide that creates a new protein sequence

Primary Structure

linear amino acid sequence; held together by covalent peptide bonds

Secondary structure

polypeptide backbone is created through hydrogen bonding between carboxyl group ‘O’ and amino group ‘N’; beta strands, beta turns, and alpha heloxes

Which amino acid is more commonly found in alpha helixes and why?

Proline because it has a cyclic structure that helps maintain the cork-screw shape of the alpha helices

Many alpha helices are _________ because there are hydrophobic or __________ amino acids ever 3-4 residues.

amphipathic; hydrophilic

Beta strands are held together by ______ bonding and form beta _______ _________.

hydrogen; pleated sheets

Beta sheets form in two directions:

parallel and anti-parallel

Beta turns connection two ____ strands in an ______ beta sheet, with _____ being the second or third residue.

beta; anti-parallel, glycine

Tertiary structure includes all _______ structures in their ________ patterns and many _______ and _______ interaction between the _____ _______.

secondary; folding; covalent; noncovalent; side chains.

Quaternary structure consists of multiple _______ _______ complexes and their respective covalent and non-covalent interaction.

subunit protein

Homodimer

Two identical protein subunits

Heterdimer

two subunits created from two different polypeptides

What are immunoglobulin proteins? What do they do?

Antibodies that bind to antigens and attract immune cells to the antigen-antibody complexes they create so intruders can be destroyed

Describe the structure of antibodies, where antigens can bind, and what bonds stabilize them.

They are heterotrimers that consist of two heavy chain and two light chain subunits that are arrange in a Y-shaped molecule.

Antigen binding sites are near the N-terminus of the H and L chains

They are stabilized by disulfide bonds.

What is the specific reducing angels that break disulfide bonds?

BME or beta mercaptoethanol