PHSC1212 Biochemistry - Lecture 5 Amino Acids pt 1

Proteins

diverse group of molecules that perform many of the functions required for life

Hydrogen, Amino, Carboxyl, R group

general amino acid components

R group

Which part of different amino acids is different?

Functional group

another name for the R group on the amino acids

Amino acids

make up proteins; "building blocks" of proteins

Peptide

two or more amino acids bound together

Polypeptide

a peptide made up of more than 50 amino acids

Negative

charge of a carboxyl group at physiological pH of 7.4

Positive

charge of an amino group at physiological pH of 7.4

Once folded into its functional conformation

When is a polypeptide considered a protein?

Peptide bond

the amide bond between two amino acids

20

How many standard amino acids used to build proteins?

Nonessential

type of amino acids that can be synthesized by the body

Essential

type of amino acids that cannot be synthesized by the body; must be in the diet

Complete proteins

have all the essential amino acids and are typically animal sources

Incomplete protein

a protein lacking one or more essential amino acids

Plant sources

typically incomplete proteins

Wheat

type of plant protein lacking sufficient Lys (lysine)

Corn

type of plant protein low in Lys (lysine) and Trp (tryptophan)

Chiral

What type of molecules are amino acids due to their stereocenters?

L-form

stereoisomer form of amino acids found in proteins

Stereoisomers

differ only in the spatial arrangement of their atoms

4

How many different groups are attached to a chiral carbon? (just enter the number)

Glycine

only standard amino acid without a chiral carbon

Glyceraldehyde

What molecule and its similarity was used to designate D and L forms?

Enantiomers (optical isomers)

What are D and L isomers?

Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Proline

nine nonpolar amino acids

Nonpolar

uncharged, hydrophobic amino acids

Aliphatic

What type of hydrocarbons are most nonpolar amino acids?

Phenylalanine and Tryptophan

nonpolar aromatic hydrocarbons

Charge

What do nonpolar and polar amino acids not have?

Thioether

What does Methionine have?

Hydrophilic

Due to the R-group being a hydrogen, Glycine is slightly what?

Proline

only amino acid with a secondary amine instead of primary amine

Secondary

What type of amine does proline have that makes it unique?

Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

six polar amino acids

Polar

uncharged amino acids that can form hydrogen bonds with water (hydrophilic)

Serine and Threonine

amino acids that are attachment sites for carbohydrates

Cysteine

amino acid with highly reactive thiol group; also binds metals; found in reaction sites of enzymes; can form disulfide bonds

Thiol group

functional group of cysteine that is highly reactive

Enzymatic reactions

What is the thiol group on cysteine important for?

Metals

What can cysteine bind to?

Hydrogen bonding and modification

What is the hydroxyl group on serine, threonine, and tyrosine good for?

Asparagine and Glutamine

amino acids that have amides

Aspartate and glutamate

two acidic amino acids (names without the acid ending)

Carboxyl group

side chain of acidic amino acids

Negatively charged at pH 7.4

Why can the acidic amino acids also be referred to as aspartic acid and glutamic acid)

Lysine, Arginine, Histidine

three basic amino acids

Positively charged

What are Lysine and Arginine at physiological pH?

Salt bridge

ionic bond formed between basic and acidic amino acids

Lysine

an important component of collagen

Weak

What type of base is Histidine's R group?

pKa close to physiological pH

Why is Histidine a basic amino acid, ionized or unionized?

Can participate in acid base reactions

Why is Histidine often found in enzyme-active sites?

6

Histidine pKa

Charged or ionized

Lysine and Arginine are considered to have permanently ____________ R groups

Much higher pKa than physiological pH

Why are Lysine and Arginine considered to have "permanently charged/ionized" R groups?

10

Lysine pKa

12

Arginine pKa

pH

affects the ionization of amino acids

Glutamate

amino acid example with three ionizable groups and thus three pKas

carboxyl

Which group is pK1?

amino

Which group is pK2?

Isoelectric point or pI

pH at which the amino acid has no net charge

Percentage in ionized state

What increases for acids further above pKa and decreases for bases further below pKa?

3rd pKa

What do amino acids with ionizable R groups have?

Hydrogen bonding, acid-base chemistry

Because they are uncharged at physiological pH, cysteine and tyrosine tend to behave more like polar amino acids and can participate in ___________ but not ___________

pKa

Certain environments can lower ____ of tyrosine and cysteine, increasing acidic behavior