Amino Acids, Peptides, and Proteins Flashcards by Ashley Wilson | Brainscape

Q

What are the amino acids encoded in the genetic code called?

A

proteinogenic amino acids

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Q

Which amino acid is achiral?

A

glycine

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Q

Amino acids in eukaryotes are D or L?

A

L

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Q

Amino acids are all S/R except for ______?

A

S except for cysteine

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Q

Which two amino acids contain sulfur?

A

methionine and cysteine

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Q

Glycine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
neither

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Q

Alanine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
hydrophobic

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Q

Valine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
hydrophobic

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Q

Leucine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
hydrophobic

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Q

Isoleucine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
hydrophobic

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Q

Methionine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
neither

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Q

Proline
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
nonaromatic
neither

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Q

Tryptophan 
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
aromatic
neither

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Q

Phenylalanine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

nonpolar
neutral
aromatic
hydrophobic

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Q

Tyrosine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
aromatic
neither

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Q

Serine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
nonaromatic
neither

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Q

Threonine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
nonaromatic
neither

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Q

Asparagine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
nonaromatic
neither

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Q

Glutamine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
nonaromatic
neither

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Q

Cysteine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
neutral
nonaromatic
neither

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Q

Aspartic Acid
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
negative
nonaromatic
hydrophilic

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Q

Glutamic Acid
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
negative
nonaromatic
hydrophilic

Q

Lysine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
positive
nonaromatic
hydrophilic

Q

Arginine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
positive
nonaromatic
hydrophilic

Q

Histidine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =

A

polar
positive
aromatic
hydrophilic

Q

How many pKa values do amino acids have and what are they?

A

at least two
the first one is the deprotonation of the carboxyl group around 2
the second one is the deprotonation of the amino group around 9/10

Q

At very acidic pH values, amino acids tend to be _____ charged.

A

positively

Q

What is the isoelectric point?

A

the pH at which the molecule is electrically neutral

Q

pI of a neutral amino acid

A

pKa amino group + pKa carboxylic acid / 2

Q

pI of a acidic amino acid

A

pKa R group + pKa carboxylic acid / 2

Q

pI of a basic amino acid

A

pKa amino group + pKa R group / 2

Q

What is a peptide bond?

A

a specialized form of an amide bond, which form between the -COO- group of one amino acid and the NH3+ group of another amino acid

Q

Peptides read from the _-terminus to the _-terminus.

A

N to C

Q

How do hydrolytic enzymes hydrolyze peptides?

A

Break apart amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon

Q

Where does trypsin cleave?

A

carboxyl end of arginine and lysine

Q

Where does chymotrypsin cleave?

A

at the carboxyl end of phenylalanine, tryptophan and tyrosine

Q

What is the primary structure of a protein?

A

the linear arrangement of amino acids coded in an organism’s DNA

Q

What is the secondary structure of a protein?

A

the local structure of neighboring amino acids

Q

What are two secondary structures?

A

alpha helix and beta sheets

Q

Which bonds hold the secondary structure together?

A

hydrogen bonds

Q

What is proline useful for?

A

found at the turns between beta sheets and start of alpha helix due to its kinking properties

Q

What are fibrous proteins?

A

structures that resemble sheets or long strands

Q

What are globular proteins?

A

structures that are spherical

Q

What is tertiary structure?

A

three-dimensional shape

Q

What determines the tertiary structure?

A

hydrophilic and hydrophobic interactions between the R groups

Q

What are quaternary structures?

A

aggregate of smaller globular peptides (multiple polypeptides chains) that function as a protein

Q

Four reasons for having quaternary structure?

A

(1) more stable by reducing the surface area of the protein complex
(2) reduce amount of DNA needed to encode the protein complex
(3) bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
(4) Cooperativity/allosteric effects

Q

What are conjugated proteins?

A

proteins with have covalently attached molecules known as prosthetic groups

Q

What are lipoproteins?

A

proteins with lipid prosthetic groups

Q

What are glycoproteins?

A

proteins with carbohydrate prosthetic groups

Q

What are nucleoproteins?

A

proteins with nucleic acid prosthetic groups

Q

What are prosthetic groups needed for?

A

can direct protein to be delivered to a certain location

- affect activity of protein

Q

Which amino acids have chiral carbons in their side chains?

A

serine and threonine