Amino Acids and Protein Structure

In every living organism, proteins are constructed from a common set of how many amino acids

20

carbon

an α-amino acid has a central carbon atom called the α-what

the α-carbon is linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive side chain called the what group

R

True or False: the α carbon is a not chiral center

False

useful for visualizing the constituent atoms of the molecule

Fischer projections

useful for visualizing the shape of the molecule

Stereochemical renderings

only the which isomers of amino acids are found in proteins

L

same chemical formula but different structure

isomers

isomers with same connectivity of atoms, but different arrangement

stereoisomers

stereoisomers that are not mirror images

diastereoisomers

stereoisomers that are mirror images

enantiomers

Interactions between Biomolecules Are what

Stereospecific

All Amino Acids Have at Least how many Charged Groups

2

The what group (NH3+) and the what group (COO−) are usually charged at neutral pH

amino, carboxyl

isoelectric

the pH at which the net electric charge is zero is the what point (pI)

zwitterions

at neutral pH most amino acids are dipoles or what

side chain

The distinct chemical properties of amino acids come from the chemical nature of the what

Amino acids can be sorted into four groups based on the general
characteristics of their R groups:

positively charged amino acids

hydrophillic

Amino acids can be sorted into four groups based on the general characteristics of their R groups:

nonpolar amino acids

hydrophobic

Amino acids can be sorted into four groups based on the general characteristics of their R groups:

polar and uncharged amino acids

hydrophilic

Amino acids can be sorted into four groups based on the general characteristics of their R groups:

negatively charged amino acids

hydrophillic

electronegative

polar amino acids that are neutral, yet they are polar because the R group contains an what atom (O, S) that hoards electrons, so the R group has a partial charge

Ser, Thr and Tyr have hydroxyl groups (-OH) with a partial charge, which makes them what

polar

Ser, Thr and Tyr are the three amino acids that can be modified by addition of a what group in eukaryotes, when proteins are what

phosphate, phosphorylated

Cys has a what -?H group

S, sulfhydryl (thiol)

Cysteine is like what

Serine

Cysteine can bond to itself to create what bonds

disulfide

Asn and Gln have electronegative O and what atoms at the end of the side chain, making them polar

N

Polar residues wish to be what-exposed

solvent

Asp and Glu have a net negative charge at what pH

neutral

Lys and Arg have significant what charge at pH 7.0

positive

imidazole

histidine has an what side chain that can be uncharged or positively charged at neutral pH depending on its surroundings

histidine

what is found in the active sites of many enzymes where it acts as a proton donor or proton acceptor

In folded proteins, positively-charged and negatively-charged amino acid side chains can or cannot interact with each other

can

Charged amino acids make a what bond also called a ‘salt bridge’

ionic

Most microorganisms can synthesize the entire basic set of 20 amino acids,
whereas human beings can make only how many of them

11

Amino acids that must be supplied by the diet and are termed what amino acids

essential

Histidine, Isoleucine. Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine

essential

Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine

nonessential

3D

The what structure of a protein determines its function

peptide

In proteins, amino acids are joined in a linear sequences through a common amide linkage, the what bond

The amino acid sequence of a protein is its what structure

primary

peptide bond:
– between amino nitrogen and what carbon

carboxyl

peptide bond:
– what bond

covalent

peptide bond:
– formed through what reaction (release of water)

condensation

Amino acid sequence numbering starts from the amino-terminal residue (?-terminal)

N

2 amino acids, 1 peptide bond

dipeptide

3 amino acids, 2 peptide bonds

tripeptide

a few amino acids

oligopeptide

many amino acids, molecular weight < 10 kDa

polypeptide

many amino acids, molecular weight > 10 kDa

protein

2+ polypeptides associated noncovalently

multisubunit protein

at least 2 identical subunits

oligomeric protein

average molecular weight of all amino acids

128 Da

molecule of water removed to form peptide bond

18 Da

average molecular weight of an amino acid in a protein

110 Da

In some proteins, the polypeptide chain is cross-linked by what bonds

disulfide

disulfide bonds form by the what of two cysteines

oxidation

cystine

the resulting unit of two linked cysteines is called what

losing H or electrons

oxidation

gaining H or electrons

reduction

prosthetic group

permanently associated chemical component

contain lipids

lipoproteins

contain sugars

glycoproteins

contain specific metals

metalloproteins

Polypeptide

What Chains Are Flexible Yet Conformationally Restricted

Rotation

What is permitted about the N–Cα bond [phi (Φ)bond) and about the Cα-carbonyl bond (psi (ψ) bond

chain

The rotation about the Φ and ψ bonds determines the path of the polypeptide what. Not all angles are permitted

Ramachandran

A what Diagram Shows the Preferred Values of Φ and ψ

The clashing of R groups leads to certain ‘what structures’ being favored

secondary

Most peptide bonds have R groups in which configuration to minimize steric clashes between neighboring R groups

trans

the spatial arrangement of the main-chain atoms in a region of the protein

secondary structure

Two main types of protein secondary structure elements are seen
- the what helix

alpha

Two main types of protein secondary structure elements are seen
- the what sheet

beta

The what Is a Coiled Structure Stabilized by Intrachain Hydrogen Bond

Alpha Helix

The α helix is a what coiled rodlike structure

tightly

R groups

The α helix is a tightly coiled rodlike structure, with the what sticking out from the axis of the helix

Each helical turn = how many residues, ∼ how many nm

3.6, 0.54

The what group of each amino acid forms a hydrogen bond with the NH group of the amino acid four residues ahead in the sequence

CO

α helices found in proteins are what-handed

right

Alpha helices are often depicted like a what diagram

ribbon

protein

Alpha helices shows path of what backbone

True or False: Alpha helices have no side chains shown

True

Stabilized by Hydrogen Bonding Between Polypeptide Strands

Beta Sheets

in a β strand the what chain is fully extended with side chain R groups sticking out above and below the plane of the backbone

amino acid

Beta sheets are formed by what bonds between backbone C=O and N-H groups from adjacent β strands

hydrogen

opposite orientation of strands

antiparallel Beta Sheets

same orientation of strands

parallel Beta Sheets

Model of a Twisted Beta Sheet
In diagrams of protein structure, b strands are shown as flat arrows with arrowhead at the which terminus

carboxy

beta turns

connect ends of adjacent segments of an antiparallel beta sheet

b turns
– what ° turn

180

b turns
– involves how many residues

4

b turns
– hydrogen bond forms between which residues

1st and 4th

residue 2

Gly

residue 3

Pro

the overall 3D arrangement of all the atoms in a protein

tertiary structure

conformation

Tertiary structure refers to the spatial arrangement of all amino acids in the protein in three-dimensions - the protein’s what

Water

Tertiary Structure: What-Soluble Proteins Fold into Compact Structures

hydrophobic

Tertiary structure is the result of interactions between the amino acid side
chains (R groups) (ionic, hydrogen bonds, van der Waals, what effect)

folded into a spherical or globular shape

globular proteins