PROTEINS AND PEPTIDES

amide plane

Peptide bonds lie along an

The peptide (C-N) bond

can not easily rotate; bonds adjacent to the peptide bond freely rotate

from the N- terminus to the C- terminus

Proteins are synthesized

polar

The polypeptide backbone as a whole is relatively ____due to the polarity of the peptide bond.

constituent amino acids

▪ The chemical and physical properties of a polypeptide strands thus, depends on the?

oligopeptides or just peptides.

Polypeptides with up to about 40 residues are often called ?

sequence of amino residues

The structure of a polypeptide can be specified through the?

Φ

is the angle arising from the rotation of the Cα— N bond

Ψ

is the dihedral angle arising from the rotation of the Cα—CO bond

The Newman projection

iT shows the torsion angles Ψ as the angle between the CO—N bond and the Cα—N bond

Ramachandran Plot

plots show the allowed pairings of dihedral angles for proteins

Secondary structures 

can allow backbone atoms to satisfy H-bonding requirements

α-helical and β-sheet structures

are two major secondary structures

α-helices , β-strands

, helices represent _____ and flat sheets with arrows represent ____

An α-helix i

s a right-handed helix that has specific characteristics

Characterized by having 3.6

how many residues every complete turn of the helix

1.5 Å vertical distance

Successive residues in aa-helix are separated by a?

5.4 Å, Helical pitch

– the height of one complete helix turn – is

intrachain hydrogen bonds

An α-helix is a stabilized by very specific,

β-sheets

are made up of β strands

β-sheets

Consists of aligned β-strands of polypeptide whose hydrogen bonding requirements are met by bonding between neighboring strands

3.5 Å,

the distance between residues of

β-sheets

inter-strand

H-bonding in β-sheets is

β-sheets

have a pleated structure

tetrahedral Cα atom (found in the folds of the pleats)

The successive amide planes have a pleated appearance due to the

β-sheets are sometimes called

Coils

are taken to mean any other structure that are not any of the previously mentioned structures or those that do not have a regular or characteristic geometric properties.

Coils

These are unordered in the sense that there is more conformational flexibility

Coils

The lack of inter- or intra- strand non-covalent interactions allow these stretches to interact with water, ligands or other proteins

The tertiary structure

it describes the overall conformation of a protein.

The tertiary structure

Describes the global arrangement of all the atoms in a protein

The tertiary structure

▪ The tertiary structure includes long-range aspects of amino acid sequence, amino acids that are distant in the sequence can be brought closer together

secondary structures

characterizes the spatial arrangement of residues that are relatively close together in the sequence

The tertiary structure

collection of secondary structures (including coils)

tertiary structure

as the way the secondary structures pack closely to form the three-dimensional structure of a protein

▪ Globular proteins ▪ Fibrous proteins ▪ Membrane proteins ▪ Intrinsically disordered proteins

On the basis of general shape and secondary structure composition, proteins are typically grouped into four major classes:

Globular proteins

are compactly folded polypeptides

Globular proteins

are compactly folded giving most, but not all, a roughly spheroidal shape

Globular proteins

The formation of turns and loops allow for the polypeptide chain to change direction multiple times and thus, for compact folding to occur.

globular proteins

As most are water-soluble, this means that this proteins have a hydrophilic exterior and a hydrophobic interior.

fibrous proteins

are large, elongated molecules

fibrous proteins

Contain long polypeptide chains that consist of long strands or sheets that are organized approximately parallel along a single axis

fibrous proteins

These long polypeptide chains can also aggregate to form even thicker structures

fibrous proteins

▪ These are mechanically strong proteins and thus mainly play a structural role in cells

fibrous proteins

▪ Relatively insoluble in water

Membrane proteins

are embedded within cell membranes

Membrane proteins

are associated with the lipid bilayer of cells.

hydrophobic.

the amino acids in the lipid-embedded surface of membrane proteins are

Membrane proteins

can be further categorized as integral (or transmembrane), peripheral, or lipid-anchored depending on the degree of their association with the membrane.

Intrinsically disordered proteins (IDPs)

have no stable threedimensional structure

Intrinsically disordered proteins (IDPs)

These proteins do not have well-ordered structures in their “native” or functional state.

Intrinsically disordered proteins (IDPs)

These are unable to fold spontaneously into stable, 3D structures and are dynamically disordered and fluctuate rapidly through a range of conformations

Intrinsically disordered proteins (IDPs)

The amino acid composition is biased towards charged and hydrophilic amino acids against bulky hydrophobic amino acids

myeloid cell leukemia sequence 1

p53 upregulated modulator of apoptosis

MEANING OF PUMA AND MCL1

PUMA and MCL1

are intracellular proteins that influence the process of programmed cell death (apoptosis)

Tertiary structures

are held together by a mixture of covalent and noncovalent interactions

salt bridges

Interactions between fully charged groups, also known as_____, are relatively strong, non-covalent interactions.

zinc fingers

PROTEINS that are common in DNA-binding proteins

Van der Waals interactions

– the general term referring to the intermolecular forces between atoms

Van der Waals interactions

these are weak interactions, but can add up when there is a collection of atoms interacting

Hydrogen bonds,

a subtype of dipole-dipole interactions, are much more stronger than dispersive forces

Disulfide bonds

formed from the oxidation of two nearby cysteine residues are an important covalent linkage that impacts a protein’s shape

Motifs

are recurring patterns of secondary structures often found in a protein’s tertiary structure

supersecondary structures

These recurring patterns are called motifs and are considered to be what is known as

The αα motif

is composed of two α-helices that may be connected by a hairpin turn or loops e.g. helix-turn-helix, helix-loop-helix

helix hairpin or an αα hairpin

Resembling a hairpin, this α-helical motif is known as a

A four-helix bundle,

another common motif, is composed of two helix hairpins.

EF hand

is a Ca2+ binding motif and is so named because the two helices involved are the E (yellow) and F (blue) helices of parvalbumin, the calcium-binding protein where this motif was originally discovered.

parvalbumin

, the calcium-binding protein where this motif was originally discovered.

A Greek key motif

has a β-hairpin folded over to form 4 anti-parallel β-strands

βαβ motif

The most common form of supersecondary structure is the_____that features two parallel strands of a β-sheet that are connected by an α-helix

Quaternary structure

Large proteins (especially those with masses larger than 10kD) typically consist of more than one polypeptide chain or subunits

homodimers, homohexamers …

If subunits are similar —

heterotetramers …

➢ Different subunits –

molecular chaperones

some proteins fold with the aid of other proteins called

TIM barrel

– first described in triosephosphate isomerase enzyme ▪ Contains a series of βαβ motifs

TIM barrel

▪ Contains a series of βαβ motifs

TIM barrel

▪ Found in ⁓10% of enzymes and is also common in membrane proteins

TIM barrel

▪ have a known enzymatic function, with only one exception, which is narbonin

Glycosylation

is the enzymatic transfer of oligosaccharides to proteins

Glycation

is a spontaneous reaction between sugar aldehydes and amino groups

disulfide bond

Oxidation of two –SH sidechains produces a

Proteolysis

occurs through hydrolysis of peptide bond

Proteolysis

breaks down proteins through the hydrolysis of peptide bonds

proenzymes or coenxymes

This modification occurs in the activation of