Biochem - Lecture 4 Learning Objectives

Proteins structure and peptide bond learning objectives

equation for peptide bond formation

condensation reaction

peptide bond conformation refers to what?

the spatial arrangement of atoms around the peptide bond, which can be cis or trans

are peptide bond conformations typically cis or trans?

trans except Pro

why is Pro not always trans?

due to its cyclic shape

N-terminus

amino acid with a free amino group, marks the beginning of the protein

C-terminus

the amino acid with a free carboxyl group, marks the end of the chain

In what direction do we read an amino acid chain?

N-terminus to C-terminus

How are amino acid residues in a protein numbered?

they are numbered starting at the N-terminus and move toward the C-terminus, you know a new amino acid residue starts when you see another alpha carbon, so you can essential count the alpha carbons

linear projection structure of a short peptide of any given sequence

What is the charge of this peptide chain at pH = 8: TNMFDKR?

+1

what does the partial double bond character of a peptide bond do?

due to resonance, it prevents rotation around the bond and forces the atoms in the peptide bond to be in a planar configuration. which will significantly restrict the possible conformations of the chain

what is a steric effect?

a nonbonding interaction in a molecule that occurs when atoms occupy space too close to one another

what does the steric affect do?

influences the chain’s folding by favoring conformations that minimize interactions between bulky groups, determining the overall protein structure

what do steric effects arise from?

the spatial arrangement of side chains

6-atom planar peptide group

refers to the six atoms that lie in the same plane within a peptide bond

what are the 6-atoms in the planar peptide group?

the carbonyl carbon, the carbonyl oxygen, the amide nitrogen, the amide hydrogen, and the two alpha carbons

What three categories can be found in the secondary structure of a protein?

alpha helix, beta sheet, and loops

alpha helix

backbone coiled (spiral) conformation with regular repeating rotation, residue by residue

in an alpha helix, what group is the hydrogen bond donor?

the amide nitrogen group

in an alpha helix, what group is the hydrogen bond acceptor?

the carbonyl oxygen

what is the chirality of the alpha helix?

right handed helix

how many residues per turn in an alpha helix?

4 amino acid residues

R groups point ___ from the helix axis

outward

what direction does the dipole moment move in on an alpha helix?

from C-terminus to the N-terminus

What terminus is negative on an alpha helix?

C-terminus

What terminus is positive on an alpha helix?

N-terminus

the packing density in an alpha helix is

relatively high, but depends on the amino acid and the environment

what components of amino acid residues in one helix directly contact what components of residues in the other helix?

the side chain of amino acid residues on one helix directly interact with the side chain of another amino caid residue

beta conformation (sheets)

an element of secondary structure in which the protein chain is nearly linear

in a beta sheet, what is the hydrogen bond acceptor group?

carbonyl oxygen group of the polypeptide backbone

in a beta sheet, what is the hydrogen bond donor group?

amide nitrogen group of the polypeptide backbone

What is the orientation of R groups in a beta pleated sheet?

the R groups on the peptide strand alternate sides in both parallel and antiparallel configurations

Are parallel beta sheets more stable or less?

less stable due to their hydrogen bond arrangement being bent

Are antiparallel beta sheets more stable or less?

more stable due to their hydrogen bond arrangement being straight

what is parallel beta conformation?

when the C-terminus of one sheet is next to the C-terminus of another sheet and their N-terminus are also next to each other

What is an antiparallel beta conformation?

when the C-terminus of one sheet is next to the N-terminus of another sheet

what is the most important noncovalent interactions stabilizing the alpha helix and beta conformations?

hydrogen bonding between the backbone amino group of one amino acid and the carbonyl oxygen of another amino acid located further down the peptide chain

what do the blue arrows represent?

beta sheets

what do the yellow and white ribbons represent?

alpha helix

what do the yellow strings represent?

loops

what does the head of the arrow represent?

C-terminus

what does the flat end of the arrow represent?

N-terminus

collagen

what is the chirality of collagen?

left handed

how many residues in a turn in a collagen helix?

3 amino acid residues

what is the pitch of a helix?

the vertical distance traveled along the axis of a helix to complete one full turn around the axis

what is the pitch of an alpha helix?

5.4 A/turn

what is the pitch for a collagen helix?

10 A/turn

collagen can form a very stable ___ ____

triple helix

collagen’s primary structure is made of

Proline, hydorxyproline (Hyp), and glycine

the individual polypeptide chain secondary structure of collagen is a

collagen helix

supersecondary structure for collagen is a

3-standard coiled coil, a triple helix

what is collagen in the human body?

a structural protein in connective tissue

is collagen flexible or inflexible?

collagen is very inflexible, or rigid

what is collagen helix stabilized by?

inherent kins in Pro and Hyp rings

the triple helix of collagen is stabilized by

H bonds between the backbone groups on different chains

secondary structure of alpha keratins

right handed alpha helix

supersecondary structure of alpha keratin

2 polypeptides with right handed alpha helices, coiled together in a left handed twist to give a 2 stranded supercoil

what is the quaternary structure of alpha keratin?

higher levels of assembly of multiple polypeptide chains

the supercoiled structure of alpha helices has great

tensile strength

What role do disulfide bridges play in alpha keratins?

they act as strong covalent bonds between cysteine amino acids, effectively cross-linking the protein chains and providing significant stability to the overall structure

What is the molecular basis for ascorbic acid definiency?

ascorbic acid acts as a cofactor for the enzymes responsible for hydroxylating Pro and Lys residues in collagen, and without it, collagen synthesis is impaired leading to weak and fragile blood vessels, skin, etc.

conformation

the spatial arrangement of atoms in a molecule

configuration

the fixed 3-D relationship of the atoms in a molecule, defined by the bonds between them

secondary structure

local regular conformations for parts of the peptide backbone of a protein

what is the rise of a helix?

the distance traveled along the axis of the helix for each amino acid residue

tertiary structure

3-D conformation of whole
polypeptide in its folded state

domain

a distinct, independently folding structural unit within a protein that carries a specific function

fibrous protein

big long extended cables (fibers) made up of proteins

globular protein

spherical proteins that are the most common and abundant proteins in nature

coiled coil (supercoil)

structural motif in proteins where two to seven alpha helices are coiled together like rope strands

amphipathic helix

an alpha helix with opposing polar (hydrophilic) and nonpolar (hydrophobic) sides

stacked beta sheets

a protein supersecondary structure where the beta sheets stack to form ribbons, then fibrils, and finally fibers