Lesson 2: Proteins

Lateral strands

in beta-sheets

can run in two different orientations, parallel or anti parallel

Parallel beta sheets

the hydrogen bonding strands run in the same direction

this results in bent hydrogen bonds that are weaker

1 Kcal/mol

Antiparallel beta sheets

The H-bonded strands run in opposite directions resulting in hydrogen bonds that are stronger

about 5 kJ/mol in bonding energy

beta turns

Occur whenever strands in the beta sheet conformation change direction

180 degree turn is accomplished over 4 amino acids

Type is twice more frequent than a type 2

Proline and glycine

Act as helix breakers, most common amino acids present in beta turns

Perpendicular to the axis and trans to each other

What is the orientation of the R groups of amino acids in beta sheets?

alanine and leucine

strong alpha-helix formers

Motifs

Specific arrangement of several elements of secondary structure (alpha-helix and beta-sheets)

super-secondary structure

Do not allow us to predict biological function

Beta Barrel motif

a large, cylinder-shaped protein structure formed by β-sheets that twist and curl until the first and last strands bond to close the cylinder

serpentine alpha helical

most membrane-bound transport proteins are?

Protein domain

A distinct, self-contained region within a protein’s structure that folds independently into a stable 3D shape and carries out certain functions

can vary in length

Beta propeller

found on the LDL receptor

a type of protein domain

Hemoglobin

an example of a quaternary strcutre

the 4 sub units are held together by Noncovalent bonds

Hypervariable Region

the loops formed by the beta basket domain of the VL and VH

This domain is found on both the heavy chain and the light chain

These Loops are the antigen bining region of an antibody

Structural motif

does not tell you anything in regards to two proteins that share it in regards to their secondary structural similarities

DNA-directed DNA polymerase

the enzyme that replicates DNA

Collagen

most numerous protein in the body

found in connective tissue and skin

Actin

The motion of _____ along the myosin chain which is energized by ATP hydrolysis is how we move ourselves

Integrins

cell-surface receptor proteins whose main role is to connect the cell's interior (cytoskeleton) to the extracellular matrix (ECM)

Myoglobin

protein that functions in the cells of the tissues to store oxygen for utilization in aerobic respiration

has tertiary structure

Bohr Effect

The release of oxygen by hemoglobin due to a small drop in pH from 7.4 to 7.2, to then be bound by myoglobin