7_27 Lecture 2 Proteins 2.txt

author "Joshua Ellis"

tags "HUCM"

description ""

fileName "7/27 Lecture 2 Proteins 2"

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What is the difference between conservative and non-conservative mutations? Give an example.

Conservative doesn't change structure too much

ie: conservative would be to change Leu to Ile... as both structure simply have a strand of CH2 chains.

non-conservative would be to change glu to val... which is sickle cell anemia in hemoglobin

What is a major character of the Peptide bond between proteins? What are its characteristics? (5) What is the common configuration? and the exception?

The partial double bond.

Shorter

No rotation

Flat

6 atoms lie in the same plane.

Flexible but conformationally restricted

Trans is the common configuration. Prolyl residue is the exception. (must complete the ring)

In the alpha helix how many residues are in each turn? What is the pitch and its actual number? What is rise and its actual number?

There are 3.6 residues per turn (3.6 amino acid per turn)

The pitch is the distance between each turn and is 5.4

The rise/ residue is the distance for each amino acid and is 1.5

How long is a 10 amino acid chain?

Rise is 1.5... so 10 * 1.5 = 15 angstroms

Alpha helix right/left hand rule

point thumb and curl fingers.

What is amphipathic

It is when one half is polar and the other half is non polar. The side chains of the helix stick outside the axis

What is the pitch and and residue amount in each turn of a Beta strand?

n=2 residues per "turn"

p= 6.8 angstrom

What is the difference between parallel and anti-parallel Beta sheets. How do they stack

They stack with chains projecting above and below... allowing sheets to form.

What is a Beta turn and a Beta loop

A Beta reverse turn occurs when a 1st residue hydrogen bonds to a 4th. (Type I and Type II)

Beta loop is more elaborate. Located on surface of proteins but do not have regular structure.

What are the Simple Tertiary Structures

Alpha domain proteins (contain mostly alpha helices)

Beta domain proteins (contain mostly beta helices)

Alpha/Beta domain proteins (contain both)

Supersecondary Structures

Otherwise known as motifs... in between secondary and tertiary.

ie:

helix-loop-helix

Ways to determin protein structure

X-ray Crystallography

NMR--advantage cuz you can look at things in solution

Helix-Loop-Helix

Feature of some transcription factors proteins that bind to DNA and direct transcription

Zinc-Finger DNA Binding Motif

2 his and 2 cys residues connected to Zn++ ion. Has a DNA binding region.