Lecture 13

Question 1

Helix-Turn-Helix

Answer 1

• motif
• two small helices connected by a turn
• DNA binding-structure
• common to the group of small proteins called transcription factors which are involved in the transcription of genetic information

Question 2

Transcription factors

Answer 2

• involved in the transcription of genetic information

- Bind the major groove of DNA thereby either activating or suppressing the transcription of an adjacent gene

Question 3

HTH structure details

Answer 3

• HTH assembly is held together by dispersion forces
• Most H-bonds maintain the two helices, but the cross-helix gln-gln interaction makes a strong contribution to the structure
• The turn is ALWAYS a short segment and always contains at least one gly (the smallest and most flexible AA)

Question 4

Calmodulin

Answer 4

• Calcium sensing and signaling protein that consists of 7 alpha helices
• Shape changes dramatically when Ca2+ binds; forming 2 hydrophobic clefts that allows calmodulin to bind to a range of other calcium processing proteins
• binds Ca2+ in specific HTH known as EF hand

Question 5

four helix bundles

Answer 5

• Domain
• helices cross one another at angles ~20º which allows R groups to mesh together efficiently
• Alpha helices are often amphipathic
• Four helix bundles align together to give a hydrophobic core

Question 6

The Globin Fold

Answer 6

More complex arrangement of alpha helices
-usually consists of several helices packed against each other with larger angles, ~50º and ~90º so helices form a hydrophobic packer for the heme active site

Question 7

Greek Key

Answer 7

Consists of four antiparallel beta strands and the loops that connect them

• strands 1,2,3 connected by hairpin turns
• strand four connected by a longer loop
• resembles greek art

Question 8

beta-alpha-beta motif

Answer 8

• basically two parallel beta strands with an alpha helix in the middle
• almost always right handed crossover loop
• stabilized by a hydrophobic core

Question 9

The Rossman Fold

Answer 9

-A motif often found in nucleic acid binding proteins

beta-alpha-beta-alpha-beta

Question 10

The beta barrel

Answer 10

• antiparallel beta are often arranged as two beta sheets that stack against each other to form a distorted barrel structure
• several structural variations of beta barrels

Question 11

beta meander

Answer 11

Simple set of 2 or more antiparallel beta strands connected by hairpin turns

Question 12

Omega loop

Answer 12

A catch all term for a loop of several residues that has no specific internal hydrogen bonding

Question 13

Domains

Answer 13

• segment of a polypeptide that can fold, function, and evolve independently of the rest of the protein
• each has its own characteristic tertiary structure
• one domain may appear in several different proteins
• vary from 25-500 AA’s

Question 14

Porins

Answer 14

membrane protein that allow movement of solutes in and out of cells

Question 15

Fibrous proteins

Answer 15

Structural molecules used for muscle fiber, bone matrix, tendons and connective tissue

• found only in animals
• usually insoluble in water
• includes keratin, collagen, and fibroin

Question 16

Fibroin

Answer 16

-Fibrous protein that forms silk

Question 17

Keratins

Answer 17

• fibrous protein

- hair skin and nails

Question 18

Collagen

Answer 18

Fibrous protein that basically is what holds an animal together

Question 19

Membrane proteins

Answer 19

Span the lipid bilayer and have several major functions including transport of molecules across the membrane, enzymatic activity, signal transduction and cell-cell recognition
-usually bundles of alpha helices with hydrophobic exterior surfaces

Question 20

Globular proteins

Answer 20

Act as catalysts, messengers, transporters, and regulators

• approximately spherical in shape, important for keeping proteins in solution by maximizing hydrogen bonding to water
• hemoglobin is a globular protein