Chapter 4: Protein Structure And Function

Front 1

Protein constitute most of the cell's what?

Back 1

Dry mass

Front 2

Proteins execute nearly all of the cell's what?

Back 2

functions

Front 3

What is proteins fuction determined by?

Back 3

by the protein's 3D structure

Front 4

What are proteins?

Back 4

Are linear chins of amino acids that are linked by peptide bonds.

Front 5

What unique type of feature does each type of protein have?

Back 5

Unique sequence of amino acids

Front 6

When proteins fold into a particular 3 D structue what is it stabilized by?

Back 6

Many noncovalent interactions
-hydrogen bonds,
-van der walls
-electrostatic attraction

Front 7

What helps proteins fold into compact conformations?

Back 7

Hydrophobic forces (contain nonpolar side chins)

Front 8

Where are Hydrogen bonds found?

Back 8

-forms on the polar side chins on the outside of the protein molecule

-between atoms of two peptide bonds (backbone+backbone)

-between peptide bond and amino acid side chain (backbone+sidechin)

-betwn 2 amino acid side chin (side chain+side chain)

Front 9

Proteins spontaneously fold into a conformation of what?

Back 9

lowest energy

Front 10

when can protein conformatin change? And why is the change in shape crucial?

Back 10

When interacting with other molecules in th cell.

Crucial for regulating protein activity

Front 11

Prion diseases

Back 11

when protein folding goes wrong

Front 12

Prion protein can adopt what?

Back 12

And abnormal misfolded form

Front 13

What do misfolded prion proteins form?

Back 13

aggregates that cause disease, plus othe neurodegenerative disorders

Front 14

How can prion diseases be spread?

Back 14

ingestion of a misfolded prion protein

Front 15

heterodimer

Back 15

prion converts normal into abnormal

Front 16

homodimer

Back 16

converts more proteins until aggregate forms

Front 17

Common folding patterns of proteins?

Back 17

Alpha helix and Beta sheet

Front 18

What bond do the common folding patterns of proteins have? And betwen what?

Back 18

hydrogne bonds between N-H
and C=O groups in polypeptide backbone

Front 19

In alpha helix, the N-H of ever peptide hond is hydrgon bonded to the C=O ___ amino acids away in the same side change

Back 19

4

Front 20

What is a segment of alpha helix often used for?

Back 20

to span a lipid bilayer

Front 21

What can beta sheets form at the core of many proteins?

Back 21

rigid structures

Front 22

Beta shets can be ---- or ----

Back 22

parallel or aniparalll

Front 23

what do dthe arrow ppoin to in beta sheets?

Back 23

C termina end of the polypeptide chain

Front 24

What protein domian is common among proteins involved in cell signaling and is 100 amiino acids long

Back 24

SH2 domain

Front 25

What domian comprimise a family of proteolytic enzymes

Back 25

Serine proteases

Front 26

What are examples of proteins with multiple copies of a single protein subunit?

Back 26

CAP and neuraminidase

Front 27

An example of protein that is formed as a symmetrical assmely of two different subunits

Back 27

Hemoglobin

Front 28

What is composed of identical protein subunits?

Back 28

An actin filament

Front 29

What can single protein subunits can pack to form?

Back 29

A filament, tube, or a spherical shell

Front 30

Example of spherical protein assemplies

Back 30

viral capsids

Front 31

What is the most abundant protein in animals?

Back 31

Collagen (20-25% total protein)

Front 32

What is collagent a component of?

Back 32

extracellular matrix (a gel like material that binds cells together to from tissues)

Front 33

What can mutations in collagen genes cause?

Back 33

cuticle defects in C. elegans resulting in Dumpy, Blister or Roller pheinotypes

Front 34

These are cross linked togeter to form rubberlike, elastic fibers.

Back 34

Elastin polypeptide chains

Front 35

What do elastin fibers do?

Back 35

Allow skin and other tissues to stretch and recoil without tearing

Front 36

What are extracellular protein structures stabilized by?

Back 36

disulfide bonds

Front 37

Where do disulfide bonds do not form? Why

Back 37

in cyston becuse of high concnetration of reducing agens present

Front 38

What are proteins?

Back 38

catalysts
strucutral supports
signal receptors
tiny motors

Front 39

What do proteins fuctions depend on?

Back 39

depend on the physical binding of a protein to another molecule

Front 40

What can proteins bind to

Back 40

proteins
small molecules (enzyme substrate, DNA)

Front 41

The binding of a protein molecule is highly---- and requires the combined effect of many ---- ----- bonds

Back 41

selective
weak noncovalent

Front 42

HOw is the biniding site formed?

Back 42

1. Folding of the polypeptide chin creates a cervice or cavity on the surface

2. Amino acids form differnt parts of the protein chain can come togeter in the binding site.

Front 43

What are imoortant for proper folding and whre can they be found?

Back 43

aminno acids
protein core

Front 44

The binding sites of what are especially versatile?

Back 44

antibodies

Front 45

What is the first step in enzymes function to catalzye chemical reactions?

Back 45

binding

Front 46

How are enzymes grouped into fuction classes?

Back 46

Based on the chemical reactions they catalyse

Front 47

Hydrolase

Back 47

enzymes that catlyze a hydrolytic cleavage reaction

Front 48

protease

Back 48

breaks down proteins by hydrolysing peptide bonds between amino acids

Front 49

Synthase

Back 49

name used for enzymes that synthesize molecules in anabolic reactions by condensing two molecules together

Front 50

Isomerase

Back 50

catalyzes the rearrangement of bonds within a single molecule

Front 51

polymerase

Back 51

catalyzes polymerization reactions such as the synthesis of DNA and RNA

Front 52

Kinase

Back 52

adds phospahte groups to proteins

Front 53

Lysozyme severs what that form what and is found in what?

Back 53

polysacchride chain
bacterial cell walls (anitibiotic)
egg white, saliva, tears

Front 54

What enzyme was the first structrurew to be determined by X-ray crystallography

Back 54

lysozyme

Front 55

HOw do enzymes lower activation energy?

Back 55

1. enzyme binds to 2 substrate molecules and orients them precisely to encourage a reaction to occur between them

2. binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and postivie charges that favor reaction

3. enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction

Front 56

Many proteins require what to peform theri fuciton? Give an example

Back 56

bound smal moleucles

heme on hemoglobin

Front 57

The number of molecules of each protein are regulated by what?

Back 57

by regulation of gene expression

Front 58

Proteins may be confined to what?

Back 58

particular subcellular compartments

Front 59

Proteins can be switched on or off very rapidly by what? and what does this do?

Back 59

by a variety of mechinaism due to change of shpe

change funciton and tus the protein.

Front 60

Feedback Inhibition

Back 60

the end product of a reaction pathway inhibits the activity of an enzyme acting early in the pathway (megatove regulation)

Front 61

In feedbakc inhibiton a molecule other than the normal substrate bind to the enzyme at a special ----- site not at the --- site, the molecule is what?

Back 61

regulatory
active
inhibitor

Front 62

Postive reguulation

Back 62

Uses a similar mechanism however the enzyme activity is timulated by binding of a regulatory molecule.

For ex. ADP stimulates enzymes invovlved in oxidation of sugars

Front 63

What does feedback inhibition at multiple sites regulates

Back 63

conncected metabolic reactions


ex. Foru amino acid biosynthetic pahtyways in bacteria and thier coordinated regulation

Front 64

Allosteric proteins

Back 64

proteins tha can adopt two or more slighly differnt conformations.

Front 65

Allosteric proteins acitivy is regulated by what

Back 65

by a shift from one conformation to another

Front 66

A specific proteiin conformation is stablized by waht?

Back 66

by the binding of a ligant to a site on the protein away from the active site.

Front 67

The ligand might stabilize an ------ or an ----

Back 67

inhibitor (inactive conformation) or activator (active confromation)

Front 68

The bacterial protein CAP (catabolite activiating protein) has one large domain and one small domin what do each domin bind to to form a dimer

Back 68

Small domin binds to DNA
Large domin binds to cyclic AMP

Front 69

What does a CAP dimer do

Back 69

Binds DNA (in presence of cAMP) which bends DNA and recruits RNA plymerase to the rpmoter

Front 70

What does cAMP binding cause

Back 70

rotation of the prtoen subunits so that the DNA binding helices are aligned with the major groove of the DNA

Front 71

Protein phoshorylation is a very common means of what

Back 71

of regulating protein activity

Front 72

HOw many proteins in a typical mammalian cells are phosphoryalated at any one time

Back 72

1/3 of the 10,000

Front 73

Why can phosphorylation dramatically affect the conformation of the protein

Back 73

because each phosphate group has two negative charges

Front 74

Protein phosprhylation is

Back 74

reversible and fast but energecialy costsly

Front 75

THe phosphorylated form of the protein can be either the --- or --- form, depend on the particular protein

Back 75

active or inactive

Front 76

Phosphorylation is not used to simly turn protein activity on or of but to what?

Back 76

to regulate the binding fo different proteins to each other

Front 77

GTP binding proteinss are regulated by what?

Back 77

cyclic gain or loss of a phosphate group.

Front 78

GTP binding proteins act as a whoat

Back 78

molecular switchers

Front 79

GTP binding proteins play a crusial role in what?

Back 79

intracelluar signalling pathways

Front 80

What do motor proteins do to genrate movment

Back 80

contrat muscles
move chormosomes druing mitosis
move organells along the cytoskeleton
move enzymes along a DNA strand

Front 81

What allow proteins to walk along a filament such as a DNA molecule or a microtuble

Back 81

Changes in conformation

Front 82

How is walking in one direction made irreversible

Back 82

by hydrolysis of ATP in every cycle

Front 83

Once ATP is hydrolyzed what can a protein ono longer do

Back 83

go back it can only go forward

Front 84

What conrols the location and assemlby of protein machines?

Back 84

covalent modifications

Front 85

what fuction as molecular machines

Back 85

large complexes formed by proteins

Front 86

protein machines are assembled at ---locations within cells

Back 86

specific

Front 87

protein machines are actived when and where

Back 87

only needed

Front 88

What protein controls how a cell responds to DNA damage

Back 88

p53

Front 89

What determines how a protein binds to other molecules and its activity

Back 89

the chemical proteris of the surfact of a protein

Front 90

What deterimnes those surface proteities of a protein

Back 90

the tree dimensinoal shape

Front 91

How are proeins regulated?

Back 91

by chainging thir shapes and surfaces