Chapter 3 Proteins:

Shape, Structure, and

Function

Proteins Execute Cell

Functions
Enzymes
Channels and pumps
Signal molecules
Messengers
Molecular machines
Structural support
Cell Recognition

Proteins are structurally complex

and functionally sophisticated

Peptide Bonds Link Amino Acids into Polypeptide

Chain

Evolution has fine-tuned the

structure and chemistry of proteins

Shape dictated by amino acid sequence

polypeptide backbone
side chains

The amino acid sequence of a

protein determines its structure

Weak non-covalent
bonds/interactions are impt to
protein folding

Stearic Interactions
Weak Noncovalent Bonds/Interactions
Distribution of Polar and Non-polar amino acids

Proteins fold into the

conformation of lowest
energy
http://www.youtube.com/watch?v=gFcp2Xpd29I

Why are alpha helices, Beta sheets

and coiled coils common folding
patterns?

There are four organization levels of

protein structure

primary= aa sequence
secondary= stretches of alpha helix, beta sheets
tertiary=3d organization
quartenary=complete structure of protein w/ > 1
poly-peptide chain

Short signature sequences identify

homologous protein domains

Protein Domain= Fundamental Unit of Organization

independently folding functional unit 40-350 aa

Protein Fold= central core of domain; comprised of beta

sheets and alpha helices in various combinations; limited
number

Domain shuffling brings about new

protein sequences

Domain shuffling

Domain Distribution Across Species

Certain domains are found together

in many proteins
Human genome
1000

immunoglobulin domains
500 protein kinase domains
250 DNA binidng
homeodomains
300 SH3 domains
120 SH2 domains

Protein modules are smaller than the

average domain and are particularly
versatile
Protein Module
generally 40-200 aa
Stable core of Beta sheet
versatile
Easily integrated into other proteins; form parts of many different
proteins

The titanic protein titin: 27,000 aa, 132

fibronectin domains and 166 immunoglobunlin
domains

Members of a protein family share

the same structure

Protein Families
similar 3d structure
portions or aa sequence conserved
non-conserved portions impart new functionality

How do we determine the structure

and function of a newly sequenced
gene?

Protein are of different size and

shape
which is related to its function

Larger proteins often contain more

than one polypeptide

Larger proteins can assemble from

identical monomeric subunits

Protein Shape and Structure

Elongated Filbrous
Globular
Unstructured Polypeptide Chains

Intrinsically unstructured proteins are common

in nature impart elastomeric properties

Larger proteins often contain more

than one polypeptide

Proteins can serve as subunits for assembly of large

structures
Self Assembly

protein function is dictated by

physical interactions with ligand
binding
specificity and ligand afforded by multiple weak noncovalent
bonds
active/binding site often cavity on protein surface

Protein conformation
determines chemistry

Regions adjacent to active or ligand binding site to restrict water & increase
ligand binding
Clustering of polar or chged residues can alter chemical reactivity
Type and orientation of exposed aa side chains govern chemical reactivity

Evoltuionary tracing can determine

sites critical to protein function
3d structure of protein family members are similar even when aa
homology <25%
Map conserved aa or homologous aa from all known family members
onto 3d structure of one family member
Most invariant positions often on surface and represent ligand
binding site

Protein bind to other proteins

through different types of interfaces

Equilibrium constant describes

binding strength

Steady state or equilibrium:

# association events/sec = # dissociation/sec
K units = Liters/mole
From conc of two molecules and complex, equilibrium constant can be
calculated

Enzymes as catalysts

Make or break covalent bonds

Speed up chemical reactions > 106 fold

Stabilize transition state

Decrease activation energy
Increase local conc of substrate at catalytic site
Hold reactants in proper orientation for chem rxn
Binding energy contributes directly to catalysis

Not consumed or changed during process

Common types of enzymes

Hydrolases
Nuclease
Proteases
Phosphatases

Isomerases
Polymerases
Kinases

OxidoReductases
ATPases
Synthases

Enzyme kinetics: the detailed study

of chemical reactions

E+S

ES

EP

E+P

Vmax= how fast enzyme can process substrate, pt at which enzyme saturated
w/substrate
Turnover Number= Vmax/[enzyme]
turnover range: 1-10,000 substrate molec/sec
Km= substrate conc at Vmax/2; measure of affinity

Lysozyme hydrolyzes
polysaccharide chains in the cell
wall of bacteria

Enzymes position substrates, bending

critical chem bonds that participate in
chem rxn

Specific Mechanism of Lysozyme Hydrolysis

Positions acidic side chain of Glu w/in active site to provide high conc of
acidifying H+ ions
2. Negatively chged Asp stabilizes positive chged transition state
1.

General Mechanism of Enzyme

Activity
Active site contains atoms that speed up rxn
Substrate driven towards transition state upon binding to enzyme;
shape of substrate chgs & critical bonds bent
Covalent bond sometimes formed btwn substrate and side chain of
enzyme
Restoration of side chain to original state

Small molecules add extra

functions to proteins

Chromophores detect light; retinal

Metal atoms assist w/ catalytic functions; Zn, Mg, Fe
Coenzymes (sm organic molec) provide functional
grps;

Protein Function

Some proteins form molecular tunnels to move

substrates through multiple active sites

Molecular Tunnels impt when intermediates:

1) Unstable
2) Could diffuse readily out of the cell
Carbamoyl Phosphate
Synthetase

Multienzyme complexes increase

the rate of cell metabolism

Product of enzyme A passed directly to enzyme B; product of enzyme B

passed to enzyme C; and so on
Simulates intracellular membrane compartment; effectively increasing
substrate conc at site of enzyme activity

Catalytic activity can be regulated

in a number of ways

Negative Feedback
Positive Regulation
Allosterism

The activity of a protein can be

altered by allosterism

Allosterism= when the conformation of a protein chgs

upon binding of a regulatory ligand, or by covalent
modification

Symmetric protein assemblies and

cooperative allosterims affords tight
regulation
sm chgs in ligand conc switches enzyme assembly from fully active to fully
inactive state via conformation changes that are transmitted across neighboring
subunits

Allosteric transition in aspartate

transcarbamolyase is afforded by 6 catalytic
and 6 regulatory subunits

The regulation of many proteins is

achieved by
phosphorylation/dephosphorylation

Protein Kinases transfer terminal P

of ATP to OH- grp of Ser, Tyr, or Thr

Protein phosphatases catalyze the

removal of a PO4 group

Some specific; some act on broad range of proteins

Protein can function as a microchip

integrating a variety of input signals

GTP binding proteins are analogous to

proteins regulated by
phosphorylation/desphorylation

Regulatory proteins control the

activity of GTP binding proteins

Large protein movements can be

generated from relatively small
movements
EF-Tu = elongation factor is involved in protein synthesis, GTPase

Motor proteins produce large

movements in cells and possess
moving parts as force generating
machines
muscle contraction
crawling and swimming of cells
movement of chromosomes
movement of organelles
enzymes on DNA

ATP hydrolysis allows unidirectional

series of conformational chgs to propel
proteins

Allosteric proteins harness energy from

ATP hydrolysis can be used to pump ions
or sm moleules across membranes

Ca2+ Pump of Sarcoplasmic Reticulum

Na/K+ Pump maintains membrane potential

Mechanism of Ca2+ Pump

Protein Function
Structure of Ca2+ Pump
10 transmembrane helices
4 transmembrane helices
provide Ca2+ binding sites for
pump
helices that bind Ca2+ wind
around ea other forming cavity
btwn helices for Ca2+
ATP hydrolysis causes
conformation chgs that enables
Ca2+ to be pushed through

Small molecules covalently attached to

proteins regulate protein function

Proteins often form large complexes that function as protein

machines: interchangeable parts make efficient use of genetic
information

SCF ubiquitin ligase

Protein structure governs protein

function

Rules for producing your questions

Ask as many questions as you can

Do not stop to discuss, judge or answer the
questions
Write down every question exactly as it is stated.
Change any statement into a question

Improve your questions

Categorize your questions as closed- or open-ended:

Closed-ended questions: can be answered with yes or no or
with
a single word
Open-ended questions: require an explanation and cannot be
answered with yes or no or with one word

Prioritize the questions

Choose

the three most important questions:

1.
2.
3.
Why did you choose these three as the most
important?