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The Structure and Functions of Biological Molecules
The Structure and Functions of Biological Molecules
Copyright 2013 John Wiley & Sons, Inc. All rights reserved.
Keys
Introduction
Understanding cellular function requires
knowledge of structure.
Structure and function in cells is closely related
to the structure of molecules and atoms.
The study of chemistry is essential for
understanding cell biology.
A representation of the
arrangement of electrons in a
number of common atoms
2013 John Wiley & Sons, Inc. All rights reserved.
Covalent Bonds
Polar and Nonpolar
Molecules
Polar molecules
have asymmetric
distributions of
electrical charge.
Nonpolar
molecules lack
polarized bonds.
Some biological
molecules, such
as proteins and
phospholipids,
have both polar
and nonpolar
regions.
A representation of the
arrangement of electrons in a
number of common atoms
Covalent Bonds
Atoms tend fill their outer electron shell by sharing electrons with other atoms.
Hydrogen forms a single covalent bond by sharing its unpaired electron.
Oxygen forms two covalent bonds by sharing two unpaired electrons.
Water results when oxygen bonds with two hydrogens.
It requires 80100 kilocalories to break a mole of covalent bonds.
Multiple bonds are formed when more than one pair of electrons are shared by two atoms.
Shared electrons stay closest to the nucleus with the highest electronegativity.
Depends upon the number of protons in nucleus.
Depends upon the distance of the shard electrons from the nucleus.
Calorie restriction:
Extends the lifespan of experimental animals.
Results in decreased production of free radicals.
A new study indicates that individuals on a diet
containing 25% fewer calories show reduced levels of
DNA damage.
2013 John Wiley & Sons, Inc. All rights reserved.
Noncovalent Bonds
Hydrogen bonds
2. Hydrogen bonds:
-- A hydrogen bond occurs when covalently bound hydrogen
has a partial positive charge and attracts electrons of a second
atom.
-- H-bonds determine the structure and properties of water.
-- H-bonds occur in biological molecules, such as between the
strands of DNA. 2013 John Wiley & Sons, Inc. All rights reserved.
Noncovalent Bonds
3. Hydrophobic interaction
and van de Waals forces:
- These occur when nonpolar
molecules associate and
minimize their exposure to
polar molecules.
- van der Waals forces, or
attractions between
nonpolar molecules, are due
to transient dipole formation.
Hydrophobic interactions
reduce exposure to
hydrophilic molecules
Noncovalent Bonds
3. Hydrophobic interaction
and van de Waals forces:
- These occur when nonpolar
molecules associate and
minimize their exposure to
polar molecules.
- van der Waals forces, or
attractions between
nonpolar molecules, are due
to transient dipole formation.
Noncovalent Bonds
Noncovalent Bonds
The Life-Supporting
Properties of Water
The properties of water
result from its structure.
It is asymmetric
both H atoms are on
one side.
It requires a lot heat
to evaporate it.
It is an excellent
solvent for many
substances.
The importance of water
in protein structure
It determines the
interactions between
many biological
solutes. 2013 John Wiley & Sons, Inc. All rights reserved.
Amphoteric
Base
molecule
Hydrogen
ion
Carbonic
acid
Hydrocarbons:
Contain only carbon
and hydrogen.
Vary in the number
of carbons, and the
number of double
and triple bonds
between carbons.
2013 John Wiley & Sons, Inc. All rights reserved.
The
structures of
sugars
Stereoisomerism of
glyceraldehyde.
Carbohydrates
Polysaccharides are polymers of sugars joined by glycosidic bonds.
Glycogen is an animal product made of branched glucose
polymers.
Starch is a plant product made of both branched and
unbranched glucose polymers.
2013 John Wiley & Sons, Inc. All rights reserved.
Peptide bonds form between the -carbonyl and the amino of participating amino acids.
Amino acids differ in the R group attached to one of
the bonds of the -carbon.
R groups may be polar charged; polar uncharged;
nonpolar.
2013 John Wiley & Sons, Inc. All rights reserved.
Formation of disulfide
bonds: oxidation and
reduction of bonds between
two cysteine residues
The ionization of
charged, polar amino
acids.
Scanning electron
micrograph:
The -helix: structure and physical characte
Red blood cell sickle cell
anemia of Proteins
The Structure
Primary structure, the sequence of amino acids in the polymer, is
critical to the protein function.
Secondary structure refers to the conformation of adjacent
amino acids into -helix, -sheet, hinges, turns, turns, loops, or
finger-like extensions.
2013 John Wiley & Sons, Inc. All rights reserved.
Types of non-covalent
An X-ray diffraction
bonds maintaining the
Ribbon model
pattern of
conformation of
of
myoglobin
proteins
ribonuclease
Tertiary structure is the conformation of the entire
polymer.
It is stabilized by noncovalent bonds.
It is studied by X-ray crystallography.
Proteins can be fibrous or globular.
2013 John Wiley & Sons, Inc. All rights reserved.
Dynamic movements
within the enzyme
acetylcholinesterase.
Domains occur when proteins are composed of two or more distinct regions.
Each domain is a functional region
Dimer: TGF-2
Cysteine residues
Hydrophobic residues
Protein-Protein Interactions
Different proteins can become
physically associated to form a
multiprotein complex.
Pyruvate dehydrogenase:
60 polypeptide chains
Proteinprotein
interactions: complementary
molecular surfaces of portions
of two interacting proteins
Protein-Protein Interactions
Can be studied using the yeast two-hybrid (Y2H).
Results from large-scale studies can be presented in the form of a network.
A list of potential interactions can be used to elucidate unknown processes.
A network of proteinprotein
interactions.
Protein-Protein Interactions
Proteinprotein
interactions of hub
proteins.
Ribonuclease A
(RNase: 124 aa; 4 disulfide
bonds)
First step:
Formation of
secondary
structure or
collapse
driven by
hydrophobic
interactions
Along
the
folding
pathway
2013 John Wiley & Sons, Inc. All rights reserved.
Formation of the A
peptide
2013 John Wiley & Sons, Inc. All rights reserved.
Identifying proteins by
mass spectrometry
Global analysis
of protein
activities using
protein chips.
2013 John Wiley & Sons, Inc. All rights reserved.
Protein Engineering
Current technology allows the making of artificial genes that
code for proteins of specific amino acids sequences.
Knowledge of a proteins amino acid sequence rarely allows
prediction of a proteins structure.
Site-directed mutagenesis allows researchers to make
alterations in single amino acids by altering the DNA
encoding a protein.
Computational
design of a
protein that is
capable of
binding to the
surface of
another protein.
Gleevac
structure
ABL protein-targeting
with Gleevac (L) and
Sprycel (R)
Distribution of polar,
charged amino acid
residues in the enzyme
malate dehydrogenase
Nucleotides and
nucleotide
strands of RNA
Nitrogenous bases
in nucleic acids
Experimental Pathways:
Helping Proteins Reach Their Proper
Folded State
Some proteins can self-assemble from purified
subunits.
Other proteins require molecular chaperones for
proper folding.
Molecular chaperones may protect protein structure
during the heat shock response.
The heat shock response involves synthesis of heat shock
proteins that prevent denaturation of existing proteins.
Experimental Pathways:
Helping Proteins Reach Their Proper
Folded State
Heat shock proteins and other chaperones prevent
aggregation of denatured or newly synthesized
proteins.
Chaperones also move newly synthesized proteins
across membranes.
The protein GroEL is synthesized in E. coli is essential
for the proper folding of other cellular proteins.
GroEL
models
Experimental Pathways:
Helping Proteins Reach Their Proper
Folded State
Conformatio
nal change
in GroEL
Experimental Pathways:
Helping Proteins Reach Their Proper
Folded State
GroEL-GroESassisted
folding of a
polypeptide