Biochemistry of Cells

Chapter 2

Covalent Bonds
•  Covalent bond - two atoms share
electrons to complete their valence
shells
–  A full atom is a happy atom
•  Strong bonds!!
•  Bond lengths and bond angles
maximize attractive and repulsive
forces
–  Determine shape of molecules
•  Bond strength
–  Amount of energy needed to break
the bond
–  Kcal/mol or kJ/mol
–  Reactivity

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 Covalent Bonds
•  Single bonds - sharing of 2 electrons (one from
each atom).
–  Free rotation
•  Double bonds - sharing of 4 electrons (two from
each atom)
–  Shorter and stronger than single bonds
–  No rotation
•  Intermediate - e.g. benzene ring
–  Electrons in double bonds are delocalized

Polar, Covalent Bonds

•  Bonds between atoms, within a molecule
–  Intramolecular bond
•  Electrons shared unequally between atoms with
different electronegativities
–  Positive charge concentrated on
one end
–  Negative charge concentrated on
the other end.
•  Oxygen and nitrogen are
highly electronegative
–  Strongly attract electrons from H
–  -O-H, -N-H Polar, covalent bond
•  **Allows hydrogen bonding

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 Polar, Covalent Bonds
•  Electrons shared unequally between atoms with
different electronegativities
–  Positive charge concentrated on
one end
–  Negative charge concentrated on
the other end.
•  Relative electronegativities of
biologically important elements
–  H – 2.2
–  C – 2.4
–  N – 3.0 O--:------H
–  O – 3.5 O----:----O Polar, covalent bond

•  How would you classify the following

bonds?
C–C Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

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•  How would you classify the following
bonds?
C–H Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

•  How would you classify the following

bonds?
O–H Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

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•  How would you classify the following
bonds?
N–H Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

•  How would you classify the following

bonds?
C–N Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

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•  How would you classify the following
bonds?
C–O Electronegativitie
A.  Non-polar covalent s of some
B.  Slightly polar covalent elements
H – 2.2
C.  Polar covalent
C – 2.4
N – 3.0
O – 3.5

Hydrogen Bonding
•  Partial electric charges in polar
molecules attract oppositely
charged areas of other
molecules.
–  Intermolecular bonding
•  Responsible for properties of
water that make it conducive to
life.
•  Responsible (in part) for
protein folding
–  Esp. 2° structure
•  Determines how hydrophilic or
hydrophobic a substance is Polar, covalent bond

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 Water = Life!
•  Each water can H-bond
with 4 other water
molecules
–  Highly organized network
–  The strength of one bond is
weak, the strength of many
bonds is strong
•  H-bonds continually break
and reform (fluidity), but
at any given time there
are many, many bonds

Hydrophobic Interactions
•  Nonpolar molecules are hydrophobic
•  In an aqueous environment, non-polar
molecules are forced together to
minimize their exposure to water
•  Hydrophobic regions of proteins tend to
tightly aggregate in the center of the
protein

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 •  Why do white bears like to go
swimming?
A.  Because they like fish
B.  Because they need to stay cool
C.  Because they’re polar!

Electronegativity difference

Ionization

Ionization
Polar covalent bond

•  The ionic character of a bond increases

as the electronegativity difference
Nonpolar covalent bond
between the two bonded atoms
increases (e.g. Na – 0.9, Cl – 3.2)
•  Ions form when atoms lose or gain
electrons
–  Charged atoms or molecules
•  Ionic interactions – attraction of
positive and negative ions
•  A salt is a dry solid composed of
atoms bonded by ionic bonds.
•  Water prevents ions from associating
strongly - dissolve

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•  Which is strongest?

A.  A covalent bond

B.  An ionic bond
C.  A hydrogen bond

•  Which is weakest?

A.  A covalent bond

B.  An ionic bond
C.  A hydrogen bond

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 Dehydration and Hydrolysis
Reactions

•  What kind of reaction is responsible for

forming glycosidic bonds?
A. Dehydration reactions
B. Hydrolysis reactions
C. Glycosidic reactions
D. Polymerization reactions

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•  What type of reaction would be required to
break a sucrose molecule (a disaccharide)
into a glucose and a fructose?
A. Dehydration reaction
B. Hydrolysis reaction
C. Glycosidic reaction
D. Degredation reaction

•  What kind of reaction is responsible for

producing an ester bond between a
glycerol and a fatty acid?
A. Dehydration reaction
B. Hydrolysis reaction
C. Ester reaction
D. Lipid reaction

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•  What kind of reaction is responsible for
producing phosphodiester bonds?
A. Dehydration reactions
B. Hydrolysis reactions
C. Posphodiester reactions
D. Nucleotide reactions

Proteins
•  Many various functions due to their shape
•  Selectively interact with other molecules
due to the shape and chemical properties
of the protein
•  Proteins do it all!

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 Amino Acids
•  Monomers of polypeptides
•  Central (α) carbon with amino group,
carboylic acid group, H, R-group

Amino Acids
•  R-group confers ‘properties’

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 Amino Acids
•  R-group confers ‘properties’

Amino Acids
•  R-group confers ‘properties’

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•  Which of the following amino acids is
hydrophobic?
A B C

•  Why?

•  Which of the following amino acids is

hydrophobic?
A B C

•  Why? C-H bonds are nonpolar

Ions dissolve in water
O-H bonds are polar

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 Proteins - 1˚ Structure
•  Proteins have a unique sequence of amino
acids
•  R groups (side chains) determine how a
protein will fold
–  Flexible polypeptide
–  Non-covalent bonds lead to higher levels of
structure
•  Ionic bonds
•  H-bonds
•  Hydrophobic interactions
•  Van der Waals attractions

Proteins - 2° Structure
•  H-bonds in backbone
–  C-C-N (not in R groups)
•  α-Helix
•  β-Pleated sheet

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 Proteins - 2° Structure
This hole is
•  α-Helix teeny weenie.
No molecules
–  H-bond between every will fit through
here!
4th peptide
•  N-H of one amino acid and
C=O of the other
•  H-bonds in backbone
•  Stabilizes coil
•  1 turn every 3.6 amino
acids
–  Only R-groups will
interact with environment
–  Common in
transmembrane proteins

Proteins - 2° Structure
•  β-Pleated sheet
–  Rigid, pleated structure
–  H-bond between amino
acids lying side by side.
–  Parallel β sheets
•  run in same direction
–  Antiparallel β sheets
•  run in opposite direction

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 Hydrophobic
interactions and

Proteins - 3° Structure van der Waals

interactions

•  Overall shape of the

Polypeptide
backbone

polypeptide
Hydrogen
bond

•  3-D structure determined by

folding via various interactions Disulfide bridge

–  H-bonds
–  Hydrophobic interactions
–  van der Waals Ionic bond

–  Ionic interactions
–  Covalent bonds - disulfide
bridges
•  Not as common
•  Interactions in R-groups
–  Some interactions in the
backbone

Collagen

Proteins - 4° Structure
•  More than one polypeptide
•  Some proteins include small,
non-proteinaceous molecules
that are necessary for their
function – prosthetic groups
–  Hemoglobin - heme groups
•  Ring shaped molecules that
include Fe
•  Fe critical to carrying oxygen
(redox reaction!)
–  Rhodopsin - retinal
•  Light sensitive pigment
•  Vitamin-A, lipid

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 Protein Folding
•  Conformation – protein’s final, stable shape due to
4 levels of structure
Chaperone
–  May change if chemistry changes protein GroEL
•  E.g. retinal in response to light Binds ATP à
conformation
–  Binding of other molecules change
•  Changes chemistry
Inside the
•  Phosphorylation cavity
–  Free energy (G) is minimized Hydrophobic
à Hydrophilic
•  Non-polar groups cluster in center
•  Polar groups on outside of protein
•  Structure = Function:
–  active sites, recognition sites, conformation changes

Chaperone Proteins
•  Chaperone proteins may bind to partially
folded (partially synthesized) polypeptides
and help them fold.
•  Important to prevent
binding with other
nascent proteins.
•  Increase efficiency of
folding but final product
unaffected
–  Sort of like enzymes

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 Binding Sites
•  Structure dictates function
•  Specificity due to shape and
chemical attraction
•  Active sites, allosteric sites,
other binding sites
•  Enzymes bind substrates to
catalyze reactions
•  Antibodies bind antigens
(foreign cells/virus)
•  Ligand - anything that binds to
a protein

Protein Structure
•  A protein may be denatured if environment if
altered
•  Effected by physical conditions of
the cell
–  pH
–  Temperature
–  Salt concentration
•  Denaturation cause protein to unfold
•  When conditions return to ‘normal’ the protein
might reconform (renature) to its functional shape
–  Might not

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•  You are examining a protein and
determine that it contains at least 3
globular polypeptides, each with several
α-helices. Which is the highest level of
structure this protein exhibits?
A.  1°
B.  2°
C.  3°
D.  4°
E.  5°

Proteins gone Wild!

•  Infectious, abnormally folding proteins
•  Transmissible Spongiform Encephalopathies
–  Scrappie in sheep
–  Mad cow in cow
–  Chronic wasting disease in deer
–  CJD in humans
•  Infectious, self replicating little buggers!
•  Alive? normal CJD

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 Prions
CJD
•  Normal protein - PrPC
–  2° structure dominated α-helices
–  Soluble, monomers
–  Degraded by protienase
•  Prion - PrPSc
–  Abnormal, disease producing protein
–  Same 1° structure as PrPC, but 2°
structure is dominated by β sheets
–  Insoluble, fibrils
–  Cannot be digested by proteinases
–  Infectious - binds to PrPc, converting
to PrPSc

Alzheimer’s Disease
•  Formation of amyloid plaques
in the brain
–  Insoluble fibrils
–  Results in death of nerve cells
–  Nontransmissable

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 Alzheimer’s Disease
•  Amyloid β-peptide (Aβ) - part of the amyloid
precursor protein (APP)
•  Cleaved from APP by β-secretase and γ-secretase
•  Aβ40 and Aβ42 both exist as soluble forms with
predominantly α-helices
•  Aβ42 spontaneously
refolds into conformation
with many β sheets
–  Self-associate to form
small complexes (leads
to death of nerve cells)
or large aggregates (Leads
to formation of plaques)

Protein Structure
•  Proteins have diverse shapes that confer
diverse functions.

–  Globular
–  Filamentous
–  Fibrous
–  Sheets
–  Rings
–  Spheres

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 Protein Motif
•  A substructure found among many
different proteins
•  Examples:
–  Helix-loop-helix
–  Zink finger
–  Greek key

Protein Domain
•  Any segment of a polypeptide that can fold
and function semi-independently ~100-250
amino acids
•  Modular - found in many proteins
–  Not specific to a gene or gene family
•  Often associated with a specific function
–  DNA binding domains
–  Ca2+ binding domain
–  cAMP binding domain
–  Membrane-spanning domain Single stranded
DNA binding domain

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 Protein Families
•  Different proteins with similar amino acid sequences,
functions, and evolutionary history
•  Hemoglobin Family
–  Hemoglobin
•  F - Fetal hemoglobin
•  A - common adult type
•  A2 - Late in 3rd trimester and in adults ~2.5% of hemoglobin
–  Myoglobin
–  Neuroglobin
•  Serine Proteases - digestive enzymes
–  Trypsin
–  Elastase
–  Chymotrypsin
–  Blood clotting proteases

Protein Complex
•  Different proteins with different functions
come together to complete a specific task.
•  Important in metabolic pathways
–  Product of one enzyme
channeled directly to the next
–  Pyruvate dehydrogenase
–  ATP synthase
–  Photosystem II

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 Protein Assemblages
•  Self organizing! Stable conformation.
•  Repeating subunits
•  Binding site on one polypeptide is complementary to
the binding site on another polypeptide
–  Subunits.
–  Dimers, helices, rings
–  Long filaments
•  Actin helix (cytoskeleton)
–  Sheets
–  Tubes
•  Microtubules
–  Spherical shells
•  Virus coat

•  What is the difference between a protein

complex and a protein assemblage?
A.  A complex is made of many different subunits,
an assemblage is made of repeating subunits
B.  An assemblage is made of many different
subunits, a complex is made of repeating
subunits
C.  A complex is smaller than an assemblage
D.  A complex does not have 4° structure, but an
assemblage does

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 Phosphorylation
•  Protein kinase - enzyme that
catalyzes the addition of a
phosphate to a protein
–  Phosphate comes from ATP or a
phosphorylated protein
–  Attaches to an R-group (Serine,
Threonine, Tyrosine)
•  Protein Phosphatase
–  Removes a phosphate from a protein,
returns it to original conformation
–  Dephosphoryltion
•  Cycle

GTP-Binding Proteins
•  GTP-bound - active protein
–  GTP binds tightly to the protein
–  Hydrolysis of GTP to GDP deactivates
•  GDP-bound is the inactive form of the protein
–  GDP is not tightly bound
–  GDP disassociates and GTP binds
to activate
•  Molecular switches in cells
–  Often activated by cellular signals
–  Regulation of enzymatic pathways

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 GTP-Binding Proteins
1.  An inactive G Protein
(GDP bound) is GTP
activated by a signal Signal

2.  The protein loses its GDP

affinity for GDP G-Protein

•  GDP leaves the Activation

binding site à cytosol GDP GDP GTP

3.  GTP (from the cytosol) G-Protein G-Protein

enters the nucleotide Inactive Active

binding site – ACTIVE! P

GTP
4.  G Proteins have intrinsic Intrinsic
GTPase GDP
GTPase activity G-Protein

GTP à GDP + P Inactivation

INACTIVE!

True or False?

•  A G-protein is active when it is bound to

GTP. In order for activation to occur GDP
is phosphorylated to GTP.
A. True
B. False

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True or False?

•  A G-protein is active when it is bound to

GTP. When it is deactivated GTP is
hydrolyzed to GDP.
A. True
B. False

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