Download - BioChem Handouts Part 1 (EAmor)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
1/127
6/13/11
1
Introduction
On Life and Chemistry..
Living things are composed of lifelessmolecules (Albert Lehninger)
Chemistry is the logic of biologicalphenomena (Garrett and Grisham)
What on earth is notbiochemistry? (Anonymous)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
2/127
6/13/11
2
Scope of this Review
Proteins
Carbohydrates
Lipids
Nucleic Acids
Metabolism
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
3/127
6/13/11
3
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
4/127
6/13/11
4
Polymer of L-amino acids
Have varied roles most important of which is catalysis and regulation
Polymer of monosaccharides
Main source of energy in most
organisms
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
5/127
6/13/11
5
informational molecules of allliving organisms
structural and functional partsof units such as the ribosome
catalytic function (ribozymes)transport and providechemical energy in the form of
phosphate groups
important in cell regulationand signal transduction
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
6/127
6/13/11
6
The language of nucleic acids
What makes us human
There are 46chromosomes,arranged in 23 pairs,in each cell in thebody
One chromosome ofeach pair iscontributed by thefather, and the otherby the mother
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
7/127
6/13/11
7
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
8/127
6/13/11
8
Biochemistry for the MED Boards
Distinctive Properties of Living Systems
Organisms are complicated and highlyorganized
Biological structures serve functionalpurposes
Living systems are actively engaged inenergy transformations
Living systems have a remarkablecapacity for self-replication
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
9/127
6/13/11
9
Biochemistry for the MED Boards
Biochemistry for the MED Boards
IN008
The sequence of monomeric units in a biological polymer has the potential to contain
information if the diversity and order of the units are not overly simple or repetitive. Nucleic
acids and proteins are information-rich molecules; polysaccharides are not.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
10/127
6/13/11
10
Methods for Separating and Purifying
Biomolecules
Salt fractionation(precipitation of
proteins with
ammonium sulfate)
Chromatography paper, ion-exchange,
affinity, thin-layer,gas-liquid, high
pressure liquid, gel
filtration
Electrophoresis paper, high voltage,
agarose, cellulose
acetate, starch gel,
polyacrylamide gel,
SDS-PAGE
Ultracentrifugation
Methods for Determining Biomolecular
Structures
Elemental analysis UV-VIS, IR, NMR
spectroscopy
Acid/base hydrolysis Enzymatic
degradation
MS Specific sequencing
methods
X-ray crystallography
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
11/127
6/13/11
11
Preparations for Studying Biochemical
Processes
Whole animal(transgenic and withgene knockout)
Isolated perfusedorgan
Tissue slice Whole cells Homogenate Isolated cell
organelles
Subfractionation oforganelles
Purified metabolitesand enzymes
Isolated genes (PCRand site-directed
mutagenesis)
Major Causes of Diseases
Physical agents mechanical trauma,extremes of T, suddenchanges inatmospheric P,radiation, electricshock
Chemical agents,including drugs:certain toxiccompounds,therapeutic drugs,etc.
Biologic agents:viruses, bacteria,fungi, higher forms ofparasites
All of the causes listed act by influencing the various biochemical mechanisms in
the cell or in the body.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
12/127
6/13/11
12
Major Causes of Diseases
Oxygen lack: loss ofblood supply,depletion of theoxygen carryingcapacity of the blood,poisoning of theoxidative enzymes
Genetic disorders congenital, molecular
Immunologicreactions anaphylaxis,autoimmune disease
Nutritional imbalances deficiencies,excesses
Endocrine imbalances hormonaldeficiencies,excesses
Amino Acids
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
13/127
6/13/11
13
What Are the Structures and Properties of Amino
Acids, the Building Blocks of Proteins?
Amino acids contain a central tetrahedralcarbon atom
There are 20 common amino acids Amino acids can join via peptide bonds Several amino acids occur only rarely in
proteins Some amino acids are not found in
proteins
Biochemistry for the MED Boards
Anatomy of an amino acid. Except for proline and its derivatives, all of the
amino acids commonly found in proteins possess this type of structure.
Amino AcidsBuilding Blocks of Proteins
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
14/127
6/13/11
14
20 Common Amino Acids
You should know names, structures, pKavalues, 3-letter and 1-letter codes
Non-polar amino acids Polar, uncharged amino acids Acidic amino acids Basic amino acids
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
15/127
6/13/11
15
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
16/127
6/13/11
16
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
17/127
6/13/11
17
Biochemistry for the MED Boards
Biochemistry for the MED Boards
The ionic forms of the amino acids, shown without consideration of any ionizations onthe side chain. The cationic form is the low pH form, and the titration of the cationic
species with base yields the zwitterion and finally the anionic form.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
18/127
6/13/11
18
pKa Values of the Amino Acids
Alpha carboxyl group - pKa = 2 Alpha amino group - pKa = 9
pKa Values of the Amino Acids
Arginine, Arg, R: pKa(guanidinogroup) = 12.5
Aspartic Acid, Asp, D: pKa = 3.9 Cysteine, Cys, C: pKa = 8.3 Glutamic Acid, Glu, E: pKa = 4.3 Histidine, His, H: pKa = 6.0
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
19/127
6/13/11
19
pKa Values of the Amino Acids
Lysine, Lys, K: pKa = 10.5 Serine, Ser, S: pKa = 13 Threonine, Thr, T: pKa = 13 Tyrosine, Tyr, Y: pKa = 10.1
Biochemistry for the MED Boards
Titration of glycine, a simple
amino acid. The isoelectric
point, pI, the pH where the
molecule has a net charge of
0, is defined as (pK1+ pK2)/2.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
20/127
6/13/11
20
Biochemistry for the MED Boards
Titration of glutamic acid.
Biochemistry for the MED Boards
Titration of lysine.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
21/127
6/13/11
21
A Sample Calculation
What is the pH of a glutamic acid solutionif the alpha carboxyl is 1/4 dissociated?
pH = 2 + log10 [1][3]
pH = 2 + (-0.477)pH = 1.523
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
22/127
6/13/11
22
Reactions of Amino Acids
Carboxyl groups form amides & esters Amino groups form Schiff bases and
amides
Side chains show unique reactivitiesCys residues can form disulfides and
can be easily alkylatedFew reactions are specific to a single
kind of side chain
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
23/127
6/13/11
23
Biochemistry for the MED Boards
Biochemistry for the MED Boards
The pathway of theninhydrin reaction,
which produces acolored product
called Ruhemanns
Purple that absorbslight at 570 nm. Note
that the reactioninvolves and
consumes twomolecules ofninhydrin.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
24/127
6/13/11
24
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
25/127
6/13/11
25
Stereochemistry of Amino Acids
All but glycine are chiral L-amino acids predominate in nature D,L-nomenclature is based on D- and L-
glyceraldehyde
R,S-nomenclature system is superior,since amino acids like isoleucine and
threonine (with two chiral centers) can be
named unambiguously
Biochemistry for the MED Boards
The configuration of thecommon L-amino acids
can be related to theconfiguration of L(-)-
glyceraldehyde as shown.These drawings areknown as Fischer
projections. The horizontallines of the Fischer
projections are meant toindicate bonds coming outof the page from the
central carbon, andvertical lines represent
bonds extending behindthe page from the centralcarbon atom.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
26/127
6/13/11
26
Biochemistry for the MED Boards
Enantiomeric molecules basedon a chiral carbon atom.
Enantiomers arenonsuperimposable mirror
images of each other.
Spectroscopic Properties
All amino acids absorb at infraredwavelengths
Only Phe, Tyr, and Trp absorb UV Absorbance at 280 nm is a good
diagnostic device for amino acids NMR spectra are characteristic of each
residue in a protein, and high resolutionNMR measurements can be used toelucidate three-dimensional structures ofproteins
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
27/127
6/13/11
27
Biochemistry for the MED Boards
Cation (a) and anion (b)exchange resins commonly
used for biochemicalseparations.
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
28/127
6/13/11
28
Proteins
Biochemistry for the MED Boards
Anatomy of an amino acid. Except for proline and its derivatives, all of the
amino acids commonly found in proteins possess this type of structure.
What Is the Fundamental Structural Pattern inProteins?
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
29/127
6/13/11
29
The Peptide Bond
is usually found in the trans configurationhas partial (40%) double bond characteris about 0.133 nm long - shorter than a typicalsingle bond but longer than a double bond
Due to the double bond character, the six atomsof the peptide bond group are always planar!
N partially positive; O partially negative
Biochemistry for the MED Boards
Anatomy of an
amino acid.
Except for proline
and itsderivatives, all of
the amino acids
commonly found
in proteins
possess this type
of structure.
The Coplanar Nature of the Peptide Bond
Six atoms of the peptide group lie in a plane!
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
30/127
6/13/11
30
Biochemistry for the MED Boards
The amide or peptide bond planes arejoined by the tetrahedral bonds of the
-carbon. The rotation parameters are and . The conformation shown
corresponds to = 180 and = 180.Note that positive values ofand correspond to clockwise rotation as
viewed from C. Starting from 0, arotation of 180 in the clockwisedirection (+180) is equivalent to arotation of 180 in the counterclockwisedirection (-180). (Illustration: Irving Geis.Rights owned by Howard Hughes MedicalInstitute. Not to be reproduced without
permission.)
The angles phi
and psi are
shown here
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
31/127
6/13/11
31
Peptides
Short polymers of amino acids Each unit is called a residue 2 residues - dipeptide 3 residues - tripeptide 12-20 residues - oligopeptide many - polypeptide
Protein
One or more polypeptide chains
One polypeptide chain - a monomeric protein
More than one - multimeric protein Homomultimer - one kind of chain Heteromultimer - two or more different chains Hemoglobin, for example, is a heterotetramer It has two alpha chains and two beta chains
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
32/127
6/13/11
32
What Architectural Arrangements
Characterize Protein Structure?
Proteins are classed according to shape andand solubility
Shape - globular or fibrous The four levels of protein structure
- Primary - sequence
- Secondary - local structures - H-bonds
- Tertiary - overall 3-dimensional shape
- Quaternary - subunit organization
Biochemistry for the MED Boards
(a) Proteins having structural roles in cells are typically fibrous and often water insoluble.
Collagen is a good example. Collagen is composed of three polypeptide chains that intertwine.
(b) Soluble proteins serving metabolic functions can be characterized as compactly folded
globular molecules, such as myoglobin. The folding pattern puts hydrophilic amino acid side
chains on the outside and buries hydrophobic side chains in the interior, making the protein
highly water soluble. (c) Membrane proteins fold so that hydrophobic amino acid side chains
are exposed in their membrane-associated regions. The portions of membrane proteins
extending into or exposed at the aqueous environments are hydrophilic in character, like
soluble proteins. Bacteriorhodopsin is a typical membrane protein; it binds the light-absorbing
pigment, cis-retinal, shown here in red.(a, b, Illustration: Irving Geis. Rights owned by Howard HughesMedical Institute. Not to be reproduced without permission.)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
33/127
6/13/11
33
Biochemistry for the MED Boards
Bovine pancreatic
ribonuclease A
contains 124 amino
acid residues, none of
which are tryptophan.
Four intrachain
disulfide bridges (S-
S) form crosslinks in
this polypeptide
between Cyc26 and
Cys84, Cys40 and
Cys95, Cys58 andCys110, and Cys65 and
Cys72. These
disulfides are
depicted by yellow
bars.
Classes of Secondary Structure
All these are local structures that arestabilized by hydrogen bonds
Alpha helix Other helices Beta sheet (composed of "beta strands") Tight turns (aka beta turns or beta bends) Beta bulge
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
34/127
6/13/11
34
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
35/127
6/13/11
35
Biochemistry for the MED Boards
The arrangement of hydrogenbonds in (a) parallel and (b)
antiparallel -pleated sheets.
Biochemistry for the MED BoardsChemistry 40 (Summer 2007)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
36/127
6/13/11
36
Biochemistry for the MED Boards
The structures of two kinds of-turns (also called tight turns or-bends) (Irving Geis)
Biochemistry for the MED Boards
Three different kinds of-bulge structures involving a pair of adjacent polypeptidechains. (Adapted from Richardson, J. S., 1981. Advances in Protein Chemistry 34:167339.)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
37/127
6/13/11
37
Supersecondary Structures
1. 2. 3. -meander4. Greek key
Domain
Distinct compactunits within a protein
consisting of various
elements of
secondary structure
25 to 300 residues Combinations of
secondary
structures that form
the core of a domain
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
38/127
6/13/11
38
Tertiary structure Disulfide bonds are
not generally foundin intracellularproteins but aresometimes found inextracellularprotein
May also holdtogether differentsubunits (i.e.,contribute toquaternarystructure)
Insulin A & B chains
Protein folding
dictated by primarystructure
Multiple intermediatesteps
Important drivingforces: Hydrophobic effect Hydrogen bonding Van der Waals Charge-charge
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
39/127
6/13/11
39
Molecular chaperones
Increase the rate ofcorrect folding of
nascent polypeptide
chains
Aid in the assembly ofmultisubunit proteins
Protect proteins fromstress-induced damage
(eg. Heat shock)
Chaperonin
Molecular chaperones assist protein
folding
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
40/127
6/13/11
40
Anfinsen experiment: Spontaneousrenaturation of Ribonuclease A
Primarystructurecontainssufficientinformationto allow
formation ofsecondaryand tertiarystructures
Predictive Algorithms
If the sequence holds the secrets of folding, can wefigure it out?
Many protein chemists have tried to predictstructure based on sequence
Chou-Fasman: each amino acid is assigned a"propensity" for forming helices or sheets
Chou-Fasman: is only modestly successfuland doesn't predict how sheets and helicesarrange
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
41/127
6/13/11
41
Biochemistry for the MED Boards
Relative frequencies of occurrence of amino acid residues in a-helices, b-sheets, and b-turns in proteins of known structure. (Adapted from Bell , J. E., and Bell , E. T., 1988, Proteinsand Enzymes, Englewood Cliffs, NJ: Prentice-Hall.)
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
42/127
6/13/11
42
Prion Misfolding Diseases
Prion- proteinaceous infectious particles(spongiform encelopathies)
Mad Cow Disease (cow) Creutzfeldt-Jacob disease (human) Scrapie (sheep)
Quaternary structure
Quaternary structure refers to theorganization and arrangement of subunits in
a protein with multiple subunits
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
43/127
6/13/11
43
Quaternary structure
Can have more thantwo subunits
Subunits areindividual
polypeptides
Pyruvate dehydrogenase complex:60 subunits!
Levels of protein structure
Primary
Secondary
Tertiary Quaternary
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
44/127
6/13/11
44
How Are Proteins Isolated and Purified fromCells?
The thousands of proteins in cells can beseparated and purified on the basis of sizeand electrical charge
Proteins tend to be least soluble at theirisoelectric point
Increasing ionic strength at first increasesthe solubility of proteins (salting-in), thendecreases it (salting-out)
1. If more than one polypeptide chain,separate.
2. Cleave (reduce) disulfide bridges 3. Determine composition of each chain 4. Determine N- and C-terminal
residues
Determining the SequenceAn Eight Step Strategy
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
45/127
6/13/11
45
5. Cleave each chain into smallerfragments and determine the
sequence of each chain
6. Repeat step 5, using a differentcleavage procedure to generate a
different set of fragments.
Determining the SequenceAn Eight Step Strategy
Determining the Sequence
An Eight Step Strategy
7. Reconstruct the sequence of theprotein from the sequences of
overlapping fragments
8. Determine the positions of thedisulfide crosslinks
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
46/127
6/13/11
46
Step 1:
Separation of chains
Subunit interactions depend on weakforces
Separation is achieved with:- extreme pH
- 8M urea
- 6M guanidine HCl
- high salt concentration (usuallyammonium sulfate)
Step 2:
Cleavage of Disulfide bridges
Performic acid oxidation Sulfhydryl reducing agents
- mercaptoethanol- dithiothreitol or dithioerythritol
- to prevent recombination, follow withan alkylating agent like iodoacetate
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
47/127
6/13/11
47
Step 3A:
Identify N- and C-terminal residues
N-terminal analysis:Edman's reagentphenylisothiocyanatederivatives are phenylthiohydantoinsor PTH derivatives
Step 3B: :
Identify N- and C-terminal residues
C-terminal analysis
Enzymatic analysis (carboxypeptidase)Carboxypeptidase A cleaves any residueexcept Pro, Arg, and Lys
Carboxypeptidase B (hog pancreas) onlyworks on Arg and Lys
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
48/127
6/13/11
48
Steps 4 and 5:
Fragmentation of the chains
Enzymatic fragmentationtrypsin, chymotrypsin, clostripain,
staphylococcal protease Chemical fragmentation
cyanogen bromide
Enzymatic Fragmentation
Trypsin - cleavage on the C-side of Lys, Arg Chymotrypsin - C-side of Phe, Tyr, Trp Clostripain - like trypsin, but attacks Arg
more than Lys Staphylococcal protease
C-side of Glu, Asp in phosphate bufferspecific for Glu in acetate or bicarbonate
buffer
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
49/127
6/13/11
49
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
50/127
6/13/11
50
Reconstructing the Sequence
Compare cleavage by trypsin and staphylococcalprotease on a typical peptide:
Trypsin cleavage:A-E-F-S-G-I-T-P-K L-V-G-K
Staphylococcal protease:F-S-G-I-T-P-K L-V-G-K-A-E
Reconstructing the Sequence
L-V-G-K A-E-F-S-G-I-T-P-K
L-V-G-K-A-E F-S-G-I-T-P-K
Correct sequence:L-V-G-K-A-E-F-S-G-I-T-P-K
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
51/127
6/13/11
51
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
52/127
6/13/11
52
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
53/127
6/13/11
53
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
54/127
6/13/11
54
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
55/127
6/13/11
55
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
56/127
6/13/11
56
Amino Acid Sequence Can Be Determined
by Mass Spectrometry
Mass spectrometry separates particles onthe basis of mass-to-charge ratio
Fragments of proteins can be generated invarious ways
MS can also separate these fragments
Do Proteins Have Chemical Groups Other
Than Amino Acids?
Proteins may be "conjugated" with otherchemical groups
If the non-amino acid part of the protein isimportant to its function, it is called aprosthetic group.
Be familiar with the terms: glycoprotein,lipoprotein, nucleoprotein, phosphoprotein,metalloprotein, hemoprotein, flavoprotein.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
57/127
6/13/11
57
What Are the Many Biological Functions of
Proteins?
Many proteins are enzymes Regulatory proteins control metabolism and
gene expression
Many DNA-binding proteins are gene-regulatoryproteins
Transport proteins carry substances from oneplace to another
Storage proteins serve as reservoirs of aminoacids or other nutrients
What Are the Many Biological Functions of
Proteins?
Movement is accomplished by contractileand motile proteins
Many proteins serve a structural role Proteins of signaling pathways include
scaffold proteins (adapter proteins)
Other proteins have protective andexploitive functions
A few proteins have exotic functions
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
58/127
6/13/11
58
Death of a protein
In a typical day, a person who is in nitrogen
balance will consume 100 grams of protein, break down
400 grams of bodily protein, resynthesize 400 grams ofprotein, and excrete/catabolize100 grams. Individual
proteins exhibit tremendous variability in their metabolic
lifetimes, from a few minutes to a few months.
Proteins in extracellular environments,
such as digestive enzymes,
polypeptide hormones, and antibodies,
turn over quite rapidly, but proteins
with predominantly structural roles,
such as collagen of connective tissue,
are much more stable.
Protein Turnover
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
59/127
6/13/11
59
Protein Turnover
Ubiquitination
Ubiquitin is a 76-amino acid residue
heat-stable protein found in all
eukaryotic cells. An ATP-dependent
reaction with proteins links ubiquitin'sC-terminal glycine to lysine amino
groups in the target protein.
PEST sequences
Virtually all short-lived proteins (i.e.,
half-lives less than 2 hours) contain
one or more regions rich in proline,
glutamate, serine, and threonine.
Insertion of these sequences into
long-lived proteins increases
their metabolic lability.
Protein Turnover
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
60/127
6/13/11
60
N-terminal amino acid residue
An N-terminal protein residue
of Phe, Leu, Tyr, Trp, Lys, orArg is correlated with short
metabolic lifetimes.
Protein Turnover
Enzymes
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
61/127
6/13/11
61
What Characteristic Features Define
Enzymes?
Enzymes endow cells with the remarkablecapacity to exert kinetic control over
thermodynamic potentiality
Enzymes are the agents of metabolicfunction
Catalytic power, specificity, regulation
Biochemistry for the MED BoardsChemistry 40 (Summer 2007)
Reaction profile showing large DG for glucose oxidation, free energy change of -2,870 kJ/
mol; catalysts lower DG, thereby accelerating rate.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
62/127
6/13/11
62
Enzyme Classification
Biochemistry for the MED BoardsChemistry 40 (Summer 2007)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
63/127
6/13/11
63
Vitamins
organic compounds essential in the diet insmall amounts
have little or no caloric value chemical composition is varied normally classified according to their
polarity
Classification of Vitamins
Fat-soluble vitamins(nonpolar)
Vitamin A
Vitamin D
Vitamin E
Vitamin K
Water-soluble vitamins(polar)
Vitamin C
Vitamin B Complex
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
64/127
6/13/11
64
Fat-Soluble vitamins: A, D, E, K
Soluble in fatty tissues Stored in the body for long periods of time Not easily excreted Can be overconsumed (overdose)
Water-Soluble Vitamins:
C and B Complex
Soluble in water Excreted in the urine and pose little threat
of overdose
However, they must be consumed insufficient amounts on a daily basis
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
65/127
6/13/11
65
Nutritional Minerals
elements,other than C, H, N, and O, neededfor good health.
many are present as ions rather than asneutral atoms
Major minerals (~4% of the bodys weight)Ca, P, Mg, Na, K, Cl, and S
Minor mineralsFe, Cu, Zn, I, Se, Mn, F, Cr, and Mo
Can the Rate of an Enzyme-Catalyzed
Reaction Be Defined in a Mathematical Way?
Enzymes can accelerate reactions as muchas 1016 over uncatalyzed rates!
Urease is a good example:Catalyzed rate: 3x104/secUncatalyzed rate: 3x10 -10/secRatio is 1x1014 !
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
66/127
6/13/11
66
Biochemistry for the MED Boards
The pH activity profiles of four different enzymes. Trypsin, an intestinal protease, has slightlyalkaline pH optimum, whereaspepsin, a gastric protease, acts in the acidic confines of thestomach and has a pH optimum near 2. Papain, a protease found in papaya, is relativelyinsensitive to pHs between 4 and 8. Cholinesterase activity is pH sensitive below pH 7 but notbetween pH 7 and 10. The cholinesterase pH activity profile suggests that an ionizable group
with pK' near 6 is essential to its activity. Might it be a histidine residue within the active site?
Biochemistry for the MED Boards
The effect of temperature
on enzyme activity. The
relative activity of an
enzymatic reaction as a
function of temperature.
The decrease in the activity
above 50C is due to
thermal denaturation.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
67/127
6/13/11
67
Specificity
Enzymes selectively recognize propersubstrates over other molecules
Enzymes produce products in very highyields - often much greater than 95%
Specificity is controlled by structure - theunique fit of substrate with enzyme controlsthe selectivity for substrate and the productyield
How Can Enzymes Be So Specific?
Lock and key was the first explanation forspecificity
Induced fit provides a more accuratedescription
Induced fit favors formation of the transition-state intermediate
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
68/127
6/13/11
68
Enzyme-Linked Immunosorbent Assay (ELISA)
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
69/127
6/13/11
69
Several terms to remember
rate or velocity rate constant rate law order of a reaction molecularity of a reaction
The Michaelis-Menten Equation
Louis Michaelis and Maud Menten's theory It assumes the formation of an enzyme-
substrate complex
It assumes that the ES complex is in rapidequilibrium with free enzyme Breakdown of ES to form products is assumedto be slower than 1) formation of ES and 2)breakdown of ES to re-form E and S
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
70/127
6/13/11
70
Understanding Km
The "kinetic activator constant" Km is a constant Km is a constant derived from rate
constants
Km is, under true Michaelis-Mentenconditions, an estimate of thedissociation constant of E from S
Small Km means tight binding; high Kmmeans weak binding
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
71/127
6/13/11
71
Understanding Vmax
The theoretical maximal velocity Vmax is a constant Vmax is the theoretical maximal rate of the
reaction - but it is NEVER achieved inreality
To reach Vmax
would require that ALLenzyme molecules are tightly bound withsubstrate
Vmax is asymptotically approached assubstrate is increased
The dual nature of the Michaelis-Menten
equation
Combination of 0-order and 1st-order kinetics
When S is low, the equation for rate is 1storder in S
When S is high, the equation for rate is 0-order in S
The Michaelis-Menten equation describes arectangular hyperbolic dependence of v on S!
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
72/127
6/13/11
72
The turnover number
A measure of catalytic activity
kcat, the turnover number, is the number ofsubstrate molecules converted to product per
enzyme molecule per unit of time, when E is
saturated with substrate. If the M-M model fits, k2 = kcat = Vmax/Et Values of kcat range from less than 1/sec to many
millions per sec
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
73/127
6/13/11
73
The catalytic efficiency
Name for kcat/KmAn estimate of "how perfect" the enzyme is
kcat/Km is an apparent second-order rateconstant
It measures how the enzyme performswhen S is low
The upper limit for kcat/Km is the diffusionlimit - the rate at which E and S diffusetogether
Enzyme Units
IU (International Unit) amount of enzymethat catalyze the formation of 1 micromole
of product in 1 minute
Katal amount of enzyme that converts 1mole of substrate to product in 1 second
Specific activity enzyme unit per mg ofprotein
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
74/127
6/13/11
74
Linear Plots of the Michaelis-Menten
Equation
Lineweaver-Burk Eadie-Hofstee Hanes-WoolfHanes-Woolf is best - why?
Smaller and more consistent errorsacross the plot
Biochemistry for the MED Boards
The Lineweaver-Burk double-reciprocal plot, depicting extrapolations that allow the
determination of thex- and y-intercepts and slope.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
75/127
6/13/11
75
Biochemistry for the MED BoardsA Hanes-Woolf plot of [S]/vversus [S], another straight-line rearrangement of the Michalelis-Menten equation.
Eadie Hofstee Linear Plot
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
76/127
6/13/11
76
What Can Be Learned from the Inhibition of
Enzyme Activity?
Enzymes may be inhibited reversibly orirreversibly
Reversible inhibitors may bind at the activesite or at some other site
Enzymes may also be inhibited in anirreversible mannerPenicillin is an irreversible suicide inhibitor
Biochemistry for the MED Boards
Lineweaver-Burk plot of competitive inhibition, showing lines for no I, [I], and 2[I]. Note that
when [S] is infinitely large (1/[S] = 0), Vmax is the same, whether I is present of not. In the
presence of I, the negative
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
77/127
6/13/11
77
Biochemistry for the MED Boards
Structures of succinate, the substrate of succinate dehydrogenase (SDH), and malonate,
the competitive inhibitor. Fumarate (the product of SDH action on succinate) is also shown.
Biochemistry for the MED Boards
Lineweaver-Burk plot of pure noncompetitive inhibition. Note that I does not alter Km but
that it decreases Vmax. In the presence of I, the y-intercept is equal to (1/Vmax)(1 + I/KI).
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
78/127
6/13/11
78
Biochemistry for the MED Boards
Lineweaver-Burk plot of pure
uncompetitive inhibition. Note
that I decreases Km and Vmax. In
the presence of I, the y-interceptis equal to (1/Vmax)(1 + I/KI).
Biochemistry for the MED Boards
Penicillin is an irreversible inhibitor of
the enzyme glycoprotein peptidase,which catalyzes an essential step in
bacterial cell wall synthesis. Penicillin
consists of a thiazolidine ring fused to a
b-lactam ring to which a variable group
R is attached. A reactive peptide bond
in the b-lactam ring covalently attaches
to a serine residue in the active site of
the glycopeptide transpeptidase. (The
conformation of penicillin around its
reactive peptide bond resembles thetransition state of the normal
glycoprotein peptidase substrate.) The
penicilloyl-enzyme complex is
catalytically inactive. The bond
between the enzyme and penicillin is
indefinitely stable; that is, penicillin
binding is irreversible.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
79/127
6/13/11
79
Are All Enzymes Proteins?
Relatively new discoveries Ribozymes - segments of RNA that display
enzyme activity in the absence of protein
Examples: RNase P and peptidyl transferase Abzymes - antibodies raised to bind the
transition state of a reaction of interest
What Are the Mechanisms of Enzyme-
Induced Rated Accelerations?
Mechanisms of catalysis:
Entropy loss in ES formationDestabilization of ESCovalent catalysisGeneral acid/base catalysisMetal ion catalysisProximity and orientation
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
80/127
6/13/11
80
What Factors Influence Enzymatic
Activity?
Six points: Rate slows as product accumulates Rate depends on substrate availability Genetic controls - induction and repression Enzymes can be modified covalently Allosteric effectors may be important Zymogens, isozymes and modulator
proteins may play a role
Biochemistry for the MED Boards
Enzymes regulated by covalent modification are called interconvertible enzymes. The
enzymes (protein kinase andprotein phosphatase, in the example shown here) catalyzingthe conversion of the interconvertible enzyme between its two forms are called converter
enzymes. In this example, the free enzyme form is catalytically active, whereas the
phosphoryl-enzyme form represents an inactive state. The -OH on the interconvertible
enzyme represents an -OH group on a specific amino acid side chain in the protein (for
example, a particular Ser residue) capable of accepting the phosphoryl group.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
81/127
6/13/11
81
Biochemistry for the MED Boards
Proinsulin is an 86-
residue precursor to
insulin (the sequence
shown here is human
proinsulin). Proteolytic
removal of residues 31
to 65 yields insulin.
Residues 1 through 30
(the B chain) remain
linked to residues 66
through 87 (the A chain)
by a pair of interchain
disulfide bridges.
Biochemistry for the MED BoardsThe proteolytic activation of chymotrypsinogen.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
82/127
6/13/11
82
Biochemistry for the MED Boards
The isozymes of lactate dehydrogenase (LDH). Active muscle tissue becomes anaerobic
and produces pyruvate from glucose via glycolysis. It needs LDH to regenerate NAD + from
NADH so glycolysis can continue. The lactate produced is released into the blood. The
muscle LDH isozyme (A4) works best in the NAD+-regenerating direction. Heart tissue is
aerobic and uses lactate as a fuel, converting it to pyruvate via LDH and using the pyruvate
to fuel the citric acid cycle to obtain energy. The heart LDH isozyme (B4) is inhibited by
excess pyruvate so the fuel wont be wasted.
Biochemistry for the MED Boards
Cyclic AMP- dependent protein kinase (also known as PKA) is a 150- to 170-kD R2C2tetramer in mammalian cells. The two R (regulatory) subunits bind cAMP (KD = 3 x 10
-8
M); cAMP binding releases the R subunits from the C (catalytic) subunits. C subunits areenzymatically active as monomers.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
83/127
6/13/11
83
Carbohydrates
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
84/127
6/13/11
84
Biochemistry for the MED Boards
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
85/127
6/13/11
85
Biochemistry for the MED Boards
Biochemistry for the MED Boards
D-Fructose and L-fructose, an enantiomeric pair. Note that changing the configurationonly at C5 would change D-fructose to L-sorbose.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
86/127
6/13/11
86
Biochemistry for the MED Boards
the sweetest of all sugars (more than 50%sweeter than table sugar)
Which structure is a Haworth projection ofI?
Which structure is a carbon-2 (position 2) epimer ofI?
Which structure(s) has/have the "beta" configuration at the anomeric carbon?
Which structure(s) is/are a ketose?
Which structure is a pentose?
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
87/127
6/13/11
87
Biochemistry for the MED Boards
D-Glucose can cyclize in two ways, forming either furanose or pyranose structures.
Biochemistry for the MED Boards
(a) Chair and boat conformations of a pyranose sugar. (b) Two possible chairconformations of-D-glucose.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
88/127
6/13/11
88
Monosaccharide Derivatives
Reducing sugars: sugars with free anomeric
carbons - they will reduce oxidizing agents, such
as peroxide, ferricyanide and some metals (Cu
and Ag)
These redox reactions convert the sugar to a
sugar acidGlucose is a reducing sugar - so these reactions
are the basis for diagnostic tests for blood sugar
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
89/127
6/13/11
89
Biochemistry for the MED Boards
Structures of some sugar alcohols.
Biochemistry for the MED BoardsSeveral deoxy sugars and ouabain, which contains -L-rhamnose (Rha). Hydrogenatoms highlighted in red are deoxy positions.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
90/127
6/13/11
90
Biochemistry for the MED Boards
Several sugar esters important in metabolism.
Biochemistry for the MED Boards
Structures of D-glucosamine and D-galactosamine.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
91/127
6/13/11
91
Biochemistry for the MED Boards
Structures of muramicacid and neuraminic
acid and severaldepictions of sialic acid.
Biochemistry for the MED Boards
Acetals and ketals can be formed from hemiacetals and hemiketals, respectively.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
92/127
6/13/11
92
What is the Structure and Chemistry ofOligosaccharides?
Be able to identify anomeric carbons andreducing and nonreducing ends
Sucrose is NOT a reducing sugar Note carefully the nomenclature of links.Be able to recognize alpha(1,4), beta
(1,4), etc
Soy milk is good substitute forlactose intolerance
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
93/127
6/13/11
93
Biochemistry for the MED Boards
The structures of several important disaccharides. Notethat the notation -HOH means that the configuration can
be either or. If the -OH group is above the ring, the
configuration is termed . The configuration is if the -
OH group is below the ring as shown. Also note thatsucrose has no free anomeric carbon atoms.
Biochemistry for the MED Boards
The structures of some interesting oligosaccharides.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
94/127
6/13/11
94
What is the Structure and Chemistry of
Polysaccharides?
Functions: storage, structure, recognition
Nomenclature: homopolysaccharide vs.heteropolysaccharide
Starch and glycogen are storage molecules Chitin and cellulose are structural molecules Cell surface polysaccharides are recognition
molecules
Starch
A plant storage polysaccharide
Two forms: amylose and amylopectin Most starch is 10-30% amylose and 70-90%
amylopectin
Branches in amylopectin every 12-30 residues Amylose has alpha(1,4) links, one reducing
end
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
95/127
6/13/11
95
Biochemistry for the MED Boards
Amylose and amylopectin are the two forms of starch. Note that the linear linkages are
(1 4), but the branches in amylopectin are (1 6). Branches in polysaccharides caninvolve any of the hydroxyl groups on the monosaccharide components. Amylopectin is ahighly branched structure, with branches occurring every 12 to 30 residues.
Starch
A plant storage polysaccharide
Amylose is poorly soluble in water, but formsmicellar suspensions
In these suspensions, amylose is helicaliodine fits into the helices to produce a blue
color
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
96/127
6/13/11
96
Glycogen
The glucose storage device in animals
Glycogen constitutes up to 10% of liver massand 1-2% of muscle mass
Glycogen is stored energy for the organism Only difference from starch: number of
branches Alpha(1,6) branches every 8-12 residues Like amylopectin, glycogen gives a red-violet
color with iodine
Structural Polysaccharides
Composition similar to storage polysaccharides,but small structural differences greatlyinfluence properties
Cellulose is the most abundant naturalpolymer on earth Cellulose is the principal strength and support
of trees and plants
Cellulose can also be soft and fuzzy - in cotton
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
97/127
6/13/11
97
Biochemistry for the MED Boards
(a) Amylose, composed exclusively of the relatively bent (14) linkages, prefers toadopt a helical conformation, whereas (b) cellulose, with (14)-glycosidic linkages, can
adopt a fully extended conformation with alternating 180 flips of the glucose units. Thehydrogen bonding inherent in such extended structures is responsible for the great
strength of tree trunks and other cellulose-based materials.
Structural Polysaccharides
Composition similar to storage polysaccharides,but small structural differences greatlyinfluence properties
Beta(1,4) linkages make all the difference! Strands of cellulose form extended ribbons
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
98/127
6/13/11
98
Biochemistry for the MED Boards
The structure ofcellulose, showing
the hydrogenbonds (blue)
between thesheets, whichstrengthen the
structure.Intrachain
hydrogen bonds
are in red andinterchain
hydrogen bondsare in green.
Other Structural Polysaccharides
Chitin - exoskeletons of crustaceans, insectsand spiders, and cell walls of fungi
similar to cellulose, but C-2s are N-acetylcellulose strands are parallel, chitins can be
parallel or antiparallel
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
99/127
6/13/11
99
Biochemistry for the MED Boards
Like cellulose, chitin,mannan, and poly(D-
mannuronate) formextended ribbons and
pack together efficiently,taking advantage ofmultiple hydrogen
bonds.
Biochemistry for the MED Boards
Glycosaminoglycans areformed from repeating
disaccharide arrays.Glycosaminoglycans are
components of theproteoglycans.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
100/127
6/13/11
100
Characteristics of GAGsGAG Localization Comments
Hyaluronate
synovial fluid, vitreous
humor,ECM of loose connective
tissue
large polymers, shock
absorbing
Chondroitin sulfate cartilage, bone, heart valves most abundant GAG
Heparan sulfatebasement membranes,
components of cell surfaces
contains higher acetylated
glucosamine than heparin
Heparin
component of intracellular
granules of mast cellslining the arteries of the
lungs, liver and skin
more sulfated than heparan
sulfates
Dermatan sulfateskin, blood vessels, heart
valves
Keratan sulfate
cornea, bone,
cartilage aggregated withchondroitin sulfates
What Are Glycoproteins, and How Do They
Function in Cells?
Many structures and functions!
May be N-linked or O-linked N-linked saccharides are attached via the
amide nitrogens of asparagine residues O-linked saccharides are attached to
hydroxyl groups of serine, threonine orhydroxylysine
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
101/127
6/13/11
101
Biochemistry for the MED Boards
The carbohydrate moieties ofglycoproteins may be linked to the
protein via (a) serine or threonine
residues (in the O-linked
saccharides) or(b) asparagine
residues (in the N-linked
saccharides). (c) N-Linked
glycoproteins are of three types:
high mannose, complex, and
hybrid, the latter of which
combines structures found in the
high mannose and complex
saccharides.
Blood Group Antigens
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
102/127
6/13/11
102
Blood Group Antigens
Lipids
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
103/127
6/13/11
103
Classes of Lipids
All biological lipids are amphipathic
Fatty acids Triacylglycerols Glycerophospholipids Sphingolipids Waxes Isoprene-based lipids (including steroids)
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
104/127
6/13/11
104
Biochemistry for the MED Boards
The structures of some typical fatty acids. Note that most natural fatty acids contain aneven number of carbon atoms and that the double bonds are nearly always cis and
rarely conjugated.
Triacylglycerols
Also called triglycerides
A major energy source for many organisms Why?
Most reduced form of carbon in natureNo solvation neededEfficient packing
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
105/127
6/13/11
105
Biochemistry for the MED Boards
Triacylglycerols are formed from glycerol and fatty acids.
Triacylglycerols - II
Other advantages accrue to users oftriacylglycerols
InsulationEnergy without nitrogenMetabolic water
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
106/127
6/13/11
106
Glycerophospholipids
Glycerophospholipids are phospholipidsbut not necessarily vice versa
Biochemistry for the MED Boards
Phosphatidic acid, the parent compound for glycerophospholipids.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
107/127
6/13/11
107
Biochemistry for the MED Boards
Structures of several
glycerophospholipids andspace-filling models of
phosphatidylcholine,phosphatidylglycerol, andphosphatidylinositol.
Ether Glycerophospholipids
An ether instead of an acyl group at C-1
Plasmalogens are ether glycerophospholipids inwhich the alkyl chain is unsaturated
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
108/127
6/13/11
108
Biochemistry for the MED Boards
A 1-alkyl 2-acyl-phosphatidylethanolamine (an ether glycerophospholipid).
Ether Glycerophospholipids
Platelet activating factor (PAF) is an etherglycerophospholipid
PAF is a potent biochemical signal moleculeNote the short (acetate) fatty acyl chain at theC-2 position in PAF
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
109/127
6/13/11
109
Biochemistry for the MED Boards
The structure of1-alkyl 2-acetyl-phosphatidylcholine, also known as platelet activatingfactor or PAF.
Biochemistry for the MED Boards
The structure and a space-filling model of a choline
plasmalogen.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
110/127
6/13/11
110
Sphingolipids
Base structure is sphingosine
Sphingosine is an 18-carbon amino alcoholCeramides are amide linkages of fatty acids tothe nitrogen of sphingosine
Glycosphingolipids are ceramides with one ormore sugars in beta-glycosidic linkage at the 1-hydroxyl group
Biochemistry for the MED BoardsFormation of an amide linkage between a fatty acid and sphingosine produces aceramide.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
111/127
6/13/11
111
Sphingolipids
Glycosphingolipids with one sugar arecerebrosides
Gangliosides - ceramides with 3 or moresugars, one of which is a sialic acid
Biochemistry for the MED Boards
A structure and a space-
filling model of a cholinesphingomyelin formed from
stearic acid.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
112/127
6/13/11
112
Biochemistry for the MED Boards
The structure of a
cerebroside. Note thesphingosine backbone.
Biochemistry for the MED BoardsThe structures of several important gangliosides. Also shown is a space-filling model ofganglioside GM1.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
113/127
6/13/11
113
Waxes
Esters of long-chain alcohols with long-chainfatty acids
Highly insoluble Animal skin and fur are wax-coated Leaves of many plants Bird feathers
Biochemistry for the MED Boards
Figure 8.15 An exampleof a wax. Oleoyl alcohol
is esterified to stearicacid in this case.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
114/127
6/13/11
114
Terpenes
Based on the isoprene structure
Know nomenclature Understand linkage modes All sterols (including cholesterol) areterpene-based molecules Steroid hormones are terpene-based
Biochemistry for the MED Boards
The structure of isoprene (2-methyl-1,3-butadiene) and the structure of head-to-tail andtail-to-tail linkages. Isoprene itself can be formed by distillation of natural rubber, a linear
head-to-tail polymer of isoprene units.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
115/127
6/13/11
115
Biochemistry for the MED Boards
Many monoterpenes are readily recognized by their characteristic flavors or odors(limonene in lemons; citronellal in roses, geraniums, and some perfumes; pinene in
turpentine; and menthol from peppermint, used in cough drops and nasal inhalers). Thediterpenes, which are C20 terpenes, include retinal (the essential light-absorbing pigment in
rhodopsin, the photoreceptor protein of the eye), phytol (a constituent of chlorophyll), andthe gibberellins (potent plant hormones). The triterpene lanosterol is a constituent of woolfat. Lycopene is a carotenoid found in ripe fruit, especially tomatoes.
Biochemistry for the MED Boards
Dolichol phosphate is an initiation point for the synthesis of carbohydrate polymers in animals. The
analogous alcohol in bacterial systems, undecaprenol, also known as bactoprenol, consists of 11isoprene units. Undecaprenyl phosphate delivers sugars from the cytoplasm for the synthesis of cell
wall components such as peptidoglycans, lipopolysaccharides, and glycoproteins. Polyprenyl
compounds also serve as the side chains of vitamin K, the ubiquinones, plastoquinones, and
tocopherols (such as vitamin E).
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
116/127
6/13/11
116
Steroids
Based on a core structure consisting of three6-membered rings and one 5-membered ring,all fused together
Cholesterol is the most common steroid inanimals and precursor for all other steroids inanimals
Steroid hormones serve many functions inanimals - including salt balance, metabolicfunction and sexual function
Biochemistry for the MED Boards
The structure of cholesterol, shown with steroid ring designations and carbon numbering.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
117/127
6/13/11
117
Biochemistry for the MED Boards
The structures of several important sterols derived from cholesterol.
Biochemistry for the MED Boards
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
118/127
6/13/11
118
The Macronutrients and the Energy
They Provide to the Body
Fats and Oils Carbohydrates
1 Cal = 1000 cal
Membranes and Membrane
Transport
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
119/127
6/13/11
119
What Are the Chemical and PhysicalProperties of Membranes?
Structures with many cell functions
Barrier to toxic molecules Help accumulate nutrients Carry out energy transductionFacilitate cell motion Assist in reproduction
Modulate signal transduction Mediate cell-cell interactions
Biochemistry for the MED Boards
Several spontaneously formed lipid structures.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
120/127
6/13/11
120
Lipids Form Ordered Structures
Spontaneously in Water
Hydrophobic interactions all!
Lipid bilayers can form in several waysunilamellar vesicles (liposomes)multilamellar vesicles (Alex Bangham)
Biochemistry for the MED Boards
Drawings of(a) a bilayer, (b) a unilamellar
vesicle, (c) a multilamellar vesicle, and (d) an
electron micrograph of a multilamellar Golgi
structure (X94,000).
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
121/127
6/13/11
121
The Fluid Mosaic Model Describes MembraneDynamics
S. J. Singer and G. L. Nicolson
The phospholipid bilayer is a fluid matrix The bilayer is a two-dimensional solvent Lipids and proteins can undergo rotational and
lateral movement Two classes of proteins:
peripheral proteins (extrinsic proteins)integral proteins (intrinsic proteins)
Biochemistry for the MED Boards
The fluid mosaic model of membrane structure proposed by S. J. Singer and G. L. Nicolson. In
this model, the lipids and proteins are assumed to be mobile, so that they can move rapidly
and laterally in the plane of the membrane. Transverse motion may also occur, but it is much
slower.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
122/127
6/13/11
122
Biochemistry for the MED Boards
Phospholipids are arranged asymmetrically in most membranes, including the human
erythrocyte membrane, as shown here. Values are mole percentages. (After Rothman andLenard, 1977. Science194:1744.)
Biochemistry for the MED Boards
Phospholipids can be flipped across a bilayer membrane by the action of flippase proteins.
When, by normal diffusion through the bilayer, the lipid encounters a flippase, it can be moved
quickly to the other face of the bilayer.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
123/127
6/13/11
123
Membranes Undergo PhaseTransitionsThe "melting" of membrane lipids
Below a certain transition temperature,membrane lipids are rigid and tightly packed
Above the transition temperature, lipids aremore flexible and mobile
The transition temperature is characteristic ofthe lipids in the membraneOnly pure lipid systems give sharp, well-definedtransition temperatures
Biochemistry for the MED Boards
An illustration of the gel-to-liquid crystalline phase transition, which occurs when a membrane
is warmed through the transition temperature, Tm. Notice that the surface area must increaseand the thickness must decrease as the membrane goes through a phase transition. The
mobility of the lipid chains increases dramatically.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
124/127
6/13/11
124
What is Passive Diffusion?
No special proteins needed Transported species simply moves down its
concentration gradient - from high [c] to low[c]
Biochemistry for the MED Boards
Passive diffusion of an
uncharged species
across a membrane
depends only on the
concentrations (C1
and C2) on the two
sides of themembrane.
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
125/127
6/13/11
125
Biochemistry for the MED Boards
The passive diffusion of
a charged species
across a membrane
depends upon the
concentration and also
on the charge of the
particle, Z, and the
electrical potential
difference across the
membrane, Dy.
How Does Facilitated Diffusion Occur?
G negative, but proteins assist Solutes only move in the
thermodynamically favored direction
But proteins may "facilitate" transport,increasing the rates of transport
Two important distinguishing features:solute flows only in the favored directiontransport displays saturation kinetics
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
126/127
6/13/11
126
Biochemistry for the MED Boards
Passive diffusion and facilitated diffusion
may be distinguished graphically. The plots
for facilitated diffusion are similar to plots of
enzyme-catalyzed processes (Chapter 13)
and they display saturation behavior.
How Does Energy Input Drive Active
Transport Processes?
Energy input drives transport
Some transport must occur such that solutesflow against thermodynamic potential
Energy input drives transport Energy source and transport machinery are
"coupled"
Energy source may be ATP, light or aconcentration gradient
-
8/6/2019 BioChem Handouts Part 1 (EAmor)
127/127
6/13/11
The Sodium Pump
aka Na,K-ATPase
Large protein - 120 kD and 35 kD subunits Maintains intracellular Na low and K high Crucial for all organs, but especially for
neural tissue and the brain
ATP hydrolysis drives Na out and K in Alpha subunit has ten transmembrane
helices with large cytoplasmic domain