1
Biochemistry
-the study of
molecular basis of life
Mgr. Marie Brázdová, Ph.D.
brazdovam@vfu.cz, brazdovam@yahoo.com, maruska@ibp.cz
Biofyzikální ústav,
Akademie věd České
republiky, v.v.i.
Královopolská 135
612 65 Brno
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Sylabus
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Literature
 MURRAY,R.K.; GRANNER,D.K.;RODWELL,V.W. Harper´s
Illustrated Biochemistry. Appleton & Lange, 2012.
 T.McKee, J.S.McKEe. Biochemistry. USA, 1996. ISBN 0-697-21159-
2.
 MURRAY,R.K.; GRANNER,D.K.;RODWELL,V.W. Harper´s
Illustrated Biochemistry. Appleton & Lange, 2006. ISBN 07-147885-
X.
 A. L. Lehninger, D. L. Nelson, M. M. Cox. Principles of biochemistry.
USA, 2005. ISBN 0716743396.
 Color Atlas of Biochemistry, Second edition, revised and enlarged, J.
Koolman, KH Roehm; ISBN-13: 978-1-58890-247-4, ISBN-10: 1-
58890-247-1
 J. Tomandl Biochemistry I Seminars, 2012
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The exam from Biochemistry:
conditions for exam
1. credit from practical course
(100% presence, credit test 80%)
2. preparation of „Seminars from Biochemistry“ (download to Moodle)
3. 60% of presence on lectures, 60% of week tests
Exam: 2 parts
- test (60% limit), majority question from „Seminars from Biochemistry,
formulas of AA, carbohydrates, vitamins, hormones, lipids, base of
NA…..
- oral examination
from A (90-95% of test)
B (90-80%), C(90-80%), D (80-70%, E (70-60%)
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Biochemistry
 Biochemistry is the study of the molecular basis of life.
 Lying at the interface between chemistry and biology,
biochemistry
 is concerned with the structure and interaction of proteins,
nucleic acids, and other biomolecules as related to their
function in biological systems.
 As one of the most dynamic areas of science,
 biochemistry has led to improved medicines and diagnostic
agents, new ways of controlling disease, and greater
understanding of the chemical factors that control our general
health and well-being.
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Biochemistry and Medicine
 Examples of two way
street connectiong
biochemistry and
medicine,
 Knowledge of the
biochemsitry –
understending of
diseases
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Central principes:
1. Cellular foundation: Cells – highly organized
structural basic of all living organism
2. Chemical foundation:
- Living processes – thousand chemical reaction,
regulation and integration – maintenance of live
- Reaction pathways (glycolysis) –all organism
3. Physical foundation: All organism utilize the same
types of molecules (carbohydrates, lipids, proteins,
nucleic acids)
4. Genetic foundation: The instruction for growth,
development, reproduction – nucleic acids
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Prokaryotic cells
-Bacteria, mostly unicellular
- cell size 1-10 mm
-Cytomplasmatic membrane,
cell wall
-No membrane organene
(subcellular comartmentation)
-No separated nucleus
-Circular DNA (mainly)
-Ribosome size 70S
-Cell division
-DNA without histones
-Protein synthesis events –
cytomplasm
-Respiration enzymes – in
plasmatic membrane
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animal plant
Eukaryotic cells – variety of membrane organelles
10-20 mm, but upto 150mm-Unicellular organism, Multicellular organism
- Cells in tissues, organs –specialized functions
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Animal cell
Eukaryotic cells – variety of membrane organelles
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The differences between the eukaryotic
and prokaryotic cells
 Prokaryotic organisms are simpler than eukaryotic organisms - that is probably the main difference that
must be taken into account.
 Among prokaryotic organisms belong unicellular organisms such as bacteria and cyanobacteria. Size
of the cell is mostly in the range 1 to 10 microns.
 Around a cell can be found at the cytoplasmic membrane and the cell wall stronger. Since the cell is
bounded by a cell wall contains cytoskeleton. The internal contents of the cell is further divided in any
way, because in prokaryotes are not talking about compartmentalization.
 Genetic information is stored in prokaryotes the circular DNA. Transcription and translation take place
in the cytoplasm, translation, specifically on ribosomes, having a size 70S.
Enzymes cellular respiration are stored at the cytoplasmic membrane.
Among the eukaryotic organisms are those which are composed of eukaryotic cells - these are
multicellular organisms, such as fungi, plants and animals.
Eukaryotic cells are larger than prokaryotic - average size is 10 to 20 micron, although some may reach
the size of 150 microns.
 On the surface of a cell is the cell membrane, cytoskeleton maintains cell shape. Similar membranes
such as those on the surface, can also be found in cell organelles, which are thus separated from the
internal environment of the cell forming the cytosol.
 Genetic information is stored in the core of the fiber in the form of DNA molecules (together with proteins
named histones produces bodies - chromosomes). DNA synthesis occurs in the nucleus, as well as
transcription. T
 ranslation takes place in the cytosol or in the smooth endoplasmic reticulum membrane, but in both
cases the size 80S ribosomes.
Enzymes cellular respiration are deposited on the inner membrane of mitochondria.
The above summarized in the following table:
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Differences between prokaryotic and
eukaryotic cells
Feature Prokyryotic cells Eukaryotic cell
Organisms Bacterie, cyanobacteria, unicellular Protozoa, fungi, plants, animals, multicellular
Cell size (uM) 1 – 10 µm 10 – 20 µm
Separated nucleus No Yes
Subcellular organels No Yes
Character of Chromosomes Circular DNA Linear DNA
Ribosome size 70S 80S
Presence of cytoskeleton No Yes
Cell division Lateral/binary fission Mitosis
DNA Free Connected with protiens (histones)
Protein synthesis events In cytoplasm Cytoplasm, ER
Location of respiratory enzymes
In plasmatic membrane In mitochondrial membrate (inner)
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Eukaryotic NUCLEUS
 is a membrane-enclosed organelle found in eukaryotic cells.
 It contains most of the cell's genetic material, organized as multiple long linear DNA
molecules in complex with a large variety of proteins, such as histones, to form
chromosomes.
 The genes within these chromosomes are the cell's nuclear genome. The function of
the nucleus is to maintain the integrity of these genes and to control the activities of
the cell by regulating gene expression—the nucleus is, therefore, the control center
of the cell.
 The main structures making up the nucleus are the nuclear envelope, a double
membrane that encloses the entire organelle and isolates its contents from the
cellular cytoplasm, and the nucleoskeleton (which includes nuclear lamina), a
network within the nucleus that adds mechanical support, much like the
cytoskeleton, which supports the cell as a whole. Because the nuclear membrane is
impermeable to large molecules, nuclear pores are required that regulate nuclear
transport of molecules across the envelope.
 The pores cross both nuclear membranes, providing a channel through which larger
molecules must be actively transported by carrier proteins while allowing free
movement of small molecules and ions.
 Movement of large molecules such as proteins and RNA through the pores is
required for both gene expression and the maintenance of chromosomes.
 The interior of the nucleus does not contain any membrane-bound sub
compartments, its contents are not uniform, and a number of sub-nuclear bodies
exist, made up of unique proteins, RNA molecules, and particular parts of the
chromosomes.
 The best-known of these is the nucleolus, which is mainly involved in the assembly
of ribosomes. After being produced in the nucleolus, ribosomes are exported to the
cytoplasm where they translate mRNA.
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Eukaryotic NUCLEUS
 Genetic information
 DNA with histones
 Metabolism:
- replication of DNA,
- synthesis of RNA,
- RNA processing
- protein biosynthesis
- RNA transport
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 The cell membrane (also known as the plasma membrane or
cytoplasmic membrane) is a biological membrane that
separates the interior of all cells from the outside environment.
 The cell membrane is selectively permeable to ions and organic
molecules and controls the movement of substances in and out
of cells.[3]
 The basic function of the cell membrane is to protect the cell from
its surroundings. It consists of the phospholipid bilayer with
embedded proteins.
 Cell membranes are involved in a variety of cellular processes
such as cell adhesion, ion conductivity and cell signalling and
serve as the attachment surface for several extracellular
structures, including the cell wall, glycocalyx, and intracellular
cytoskeleton. Cell membranes can be artificially reassembled
Cell membranes:
- plasmatic membrane
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Cell membranes:
- plasmatic membrane
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Cytoplasm
 Cytoplasm form a uniform environment in
which the other cellular organelles, located
between them and the cell wall.
 Its main component is water in which is
located a number of other substances (from
simple inorganic substances to complex
enzyme complexes).
 Important role in cell metabolism and
distribution of the ions.
 In the cytoplasm are the cations K +, Mg2 +,
Na +, anions then phosphates, sulfates,
anionic proteins (proteins) and
bicarbonates.
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Mitochondria
 Mitochondria are semi-autonomous organelles that contain their own DNA,
own proteosynthetic apparatus and are wrapped in a double membrane.
 The outer membrane is relatively high penetrability, the inner membrane is
almost impermeable and therefore contains a number of protein carriers, which
allow transfer of the necessary substances.
 Besides the transporters are located inner mitochondrial membrane as
well as enzymes of the respiratory chain and ATP-synthase enzyme,
which occurs aerobic ATP formation phosphorylation.

The material filling the content of mitochondria is called the mitochondrial
matrix. It takes place in the series of important events, such as the Krebs
cycle, urea synthesis, heme synthesis, synthesis of ketones, β oxidation
of fatty acids ...
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The endoplasmic reticulum

The endoplasmic reticulum is composed of a
system of cisterns and vesicles.
 We distinguish between smooth ER (mainly
consisting of vesicles on the surface is not bound
ribosomes) and rough ER (composed mainly
tanks, are located on the surface of ribosomes).
 In muscle cells, the ER is called sarcoplasmic
reticulum, and contains in its vesicles large
amount of calcium ions.
The rough ER occurs desaturation of fatty
acids or hydroxylation various other
substances (eg. Xenobiotics). Both types of
reactions are involved in cytochrome P-450
(CYP).
 smooth ER (mainly consisting of vesicles on the
surface is not bound ribosomes-
proteosynthesis)
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Golgi apparatus
 Golgi apparatus consisting of
tanks and transport vesicles.
 This is a polarized organelle - we
can distinguish the trans-side
(which are received by agents especially
proteins - for editing
and roztřízení) and cis-side on
which these substances are also
released.
 Part of the cellular endomembrane
system, the Golgi apparatus
packages proteins inside the cell
before they are sent to their
destination; it is particularly
important in the processing of
proteins for secretion.
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Peroxisomes
Peroxisomes are coated membrane vesicles,
which are intended primarily for the disposal
of hydrogen peroxide.
They contain the enzyme catalase, which is
responsible for the two types of reactions:
a) the decomposition of hydrogen peroxide
2 H2O2 → 2 H2O + O2
b) the use of hydrogen peroxide to oxidize the
substrate
RH2 + H2O2 → 2 H2O + R
Reactions of type b) is for example used for the
degradation of ethanol in the event that it is
too much in the organism and enzyme
alcohol dehydrogenase has not worked:
Ethanol + H2O2 → 2 H2O + acetaldehyde
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Lysosomes
 Lysosomes are organelles of the cell digestion.
 In its membrane comprises a hydrogen pump, which is involved in
maintaining an acidic pH within them.
 Distinguish between primary and secondary lysosomes.
 Primary are those that have not participated in the digestion process,
and do not contain remnants of organelles, proteins etc.., And their
enzymes have not yet been used.
 Secondary lysosomes are those that are already involved in digestion.
Most enzymes found in lysosomes, belongs to the group of
hydrolases, and the cleavage of various bonds on different molecules.
 They are structurally and chemically spherical vesicles containing
hydrolitic enzymes, which are capable of breaking down virtually all
kinds of biomolecules, including proteins, nucleic acids, carbohydrates,
lipids, and cellular debris. They are known to contain more than fifty
different enzymes which are all active at an acidic environment of about
pH 5.
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The enzyme - type bonds
• α-glucosidase cleaves α-glycosidic linkage between the glucosamine
• β-galactosidase cleaves the β-glycosidic linkage between galactose
• Hyaluronidase cleaves a bond between molecules of hyaluronic acid
• arylsulphatase cleaves the bond sulfoesterovou
• Lysozyme cleaves the glycosidic bond
• cathepsin cleave a peptide bond (the protease)
• collagenase cleaves the triple helix collagen chain
• elastase cleaves a peptide bond (the protease)
• ribonuclease cleaves ribonucleotides diester linkage between
• lipase cleaves the ester bond between glycerol and fatty acids
• phosphatase cleaves the ester linkage (cleaves phosphate)
• ceramidasa cleave the ester bond between the ceramide, and fatty acid
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The cytoskeleton
 The cytoskeleton is a structure that
contributes to the maintenance of cell
shape, cell division and
movement within the cell.
 It consists of three main types of
fiber:
a) microfibrils
b) microfilaments
c) intermediate filaments
 The microfibrils are used dynein
and kinesin proteins that serve as
cell engines and can move along the
fiber (thus allowing intracellular
movement).
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The cytoskeleton The cytoskeleton of eukaryotes (including human and all animals
cells) has three major components:
 microfilaments composed of the protein actin and
 microtubules composed of the protein tubulin are present in all
eukaryotic cells.[2]
 By contrast intermediate filaments, which have more that 60
different building block proteins have so far only been found in
animal cells (apart from one non-eukaryotic bacterial intermediate
filament crescentin).[4]
 The complexity of the eukaryotic cytoskeleton emerges from the
interaction with hundreds of associated proteins like molecular
motors, crosslinkers, capping proteins and nucleation promoting
factors.[2][3]
 There is a multitude of functions the cytoskeleton can perform: It
gives the cell shape and mechanical resistance to deformation;[1]
through association with extracellular connective tissue and other
cells it stabilizes entire tissues;[1][4] it can actively contract, thereby
deforming the cell and the cell's environment and allowing cells to
migrate;[3] it is involved in many cell signaling pathways; it is
involved in the uptake of extracellular material (endocytosis);[5] it
segregates chromosomes during cellular division;[1] it is involved in
cytokinesis - the division of a mother cell into two daughter cells;[2]
it provides a scaffold to organize the contents of the cell in space
[3] and for intracellular transport (for example, the movement of
vesicles and organelles within the cell);[1] it can be a template for
the construction of a cell wall.[1] Furthermore, it forms specialized
structures such as flagella, cilia, lamellipodia and podosomes.
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Cytoplasm is organized by the cytoskeleton
is highly dynamic
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Comparison -Cytoskeleton types
Cytoskeleton
type[8]
Diameter
(nm)[9] Structure Subunit examples[8]
Microfilament
s
6 double helix actin
Intermediate
filaments
10 two anti-parallel helices/dimers, forming tetramers
vimentin (mesenchyme)
glial fibrillary acidic
protein (glial cells)
neurofilament proteins
(neuronal processes)
keratins (epithelial cells)
nuclear lamins
Microtubules 23
protofilaments, in turn consisting of tubulin
subunits in complex with stathmin[10] α- and β-tubulin
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Localization of metabolic processes

We continue to focus on eukaryotic cell. They occur in the
organism in many types - each type is designed to perform
different functions, there are other active enzymes like.
 Cells produce a single type of tissue, which are also specialized
to perform certain functions. The following table lists some of the
metabolic process, and cells which take place:
The Process Where to find
glycogen synthesis hepatocytes, muscle cells
oxygenation of hemoglobin lung cells
synthesis of adrenaline cells of adrenal medulla
urea synthesis hepatocytes
lipid deposition adipocyte
actin and myosin synthesis muscle cells
Synthesis of the insulin β-cells of the islets of Langerhans
conjugation of toxic substances hepatocytes
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Many Important Biomolecules
are Polymers
• Biopolymers - macromolecules created by joining many
smaller organic molecules (monomers)
• Condensation reactions join monomers
(H2O is removed in the process)
• Residue - each monomer in a chain
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Molecular Organisation of a cell
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2. Chemical Foundations
 Biochemistry aims to explain biological form and function in chemical
terms.
 Composition of living matter – C, O, N, P (99%)
- 30 elements are essential
- trace elements – Fe hemoglobin (0.3%)
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Biomolecules
 Organic chemistry is the study of Carbon compounds.
 Organic compounds are compounds composed primarily of a
Carbon skeleton.
 All living things are composed of organic compounds.
 Are Compounds of Carbon with a
Variety of Functional Groups
Organic Chemistry
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Carbon can form immensely diverse
compounds, from simple to complex.
Methane with 1 Carbon
atom
DNA with tens of Billions of
Carbon atoms
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Tetrahedral
structure
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Hydrocarbons in biochemistry
 Most biomolecules are derivated from hydrocarbons
 Nonpolar (bonding electrones are shared equally between
atoms), in water-insoluble, hydrophobic
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Major classes of small biomolecules
 Amino acids
 Sugars
 Fatty acids
 Nucleotides
TEST
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 Just like cells are building blocks of tissues likewise molecules are building
blocks of cells.
 Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-
molecules)
 Water constitutes 50-95% of cells content by weight.
 Ions like Na+, K+ and Ca+ may account for another 1%
 Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)
 Infinite variety of molecules contain C.
 Most bio-molecules considered to be derived from hydrocarbons.
 The chemical properties of organic bio-molecules are determined by their
functional groups. Most bio-molecules have more than one.
Bio-molecules
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Biomolecules – Structure
 Building block
 Simple sugar
 Amino acid
 Nucleotide
 Fatty acid
 Macromolecule
 Polysaccharide
 Protein (peptide)
 RNA or DNA
 Lipid
Anabolic
Catabolic
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Important reaction types in biochemical
processes
 Nucleophilic substitution reaction
 Elimination reaction
 Isomerization reaction
 Oxidation-reduction reaction
 Hydrolysis reaction
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Nucleophilic substitution reaction
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Elimination
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Izomerization
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Oxido-reduction reaction
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Hydrolysis reactions
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Non covalent interactions
 Coherence of cells and their interaction with each other between
molecules (eg. interaction between molecules and receptor molecules
and enzymes, etc.)
 And similar interactions are based on non covalent interactions The
most important non covalent interactions are:
hydrogen bonds
electrostatic interactions
hydrophobic interactions
Their main use in various situations described by the following table:
Structure / system prevailing type of non-covalent interactions :
Proteins: Structure secondary hydrogen bonding
Proteins: the tertiary structure hydrophobic and electrostatic interactions
Proteins: Structure quaternary electrostatic interactions
DNA hydrogen bonds
Phospholipid bilayer hydrophobic interactions
Binding of the enzyme-substrate electrostatic interactions
Binding of antibody-antigen electrostatic interactions
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Protein structure
Description
The amino acid sequence
Helices and Sheets
Disulfide bridges
Multiple polypeptides connect
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Biomolecules – Structure
 Building block
 Simple sugar
 Amino acid
 Nucleotide
 Fatty acid
 Macromolecule
 Polysaccharide
 Protein (peptide)
 RNA or DNA
 Lipid
Anabolic
Catabolic
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Linking Monomers
Cells link monomers by a process
called dehydration synthesis
(removing a molecule of water)
This process joins two sugar monomers
to make a double sugar
Remove
H
Remove OH
H2O Forms
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Breaking Down Polymers
 Cells break down
macromolecules by
a process called
hydrolysis (adding a
molecule of water)
Water added to split a double sugar
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Sugars
 Carbohydrates most abundant organic molecule
found in nature.
 Initially synthesized in plants from a complex series
of reactions involving photosynthesis.
 Basic unit is monosaccharides.
 Monosaccharides can form larger molecules e.g. glycogen,
plant starch or cellulose.
Functions
 Store energy in the form of starch (photosynthesis in
plants) or glycogen (in animals and humans).
 Provide energy through metabolism pathways and cycles.
 Supply carbon for synthesis of other compounds.
 Form structural components in cells and tissues.
 Intercellular communications
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Monosaccharides -Polysaccharides
Glycosidic bonds connecting
glucose residues are in red
Glucose - Cellulose
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Fatty acids - Lipids
 Are monocarboxylic acid contains even number C atoms
 Two types: saturated (C-C sb) and unsaturated (C-C db)
 Fatty acids are components of several lipid molecules.
 E,g. of lipids are triacylglycerol, steriods (cholestrol, sex
hormones), fat soluble vitamins.
Functions
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones
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Triglyceride
Glycerol Fatty Acid Chains
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Structure of a biological membrane
• A lipid bilayer with associated proteins
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Steroids
The carbon skeleton of
steroids is bent to form 4
fused rings
Cholesterol is the
“base steroid” from
which your body
produces other
steroids
Estrogen &
testosterone are also
steroids
Cholesterol
Testosterone
Estrogen
Synthetic Anabolic Steroids are variants of testosterone
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Nucleic Acids
Store hereditary information
Contain information for making all the
body’s proteins
Two types exist --- DNA & RNA
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Amino acids - Proteins:
 Amino acids:
• Building blocks of proteins.
• R Group (side chains) determines the
chemical properties of each amino acids.
• Also determines how the protein folds and
its biological function.
• Functions as transport proteins, structural
proteins, enzymes, antibodies, cell
receptors.
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Proteins as Enzymes
 Many proteins act as biological catalysts or enzymes
Thousands of different enzymes exist in the body
Enzymes control the rate of chemical reactions by
weakening bonds, thus lowering the amount of
activation energy needed for the reaction ->
Catalysator
-> No not interfere with the equilibrium of reaction
-> Enzymes are reusable !!!!
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Enzymes:
• Active site - a cleft or groove in an enzyme that binds the
substrates of a reaction
Egg white lysozyme
The nature and arrangement of amino acids in the
active site make it specific for only one type of
substrate. (accepts just one enaniomer)
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Macromolecules
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Macromolecules
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Concepts of Life
Life is characterized by
 Biological diversity: lichen, microbes, jellyfish,
sequoias, hummingbirds, manta rays, gila monsters,
& you
 Chemical unity: living systems (on earth) obey
the rules of physical and organic chemistry – there
are no new principles
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Life needs 3 things:
(1) ENERGY, which it must know
how to:
 Extract
 Transform
 Utilize
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The Energetics of Life
• Photosynthetic
organisms capture
sunlight energy and use
it to synthesize organic
compounds
• Organic compounds
provide energy for all
organisms
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Using toxic O2 to generate energy
2 H2O  O2 + 4e- + 4H+ (photosynthesis)
Glucose + 6O2  6CO2 + 6H2O + Energy
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Glycolysis: the preferred way for the
formation of ATP
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Life needs (2) SIMPLE MOLECULES,
which it must know how to:
 Convert
 Polymerize
 Degrade
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Life needs (3) CHEMICAL MECHANISMS,
to:
 Harness energy
 Drive sequential chemical reactions
 Synthesize & degrade macromolecules
 Maintain a dynamic steady state
 Self-assemble complex structures
 Replicate accurately & efficiently
 Maintain biochemical “order” vs outside
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Trick #1: Life uses chemical coupling to drive
otherwise unfavorable reactions
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Trick #2: Life uses enzymes to speed up
otherwise slow reactions
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How does an enzyme do it,
thermodynamically?
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How does an enzyme do it, mechanistically?
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Chemical reaction types encountered in biochemical
processes
1. Nucleophilic Substitution
 One atom of group substituted for another
2. Elimination Reactions
 Double bond is formed when atoms in a molecule is removed
3. Addition Reactions:
 Two molecules combine to form a single product.
 A. Hydration Reactions
 Water added to alkene > alcohol (common addition pathway)
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4. Isomerization Reactions.
 Involve intramolecular shift of atoms or groups
5. Oxidation-Reduction (redox) Reactions
 Occur when there is a transfer of e- from a donor to an
electron acceptor
6. Hydrolysis reactions
 Cleavage of double bond by water.
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Summary of Key Concepts
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Biochemical Reactions
 Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity)
a. Anabolism- energy requiring biosynthetic pathways
b. Catabolism- degradation of fuel molecules and the production of
energy for cellular function
 All reactions are catalyzed by enzymes
 The primary functions of metabolism are:
a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO
c. Removal of waste products
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Even though thousands of pathways sound very
large and complex in a tiny cell:
 The types of pathways are small
 Mechanisms of biochemical pathways are simple
 Reactions of central importance (for energy production &
synthesis and degradation of major cell components) are
relatively few in number
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Energy for Cells
 Living cells are inherently unstable.
 Constant flow of energy prevents them from becoming
disorganized.
 Cells obtains energy mainly by the oxidation of bio-molecules
(e- transferred from 1 molecule to another and in doing so
they lose energy)
 This energy captured by cells & used to maintain highly
organized cellular structure and functions
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