Chemistry for
biology
Dr. Öykü GÖNÜL GEYİK
oyku.geyik@istinye.edu.tr
PSY106
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What is biochemistry?
Structure
Energetics
Cell
Synthesis
Reactions
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Terminology
o Biochemistry is the branch of science that explores the chemical processes within
and related to living organisms. It is a laboratory-based science that brings together
biology and chemistry. By using chemical knowledge and techniques, biochemists
can understand and solve biological problems.
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http://natural-sciences.nwu.ac.za/biochemistry
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Elements of Life
• Periodic table contains 118 elements
• 92 elements are found in nature
• 28 elements are essential for human body
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Elements in the
Human Body
Present in human
body at mg levels
Elements in the
human body
%99’dan fazlası
Present in human
body at µg levels
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Chemical components of the cell
Inorganic Compounds: Water and elements
Organic Compounds: Carbohydrates, lipids, proteins
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o Organic substances
Inorganic substances
• Carbohydrates
• Water
• Proteins, amino acids, peptides
• Enzymes
• Lipids
• Nucleotides and nucleic acids
• Hormones
• Vitamins
• ATP
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They are found in
the structure of
living things, they
are not produced.
They are taken from
nature ready.
• Minerals
• Salt
• Acid
• Base
Carbon and Its Functional Groups
• Many functional groups can attach to carbon skeleton
• esters, amino, carboxyl, phosphate groups
• Very large molecules are called macromolecules (or “polymers”
if all the monomer subunits are similar)
• Isomers have the same molecular formulas but different
structures (glucose & fructose are both C6H12O6)
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Water
• Is the most important and abundant inorganic compound in all living
systems.
• Water’s most important property is polarity, the uneven sharing of valence
electrons.
• Enables reactants to collide to form products.
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Polar Water Molecules
• In a solution the solvent dissolves the solute.
• Substances which contain polar covalent bonds
and dissolve in water are hydrophilic, while
substances which contain non-polar covalent
bonds are hydrophobic.
• The polarity of water and its bent shape allow it
to interact with several neighboring ions or
molecules.
• Water’s role as a solvent makes it essential for
health and survival.
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Body Fluid Compartments
o In lean adults, body fluids constitute 55% of female and 60%
of male total body mass
• Intracellular fluid (ICF) inside cells
• About 2/3 of body fluid
• Extracellular fluid (ECF) outside cells
• Interstitial fluid between cell is 80% of ECF
• Plasma in blood is 20% of ECF
• Also includes lymph, cerebrospinal fluid, synovial fluid, aqueous
humor, vitreous body, endolymph, perilymph, and pleural,
pericardial, and peritoneal fluids
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Types of Chemical Reactions
• Synthesis reactions -- Anabolism
• Decomposition reactions-- Catabolism
• Exchange reactions
• Reversible reactions
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Metabolism
Inorganic Compounds and Solutes
• Inorganic compounds usually lack carbon and are simple molecules; whereas
organic compounds always contain carbon and hydrogen, usually contain
oxygen, and always have covalent bonds.
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3 Common Mixtures
A mixture is a combination of elements or compounds that are
physically blended together but are not bound by chemical bonds.
o Solution: a substance called the solvent dissolves another substance called
the solute. Usually there is more solvent than solute in a solution.
o A colloid differs from a solution mainly on the basis of the size of its
particles with the particles in the colloid being large enough to scatter
light.
o Suspension: the suspended material may mix with the liquid or
suspending medium for some time, but it will eventually settle out.
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Concentration
o The concentration of a molecule is a way of stating the amount of that
molecule dissolved in solution.
o Percent gives the relative mass of a solute found in a given volume of
solution.
o A mole is the name for the number of atoms in an atomic weight of
that element, or the number of molecules in a molecular weight of
that type of molecule, with the molecular weight being the sum of all
the atomic weights of the atoms that make up the molecule.
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Dissociation of Acids, Bases, and Salts
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Concept of pH
o pH scale runs from 0 to 14 (concentration of H+ in
moles/liter)
o pH of 7 is neutral
(distilled water -- concentration of OH- and H+ are equal)
o pH below 7 is acidic ([H+] > [OH-]).
o pH above 7 is alkaline ([H+] < [OH-]).
o pH is a logarithmic scale
Example: a change of two or three pH units
pH of 1 contains 10x10=100 more H+ than pH of 3
pH of 8 contains 10x10x10=1000 more H+ than pH of 11
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The pH Scale
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Maintaining pH: Buffer Systems
o The pH values of different parts of the body are maintained fairly
constant by buffer systems, which usually consist of a weak acid
and a weak base.
• convert strong acids or bases into weak acids or bases.
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Acid-base balance
o Concentration of hydrogen
ions regulated sequentially by
• Chemical buffer systems: rapid;
first line of defense
• Brain stem respiratory centers:
act within 1–3 min
• Renal mechanisms: most
potent, but require hours to
days to effect pH changes
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Chemical Buffer Systems
o
Chemical buffer: system of one or more compounds that act to
resist pH changes when strong acid or base is added
•
1.
2.
3.
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Bind H+ if pH drops; release H+ if pH rises
Bicarbonate buffer system
Phosphate buffer system
Protein buffer system
Acid-base imbalances
• Normal pH range of arterial
blood 7.35-7.45
• Acidosis – blood pH below 7.35
• Alkalosis – blood pH above 7.45
• Major physiological effect of
• Acidosis – depression of synaptic
transmission in CNS
• Alkalosis – overexcitability of CNS and
peripheral nerves
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o Homeostasis
o Maintaining a constant
cellular environment requires
complex metabolic
regulation that coordinates
the use of nutrient pools.
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Biochemistry: A Short Course, Third Edition, John L. Tymoczko, Jeremy M. Berg, Lubert Stryer
• First, the amounts of some
enzymes are controlled by
regulation of the rate of
synthesis and degradation.
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Biochemistry: A Short Course, Third Edition, John L. Tymoczko, Jeremy M. Berg, Lubert Stryer
• Second, the catalytic
activities of many enzymes
are regulated by allosteric
interactions (as in feedback
inhibition) and by covalent
modification.
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Biochemistry: A Short Course, Third Edition, John L. Tymoczko, Jeremy M. Berg, Lubert Stryer
• Third, the movement
of many substrates
into cells and
subcellular
compartments also
is controlled.
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https://doi.org/10.1002/biot.201700052
• The energy charge, which
depends on the relative
amounts of ATP, ADP, and
AMP, plays a role in
metabolic regulation. A highenergy charge inhibits ATPgenerating (catabolic)
pathways, whereas it
stimulates ATP-utilizing
(anabolic) pathways.
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Chemical compositions of extracellular
and intracellular fluids
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Diffusion
• All molecules and ions in the body fluids, including water molecules and
dissolved substances, are in constant motion, each particle moving its
own separate way.
• Diffusion: Continual movement of molecules among one another in
liquids or in gases.
• Transport pathways through the cell membrane and the basic
mechanisms of transport
• Simple diffusion
• Facilitated diffusion
• Active transport
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Osmosis
• Process of net movement of water caused by a concentration difference
of water
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Active transport
• Situation when a cell membrane moves molecules or ions “uphill” against
a concentration gradient (or “uphill” against an electrical or pressure
gradient).
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Isoosmotic, Hyperosmotic, and
Hypoosmotic Fluids
• Solutions with an osmolarity the same as the cell are called isoosmotic,
regardless whether the solute can penetrate the cell membrane
• Hyperosmotic and hypoosmotic refer to solutions that have a higher or lower
osmolarity, respectively, compared with the normal extracellular fluid, without
regard for whether the solute permeates the cell membrane.
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Homeostasis of body fluids
• The maintenance of a
relatively constant volume
and a stable composition
of the body fluids is
essential for homeostasis.
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Macromolecules
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PROTEINS
o They are the most common biological
macromolecules in all cells and in all parts of the
cells.
o There are thousands of different types and sizes in
a single cell.
o Proteins are linear, unbranched polymers consisting
of 20 amino acids encoded by DNA.
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o As a result of the different sequences of these 20 amino acids,
different organisms form products with numerous different biological
activities such as enzymes, hormones, antibodies, carriers, muscle,
feathers, spider webs, horns, mushroom poisons.
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Enzymes
• Catalysts in living cells are called
enzymes.
• Enzymes are highly specific in terms of
the “substrate” with which they react.
• Enzymes are subject to variety of cellular
controls.
• Enzymes speed up chemical reactions by
increasing frequency of collisions,
lowering the activation energy and
properly orienting the colliding
molecules.
Catalysts and chemical reactions
Copyright 2009, John Wiley & Sons, Inc.
Protein Structure
o The polypeptide chain consisting of amino acid residues linked by covalent bonds
(mainly peptide bonds and disulfide bonds) is the primary structure. The most
important aspect of primary structure is the sequence of amino acid residues.
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Structure of Aminoacids
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D and L types of the aminoacids
o The carboxyl group of the amino acid is plotted at
the top to draw as the stereoisomer.
o Side groups are written at down.
o If the amino group remains on the right side of the
molecule, it is L-amino acid and on the left side it is
D-amino acids.
o Human proteins contain only L-amino acids
o In nature, D-amino acids appear in several places.
o For this reason, alanine means L-alanine.
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Only L-amino acids are present in
human proteins.
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Peptide bond formation
o Two amino acids combine to form a peptide bond (amide bond)
o Condensation-type junction, water is out
o The a-carboxyl group of the first amino acid and the a-amino group of the other
amino acid combine
o This type of condensation reaction does not occur spontaneously in the aqueous
medium.
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Properties of Peptide Bond
o They are covalent bonds (strongest).
o They are not degraded when heated or treated with high concentration of proteins
denaturing agents. (High acid or high alkali)
o Partial double bonding. There is no rotation in the bonds that bind C and N atoms.
Peptide bond
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Disulfide bond: Subunits in a protein are generally held together
by disulfide bond. The disulfide bond may also be in the subunit.
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The proteins in the hair contain a disulfide bond. Break the bond, shape it,
and recreate the bond. When you have your hair permed, these operations
are performed respectively.
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Amino acids are classified according to R groups
Amino acids are grouped into 5 main classes according to the properties of the R
groups, in particular their polarity or their tendency to react with water at biological pH.
 Nonpolar, Aliphatic R groups
 Aromatic R Groups
 Polar, Unloaded R Groups
 Positive Charged (Basic) R Groups
 Negative Charged (Acidic) R Groups
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Non-polar, aliphatic R groups
Aromatic R groups
Phenyl ring (light absorption at 240-290 nm)
Indole ring
(280 nm)
Positively charged R groups
Imidazole
ring
Polar, uncharged R groups
Guanidino
group
(urea
synthesis)
Negatively charged R groups
Pyrrole ring
(imino acid)
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Amino acids are classified into 2 main groups:
Essential and non-essential amino acids
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o Essential amino acids cannot be synthesized in the body and must be
taken from outside.
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CARBOHYDRATES
o Carbohydrates are the most important part
of human nutrition.
o About 300 g carbohydrates are taken in our
body per day
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•
•
•
starch (~160 g)
sucrose (~120 g)
lactose (~30 g)
glucose and fructose (~10 g)
o Abundant cellulose, starch and sucrose are
taken with plant nutrients; glycogen and
lactose are taken with animal-sourced foods
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Functions of
carbohydrates
o They are basic energy providers
o They are precursors for the formation of some
other biomolecules
o They lubricate skeletal joints and provide
adhesion between cells
o They function as structural and protective
elements
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Carbohydrates
o Fruit
o Vegetables
o Dairy products
o Grains
o Processed foods
Digestion and metabolic ways vary
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Carbohydrate
metabolism
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CLASSIFICATION OF CARBOHYDRATES
Complex
Simple
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Monosaccharides
Disaccharides
Glucose
Fructose
Galactose
Sucrose
Maltose
Lactose
Polysaccharides
Storage
Structural
Glycogen
Starch
Cellulose
Chitin
Disaccharides: When hydrolyzed, different or the same two
monosaccharides are formed
o Lactose  Glucose- b[1-4] Galactose, sugar of milk
o Sucrose  Glucose – a[1-2] Fructose, sugar of tea
o Maltose  Glucose- a[1-4] Glucose, starch
o Isomaltose  Glucose- a[1-6] Glucose
o Trehalose  Glucose – a[1-1] glucose.
o Cellabiose  Glucose- b[1-4] Glucose
o Laktulose  Galactose- b[1-4] fructose
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o Sugars are linked to each other by an
o-glycosidic bond
o It is a type of covalent bond but easy to
hydrolyse
o An oxygen is shared
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o An animal cell stores
glucose in the form of
glycogen, while the plant
cell stores starch.
o When the energy
requirement increases,
glucose is released from
storage polymers and
used in aerobic or
anaerobic ATP
production.
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LIPIDS
o Amphipathic molecule (ether, benzene chloroform)
o Fatty acids:
• a long hydrocarbon chain (hydrophobic)
• Carboxyl group (hyrophilic) interacts with water
o Properties of fatty acids:
• They are used for energy
• They participate in the structure of the cell
membrane
• They participate in the structure of proteins
• They participate in the structure of hormones and
other messenger molecules
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Functions of lipids in human organism
o Provides energy (2nd place after carbohydrates)
o They are carriers and sources of vitamins A, D, E, and K
o Growth and normal metabolic events
o
o
o
o
o
o
o
o
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It helps to create a sense of saturation
Surrounds organs (support and protection)
Prevents heat loss from the body
Essential fatty acids that cannot be synthesized in the body are taken with fats
It has effects on protein metabolism
It has a positive effect on the nervous system and regulation of the digestive metabolism
Serve as glycolipids, lipoproteins, steroids, vitamins and hormones
Phospholipids are an important component of the cell membrane
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NUCLEIC ACIDS
o The monomer of the nucleic acid polymer is called nucleotide (polymerization of
monomer nucleotides produces nucleic acid)
glycosidic bond
phosphodiester bond
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Questions? Feedback?
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