BIOCHEMISTRY
PRELIMINARY
INTRODUCTION TO BIOCHEMISTRY
Biochemistry
- Chemistry of life
- Study of life processes, structures, mechanisms,
reactions at the molecular level
- Chemistry, Biology, & Genetics
Vitalism Theory
- Idea that substances and processes associated
with living organisms did not behave according
to the known laws of physics and chemistry
- Organic vs. Inorganic
Evidences for Vitalism
- Only living things have a high degree of
complexity
- Only living things extract, transform and utilize
energy from their environment
- Only living things are capable of self assembly
and self replication
Origins of Biochemistry: a challenge to vitalism and…
Famous Dead Scientists
1. Friedrich Wohler (19th century)
- Synthesized urea from inorganic
substance—ammonium cyanate.
2. Eduard Buchner and Hans Buchner (1897)
- found that glucose + dead yeast cells
are still able to undergo fermentation,
demonstrating that reactions can occur
in vitro.
3. Emil Fischer (1894)
- Each enzyme can only catalyze specific
complex molecules called substrates.
- proposed the lock and key theory, which
states that enzymes have a specific
shape that directly correlates to the
shape of the substrate.
4. James Batcheller Sumner
- studied the enzyme urease, which
breaks down urea into ammonia and
carbon dioxide
- An enzyme is protein
5. Gregor Mendel (mid-1900)
- Started describing genes.
- Father of Genetics
6. Oswald Avery, Colin McLeod, Maclyn
McCarty (1944)
- identified DNA as information molecules
7. James Watson (still alive) and Francis Crick
(1953)
- proposed the structure of the DNA
- In 1958 Crick proposed the central
dogma of biology
Central Dogma
- Flow of information
IGANO, CIENNA CHARRISE
- DNA -> RNA (mRNA) -> Protein
- Replication -> Transcription -> Translation
Areas of Biochemistry
- Biomolecules. Structure and function of
biological macromolecules
- Metabolism
- Catabolism: Destructive phase
- Complex substance to subunits
(simpler substance)
- Anabolism: Constructive phase
- From simpler substance to
complex substance
- Molecular Genetics
- How life is replicated
- Regulation of protein synthesis
Objective of Biochemistry
- determine how the collections of inanimate
molecules that constitute living organisms
interact with each other to maintain and
perpetuate life
Scope of Biochemistry
- LIFE. chemistry of living matter in its different
phases of activity, from the smallest
microorganisms such as viruses to the most
complex ones as human
- Virus: has either DNA or RNA
- Cell: has both DNA and RNA
Chemical Reactions Occurring in Living Organism
Oxidation
- gains oxygen or loses hydrogen/electron
⇀ aerobic oxidation – takes place in the
presence of oxygen
⇀ anaerobic oxidation – occurs in the
absence of oxygen
Reduction
- gains hydrogen/electron or loses oxygen
Condensation
- Dehydration synthesis(union)
- Removal of water
1
 TRANSES: BIOCHEMISTRY

Hydrolysis Cell Size

- Lysis = splitting - Most cells are relatively small because as size
- Large molecules broken down increases, volume increases much more rapidly.
- Cell size and shape are related cell functions.
A Scale of Visibility

Transfer Reactions
a. Phosphorylation - addition of phosphate group
b. Transamination - transfer of amino group
c. Acetylation - addition of acyl group
d. Transmethylation - transfer of methyl group
Decarboxylation
- Removal of carboxyl group
Classification of Cells
There are two major types of cells
Uses of Biochemistry - Prokaryotic
The results of biochemical research are used extensively - lacks a nucleus and does not have an
in the world outside the laboratory extensive system of internal membranes
- Agriculture - all bacteria and archaea have this cell
- Pharmacology and Toxicology type
- Medical Sciences - Eukaryotic
- Clinical Chemistry - has a nucleus and has internal
- Nutrition membrane-bounded compartments
- all organisms other than bacteria or
THE CELL AND ITS CHEMISTRY archaea have this cell type

Cells Prokaryotic Cells

- Basic functional and structural unit of life Prokaryotes are the simplest cellular organisms. They
have a plasma membrane surrounding a cytoplasm without
- All living things are composed of cells, cell parts,
interior compartments (some bacteria have additional outer
or cell products layers to the plasma membrane)
- Organisms may be: - Cell wall - comprised of carbohydrates to confer rigid
- Unicellular: prokaryotes structure
- Multicellular: human - Capsule may surround the cell wall
Cell theory - Cytoplasm is uniform with little or no internal support
- All organisms are composed of one or more framework
cells. - Ribosomes (sites for protein synthesis) are scattered
throughout the cytoplasm
- Cells are the smallest living units of all living - Nucleoid region (an area of the cell where DNA is
organisms. localized)
- Cells arise only by division of a previously - not membrane-bounded, so not a true
existing cell. nucleus
- Cells vary in size and shapes. - Flagellum (plural, flagellae) is a threadlike structure
made of protein fibers that extends from the cell
Cell Requirements surface
- may be one or many
- Genetic material
- aids in locomotion and feeding
- Single circular molecule of DNA in - Pilus (plural, pili) is a short flagellum
prokaryotes - aids in attaching to substrates and in
- Double helix located in nucleus in exchanging genetic information between
eukaryotes cells
- Cytoplasm
- Fills cell interior (sugars, amino acids,
proteins, organelles)
- Plasma Membrane
- Encloses the cell

IGANO, CIENNA CHARRISE 2

 TRANSES: BIOCHEMISTRY

The Plasma Membrane

The plasma membrane is conceptualized by the fluid
mosaic model–a sheet of lipids with embedded proteins. The
lipid layer forms the foundation of the membrane. The fat
molecules comprising the lipid layers are called
phospholipids.
- A phospholipid has a polar head and two non- polar
tails
- The polar region contains a phosphate chemical
group and is water-soluble
- The non-polar region is comprised of fatty acids and
is water-insoluble
Eukaryotic Cells
Eukaryotic cells are larger and more complex than
prokaryotic cells. They have a plasma membrane encasing the
cytoplasm, internal membranes form compartments called
organelles. The cytoplasm is semi-fluid and contains a
network of protein fibers that form a scaffold called a
cytoskeleton.
- Nucleus - a membrane-bounded compartment for
DNA that gives eukaryotes (literally, “true-nut”) their
name
- Endomembrane system - gives rise to the internal
membranes found in the cell. Each compartment can
provide specific conditions favoring a particular - A lipid bilayer forms spontaneously whenever a
process. collection of phospholipids is placed in water
- The cells of plants, fungi, and many protists have a
cell wall beyond the plasma membrane
- All plants and many protists contain organelles called
chloroplasts
- Plants contain a central vacuole
- only animal cells contain centrioles

- The interior of the lipid bilayer is completely nonpolar

- no water-soluble molecules can freely cross
through it
- cholesterol is also found in the interior
- it affects the fluid nature of the
membrane
- its accumulation in the walls of
blood vessels can cause plaques
- plaques lead to cardiovascular
disease
- Another major component of the membrane is a
collection of membrane proteins
- some proteins form channels that span the
membrane
- these are called transmembrane
proteins
- other proteins are integrated into the
structure of the membrane
- for example, cell surface proteins
are attached to the outer surface of
the membrane and act as markers
- Proteins are embedded within the lipid bilayer

IGANO, CIENNA CHARRISE 3

 TRANSES: BIOCHEMISTRY
The Endomembrane System
The Nucleus: The Cell’s Control Center
- The nucleus is the command and control center of the
cell
- it also stores hereditary information
- The nuclear surface is bounded by a double-
membrane called the nuclear envelope
- groups of proteins form openings called
nuclear pores that permit proteins and RNA
to pass in and out of the nucleus
- The DNA of eukaryotes is packaged into segments
and associated with protein
- this complex is called a chromosome
- the proteins enable the DNA to be
wound tightly and condense during
cell division
- when the cell is not dividing, the
chromosomes exist as threadlike strands
called chromatin
- protein synthesis occurs when the
DNA is in the chromatin form
- The cell builds proteins on structures called
ribosomes
- ribosomes consist of ribosomal RNA (rRNA)
and several different kinds of proteins
- Ribosomes are assembled in a region of the nucleus
called the nucleolus
IGANO, CIENNA CHARRISE
- The endoplasmic reticulum (ER) is an extensive
system of internal membranes
- some of the membranes form channels and
interconnections
- other portions become isolated spaces
enclosed by membranes
- these spaces are known as
vesicles
- The portion of the ER dedicated to protein synthesis
is called the rough ER
- the surface of this region looks pebbly
- the rough spots are due to embedded
ribosomes
- The portion of the ER that aids in the manufacture of
carbohydrates and lipids is called the smooth ER
- the surface of this region looks smooth
because embedded ribosomes are scarce
- After synthesis in the ER, the newly-made molecules
are passed to the Golgi bodies
- Golgi bodies are flattened stacks of
membranes scattered through the cytoplasm
- their numbers vary depending on the cell
- their function is to collect, package, and
distribute molecules manufactured in the cell
- the Golgi bodies of a cell are collectively
called the Golgi complex
- The ER and Golgi complex function together as a
transport system in the cell
4
 TRANSES: BIOCHEMISTRY
- The Golgi complex also gives rise to lysosomes
- these membrane-bound structures contain
enzymes that the cell uses to break down
macromolecules
- worn-out cell parts are broken down
and their components recycled to
form new parts
- particles that the cell has ingested
are also digested
Organelles That Harvest Energy
- Eukaryotic cells contain energy harvesting organelles
that contain their own DNA
- these organelles appear to have been
derived from ancient bacteria that were
taken up by eukaryotic cells
- these organelles include mitochondria and
chloroplasts
- Mitochondria are cellular powerhouses
- Sites for chemical reactions called oxidative
metabolism
- The organelle is surrounded by two membranes
The Cytoskeleton and Related Structures
- Chloroplasts are the sites of photosynthesis
- The organelle is also surrounded by two membranes
The protein fibers of the cytoskeleton
- Both mitochondria and chloroplasts possess their own
molecule of circular DNA
- They cannot be grown free of the cell
- they are totally dependent on the cells within
which they occur
- The theory of endosymbiosis
- states that some organelles evolved from a
symbiosis in which one cell of a prokaryotic
species was engulfed by and lived inside of
a cell of another species of prokaryote that
was a precursor to eukaryotes
- the engulfed species provided their hosts
with advantages because of special
metabolic activities
- the modern organelles of mitochondria and
chloroplasts are believed to be found in the
eukaryotic descendants of these
endosymbiotic prokaryotes
IGANO, CIENNA CHARRISE
- In addition to the double membranes and circular
DNA found in mitochondria and chloroplasts, there is
a lot of other evidence supporting endosymbiotic
theory
- mitochondria are about the same size as
modern bacteria
- the cristae in mitochondria resemble folded
membranes in modern bacteria
- mitochondrial ribosomes are similar to
modern bacterial ribosomes in size and
structure
- mitochondria divide by fission, just like
modern bacteria
- The cytoskeleton is comprised of an internal
framework of protein fibers that
- anchors organelles to fixed locations
- supports the shape of the cell
- helps organize ribosomes and enzymes
needed for synthesis activities
- The cytoskeleton is dynamic and its components are
continually being rearranged
- Three different types of protein fibers comprise the
cytoskeleton
- Intermediate filaments
- thick ropes of intertwined protein
- Microtubules
- hollow tubes made up of the protein
tubulin
- Microfilaments
- long, slender microfilaments made
up of the protein actin
- Centrioles are complex structures that assemble
microtubules in animal cells and the cells of most
protists
- they occur in pairs
- they are found near the nuclear envelope
- they are composed of microtubules
5
 TRANSES: BIOCHEMISTRY

- Cellular motion is associated with the movement of

actin microfilaments and/or microtubules
- some cells “crawl” by coordinating the - Manufacture
rearrangement of actin microfilaments - Nucleus, ribosomes, RER, SER, Golgi
- some cells swim by coordinating the beating complex
of microtubules grouped together to form - Breakdown
flagella or cilia - Lysosomes, peroxisomes, vacuoles
- Cilia and Flagella are hairlike structures projecting - Energy Processing
from the cell that function to move the cell by their - Chloroplasts, mitochondria
movements - Support, Movement and Communication Between
- Cilium (Cilia) - the short, numerous Cells
appendages - Cytoskeleton, cell walls, extracellular matrix,
- Flagellum (Flagella) – the longer, less junctions
numerous appendages
Transport of Materials
- Passive Transport: does not require energy. Moves
along concentration gradient
- Diffusion
- Osmosis
- Facilitated Diffusion
- Active Transport: requires energy.
- Endocytosis
- Exocytosis

Diffusion and Osmosis

Eukaryotic Cell Surfaces and Junctions
- Cells interact with their environments and with each
other via their surfaces.
- Plant cells are supported by rigid cell walls made
largely of cellulose.
- Plant cells connected by plasmodesmata.
- Animal cells are embedded in an extracellular matrix
consisting mainly of glycoprotein. This matrix is
responsible for binding cells together in tissues.
Diffusion
- Movement of water and nutrients into a cell or
elimination of wastes out of cell is essential for
survival
- This movement occurs across a biological membrane
in one of three ways
- diffusion
- membrane folding
- transport through membrane proteins
- Molecules move in a random fashion but there is a
tendency to produce uniform mixtures
- The net movement of molecules from an area of
higher concentration to an area of lower concentration
is termed diffusion
- Molecules diffuse down a concentration gradient from
higher to lower concentrations
- diffusion ends when equilibrium is reached

IGANO, CIENNA CHARRISE 6

 TRANSES: BIOCHEMISTRY

- The concentration of all molecules dissolved in a Exocytosis

solution is called the osmotic concentration of the
solution
- if the osmotic concentrations of two solutions
is equal, the solutions are each called
isotonic
- if two solutions have unequal osmotic
concentration, the solution with the higher
solute concentration is said to be
hypertonic, and the solution with the lower
solute concentration is said to be hypotonic
- Movement of water by osmosis into a cell causes Chemistry of Life
pressure called osmotic pressure - Inorganic Compounds
- enough pressure may cause a cell to swell - Water
and burst - Gases
- osmotic pressure explains why so many cell - Minerals
types are reinforced by cell walls - Organic Compounds
Osmotic pressure in plants and animal cells - Carbohydrates
**Osmos means to push - Proteins
- Lipids
- Nucleic acids
- Vitamins

Hydrogen Bonds Give Water Unique Properties

- Water is essential for life
- the chemistry of life is water chemistr
- Water is a polar molecule
- water can form hydrogen bonds
- hydrogen bonding confers on water many
different special properties
- Heat Storage
- water temperature changes slowly and holds
temperature well
- Ice Formation
Forms of Endocytosis - few hydrogen bonds break at low
- Phagocytosis is endocytosis of particulate (solid) temperatures
matter. “eat” - water becomes less dense as it
- Pinocytosis is endocytosis of liquid matter. “drink” freezes because hydrogen bonds
stabilize and hold water molecules
farther apart
- High Heat of Vaporization
- water requires tremendous energy to
vaporize because of all the hydrogen bonds
that must be broken
- when water vaporizes, it takes this heat
energy with it, allowing for evaporative
cooling
Ice formation

IGANO, CIENNA CHARRISE 7

 TRANSES: BIOCHEMISTRY
- Water molecules are attracted to other polar
Molecules
- cohesion – when one water molecule is
attracted to another water molecule
- adhesion – when polar molecules other than
water stick to a water molecule
- High polarity
- in solution, water molecules tend to form the
maximum number of hydrogen bonds
- hydrophilic molecules are attracted
to water and dissolve easily in it
- these molecules are also
polar and can form
hydrogen bonds
- hydrophobic molecules are repelled
by water and do not dissolve
- these molecules are
nonpolar and do not form
hydrogen bonds
Water Ionizes
- The covalent bond within a water molecule
sometimes breaks spontaneously
H2O ↔ OH- + H+
- This produces a positively hydrogen ion (H+) and a
negatively charged hydroxide ion (OH-)
- The amount of ionized hydrogen from water in a
solution can be measured as pH
- The pH scale is logarithmic, which means that a pH
scale difference of 1 unit actually represents a 10-fold
change in hydrogen ion concentration
IGANO, CIENNA CHARRISE
- Pure water has a pH of 7
- there are equal amounts of [H+] relative to
[OH-]
- Acid – any substance that dissociates in water
- and increases the [H+]
- acidic solutions have pH values below 7
- Base – any substance that combines with [H+] when
dissolved in water
- basic solutions have pH values above 7
- The pH in most living cells and their environments is
fairly close to 7 (6.9–7.3)
- proteins involved in metabolism are sensitive
to any pH changes
- Organisms use buffers to minimize pH disturbances
- a buffer is a chemical substance that takes
up or releases hydrogen ions
Organic compounds
Biomolecules - associated with living things. Organic
molecules
- Carbohydrates – major source of energy (a.k.a.
sugars)
- Proteins – for tissue repair
- Lipids – constituents of membranes, also a source of
energy (a.k.a. Oils and fats)
- Nucleic Acids – genetic material and for protein
synthesis
CARBOHYDRATES
Carbohydrates
- provide energy through oxidation
- serve as a form of stored chemical energy
- supply carbon for the synthesis of cell components
- form part of the structures of some cells and tissues
- a molecule that contains the elements CHO in a 1:2:1
ratio
- sizes vary (simple and complex carbohydrates)
- building block is simple sugar or monosaccharide
- Carbohydrates or saccharides (saccharon) are
polyhydroxy aldehydes or ketones, or substances that
yield such compounds on hydrolysis
- An aldehyde is an organic compound in
which the carbonyl group is attached to a
carbon atom at the end of a carbon chain. A
ketone is an organic compound in which the
carbonyl group is attached to a carbon atom
within the carbon chain.
Stereochemistry of Carbohydrates
- Two Forms of Glyceraldehyde (enantiomers)—not
the same as each other; one enantiomer cannot be
superimposed on the other. Enantiomers are mirror
images of each other.
- D-glyceraldehyde
8
 TRANSES: BIOCHEMISTRY

- L-glyceraldchyde - The presence of an aldehyde is indicated by

the prefix aldo- and an ketone by the prefix
Chiral Carbons keto-
- any carbon atom which is connected to four different - Properties of Monosaccharides
groups will be CHIRAL, and will have two (Carbohydrates)
nonsuperimposable mirror images (The mirror images - monosaccharides & disaccharides
are called enantiomers) are white crystalline substance;
- An achiral object is identical with (superimposable on) starches are amorphous powder;
its mirror image. cellulose is fibrous
- solubility to ordinary solvents is
2 raised to n Rule inversely proportional to the
- when a molecule has more than one chiral carbon, complexity of their structures
each carbon can possibly be arranged in either the - monosaccharides & disaccharides
right-hand or left-hand form, thus if there are n chiral are sweet; starch and cellulose are
carbons, there are 2n possible stereoisomers tasteless
- Reducing power - the potential or
power of any substance to reduce
another substance. Substance is
able to donate electrons.
- Fermentation - Sugar undergoing
fermentation (with yeast) produces
Fischer Projection ethyl alcohol and carbon dioxide
- are a convenient way to represent mirror images in - Osazone formation - The reaction
two dimensions (oxidation) between three moles of
- Place the carbonyl group at or near the top and the phenylhydrazine and one mole of
last achiral carbon at the bottom aldose produces a crystalline
product known as phenylosazone
- Action of alkalis - Strong alkalies,
like strong acids, decompose the
sugars. This process identifies the
reducing property of sugar
- Action of acids - acid-catalyzed
aldolized glycosides hydrolyzed
back to alcohol & sugar
- Oxidation - Oxidized to
Naming Stereoisomers carboxyl/COOH
- look at the chiral carbon farthest from the carbonyl
group:
- if the hydroxyl group points to right when the
carbonyl is up, it is the D-isomer
- if the hydroxyl group points to left when the
carbonyl is up, it is the L-isomer

Chiral Carbon Atoms

- Reduction - Reduced to sugar

alcohol
- monosaccharides do not usually
exist in solution in their
"open-chain" forms
- an alcohol group can add into the
carbonyl group in the same
molecule to form a pyranose ring
Classes of Carbohydrates containing a stable hemiacetal
A. Monosaccharides (aldehyde) or hemiketal (ketone)
- simplest of the carbohydrates,since they - Haworth projection is a common way of
contain only one polyhydroxy aldehyde or writing a structural formula of sugars
ketone (monosaccharides and disaccharides) with
- Monosaccharides are classified according to an unpretentious three-dimensional
the number of carbon atoms they contain: perspective. Pyranose Ring (piattos)
- 3 carbon atoms - triose
- 4 carbon atoms - tetrose
- 5 carbon atoms - pentose
- 6 carbon atoms - hexose

IGANO, CIENNA CHARRISE 9

 TRANSES: BIOCHEMISTRY

- Common Disaccharides
- Sucrose
- table sugar
- Formation of Phosphate Esters - glucose + fructose
- Phosphate Esters - Lactose
- a class of - found in mammary milk
organophosphorus - glucose + galactose
compounds with the - Maltose
general structure O=P(OR) - found in molasse
3, a central phosphate - used to ferment beer
molecule with alkyl or - glucose + glucose
aromatic substituents. D. Polysaccharides
- phosphate esters can form - Contains hundreds/thousands carbohydrate
at the 6-carbon of units
aldohexose and - Not reducing sugar
ketohexose - Two types:
- sugar-phosphate - Homopolysaccharides - one type of
backbone of DNA & RNA, monosaccharides
ATP - Heteropolysaccharides - multiple
- Monosaccharide derivatives types of monosaccharides
- Deoxy sugars - Starch
- Sugars that have had - polymer consisting of glucose units
hydroxyl group replaced - insoluble in water because of high
with hydrogen atom molecular weight
- Amino sugars - forms of starch:
- Sugars where hydroxyl 1. Amylose
group is replaced with an - unbranched
amino group chains connected
- Alcohol sugars by (1-4)
- Polyhydric alcohols glycosidic
(polyols) formed when the linkages
carbonyl group of the - 10-20% in plants
monosaccharide is - amylose chain is
reduced to hydroxyl group flexible enough to
(one -OH/hydroxyl group allow the
attached to each carbon) molecules to twist
- Carboxylic Acid sugars into shape of a
- A carbonyl or hydroxyl helix
group is oxidized to a 2. Amylopectin
carboxylic acid group - consists of long
- Common Monosaccharides chains of glucose
- Glucose connected by
- Fructose (1-4) glycosidic
- Galactose linkages, with
B. Oligosaccharides (1-6) branches
- Contain 2-10 monosaccharide units every 24 to 30
C. Disaccharides glucose units
- Two monosaccharides linked together along the chain
through a glycosidic linkage - 80-90% of the
starch in plants is
in this form

IGANO, CIENNA CHARRISE 10

 TRANSES: BIOCHEMISTRY

- Glycogen - Functional group gives amino acids their

- aka animal starch chemical identity
- structurally similar to amylopectin, - Basic Structure of an Amino Acid
containing both (1-4) and (1-6)
glycosidic linkages
- abundant in the liver and muscles
- on hydrolysis, it forms glucose

- Cellulose - Things to remember about amino acids:

- polymer consisting of long, - only 20 L-amino acids are used to make
unbranched chains of glucose proteins; AA are joined by peptide bonds
connected by (1-4) glycosidic - side chains or side groups are what
linkages distinguish amino acids from each other
- most important structural - amino acids can exist as zwitterions (a
polysaccharide; single most molecule or ion having separate positively
abundant organic compound on and negatively charged groups)
earth
- dietary fiber

AMINO ACIDS AND PROTEINS

- Writing AA starts from N-terminus to
C-terminus
Proteins
- Classification of Amino Acids:
- are complex macromolecules that are polymers of
I. Polarity
many subunits called amino acids
- polar
- roles in living things
- acidic
- catalysts-enzymes
- basic
- hormones
- neutral
- transport molecules
- nonpolar
- key part of structures
II. R group
- muscle action
- acidic
- immune response
- basic
- visual process
- neutral
- operation of the nervous system
III. Nutrition
- Proteins come in all shapes and sizes
- essential
- non-essential
Amino Acids
- these are small molecules with a simple basic
structure, a carbon atom to which three groups are
added
- amino group (-NH2)
- carboxyl group (-COOH)

IGANO, CIENNA CHARRISE 11

 TRANSES: BIOCHEMISTRY

Polypeptide
- Count the amino acid residue
- To find the peptide bond locate the carbonyl

Proteins structure
- protein structure is complex
- the order of the amino acids that form the
polypeptide affects how the protein folds
together
- the way that a polypeptide folds to form the
protein determines the protein's function
- some proteins are comprised of
more than one polypeptide
- Primary Protein Structure
- Sequence of a chain of amino acids

- Secondary Protein Structure

- Local folding of the polypeptide chain into
helices or sheets

Proteins
- the covalent bond linking two amino acids together is
called a peptide bond
- the assembled polymer is called polypeptide
- Tertiary Protein Structure
- Three-dimensional folding pattern of a
protein due to side chain interactions

IGANO, CIENNA CHARRISE 12

 TRANSES: BIOCHEMISTRY

- Quaternary Protein Structure Enzymes Parts

- protein consisting of more than one amino - Apoenzyme
acid chain - enzymatically inactive protein part of an
enzyme, which requires a cofactor for its
activity
- Cofactor
- a non-protein chemical compound or metallic
ion that is required for an enzyme's role as a
catalyst
Properties of proteins - Proenzyme or zymogen
- very large molecules - a biologically inactive substance which is
- have characteristic amino acid composition metabolized into an enzyme.
- some proteins contain prosthetic group - Coenzyme
- generally tasteless, mostly colorless - organic compounds required by many
- insoluble in non-polar solvents; varied degrees of enzymes for catalytic activity
solubility in water, salt solution, dilute acids and bases
- Amphoteric - able to react both as a base and as an Enzymes Nomenclature
acid - Trivial System
- very reactive and highly specific - based on the substrate of the enzyme and
the type of reaction catalyzed
Classifications of proteins - use of -ase ending
I. According to structure - International Enzyme Commission
- simple proteins - groups enzymes into six classes
- compound proteins
II. According to shape Main Classes of Enzymes
- globular
- fibrous
III. According to function
- contractile
- defense
- enzymes
- regulatory
- storage
- structural
- transport

Proteins Denaturation
- changes to the environment of the protein may cause
it to unfold or denature
- increased temperature or lower pH affects hydrogen
Properties of Enzymes
bonding, which is involved in the folding process
- enzymes are proteins
- a denatured protein is inactive
- enzymes are catalysts
- enzymes are highly specific

Chemical Reactions
- All chemical reactions require an initial input of energy
called activation energy
- reactions become more likely to happen if their
activation energy is lowered
- this process is called catalysis
- catalyzed reactions proceed must faster than
non-catalyzed reactions
ENZYMES
Main Classes of Enzymes
What are enzymes?
- Catalysts
- substances that speed up chemical reactions
- enzymes are specific for one particular reaction or
group of related reactions
- many reactions cannot occur without the correct
enzyme present
General Characteristics of Enzymes
Enzymes are well-suited to their roles in three major ways:
- they have enormous catalytic power
- they are highly specific
- their activity can be regulated

IGANO, CIENNA CHARRISE 13

 TRANSES: BIOCHEMISTRY

How Enzymes Work

- enzymes bind specifically to a molecule and stress
the bonds to make the reaction more likely to proceed
- active site is the site on the enzyme that binds to a
reactant
- binding site is the site on the reactant where the
enzyme binds
- the binding of the reactant to an enzyme causes the
enzyme's shape to change slightly - leading to an
"induced fit"
- the enzyme lowers the activation energy for the How cells regulate enzymes?
reaction Cells can control enzymes by altering their shape
- the enzyme is unaffected by the chemical reaction - Repressors
and can be reused - feedback inhibition
- Activators
Mechanism of Enzyme Action
- Lock and Key Theory
- enzymes have a specific shape that directly
correlates to the shape of the substrate.
- Induced Fit Theory
- an enzyme's shape and conformation
changing over time in response to substrate
binding.

Enzyme Inhibition
- a decrease in enzyme-related processes, enzyme
production, or enzyme activity.

How Enzymes Work

- Temperature and pH affect enzyme activity
- enzymes function within an optimum
temperature range
- enzymes function within an optimal pH range

IGANO, CIENNA CHARRISE 14