Chapter 1
Introduction - Cell
Structure
Section 18.1
The Study of Living Things
•
•
•
Biochemistry is the systematic
study of the chemical substances
found in living organisms, their
organization & chemical
interactions with each other, and
the principles of their participation
in the processes of life.
Its importance is due to the
increasing recognition that
underlying each and every
biological function is a chemical
reaction.
Hundreds/thousands of chemical
reactions are taking place in our
cells every minute of our lives.
•
Biochemical investigations have
been directed towards the study of
the chemical composition of cells
and the chemical processes in
which they participate.
•
A biochemical substance is a
chemical substance found within a
living organism.
•
Two types of biochemical
substances:
-
-
Bioinorganic substances :
water and inorganic salts.
Bioorganic substances:
carbohydrates, lipids,
proteins, and nucleic acids
Section 18.1
Biochemical substances
BIOINORGANIC
SUBSTANCES
Substancesthatdo
notcontaincarbon
BIOCHEMICAL
SUBSTANCES
-
BIOORGANIC
SUBSTANCES
Substancesthat
containcarbon
-
•
Water(about70%)
•
Inorganicsalts(about5%)
Proteins(about15l})
•
Lipids(about81«·)
energy.
Carbohydrates(about2 ,)
•
ucleicacids(about2i)
As isolated compounds,
bioinorganic and bioorganic
substances have no Iife in
and of themselves.
Yet when these substances
are gathered together in a
cell, their chemical
interactions are able to
sustain Iife.
A cell in particular, and a
whole organism in general,
has three basic needs:
materials, information, and
Without the daily satisfaction
of these, human life would
be severely constrained.
Section 18.1
Main classes of foodstuffs - Materials
•
The bioorganic materials of life
will be considered, starting with
the three main classes of
foodstuffs - carbohydrates,
lipids, and proteins.
•
Lipids serve many purposes.
They are used, both by plants and
animals, as materials to make cell
membranes and as sources of
chemical energy.
•
Humans use these molecules to
build and run their bodies and to
try to stay in some state of repair.
Plants rely heavily on
carbohydrate for cell walls, and
animals obtain considerable
energy from carbohydrates made
by plants.
•
Proteins are particularly important
in both the structures and
functions of cells.
Because of the catalytic role of
proteins in regulating chemical
events in cells, the study of
proteins will be immediately
followed with an examination of
enzymes, which make up a
particular family of proteins.
•
•
Section 18.1
Information system
•
Every cell has an information
system - enzymes, hormones,
and neurotransmitters are
components of the intricate
information system in the body.
•
Without information, the materials
and energy delivered to the body
could produce only rubbish.
•
Although enzymes are major
players in the cells' information
system, they do not originate the
cellular script.
•
They only help to carry out
directions that are encoded in the
molecular structures of the
nucleic acids, which are
compounds that are able to direct
the synthesis of enzymes.
•
Thus the study of the enzyme
makers, the nucleic acids, is
included in any study of the
molecular basis of life.
•
Hormones & neurotransmitters,
two other components of cellular
information, depend on the
presence of right enzymes not
only for their existence but for their
functions.
Section 18.1
Biochemical substances
• To supply materials for
any use - parts,
information, or energy each organism has basic
nutritional needs.
• These include not just
bioorganic materials,
including vitamins, but
also bioinorganic
materials including
minerals, water, and
oxygen.
• Thus, together with
learning about the
bioorganic materials of
life and how they are
processed and used, the
need for vitamins,
minerals, water, and
oxygen will also be
considered.
Section 18.1
Metabolism
•
•
•
All life processes consist of chemical
reactions catalyzed by enzymes.
The reactions of a living cell, which
are known collectively as
metabolism, result in highly
coordinated and purposeful activity.
Among the most frequent reactions
encountered in biochemical
processes are:
-
nucleophilic substitution
-
elimination
-
addition
isomerization
-
hydrolysis
-
oxidation - reduction
•
The redox chemistry of
carbohydrates is fundamental
to life.
•
Glucose is the most important
carbohydrate in biochemistry.
Almost all cells derive energy
from the oxidation of glucose
through glycolysis, citric acid
cycle, and oxidative
phosphorylation
•
The energy yield from the
oxidation of glucose is shown
below.
Section 18.1
The Study of Living Things - The CELL STRUCTURE
•
•
•
Based on their cell structures,
organisms are divided into two
ma•in groups:
Prokaryote: Greek - meaning
"before the nucleus"; single
celled organisms
Eukaryote: Greek - meaning
"true nucleus"
contain a well-defined nucleus
surrounded by a nuclear
membrane
- can be single celled, such as
yeasts and Paramecium, or
multicellular, such as animals
and plants
•
•
•
•
•
•
•
Five kingdoms:
Monera - prokaryotic organisms;
includes bacteria and
cyanobacteria
Protista - unicellular eukaryotes:
yeast, Euglena, Volvox, Amoeba,
and Paramecium
Fungi - molds and mushrooms
Plantae
Animalia
Fungi, plants, and animals are
multicellular eukaryotes
(with few unicellular eukaryotes)
Section 18.1
The Study of Living Things - The CELL STRUCTURE
•
•
The main difference between prokaryotic and eukaryotic cells is the
existence of organelles, especially the nucleus, in eukaryotes.
An organelle is a part of the cell that has a distinct function; it is
surrounded by its own membrane within the cell.
Organelle
Nucleus
Prokaryotes
N o deFanite n u c l e u s ; D N A
present butnotseparate
f r o m t h e r e s t o f t h e cell
Eukaryotes
Present
Cell membrane
Present
Present
Mitochondria
N o n e ; enzy mes for oxidation
are onplasma membrane
Present
Endoplasmic
reticulum
None
Present
Ribosomes
Present
Present
Chloroplasts
None;photosynthesis
localized in chromatophores
P r e s e n t in
g r e e n plants
-- --
Section 18.1
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Section 18.1
The CELL STRUCTURE - Functions of the organelles
Table 1.2
Eukaryotlcorganelles.theirconstituent biomolecules,andbiological function
Strucrural Feature
!vlolecular Composition
Biological Function
Cell membrane
Bilayer of proteins (50%) and lipids (50%)
and some carbohydrate
Nucleus
Contains genomic DNA, and histone
proteins as chromatin: RNA
Flat,single-membraned vesicles of lipid
and protein; ribosomes consist of RNA
and proteins
Flattened vesicles of lipid. protein, and
polysaccharide
Selectively permeable boundary for entry and
exit of nutrients and waste:some important
enzyme activities; location of receptors for signaling
Storage of genetic information;site of DNA
replication and transcription 10 RNA
Surfaces on which ribosomes bind for protein
synthesis
Endoplasmic reticulum
with ribosomes
Golgi appararus
Mitochondria
Lysosomcs (animal)
Peroxisomcs (animal)
or gJyoxysomcs (plant)
Chloroplasts (plant)
Cytoplasm
Double-membraned with protein and lipids;
interior (matrix) contains soluble and
insoluble enzymes. RNA. anclONA
Single-membraned vesicles containing
enzymes ror hydrolysis
Single-membraned vesicles containing
cata lase and other oxidaiive enzymes
Double-membraned organelles containing
protein, lipid.chlorophyll. RNA, ONA.
and ribosomes
Cy1oskelc1on made of proteins;small
molecules,soluble proteins,enzymes,
nutrients. and salts in aqueous solution
Table 1·2 Concepts in Biochemistry 3/e
0 2 0 0 6 J o h n Wiley & Son,
Secretion of cell waste products;site of protein
processing
Sile of energy metabolism and syotbesis of
high-energy ATP
Metabolism of materials ingested by endocytosis
Oxidative metabolism of nutriCnlSu i n g 0 2 to
genera1e H202
Sites of photosynthesis: conver1light energy into
chemica I energy (ATP)
Provides shape 10 cell; region where many
metabolic reactions occur
Section 18.1
The cell membrane
•
•
•
•
•
•
a semi-permeable membrane
surrounding the cell separating its
internal environment from the
external environment;
permits and/or enhances the
absorption of essential nutrients
into the cell while preventing the
diffusion of needed metabolites
a lipid bilayer that mechanically
holds cell together
component biomolecules:
- Lipids: phospholipids,
cholesterol
Lipids provide the basic structure
of biological membranes
Proteins are embedded in the
membranes and provide
channels/carriers for the transport
of ions and nutrients
Pn>tmo,th
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Section 18.1
The cytoplasm
• structureless and highly
•
VISCOUS
• the aqueous phase of the
cell in which many
particulate constituents
like mitochondria
'
ribosomes, etc. are
suspended
• contains a wide variety of
solutes including proteins,
enzymes, nucleic acids
(RNA), a number of
electrolytes, metabolites
for cellular utilization
(e.g., glucose), and waste
products of cellular
activity (e.g., urea,
creatinine, uric acid, etc.)
Section 18.1
Nuclear
Envelope,
Biochemistry - An Overview
Anatomy
of the
Nucleus
Chromatin
Nucleolus
The nucleus
•
•
•
the "information center" of the cell;
enclosed by a nuclear membrane
and contains the cell's genetic
information and the machinery for
converting that information into
protein molecules
site of DNA and RNA synthesis
contains a comparatively large
amount of nucleoprotein (50%
DNA and 50% proteins, histones
and prolamines located in the
chromosomes, and a small
amount of RNA; >95% of nucleic
acids of the cell is in the nucleus
Endoplasmic
Reticulum
Figure 1
Ribosomes
•
nucleolus, - small, round dense
body present within the nucleus;
not surrounded by a membrane;
essentially a cluster of looped
chromosomal segments; contains
10-20% of the total RNA of the
cell, chiefly mRNA
•
serve as a storehouse for mRNA
prior to its movement into the
cytoplasm by way of the nuclear
pores
Section 18.1
The mitochondria
•
•
•
•
the second largest organelle
the powerhouse of the cell
where carbohydrates, lipids,
and amino acids are oxidized
to CO 2 and H20 by molecular
0 2 and the energy set free is
converted into the energy of
ATP
•
The inner membrane, in which
the enzymes of electron
transport and energy
conversion are located, is
convoluted to form shelves
termed cristae.
Inner membrane
Outermembrane
has a double-membrane
structure, an outer membrane
and an inner membrane
site for cellular respiration
Matti)(
lntermembra.ne
Crisi,e
ATPoynthase
complex
space
A schematic representationofamitochondrion, showing key
features of itsinternal structure.
Section 18.1
The endoplasmic reticulum
•
appears to be a system of
interconnected tubules or
canaliculi extending throughout
the cell cytoplasm and is
continuous with the outer nuclear
membrane
•
•
two types: rough and smooth er
rough er is lined with a number
of small, spheric, electron-dense
particles called ribosomes
- primarily involved in synthesis
of membrane proteins and
proteins for export from the
cell
•
smooth er lacks ribosomes
- appears to be involved in
the biosynthesis of
steroids, phospholipids,
and complex
polysaccharides
- functions also include
biotransformation, a
process in which water
soluble organic molecules
are prepared for excretion
Section 18.1
The ribosomes
• consist of ~50°/o RNA
(rRNA) and 50°/o protein
• involved in protein
synthesis in the cell and
are sometimes referred to
as the "workbench" for
protein synthesis
• complex structures
containing two irregularly
shaped subunits of
unequal size
• they come together to
form whole ribosomes
when protein synthesis is
initiated
•
when not in use, the
ribosomal subunits
separate
Rbosomal
Largesubunit
subllll11s
Ribosome
Smallsubunit
Section 18.1
The golgi apparatus / golgi complex
•
•
•
structures composed of
flattened sacs with vesicles,
located near the nucleus,
probably continuous with er
the organelles to which
synthesized proteins are
transported and temporarily
stored before release from the
cell
the "packaging stations" of the
cell
•
•
•
the primary site for packaging
and distribution of cell products
to internal and external
compartments
there is a continuous flow of
substances through the Golgi
apparatus
responsible for sorting and
packaging several types of
proteins, small molecules, and
new membrane components
Section 18.1
The lysosomes
•
membrane-bound organelles
containing a variety of
hydrolytic and degradative
enzymes and having an
optimum pH of 5.0
•
has regulatory and defense
function
•
function in the digestion of
materials brought into the cell
by phagocytosis and
pinocytosis
•
also serve to digest cell
components after eelI death
•
the "suicide bags" of the cell
•
upon death of the eelI or its
exposure to environmental
conditions, the lysosomal
membrane disintegrates,
releasing its contents, which
cause the self-digestion or
autolysis of the cell
constituents
Section 18.1
The peroxisomes
• contains oxidative
enzymes that oxidize
amino acids, uric acid,
and various 2hydroxyamino acids using
0 2 with the formation of
H202
• H 2 0 2 is then converted to
H 2 0 and 0 2 b y t h e
enzyme catalase also
present in the
perox1• somes
• thus the cell protects itself
from the toxicity of H 2 0 2
Section 18.1
Water in the cell
•
the solvent
- the agency that enables
water-soluble, water-miscible,
or emulsifiable substances to
be transferred in the body not
only in the blood but also
intercellularly and
intraceIIularly
•
in biochemical reactions
- ionization is a prerequisite to
many biochemical reactions
and ionization takes place in
water
Section 18.1
Water in the cell
•
in physiologic regulation of body
temperature
high specific heat (amount of
heat required to raise the
temperature of 1g of H 20 1°C)
enables the body to store heat
effectively without greatly raising
its temperature
high heat conductivity permits
heat to be transferred readily
from the interior of the body to
the surface
high latent heat of evaporation
causes a great deal of heat to be
used in its evaporation and thus
cools the surface of the body
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Section 18.1
Characteristics of biochemical reactions
•
•
Chemical reactions occurring
in vivo have the following
properties:
•
Mildness
-
Speed
-
glucose, for instance, is
oxidized in the body with
surprising speed, while in
vitro, the same reaction is
quite a long and tedious
process.
- this is due to the presence of
enzymes, without which life
as we know it would not be
possible
•
energy is taken up and
released in a gentle way, not
violently as those occurring in
vitro (because of high specific
heat of water which makes up
a large proportion of the
protoplasm)
Orderliness
-
a high degree of orderliness is
due to the existence of cell
specialization within the
different organs of the body