Biochemistry lecture 1

Ma. Cristina F. T Dimaculangan

With the cell, biology discovered its atom . . .
To characterize life, it was henceforth essential to study the
cell and analyze its structure: to single out the common
denominators, necessary for the life of every cell;
alternatively, to identify differences associated with the
performance of special functions.

François Jacob,
La logique du vivant: une histoire de l’hérédité
(The Logic of Life: A History of Heredity), 1970
 Cell biology

Physiology Genetics

Biochemistry

Pharmacology Immunology

Microbiology
 Biochemistry
Shows how the collections of inanimate
molecules that constitute living organisms
interact to maintain and perpetuate life
animately solely by the physical and chemical
laws that govern the nonliving universe.
 Why study biochemistry?
1. Biochemistry is beautiful and fascinating.
2. Biochemistry is important to many fields
3. Advances in biochemistry provide answers to
questions in biology and medicine.
Common Features of Living Things
1. High complexity and organization
2. Energy systems
3. Precise replication and reproduction
4. Response mechanism
5. Defined components and regulated functions
6. Evolution
Lodish et al. Molecular Biology of the Cell 5th ed. 2004
Though there are many common features, there
is enormous diversity among living things
Lehninger. Biochemistry 4th Ed. 2005
 Biochemical Evolution
4.5 billion years: approximate Earth age
3.5 billion years: organisms: resembling certain modern bacteria
Generation of molecules (C,P, L, NA) by non-biological process

Transition from prebiotic chemistry to replicating systems

Energyy interconvertion from chemical sources and sunlight tp be utilized to

drive biochemical reactions.

cells adjust to different environments, form colonies of interacting cell groups

or evolved into complex multicellular organisms
 Evolution theory of the Cell
3.5 million years ago
– Macromolecules is primordial soup
– Series of building blocks
• Act of duplication
• Transmission of information
– Catalyzes own replication
– Building blocks
– RNA – believed to be the 1st replicating
molecule
2.5 million years ago
– Chemical assembly
» RNA + DNA, proteins and enzymes
» To capture energy in the chemical form of CHO ( thru
metabolic pathways) from the environment
» The bridge between living and non-living
» Viruses
• Chemical assembly – nutrients from the environment
1.5 million years ago
• Chemical assembly + lipids
• lipids are the building blocks of membranes
• purpose: maintain own chemical environment
• result: efficient metabolic pathways
Trial and error
Protocell

Bacteria and prokaryotes

Eukaryotes

Multi-celled eukaryotes
Prebiotic world

Theory:
– Earth's early atmosphere was highly reduced
– rich in methane (CH4)
– Ammonia (NH3)
– water (H2O)
– hydrogen (H2)
– atmosphere was subjected to large amounts of
solar radiation and lightning
• Stanley Miller and Harold Urey - 1950s
The cell is the basic unit of life
 no true nucleus
genetic material - nucleoid/nuclear zone
Difference between prokaryotes and
eukaryotes has true nucleus
genetic material- nucleus

1. Prokaryotes do not have a nucleus; genetic

material is suspended in the cytoplasm.
2. Prokaryotes do not have membrane bound
organlles eukaryotes- have membrane bound organelles
3. Prokaryotes have a single chromosomal DNA
4. Prokaryotic cytoplasm is not mobile
5. Prokaryotes have no reports of having a
cytoplasm
 Basic components
Prokaryotes 1.) nucleoid (genetic material)
2.)cell membrane
3.) ribosomes
4.)cytosol

1. Archaebacteria – survives in extreme conditions

– Methanobacteria – anaerobic bacteria that reduce CO2 to CH4
– Sulfur bacteria – anaerobic bacteria in hot acidic conditions and are
also called thermoacidophiles
– Halobacteria – aerobic bacteria in high salt conditions and are also
called halophiles
Basic components of
eukaryote
2. Eubacteria 1.) nucleus
2.)cell membrane
– Cyanobacteria 3.)ribosomes
4.)cytosol
– Green photosynthetic bacteria 5.) endoplasmic
– Purple photosynthetic bacteria reticulum
6.) golgi bodies
– Gram + bacteria 7.) etc

– Gram – bacteria
The tree of life

Lehninger. Biochemistry 4th Ed. 2005

 Cells are either
prokaryotic or eukaryotic

Lodish et al. Molecular Biology of the Cell 5th ed. 2004

The Prokaryotic Cell

Lehninger. Biochemistry 4th Ed. 2005

cell wall
rigid structure found outside the
cytoplasmicmembrane w/c defines the
shape of the prokaryotic cell composed of
peptidogyclan

capsule
organized layer of viscous material
directly attached to the cell wall.
Usually used for adherence

flagella – filamentous helical hollow

structures attached to the CW and CM
and is used for locomotion

Pilus
hollow non – helical structure
projecting from the cell wall; used for
conjugation or exchange of genetic
material
cytoplasmic membrane
phospholipids bilayer containing the
cytoplasm

DNA – genetic material

ribosome – structures
responsible for protein synthesis
and are not membrane bound

mesosomes – cytoplasmic
extension of the cytoplasmic
membrane also called
cytoplasmic invaginations

inclusion bodies – glycogen,

polyhydroxybutrates,
metachromatin granules and
polyphosphates
The animal cell

Lehninger. Biochemistry 4th Ed. 2005

The plant cell

Lehninger. Biochemistry 4th Ed. 2005

Cell Membrane – (plasma membrane)
border/ barrier
• separates a cell from other cells and from surrounding fluids
• holds the cell together and can give shape to the cell.
• Encloses and protects the entire cell.
• Selectively permeable; double layer of lipids and 1 layer of
proteins

fluid mosaic model

by layer

http://psychology.wikia.com/wiki/Cell_membrane
Cell Wall
• surrounds the plasma membrane of most
plant cells
• protects and support plant cells.
– contains pectin (jelly-like substance)
released during cooking and forms a gel as
it cools.

Parts:
1. middle lamella – first layer that contains pectin
2. primary walls – attached to the middle lamella formed by the cells on
either side
- contains cellulose and pectin
3. secondary walls – firm, rigid walls that remain long after the cells are
dead.
http://library.thinkquest.org/C004535/cell_wall.html
Protoplasm
• jelly-like living substance of the cell that is
translucent, grayish, and slimy. (colloidal
suspension – often moves or streams within
the cell.)
• it may be granular or foam-like or contain small
fibers or threads.
• comprises water, minerals, salts and many
kinds of organic compounds.

Types:
a. cytoplasm – protoplasm that surrounds
the nucleus of the cell.
b. Nucleoplasm/karyoplasm – that which
made up the nucleus.

http://www.learner.org/courses/essential/life/session1/closer1.html
 Nucleus
• control center of the cell
• cellular reproduction store dna
• differentiation a cell undergo and what
form it will exhibit at maturity
• directs the metabolic activities of the
living cell.

replication transcription translation

Parts: DNA ——> RNA —-> PROTEIN

1. Nuclear membrane – double layer of lipids and proteins; separate

the nuclear material from the cytoplasm; porous
2. Nucleolus – at least one is present in most nuclei; takes part in
protein synthesis.
3. Chromatin – fine strands spread through the nucleoplasm
DNA
4. Chromosomes – contracted and distinct chromatin when a cell is
dividing. condensed structure
not dividing
threadlike structure

dividing
Endoplasmic reticulum
• system of double membranes that lie parallel to one another,
appearing to form channels.
• seem to be attached to the cell membrane and to the nuclear
membrane
• routes of transport for the materials within the cell.
• separate different areas of the cell
• surface to which enzymes and certain other cell structures are
attached, thus providing a surface for chemical reactions.

Kinds:
1. Rough E.R. – are lined with ribosomes on their outer
surfaces.
2. Smooth E.R. – lack ribosomes
http://liquidbio.pbworks.com/w/page/11135266/Matthew-Damstrom-Organelles-Project
Ribosomes
• tiny, grainy structures attached to the E.R.
• contain enymes that carry out the synthesis of proteins (proteins
factories)
• contain large amounts of RNA made in the nucleolus

http://marionkatiemaggie.blogspot.com
http://www.palaeos.com/Eukarya/Lists/EuGlossary/EuGlossaryS.htm/
Mitochondria
• small, rod-shaped organelle; rounded cylinders or
globules enclosed by membranes.
• The power-house of the cell

http://en.wikipedia.org/wiki/Mitochondrion
Golgi Complex (Bodies or Apparatus)
• discovered by Camillo Golgi in 1898
• a system of membrane-enclosed
vesicles arranged parallel to each
other
• stacks of flattened sacs separated by
membranes piled one on top of the
other.
• Functions
– secretion of several chemical
products
– membrane repair
– transport of materials in and out
of the cell.
– Protein packaging factory
– Wrap enzymes into separate
organelles.
http://micro.magnet.fsu.edu/cells/golgi/golgiapparatus.html
Centrosome
• contains one to two centrioles
centrioles - small dark bodies located above the nucleus in
many eukaryotic animal cells.
• made up of nine sets of microtubules with 3 microtubules in
each set.
• role :organizing the spindle during cell division

http://scienceblogs.com/transcript/2006/08/new_evidence_for_endosymbiotic.php
Lysosomes
• found in the cytoplasm
of most animal cells
• smaller than
mitochondria and have a
simple membrane.
• Contain digestive
enzymes that breakdown
proteins

http://www.daviddarling.info/encyclopedia/L/lysosome.html
Peroxisomes detoxification

• Microbodies
• participate in the oxidation of certain nutrients
• converts hydrogen peroxide to H2O and O2.

http://micro.magnet.fsu.edu/cells/peroxisomes/peroxisomes.html
Plastids
• large cytoplasmic organelles
found in the cells of most plants
but not in fungal or animal cells.
Types
a. Chromoplasts – colored plastids;
contain pigments
1. chlorophyll – green
2. carrotenoids – yellow and
orange
3. phycoerythrin – red
4. phycocyanin – blue
5. fucoxanthin – brown

b. Leucoplasts – colorless plastids;

storage of starch, oils and
proteins.
https://www.etap.org/demo/grade7_science/instruction2tutor.html
http://www.skoolbuz.com/library/content/407
 Vacuoles – membrane – enclosed cavities filled with
either fluid
or granular material.

Types:
1. Food – contain food particles
2. Contractile – expel excess water and wastes from the
cell. like urinary bladder

http://www.biologycorner.com/lesson-plans/phyla/kingdom-protista/
http://www.biologycorner.com/APbiology/cellular/(notes)cells2.html
Cytoskeleton
• Interconnected system of fibers, threads,
and lattices extends between the nucleus and
plasma membrane of eukaryotic cells,

Functions:
1. internal cellular organization,
2. cell shape
3. Cell’s capacity to move.
4. Reinforces the plasma membrane and
nuclear membrane holds their proteins in
place.
5. Serves as scaffolds
6. stabilizes the enzyme systems of protein
synthesis and other activities.
Types:

1. Microfilaments
– part of the cytoplasmic
matrix
- responsible for the
contraction of the cell.

2. Microtubules
–maintenance of the cell
shape, cell division and the
movement of inclusions and
organelles

3. Intermediate Filaments

http://notesforpakistan.blogspot.com/2010/09/cytoskeleton-short-note.html
Cilia
– short and numerous
movable hair-like
structures projecting
from the free surfaces.
Functions:
• cell locomotion
• moving liquids or small
particleson the surface of
the cell.
Flagella
- few appendages and
are relatively long in
proportion to the size of
the cell

http://www.technovelgy.com/ct/Science-Fiction-News.asp?NewsNum=845
Microvilli
– minute fingerlike projections of the cell
membrane.
– sites of osmosis where fluids may pass in and out
of the cell.

http://www.daviddarling.info/encyclopedia/S/small_intestine.html
Pinocytic Vesicles
– in-pocketings of the cell membrane filled with
water.
- when water is needed by the cell, the plasma
membrane engulfs a droplet of water in a
process of pinocytosis.

http://cellbiology.med.unsw.edu.au/units/science/lecture0806.htm
Plasmodesma (plasmodesmata, pl.) - of
multicelled plants; a junction between linked
walls of adjacent cells through which nutrients
and other substances flow.
http://www.nature.com/nrm/journal/v5/n9/fig_tab/nrm1470_F1.html
Lehninger. Biochemistry 4th Ed. 2005
 Chemical Bonds in Biochemistry
Covalent bonds
– Formed by sharing and the strongest present
biochemicals
– Requires high amount of energy to be broken
– Resonance structures

Stryer. Biochemistry 5th ed. 2001

 Chemical Bonds in Biochemistry
Non covalent bonds
1. Electrostatic interactions
– Based on electric charges

2. Hydrogen bonding
– H-atom is partly shared b/n electronegative atoms (F,
O, N)

3. Van der waals interactions

– Based on the electronic charge distribution
 Importance of water
• Biological molecule shapes respond to the
physical and chemical properties of water
• Water is the medium of most biochemical
reactions
• Water participates in chemical reactions
 Physical properties of water
• Colorless
• Odorless
• Tasteless
• solvent
1. Structure •Water molecules form hydrogen bonds
• water is polar

Lehninger. Biochemistry 4th Ed. 2005 Stryer. Biochemistry 5th ed. 2001
http://www.goalfinder.com/images/articles/water%20expands%20when%20frozen%20t
o%20ice.html
2. Water is a solvent
• Solubility – the ability of a solvent to interact
eith a solute more strongly than solute
particles with each other Polar and ionic
materials
• Dissolves Hydrophilic materials and ionic
compounds

Lehninger. Biochemistry 4th Ed. 2005

3. Hydrophobic effect
The tendency of water to minimize its
contacts with hydrophobic molecules

Amphiphiles – have both polar and non polar

parts (both hydrophilic and hydrophobic)
- Forms micelles
4. Osmosis and diffusion

http://qwickstep.com/search/what-is-osmosis-and-diffusion.html
Osmosis – the movement of a water from higher
concentration to a lower concentration
passing though a semi-permeable membrane

Diffusion – the movement of molecules from an

area with high concentration to an area with
low concentration
 Chemical Properties of water
1. Ionization of water
2. Acid – base chemistry
3. Buffers