Microsoft PowerPoint - Biochemistry_Chapter 1.1 and 1.2_2009.ppt







ΨΨΨΨwavefunction
ΕΕΕΕenergy

chap 1.1 to 1.2 4
Chapter 1 Foundations of Biochemistry
What is Chemistry This science that tries to understand (A)The properties of substances
(B)The changes that substances undergo
The realm of substances (A)Natural substances e.g.water, air, element, salt...
(B)New compounds created by chemists
e.g.polymer ,nylon...
(B)The changes that biomolecules undergo
chap 1.1 to 1.2 5
1. A high degree of chemicail complexity &
microscopic organization
“energy” from their environments, usually in the
form of chemical nutrients or sunlight.
3. Defined functions for each of an organism’s
components and regulated interactions among
them
alterations in their surrounding
and self-replication
evolution
chap 1.1 to 1.2 6
Biochemistry explains diverse forms of life in
unifying chemical terms
cellular and chemical levels
animalsplants
shared by all organisms in “molecular terms”
2.Provides organization principles that underlie life
The molecular logic of life
chap 1.1 to 1.2
• Consider the properties of living organisms
• Describe a set of principles that characterize
all living organism
Diverse living organisms
share common chemical
Cells:
cell, separating its contents
protein molecules that form
a thin, tough, pliable,
around the cell.
1.1 Cellular Foundations
Cells are the structural and functional units of all living organisms
chap 1.1 to 1.2 9
2. Cytoplasm
3. Nucleus or Nucleoid
Eukaryotes ()
Prokaryotes () without nuclear envelopes
chap 1.1 to 1.2 11
• Animal and plant cells are 5 to 100 µµµµm in diameter
• many bacteria are only 1 to 2 µµµµm long
• the smallest cellsmycoplasmas (), ~300nm in
diameter, and ~10-14 ml in volume
•Upper limit of cell sizedefined by the rate of diffusion
of solute molecules in aquaous systems
•Lower limit of cell sizeSet by the minimum number of
each type of biomolecule (supramolecules and organelles)
required by the cell (e.g. ribosome~20nm long)
Cellular Dimensions Are Limited by Oxygen
Diffusion
There Are Three Distinct Domains of Life
1. bacteria () inhabits soils, surface waters, tissues.
e.g. E. Coli
2. Archaea () inhabits more extreme environments (salt lakes, hot
springs…) e.g. methanococcus jannasch
prokaryotesGroups
chap 1.1 to 1.2 14
Organisms can be classified according to their
energy source (sunlight or oxidizable chemicals)
chap 1.1 to 1.2 15
Escherichia coli () is the most-studied
prokaryotic cell : 5 µµµµm in length; 2 µµµµm in diameter
ribosomes
prokaryotic cell
metabolites, and cofactors
Resistance to toxins and antibiotics.Amenable
to manipulation for molecular genetic study
chap 1.1 to 1.2 17
Cell envelopes
, etc)
staphylococcus aureus, archaebacteria, etc.)
prokaryotic cell
Cell envelopes Gram negative and positive bacteria
chap 1.1 to 1.2
Typical Eukaryotic cells

Plant cell




Eukaryotic Cells Have a Variety of Membranous
Organelles, Which Can Be Isolated for Study
chap 1.1 to 1.2 22
Plasma membrane Lipid bilayer, contains transporter and receptors
1.Transportersproteins that span the membrane and
carry nutrients into the cell and products out
2.Signal receptorsbind with extra-cellular signaling
molecules (ligands): receptors recognize ligands (can be small
molecules or macromolecules).
e.g. drugs – receptor
formed by cellulose & carbohydrate polymers outside
the plasma membrane
Organelles

Endoplasmic reticulum(ER)
and enclosing a subcellular compartment(the lumen of
the ER)
Rough ER
Smooth ER
2. metabolism of certain drugs and toxic compound
3. In some tissues(e.g skeletal muscle), storage and
release Ca+2
Rough ER
Golgi complex
smooth ER
Golgi complex
• Medial element
• Proteins will be modified (e.g. adding sulfate, lipid,
carbohydrate groups)

chap 1.1 to 1.2 26 Proteins(during the synthesis on ribosomes on rough ER)
Inserted into rough ER lumen
Move to the Golgi complex (Proteins will be modified e.g. adding sulfate, lipid, carbohydrate groups)
Bud
Small membrane vesicles (Transport vesicles)

Ribosome
be
3.Inserted into nuclear or plasma membranes
• Cytoplasmic ribosomes synthesize proteins that will
remain and function in cytosol

Lysosomes()(Only in animal cells)
polysaccharides, nucleic acids, and lipids.
• act as recycling centers
a.a, monosaccharides, fatty acids.
• pH of lysosomal compartment < 5
enzymes inside are more active in acidic pH

Peroxisomes() contain catalase
2H2O2 2H2O +O2
• contain high conc. of enzymes of glyoxylate cycle
fats Carbohydrates
Vacuoles of plant cells
•Tonoplast (the membrane surrounding the vacuole):
regulate the entry of ions, metabolites etc. for
degradation.
biomolecules enzymes
cell.(saltcytosolosmotic pressure or
call turgor pressure cell)
Nuclear Pore
Nucleuscontains the genome
nuclear pore complexes specific transporters
Chromatin()contain DNA and proteins (histones)
bound tightly together
coding ribosomal RNAs (transcribe into ribosomal
RNA)ribosomes
enzymes for
DNA replication
DNA repair
MitosisNuclear division
Cytokinesis, (cell division)
Chromatin fiber

Somatic cells()
Gametes() (egg, sperm ):
• zygate ()
2m
packed200μμμμm
•1μμμμm in size
•two membrane
outer membrane
yielding metabolism.
Aerobic Eukaryotic cells
• mitochondria are produced only by division of
previously existing mitochondria.
ribosomes.
the mitochondria inner membrane.
Aerobic Eukaryotic cells
Pigment molecules (chlorophyll,)
adsorb solar light
endosymbiotic bateria ().

Cytoskeleton
(location in cells, not rigidly fixed, change during
mitosis, cytokinesis….)
cytoskeleton and is highly dynamic
constantly disassemble & reassemble
Microtubules radiating
is highly dynamic
2. Microtubules (in green)
The Cytoplasm is organized by the cytoskeleton and
is highly dynamic (B)
Actin sununits
cytoplasmic organelle)
filament (called cytoplasmic streaming)
chap 1.1 to 1.2
*muscle contraction
mitosis, microtubules highly organized & help
the separation of chromosomes (provide motive
force) chap 1.1 to 1.2 44
Microtubules +
kinesin
dynesin +
ATP
e.g. cilia
(3)Intermediate filaments (8-10nm) provide internal mechanical support for the cell and
to position its organelles
the specific location
• Cytoplasm meshwork of structural fibers (protein fibers)
membrane-bound organelles locate
Endocytosis and Exocytosis carry traffic across
the plasma membrane
surrounding medium deep into the cytoplasm
Phagocytosis()
other smaller cells
A vesicle in the cytoplasm moves to the inside surface
of the plasm membrane fuses with it, then release the
contents outside the membrane
Cells Build Supramolecular Structures
Cells Build Supramolecular Structures
+ Fatty acids
(D)Polysaccharides
cellulose
Structural hierarchy in the molecular organization of
cells
Covalent bonds
Van der Waals forces
Complexity of life Simplicity of “element”world
1.2 Chemical Foundations
Bulk elementsrequired in gram(only H, C, N, O, Na,
P, S, Cl, K, Ca, in red) 99%99%99%99%
Trace elementsrequired much less (colored in yellow)
Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Mo, I chap 1.1 to 1.2 54
biomoleculeCovalent bonding
with a Variety of Functional Groups
Some common functional
groups of biomolecules
groups, (2) 3-dimensional structure
chap 1.1 to 1.2 57
• In cytosol:a collection of a thousand of small
molecules (Mr ~ 100 to 500), the central
metabolites in the major pathway in cells.
• including amino acids, nucleotides, sugars, etc.
Polar or charged, in µµµµM to mM
• may contain secondary metabolites (in specific
plant cells that gives plants characteristic scents,
e.g morphine, caffeine etc)
molecules
Macromolecules Are the Major Constituents of Cells
Proteins and nucleic acids are informational
macromolecules
Three-Dimensional Structure Is Described
by Configuration and Conformation
(a) Structure Formula
bond angles
Configuration changed only by bond-breaking
Configuration fixed spatial arrangement of atoms in a
molecule
In the presence of (1) double bonds (2) chiral center
configurational isomers
respected to
double bond
Configurational isomers can be isolated (if use proper
separating methods) chiral centeratomC • Enantiomers will notate the plane of plane-polarized light
• Racemic mixtures(equimolar mixture of two enantiomers)
will not rotate the plane-polarized light chap 1.1 to 1.2 62
Molecular Conformation is Changed by Rotation
about Single Bonds
Structures
structures (, complementarity)
Substrate with the catalytic site of an enzyme
TAR region of HIV
In vivo, biomolecules are usually present in only one
of their chiral forms.
Glucose Only D form
Enzymes have the ability to distinguish between
isomers. (Enzymes are stereospecific)
(a)Carvone Smell as spearmint (R form)
caraway (S form)