Chapter 1 The Foundations of Biochemistry
-The ff are distinguishing features of living organisms:
-The cell is the basic unit of life (there are debates whether it is the cell/gene)
-A high degree of chemical complexity & microscopic organization (*polymers)
-Systems for extracting, transforming & using energy from the environment (*organic or
inorganic, eg. falcon acquires nutrients by eating a smaller bird)
-Defined functions for each of an organisms components & regulated interactions among
them (*life is dynamic)
-defined functions for specific subcellular components, cell types & tissues and
dynamic interregulation b/w them.
-Mechanism for sensing & responding to alterations in surroundings
-via biosignaling, eg. ligands, receptors, signal transduction/kinase cascades
commonly used for vision, taste, smell & neurons, paracrine &endocrine systems
-A capacity for self-replication & self-assembly
-Clonal vs. Non-clonal self-replication: No organism is perfectly clonal. Clonal
refers to the mutation rate being the element of change, eg. bacteria & viruses. Non-
clonal refers to genetic recombination being the mechanism of change, eg. animals &
humans. Bacteria & viruses have high mutation rates compared to any other living
organism. Mutation leads to diff isoforms of gene products
-A capacity to change over time by gradual evolution
-Relatedness of life forms credited to Darwin (origin of species)/Wallace
(individual life form is unit of selection). Darwin came up with the theory first but didn’t
want to expose it just yet and then Wallace came up w/ it sent it to Darwin & Darwin
published his work in his name. Richard Dawkins in 1989 determined the selfish gene &
that the gene is the unit of selection
-Supernova: the explosive death of a massive star whose energy output causes its expanding
gases to glow brightly for weeks/months.
-Supernova remnant: the glowing, expanding gaseous remains of a supernova explosion; E from
supernova can fuse nuclei.
-Nebula: a diffuse mass of interstellar dust, gas/both visible as luminous patches/
areas of darkness depending on the way the mass absorbs/reflects incident radiation (some nebula
are remnants of supernova)
What is Biochemistry?
-Biochemistry is the structures, mechanisms & chemical processes shared by all organisms &
provides organizing principles that underlie life in all its diverse forms, ie. The molecular logic of
-Elements are used to make biomolecules (from other molecules=metabolism) by life forms. They
interact to extract energy from the environment (organic/ sunlight) & to replicate, ie. Biochem is
the study of how biomolecules from a living organism interact.
-10^27 atoms make a human body
-Life obeys physical laws and cells are a fundamental unit of life. Biomolecules are formed from
elements (C,H,N,Omoleculesbiomolecules [AA, NA, CHO, FAT]. Water is the solvent for
biochem (amount of pro in water makes up the pH scale)
The Origins of life
T=0 :20 billion years ago, the BIG BANG occurred
T=sec :H & He formed
T=billions of years :universe expanded & cooled; gravity formed stars & gravity from dark
matter produced planets; some stars expanded & exploded into Supernova & the energy from that
formed the periodic table of elements
T=16 billion years :First life began (earth was formed 4 billion years ago (BYA) What is Life?
-A book by Erwin Shrodinger, 1944 that was revisited in 1994 that says Life must be explained
by physical laws. There is NO “vital force” or vitalism and that the sum of individual molecules
& physical laws, results in life.
-Life appears to be very diverse but at the biochemical level, life is very uniform, ie. Virus,
bacteria, yeast, humans, etc have the same types of elements, same types of monomeric
macromolecule subunits (AA—proteins, NA—DNA/RNA, CHO—starch/glycogen & FA—
lipids), same structural units (cell/gene), same metabolic pathways (catabolism—breaking
down/anabolism—synthesis), same genetic code & same evolutionary ancestors
-Where did life come from? Studied by the Pluto mission in 2006…2015?; life may have come
from abiotic factors with RNA being the first molecules since its able to replicate, act as an
enzyme (due to peptide bonds) & is an info-containing molecule.
-Life began 4 BYA. The basic unit is either a cell/gene. Life has a complexity which requires
energy, can self replicate, can sense environment, has specialized, regulated components & has an
evolutionary history. Life appears to be diverse but uniform at the level of biochemistry.
1.1 Cellular Foundations
Cells are the structural & functional units of all organism
-The smallest living unit is the cell.
-The smallest cell is the mycoplasma: eg. obligate parasites—not free living; 300nM in
diameter & 1x10^-4 mL volume. Size is limited by a minimum # of molecules required to
replicate & extract energy. Craig Venting synthesized a human genome based on mycoplasma,
aka mycoplasma laboratorium; started eliminating genes from it that are useful or notsynthetic
life form has been made.
-The largest cell is the Green Algae Nitella: 2 cm in diameter & size is limited by rate of
diffusion of solutes in water
*with inc cell size, surface-vol ratio dec making it harder for diffusion to occur
-Intestinal cells have fingerlike projections that increase surface volume/ratio
-Neuronal cells are 10nm wide & 10mm long; the neuronal theory of cell was made by
Santiago Ramon y Cajal who noticed that cells in the neuronal system are not continuous but are
separated by gaps.
-The smallest free living cell is SAR11 which is a bacteria; 100 000:1million per seawater
teaspoon; the most abundant sea organism & a 2 million bases size genome which codes for 1-
-The biggest living organism is Armillaria ostoyae (a fungus), it covers 2200 hectares and is
24,000 years old.
-Next on the list are humans, aka homo sapiens made up of 1x10^14 human cells + 1x10^15
bacterial cells. Each human cell has 3 billion bases of DNA, 30-40 000 genes (rRNA, tRNA,
mRNA—codes for proteins in the form of codons which form the genetic code). Virolution is the
theory that viruses orchestrate our evolution, eg. a virus is responsible in making our placenta but
its not in our genome instead the virus actually infected us, gets deactivated inside our body &
through mutations are no longer able to make other viral copies, eg. sinisitin 1 &2 provided us w/
an advantage know as endosymbiosis w/ retrovirus. “Encode”(Encyclopedia of DNA elements) is
a project that systematically mapped regions of transcription, transcription factor assoc’n,
chromatin structure & histone modification which enabled us to assign biochemical functions for
80% of our genome. -Has specializations such as muscle cells, neuronal cells & blood cells. Differentiation occurs in a
single cell that results in all cell types, particularly stem cells; its due to differential gene
expression mostly at the level of transcription, eg. Spermatozoa (1 N), 2 cell stage embryo
(mitochondrial DNA is maternally related; doesn’t recombine; very easy to track lineages w/ Y
chromosome & mitochondrial DNA), Pancrease secretory cell (2N), skeletal muscle (2N) &
Erythrocytes hemoglobin (2N), plant stem cells
-Monoploid (1 set of chromosomes; majority of prokaryotes), diploid/haploid (2 sets of
chromosomes/half the normal 2 sets), polyploidy (>2 sets of homologous chromosomes, triploid,
tetraploid, etc) & aneoploid (numerical change in only a part of a chromosome set; usually
Receptors & transport across membranes (G protein coupled signal transduction)
-Transporter proteins in the p.m. allow passage of certain ions & molecules. There are receptor
enzymes/proteins such as ligands that transmit signals into the cell & participate in reaction
pathways. Gated ion channels are also present on p.m. of cells activated by ligands to bring ions
in. These are ways that we sense & react to the external world. These components in pm are not
covalently linked providing its flexibility allowing for changes in shape & size of cell. This
growth & cell division occurs w/o loss of membrane integrity
-Tight junctions= cells are juxtaposed, ie. Beside each other & there are no extracellular
-Desmosomes=fibrous plaque that welds cells; extracellular space is present for
movement of solutes
-Gap junctions=called plasmodesmata in plants; provides connections w/ openings b/w
-Plasmodesmata=called gap junctions in animals; same function
Prototypical cells for biochemistry:
1. Prokaryotes=microorganisms w/o nuclear envelopes. Seemed to be more involved in
terms of respiration. Divided into bacteria & archaea
*Eschericia coli (E.coli)—non photosynthetic; a harmless inhabitant of the human
intestinal tract. Has a protective outer membrane & inner membrane that encloses
nucleoid; b/w them is a thin but strong layer of polymer (peptidoglycan) which gives cell
its shape & rigidity. In archae rigidity is due to pseudopeptidoglycan & their membranes
also have a thin lipid bilayer penetrated by pro but their lipids are different from those in
Nucleoid contains single, simple, long circular DNA, aka plasmids (found in bacteria,
self-replicating, circular, relatively small, specialized function such as antibiotic
resistance & used in molecular cloning of DNA). Many bacteria exist as individual cells
but some show simple social behaviour forming many-celled aggregates (eg.
*Cyanobacteria (eg. Synechocystis sp PCC6803)—photosynthetic.
2. Eukaryotes=nucleus consists of nuclear material enclosed w/in a double membrane, aka
nuclear envelope. Eg. Saccharomyces Cereviciae (S. ceriviciae)—non-photosynthetic;
easier to work w/ than humans & Chlamydomonas reinhardtii (C. reinhardtii)—
photosynthetic; unicellular algae.
Features of cells
-Plasma membrane: tough, flexible lipid -Cytoplasm: internal volume of the cell;
bilayer selectively permeable to polar when centrifuged at 150000g, seperates into:
substances; incl membrane pro that help w/ -Supernatant: cytosol is a
transport, signal reception & as enzymes. concentrated soln of enzymes, RNA,
monomeric subunits, metabolites & inorganic ions; can be -Coenzymes: compounds essential to many
decanted/poured out easily enzyme-catalyzed rxns
-Pellet: particles & organelles eg. -Ribosomes: supramolecular structures
ribosomoes, storage granules, -cells must replicate DNA & transcribe
mitochondria, chloroplasts, genes; DNA is useless unless it goes through
lysosomes, ER; mostly sticks at the transcription & becomes RNA.
bottom of the tube -Must translate mRNA into proteins.
-Cytosol: aq cell contents & suspended -Cells are mostly 5-100uM long
particles & organelles; liquid of cytoplasm -Prokaryotes vs. eukaryotes (table 2-1 in
-Metabolites: small organic molecules that ppt)
are intermediates in biosynthetic & -Have organelles, eg. mitochondria, nucleus
degradative pathways & ribosomes in eukaryotes; ribosomes,
nucleoid in prokaryotes.
Three Domains of Life (Fig 1-4)
-Phylogeny relationships b/w the 2 domains are illustrated by the family tree based on the
similarity in nucleotide sequences of the rRNAs for each group. The more similar, the closer the
location of the branches w/ the dist b/w them representing the degree of diff b/w the 2 sequences.
Family trees like this can also be based on similarities across species of the a.a. sequences of a
1 &2. Prokaryotes are divided into:
-Bacteria: inhabits soils, surface waters & tissues of living/decaying organisms
-Archaea: recognized by Carl Woese inhabit extreme environments eg. salt lakes, hot
springs, highly acidic bogs & ocean depths.
*Have subgroups distinguished as either anaerobic (no O2 thus adapt by transferring e-s
to nitrate (N2), sulphate (H2S) & CO2 (CH4); some are obligate anaerobes—die b/c of
exposure to O2 & some are facultative anaerobes—able to live w/ or w/o O2)/aerobic
3. Eukarya: evolved from the same branch that gave rise to 2 groups of prokaryotes, ie. Are more
closely related to archae than to bacteria.
-We can also classify organisms based on how they obtain energy & C needed for synthesis (fig
-Phototrophs=trap & use sunlight
-autotrophs=obtain C from CO2
-heterotrophs=obtain C from organic compounds
-Chemotrops=derive energy from form oxidation of chemical fuel
-lithotrophs=oxidize inorganic fuels
-organotrophs=oxidize organic fuels
Eukaryotic cells have various membranous organelles which can be isolated for study
-Albert Claude, Christian de Duve & George Palade developed methods for separating
organelles from cytosol & from each other, ie. Fractionated into sub-cellular components:
*Typical cell fractionation, cell/tissues in soln are gently disrupted by physical shear which
ruptures the pm but leaves most of the organelles intact; homogeneate is centrifuged, organelles
differ in size thus sediment at diff rates
a. Homogenization of tissue: breaks cells & disperse their contents in an aq buffer; the
sucrose medium has similar osmotic pressure to organelles creating equilibrium for water in/out
of organelles which would swell & burst if in a soln of low osmolarity.
b. Differential centrifugation: results in rough fractionation of cytoplasmic contents
which may be further purified by isopycnic centrifugation. Large & small particles in suspension
can be separated by centrifugation at diff speeds
c. Isopycnic (ie. Same density) centrifugation (sucrose-density): particles of differing
buoyant densities (due to diff lipid:pro ratios in each organelle) are separated by this type of centrifugation via a column of a solvent w/ a graded density (inc from top to bottom); a solute eg.
sucrose is dissolved at diff [ ] to produce a density gradient. When the mix of organelles is
layered on top of the density gradient & tube is centrifuged at high speed, individual organelles
sediment until their buoyant densities is exactly the same as the gradient’s. Each layer can then be
collected for further study.
Cytoskeleton of cells
-cytoskeletal/cytoplasmic filaments are dynamic, 6-22 nm in width & composed of polymerized
subunits. The 3 general types of filaments differ in width, composition & specific func but all
provide structure & organization to the cytoplasm & shape to the cell: actin filaments
(mircrofilaments), microtubules & intermediate filaments; actin & microtubules help produce
motion of organelles/the whole cell.
-Filaments are not permanent structures, they undergo constant disassembly & reassembly;
locations are not fixed but may change due to mitosis, cytokinesis, amoeboid motion/changes in
cell shape; these are regulated by other pro.
-Motion of organelles are powered by energy dependent motor pro: enodmembrane system
(segregates specific metabolic processes & provides surfaces for enyzyme-catalyzed rxns to
occur), exocytosis & endocytosis (transport in/out of cell, respectively involving membrane fusion
& fission), provide paths b/w cytoplasm & surrounding medium, allowing for secretion of inside
cell substances & uptake of extracellular materials.
-The motion & position of organelles & cytoskeletal elements are under tight regulation;
interaction b/w them are non-covalent, reversible & subject to regulation in response to various
Cells build supramolecular structures
-Macromolecules are built from monomeric subunits—greatly differs in size
-Proteins are much smaller than ribosomes(~20nm diameter) which are much smaller than
organelles; RNA has a hydroxyl group at C2 which makes it more unstable than DNA—H in C2
makes it less reactive. Nucleic acids are built from 5 nitrogenous bases (A,C,T,G,U), 2 5C sugars
(RNA & DNA) & a phosphate ion.
-Cellular materials are constructed from 20 aa, nucleic acids, 5 components of membrane lipids
& the parent sugar which is glucose. *Phosphate is a component in both lipids & nucleic acids
-Macromolecules are used to make supramolecular complexes; they’re held together by
noncovalent interactions such as H bonds, ionic interactions, hydrophobic interactions& van der
Waals forces, all are weaker than covalent bonds but together stabilize these complexes.
*extinct: no longer in existence vs. extanct: in existence
*in vitro—in glass vs. In vivo—in the living; in vitro is used to study purified molecules to
understand biological processes but a given molecule may behave diff in the cell & in vitro
-all cells are bounded by a pm, have a cytosol containing metabolites, coenzymes, inorganic ions
& enzymes, they have a set of genes housed in nucleus/nucleiod of bacteria/archae or eukaryotes,
-phototrophs use sunlight & chemotrophs oxidize fuels by passing e-s to good e- acceptors
-cytoskeleton give the cell its shape & rigidity & serve as rail tracks for organelles
-there are 3 domains of life. Macromolecules are made from monomeric
subunitssupramolecular complexes are made from macromoleculescells are made from
1.2 Chemical Foundations
-Antoine Lavoisier noted the relative chemical simplicity of the mineral world & compared it to
the complexity of the plant & animal worlds in which he know were composed of compounds
rich in H(1b), O (2b), N (3b),C (4b),; these elements make up 99% of cellular mass+ tiny amt of
trace elements. Thus the lightest elements form the strongest bonds. C is the main element in biomolecules capable of making 4 bonds (high e.n. high versatility; H has a partial + charge
which results in H bonding w/ other molecules thus important 3D structures can form) ; organic if
C-H but H. Trace elements are essential to the func of specific pro incl enzymes, ie. As cofactors
to move things around & catalyze rxns; mg/day. Bulk elements (eg. H,O,N,C) are structural
components measured in g/day
-Biochemical processes are very similar in all life forms. Eg. A study by Jacques Monod
confirmed that all organisms share a common evolutionary origin based in the universality of
chemical intermediates & transformations, aka “biochemical unity”
-Non-covalent H bonds require 23kJ/mol which is the same amt of energy that comes form molec
motion. The greater the energy required for bond dissociation/breakage, the stronger the bond.
Biomolecules are compounds of C w/ various functional groups
-C is 50% dry weight of cells
-C single bonds: w/ H atoms; tetrahedral & free rotation
-C double bonds: w/ O & N atoms; constrained in the same plane, ie. Shorter bonds & no
-C triple bonds: rare in biomolecules
-Organic compounds are molecules w/ covalently bonded C compounds. These covalently linked
C atoms can form linear chains, branched chains & cyclic structures. Functional groups (fig 1-
15) are groups of atoms attached to an organic compound C-H backbones which gives it a special
functionality & it’s what determines chemical properties. Many biomolecules are polyfunctional
meaning they contain 2/more types of func groups. *Carbonyl groups are present for every pro. S
func groups can form connections b/w pro.
Cells contain a universal set of molecules
-Genome is the genetic makeup. Proteome is the protein makeup. Metabolome are the small
molecules in the cell incl AA, NA, lipids, sugars & their phosphorylated derivatives &
mono-/di-/tri-carboxylic acids. There are also secondary metabolites only present in certain types
of cells & organisms, eg. vascular plants which incl compounds like morphine, quinine, nicotine
& caffeine that give plants their scents.
*2 ways to describe molec mass: molec weight which is defined as the ratio of the bass of a
molecule of that substance to 1/12 mass of 12C; no units. Relative molec mass is the mass of one
molec or the molar mass divided by Avogadro’s num; expressed in Daltons/Da (1 Da=1/12 mass
Macromolecules are the major constituents of cells
-Many biomolecules are macromolecules which are polymers of high molec weight made from
simple subunits. Polymers contain tens-millions of subunits; requires large input of energy for
synthesis; can assemble into components of supramolecular complexes eg. ribosomes. Shorter
polymers are called oligomers
-Examples: Proteins (20 aa types; some catalyze rxns, are enzymes & used as structural
components, signal receptors, transporters; maybe the most versatile), DNA (A,C,T,G base pairs)
& RNA (A,C,G,U base pairs)—store, transmit genetic info OR have structural, catalyctic roles in
supra complexes), polysaccharides (simple sugars, eg. glucose; energy-rich fuel stores, rigid
structural components of cell walls & extracellular recognition elements), lipids (hydrocarbon
derivatives; energy-rich fuel stores, pigments, intracellular signals & structural elements)
-Water comprises the majority of the weight in cells, next are pro; lipids & inorganic ions make
up a smaller %. Pro & nucleic acids are often referred to as informational macromolecules b/c of
their info-rich subunits seq.
3D structure is defined by configuration & conformation
-3D structures of biomolecules vary: Stereochemistry is the arrangement of a molecule’s atoms in
3D space; a C containing compounds commonly exist as stereoisomers meaning the molec have
same chemical bonds but diff configuration (fixed spatial arrangement of atoms) Biomolecules
interact stereospecifically. *[1 chiral C=2 stereoisomers=2^#chiral C] -Configuration (fixed) is determined by the presence of: 1) = bonds (cis vs. trans) in which there
is no free rotation, 2) chiral centers resulting in an asymmetric carbon w/ 1 C forming 4 bonds w/
4 diff substituents. Stereoisomers are unique in that they can’t be interconverted w/o temp
breaking one/more covalent bonds.
-Maleic acid (ci