1.1- What is Life?
All organisms obey the same chemical and physical laws that rule the universe.
1. Life is complex and dynamic. All organisms composed of the same elements
(mainly carbon, nitrogen, oxygen, hydrogen, sulfur and phosphorus). Living
processes are comprised of thousands of reactions where vast numbers of
2. Life is organized and self-sustaining. Living organisms are organized from
smallest to largest (atom to organism). The functional capacity of each level
depends on the structural/chemical properties of the one below it. Complex
structures are made of biomolecules and macromolecules. Hundreds of
biochemical reactions sustain life and are catalyzed by enzymes and organized
3. Life is cellular. Cells are the basic unit of life, they differ greatly in structure in
function but all have a membrane (to control transport). Cells can only arise from
the division of existing cells.
4. Life is information based. Living organisms are information-processing
systems. Maintenance of structural integrity and metabolic processes involves
interaction of molecules between cells. Information is expressed in coded form
inherent in the three dimensional structure of biomolecules. Protein synthesis is
regulated by genes. Protein has a specific structure that allows it to interact with
specific molecules with complementary shapes information is transferred during
this binding process.
5. Life adapts and evolves. All life has a common origin. New forms arise from
older forms. Competitive advantage from organisms that may exploit a specific
energy source within a habitat. Interplay between environmental change and
genetic variation can lead to the accumulation of favorable traits and eventually
to increasingly different forms of life.
1.2 – Biomolecules
- living organisms comprised of thousands of different organic and inorganic molecules
- Water is 50-95% of a cell’s weight - sodium, potassium, magnesium, and calcium ions may all make up 1% of a cells
- organic molecules make up the rest, comprised of six elements: carbon, hydrogen,
oxygen, nitrogen, phosphorus, sulfur.
- trace amounts of metallic and non-metallic elements
- structural complexity/diversity of organic molecules is thanks to the ability of carbon to
form four strong, single covalent bonds to other carbon atoms or other atoms from other
elements. Organic molecules with many carbons can form complicated structures.
Functional Groups of Organic Biomolecules
- Organization of the functional groups determine chemical properties of the
- Most biomolecules contain more than one functional group
- Contribute to the behaviour of any molecule that contains it
Alcohol ROH Hydroxyl Polar (watersoluble).
Aldehyde RCOH Carbonyl Polar, found in some
Ketone RCOR’ Carbonyl Polar, found in some
Acids RCOOH Carboxyl Weakly acidic. Has a
negative charge when
it donates a proton
Amine RNH 2 Amino Weakly basic. Has a
positive charge when
it accepts a proton
Amide RCONH 2 Amido Polar but does not
bear a charge
Thiol RSH Thiol Easily oxidized. Can
form disulfide bonds
Ester RCOOR’ Ester Found in some lipid
molecules Alkene RCH=CHR’ Double bond Important structural
component of many
in lipid molecules
Major Classes of Small Biomolecules
- Cells contain four families of small molecules = amino acids, sugars, fatty acids,
- They are used in the synthesis of larger molecules (many are polymers)
- Some molecules have special biological functions. Ex: ATP = cellular reservoir for
- Many small organic molecules involved in complex reaction pathways
- Amino acids proteins catalysts & structural elements
- Sugars carbohydrates energy sources & structural elements
- Fatty acids energy sources & structural elements of complex lipid molecules
- Nucleotides DNA/RNA Genetic information/Protein synthesis
Amino Acids and Proteins
Amino acids = amino group (NH ) and2carboxyl group (CO-OH).
o Amino group can be alpha (attached to the carbon atom immediately
adjacent to the carboxyl group. Most common), beta (attached to the 2
carbon), or gamma (attached to the 3 carbon).
Many naturally occurring amino acids are not alpha. Ex: beta-
o Side chain (R group) also attached to the alpha carbon. Determines the
chemical properties of the amino acids once it has been incorporated into
protein (like solubility)
- Some standard amino acids have unique functions (ex: neurotransmitters glycine
and glutamic acid) o Protein also has nonstandard amino acids that are modified versions of
the standard amino acids
o Structure and function of amino acids are often altered by conversion of
certain amino acid residues to derivatives via phosphorylation,
hydroxylation, and other chemical modifications
- Amino acids primarily used in synthesis of polypeptides (which play a variety of
roles in living organisms transport proteins, structural proteins,
- Individual amino acids are connected in peptides and polypeptides with a peptide
Alpha amino acids Beta
Gamma amino acids
Sugars and Carbohydrates
Sugar = has alcohol and carbonyl functional groups. Basic unit of carbohydrates (the
most abundant organic molecules found in nature).
- ketoses and aldoses. Ex: glucose is an aldohexose (six-carbon ending with an
aldehyde), fructose is a ketohexose (six-carbonending with a ketone)
Carbohydrates = monosaccharides (glucose & fructose) or polysaccharides (starch &
Some biomolecules contain carbohydrate components: nucleotides (contains ribose or
deoxyribose), proteins, lipids, glycoproteins/glycolipids appear on the external surface of
cell membranes in multicellular organisms (important for cell interactions).
Fatty acids = monocarboxylic acids usually having an even number of carbon atoms.
Formula is R-COOH. Can be saturated or unsaturated
- Under physiological conditions the carboxyl group exists in the ionized state (R—
COO) - o Charged carbonyl group has an affinity for water but the long nonpolar
hydrocarbon chain usually renders most fatty acids insoluble in water
- Don’t usually appear as independent/free molecules usually components of lipid
Nucleotides and Nucleic Acids
Nucleotides have three components: five-carbon sugar (ribose or deoxyribose), a
nitrogenous base, and one or more phosphate groups.
- Nitrogenous bases are heterocyclic aromatic rings with a variety of substituents
o Either a bicyclic purine, or a monocyclic pyrimidine
Purines = Adenine (A), Guanine (G)
Pyrimidines = Thymine (T), Cytosine (C), Uracil (U)
Nucleotides participate in many biosynthetic/energy-generating reactions. Also are the
building blocks for nucleic acids
Nucleic acid = DNA and RNA
- DNA deoxyribonucleic acid. Repository of genetic information. Structure
involves two anti-parallel polynucleotide strands wound around eachother to form
a right-handed double helix.
o Contains purines (A/G) and pyrimidines (T/C) pair A—T and G—C
o Double helix forms due to complementary pairing b/w bases due to
formation of hydrogen bonds
o DNA is made up of coding and noncoding sequences
Coding sequences = genes. Specify the structure of functional gene
products like polypeptides and RNA molecules.
Some noncoding sequences have regulatory functions (controlling
the synthesis of certain proteins), while some have undetermined
- RNA = ribonucleic acid. Contains ribose instead of deoxyribose and uracil instead
of thymine. Single stranded. Fold into complex three-dimensional structures
created by local regions of complementary base pairing. Strand can serve as a
template when the DNA double helix unwinds. o RNA molecules synthesized via transcription.
Complementary base pairing specifies the nucleotide base
sequence of RNA
o Three types: messenger RNA (mRNA), ribosomal RNA (rRNA), and
transfer RNA (rRNA)
mRNA each sequence possesses information that codes directly
for the amino acid sequence of a polypeptide.
rRNA makes up ribosomes which convert the mRNA base
sequence into the amino acid sequence for the polypeptide.
tRNA transfer RNA molecules to the ribosome during protein
o Also noncoding RNA (ncRNA) was discovered and is not involved in
protein synthesis. Have roles in other cell functions.
Short interfering RNA (siRNA) important in RNA interference, an
antiviral defense mechanism
Micro RNA (miRNA) regulate the timing of mRNA synthesis
Small nuclear RNA (snRNA) facilitate the process by which mRNA
precursor molecules are transformed into functional mRNA
Small nucleolar RNA (snoRNA) assist with maturation of
ribosomal RNA during ribosome formation
Gene expression controls when/if the information encoded in a gene will be accessed.
- Begins with transcription where a base sequence of a DNA segment is used to
synthesize a gene product.
- Transcription factors regulate the expression of protein-coding genes when they
bind to specific regulatory DNA sequences referred to as response elements.
o Transcription factors are synthesized and/or regulated by an information-
processing mechanism initiated by a signal molecule (ex: insulin) or an
abiotic factor like light.
1.3 – Is the Living Cell a Chemical Factory? Autopoiesis is used to describe living organisms. Life emerges from thousands of self-
regulating biochemical reactions.
- Metabolism is made possible via the constant flow of energy and nutrients and
functionality of enzymes.
o Functions of metabolism
Acquisition and utilization of energy
Synthesis of molecules needed for cell structure and functioning
(proteins, carbs, lipids, nucleic acids…)
Growth and development
Removal of waste products
o Metabolism requires lots of useful energy!
1) Nucleophilic Substitution Reactions = one atom/group is substituted for another
Attacking species = nucleophile anions/neutral species w/ non-bonding electron
Electrophiles = deficient in electron density, so are easily attacked by the
Outgoing nucleophile = leaving group
Ex: reaction of glucose with ATP, hydrolysis reactions 2) Elimination Reactions = double bond is formed when atoms in a molecule are
ex: removal of water from biom