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Biochemistry - Reviewer
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  • Course
  • BIOL 121 (BIOL211)
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  • Saint Louis University
  • Book
  • Principles of Biochemistry 7e

Unlock the secrets of life with our meticulously crafted notes on Biomolecules and Biochemistry! Dive deep into the molecular foundations of living organisms, exploring the intricacies of proteins, carbohydrates, lipids, and nucleic acids. Our comprehensive notes distill complex concepts into diges...

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  • March 26, 2024
  • 71
  • 2023/2024
  • Class notes
  • Prof. r. dimaguiba
  • All classes

Subjects

  • biochemistry
  • biomolecules
  • lipid
  • dna
  • carbohydrates
  • proteins

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BIOMOLECULES
Prelims Reviewer – Lecture

FOUNDATIONS OF BIOMOLECULES - Prokaryotes (without the nuclear
Biochemistry – describes in molecular terms the envelopes “pro is before; karyon is
structures, mechanisms, and chemical nucleus”)
processes shared by all living organisms and
provides organizing principles that underlie life
in all of its diverse forms.
CELLULAR FOUNDATIONS
Universal Features of Living Cells
1. Plasma Membrane
- With lipid and protein molecules
- Hydrophobic barrier
- Passage of inorganic ions and most
charged and polar particles through
transport proteins
- Receptor proteins transmits signals into
the cells
2. Cytoplasm
- The internal volume bounded by the
plasma membrane
Cytosol – the aqueous solution, highly
concentrated solution containing
enzymes and the RNA molecules that
encode them
- Hundred of small organic molecules
(metabolites), intermediates in
biosynthetic and degenerative
pathways
- Coenzymes, compound essential to
many enzyme-catalyzed reactions and
also proteasomes
- Ribosomes – small particles composed
of protein and RNA molecules that are
the sites of protein synthesis
3. Nucleus or Nucleoid
- Storage of genetic material
- Where the genome (the complete set o
genes composed of DNA) is stored and
replicated.
- Nucleoid (bacteria and archaea)
- The nucleoid in bacteria is not
separated from the cytoplasm by a
membrane
- Nuclear membranes (eukaryotes “eu is
true and karyon is nucleus”)

,Eukaryotic Cytoskeleton - Polyfunctional: with 2 or more types of
1. Actin (Red) functional groups
2. Microtubules (green) – surrounding the
nucleus
3. Intermediate Filaments
Bacteria also have filaments (actin like) and
microtubules to organize their cytoplasm.
Subcellular Fractionation
- Separation of organelles from the
cytosol by differential centrifugation
- For investigating structures and functions
- Developed by Albert Claude, Christian
De Duve, and George Palade




Universal Set of Small Molecules
1. Metabolites – different small organic
molecules in the cytosol
Types: amino acids, nucleotides, sugars and
their phosphorylated derivatives, and mono-,
di-, and tricarboxylic acids
2. Polar/Charged – water soluble
3. Secondary Metabolites – plants
CHEMICAL FOUNDATIONS
(morphine, quinine, nicotine, and
- Formation of bonds (single, double,
caffeine)
triple, and tetrahedron)
BIOLOGICAL MONOMERS
- Covalently linked (linear and branched
Functional Groups: amino, carboxyl, carbonyls,
chains, cyclic structures)
alcohol, methyl, phosphate. Sulfhydryl, and
- Most are derivatives of hydrocarbons (H
others
atoms replaced by a variety of
Covalent Bonds – single, double, and triple
functional groups)
Ionization State (or not)
Solubility
Monomer Polymerization
Weak Bonds = H-bonds, Ionic bonds,
hydrophobic interactions, and Van der Waals
forces

Metabolome – entire collection of small
molecules in a given cell
Macromolecules – major constituents of cells
- Polymers with molecular weights above
5,000
Oligomers – short polymers
Examples: - Types: Proteins, nucleic acids, and
- Alcohols, amines, aldehydes, ketones, polysaccharides (MW: 500 or less)
and carboxylic acids
Biochemistry uses both molecular weight (M r)
or Molecular Mass (m) in “Daltons”

,Carbon has Mr = 12 or m+12D 1. Ball and Stick Model – bond angles and
- Very small proteins have a mass of center-to-center bond, bond lengths
10,000D = 10kD representation
- Very large ones have mass of >1million 2. Space-filling Model – the radius of each
D = 1,000kD atom is proportional to its van der Waals
- Titin a muscle protein is approximately 3 radius
million D - Contours define the space occupied by
PROTEINS the molecule
- Long polymers of amino acids Configuration is conferred by:
- Largest fraction of the cell 1. Double bonds – no freedom of rotation
- Types: Enzymes, structural, signal 2. Chiral centers – substituent groups are
receptors, transporters arranged in a specific orientation
Proteome – sum of all proteins functioning in
a given cell
NUCLEIC ACID
- DNA and RNA – polymers of nucleotide
- Stores and transmit genetic information
RNA – structural, catalytic roles in
supramolecular complexes
POLYSACCHARIDES
- Polymers of simple sugar (glucose)
Functions
1. Energy-rich fuel stores
2. Rigid structural components of the cell Geometric Isomers
wall 1. Cis (L. “on the side”) – groups on the
3. Extracellular recognition elements same side of the double bond
Oligosaccharides – attached to proteins or 2. Trans (“across”) – groups on the
lipids, for cellular signals opposite side
LIPIDS
- water-insoluble hydrocarbon derivatives
- Structural components of membranes
- Energy-rich fuel stores
- For pigments
- Intracellular signals
3D Structure is Described by Configuration and
Conformation
Stereochemistry – the arrangement of the
molecule’s constituent atoms in #D space
In the vertebrate retina, the initial event in light detection is the absorption of visible light by the 11-cis-
Stereoisomers – molecules with the same retinal. The energy of the absorbed light converts 11-cis-retinal to all-trans-retinal triggering electrical
changes in the retinal cell that lead to a nerve impulse.
chemical bonds but different configuration,
fixed spatial arrangement of atoms.
REPRESENTATION OF MOLECULES

, Enantiomers – represent nonsuperimopasable - the rate of synthesis balances the rate
mirror images of each other of breakdown, consumption, or
Chiral Atom/Chiral Center – asymmetric conversion to other product
carbon atom The Flow of Electrons Provides Energy for
Achiral Atom – a tetrahedral carbon has only Organisms
dissimilar groups, only one configuration is - energy from the sunlight (derived
possible indirectly or directly)
- The molecule is symmetric
- The molecule is superimposable on its
mirror image
Diastereoisomers – pairs of stereoisomers that
are not mirror images of each other


Bioenergetics – the study of energy
transformation in living systems




RS SYSTEM
- A nomenclature for compounds with
more than one chiral center
- Each group attached to a chiral carbon
is assigned a priority
- R (L. Rectus “right”) – priority decreases Related Enzymatically Catalyzed Reactions
in clockwise order forms a Pathway
- S (L. Sinister “left”) - counterclockwise 1. Metabolic Pathway – produces energy
or valuable materials
2. Signal Transduction Pathway – transmits
information
Metabolism is regulated to achieve balance
and economy.



PHYSICAL FOUNDATIONS
- living organisms exist in a dynamic
steady state
- small molecules, macromolecules,
supramolecular complexes are
continuously synthesized and broken
down in chemical reactions
(hemoglobin molecules, glucose like
CO2 and fat)

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