Chapter–2
Fundamentals
Biochemistry–1
(1427-101)
2.1 Biochemistry Fundamentals
2.2 Structure of Prokaryotic Cells
Dr. Ahmed Almehdi
2.3 Structure of Eukaryotic Cells
Biochemistry–1
Biochemistry, the molecular basis of life – McKee , 7th Ed (2020) , Oxford University Press
2.1 Biochemistry Fundamentals
▪ Understanding of the biological context of biochemical
processes is enhanced by examining following concepts:
water, biological membranes, self-assembly, molecular
machines, molecular crowding, proteostasis, signal
Biochemistry , Dr. Ahmed Almehdi
transduction, calcium, and metabolism
1) Water:
✓ Has unique polar structure and interacts with a wide range
of substances, such as hydrophobic interactions
between water and a nonpolar substance
2) Biological Membranes:
✓ thin, flexible, and stable sheet-like structures
✓ are selective physical barrier made of
phospholipid bilayer with integral and peripheral proteins
Cont. …2.1 Biochemistry Fundamentals
3) Self-Assembly:
✓ many parts of living organisms are supramolecular structures,
such as (i) ribosomes (the protein-synthesizing particle that are
Biochemistry , Dr. Ahmed Almehdi
formed from several types of proteins and RNA
(ii) proteosomes (large protein complexes that degrade proteins)
✓ Self-assembly involves a balance between the
✓ Interactions of hydrophilic groups with water and the water to be
excluded by hydrophobic groups)
✓ Some self-assembly need assistance,
molecular chaperones (protein molecules
that, among other functions, prevent
inappropriate interactions during the
folding process
Cont. …2.1 Biochemistry Fundamentals
4) Molecular Machines:
✓ many multisubunit complexes (mainly proteins) function as molecular
machines: physically moving parts, that convert energy into motion
(energy-driven changes in the three-dimensional shapes of proteins)
Biochemistry , Dr. Ahmed Almehdi
✓ biological machines binds to and hydrolyze ATP nucleotide to get energy.
The binding referred to as motor proteins
✓ The energy gained from ATP hydrolysis, result in
a change in the subunit’s shape of motor protein
and transmitted to nearby subunits in a process
that resembles a series of dominoes falling.
Such as binding of first subunit of hemoglobin to
oxygen affects the binding (or the release)
in an orderly change in the shape of adjacent subunits
Cont. …2.1 Biochemistry Fundamentals
5) Macromolecular Crowding:
✓ the interior space within cells is crowded
Biochemistry , Dr. Ahmed Almehdi
✓ the concentrations of proteins (the dominant
macromolecule), may be as high as 400 mg/mL
✓ the volume occupied by macromolecules, in a cell is between 20 and
40% and the remaining ~70% of the space is for the small molecules
✓ macromolecular crowding is significant, It is now believed to be an
important for: biochemical reaction rates, protein folding, protein–
protein binding, chromosome structure, gene expression, and signal
transduction
Cont. …2.1 Biochemistry Fundamentals
6) Proteostasis:
✓ each type of living cell has its own characteristic set of proteins,
(proteome) which changes in response to environmental conditions
Biochemistry , Dr. Ahmed Almehdi
✓ mammalian cells have an average of 10,000 types of protein, most of
which are produced in multiple copies (estimated total of 1 billion/cell)
✓ following their synthesis, these enormous numbers of proteins must
fold into their functional shapes, and be transported to their proper
destinations
✓ cells must protect themselves from proteotoxic stress (a lethal
condition results in accumulation of misfolded proteins caused by
oxidative stress, elevated temperatures, and exposure to toxins
✓ cells that have high protein quality control is said to be proteostasis
Cont. …2.1 Biochemistry Fundamentals
6) Cot. Proteostasis :
✓ oxidative damage include infection, inflammation, overconsumption
of certain drugs or exposure to intense radiation, and tobacco smoke
✓ oxidative damage has been linked to at least 100 human diseases
Biochemistry , Dr. Ahmed Almehdi
including cancer, Parkinson’s disease, and Alzheimer’s disease
✓ The processes that monitor and restore proteostasis are referred to
as proteostasis network (PN)
✓ the PN in mammalian cells consists of at least 2000 proteins, including
molecular chaperones (proteins that assist in protein folding or
unfolding, p. 170–172), and proteolytic enzymes
✓ significant research been devoted to proteostasis because PN
deficiencies are an important feature of numerous human diseases.
including: diabetes, cardiovascular disease, and neurodegenerative
diseases such as Alzheimer’s, Parkinson’s, and Huntington’s
Cont. …2.1 Biochemistry Fundamentals
7) Signal Transduction:
✓ biochemical information processes specifies how, when, and where each
type of biomolecule is to be synthesized, utilized, and degraded
Biochemistry , Dr. Ahmed Almehdi
✓ Living organisms require energy and information (signals) for its survival
✓ signal transduction, is the process that organisms receive and interpret
information, examples of eukaryotic signal molecules include
neurotransmitters and hormones
✓ information-processing phases are:
a) Reception: binding of a ligand to a receptor
b) Transduction: the conversion of a primary signal (binding to a receptor
and changing its 3D structure) to a secondary message across a
membrane
Cont. …2.1 Biochemistry Fundamentals
6) Cot. Signal Transduction :
c) Response: a series of reactions cascade that involve covalent
modifications (phosphorylation) of intracellular proteins, that will
Biochemistry , Dr. Ahmed Almehdi
change enzyme activities
d) Termination: living organisms use a variety of signal termination
methods, including destroying or removing signal molecules, or
covalent modification such as activation by phosphorylation are
inactivated by dephosphorylation (removal of phosphate group)
✓ Calcium ion (Ca2+) is a signal molecule that triggers changes of certain
proteins structure and function, such as: release of neurotransmitters
and hormones, protein folding, and muscle contraction
✓ for example the release of insulin from pancreatic β-cells is triggered
by calcium ions
2.2 Procaryotic Cells
▪ Prokaryotes include bacteria and archaea
▪ they have common features: cell wall, plasma
membranes, circular DNA, and no organelles
Biochemistry , Dr. Ahmed Almehdi
▪ prokaryotic cell wall: is a complex structure
Bacteria
primarily for support and protection, made of
peptidoglycan
▪ Plasma Membrane: is directly inside the
cell wall made of phospholipid bilayer
▪ Cytoplasm: contains functional region
such as nucleoid (contains the circular
chromosome). Cytoplasm also contains
small DNA plasmids
Cell membrane
2.3 Eukaryotic Cells
▪ Eukaryotic cells are structurally complex
▪ contains membrane-capsulated organelles
Biochemistry , Dr. Ahmed Almehdi
▪ some of main organelles are: plasma
membrane, endoplasmic reticulum, Golgi
apparatus, nucleus, lysosomes,chloroplast,
mitochondria, and ribosomes Human/anim
▪ Endoplasmic Reticulum: is of two types: al cells
✓ Rough ER: functions as protein
synthesis, folding, and glycosylation
✓ Smooth ER: functions include lipid
biosynthesis and Ca2+ storage
Plant cells
Cont. …2.3 Eukaryotic Cells
▪ Nucleus: contains the hereditary genetic information
▪ Lysosomes: are vesicles that contain digestive
enzymes (recycles biomolecules)
Biochemistry , Dr. Ahmed Almehdi
▪ Mitochondria: are the principle source of
cellular energy
▪ Peroxisomes: are small organelle containing Mitochonderia
oxidative enzymes
▪ Chloroplasts: are organelles found only in plants,
algae, and some protists, specialized for
photosynthesis
Chloroplast
Biochemistry Fundamentals
