3. What is Biochemistry?
• The chemistry that take places within living
systems
• “The study of life at the molecular level”
• “The study of the chemistry of life processes”
2 components: Biology & Chemistry
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4. Biochemistry
• What is the important characteristics of life?
– Extract energy from molecules (nutrients)
– Growth, differentiation & reproduction
– Respond to changes in their environments
• What is the overall goal of Biochemistry?
– To better understand how biochemistry works to
describe biological processes.
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5. The overall goal of biochemistry
• is to describe life’s processes using the language
of molecules, that is, applying the principles and
methods of chemistry to determine molecular
structure from which it is often possible to
explain biological function.
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6. Why should we learn biochemistry?
• Lead us to a fundamental understanding of life
-How do our bodies work?
-What are the biochemical similarities and differences among the
many forms of life?
-How do organisms store and transfer information necessary to
reproduce themselves?
-What primary molecules and processes were involved in the origin
of life?
-How is food digested to provide cellular energy?
-How does a brain cell store mathematical and chemical formulas?
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7. Why should we learn biochemistry?
• Impact on our understanding of Medicine, Health,
Nutrient & the Environment: molecular understanding
of diseases ---such as diabetes, sickle-cell anemia.
Biotechnology: enzymes are used in the
pharmaceutical industry to synthesize complex drugs,
manufacturing fuel alcohol, cleaning up oil and other
toxic spills.
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9. Early history of Biochemistry
• The Chinese in the fourth century B.C. believed
that humans contained five elements:
water, fire, wood, metal, and earth.
• When all elements were present in proper
balance, good health is resulted.
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11. Biological processes and
macromolecules
• Even the smallest living cell contains thousands
of organic and inorganic chemicals, many of
them large molecules called macromolecules.
• All biological processes, including vision,
thinking, digestion, immunity, motion, and
disease conditions result from how molecules
act and, sometimes, misbehave.
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13. Structural and functional
biochemistry
1. Structural and functional biochemistry focuses initially on
discovering the chemical structures and three-dimensional
arrangements of biomolecules, those chemicals that are found in
living matter. To describe biological processes, one must have a
knowledge of the molecular structures of the participating
biomolecules, which then often leads to an understanding of the
function or purpose of the cellular molecules.
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14. Informational biochemistry
2. Informational biochemistry defines the language(s) for storing
biological data and for transmitting that data in cells and
organisms. This area includes molecular genetics, which describes
the molecular processes in heredity and expression of genetic
information and also processes that communicate molecular
signals to regulate cellular activities (i.e.,hormone action).
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15. Bioenergetics
3. Bioenergetics describes the flow of energy in living organisms
and how it may be transferred from one process to another.
(endergonic and exergonic reactions).
How organisms use biochemical reactions and biomolecules to
transfer energy from exergonic to endergonic events will be pivotal
in our understanding of life processes.
The transfer of energy usually means the transformation of one type
of energy to another.
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16. All living matter contains C, H, O, N, P,
and S
Of the 100 plus chemical elements, only about 31 (28%) occur
naturally in plants and animals.
•Elements present in biological material can be divided into 3
categories:
1.Elements found in bulk form and essential for life: Carbon,
hydrogen, oxygen, nitrogen, phosphorus, and sulfur make up about
92% of the dry weight of living things.
2.Elements in trace quantities in most organisms and very likely
essential for life, such as calcium, manganese, iron, and iodine.
3. Trace elements that are present in some organisms and may be
essential for life, such as arsenic, bromine, molybdenum, and
vanadium.
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17. The biochemist’s periodic table. Elements in red: present in bulk form in living cells and
are essential for life. Yellow: trace elements, very likely essential. Blue: present in some
organisms and may be essential.
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18. How these elements were selected by primitive
life-forms during the early stages of evolutionary
development?
•Two hypotheses to explain the selection:
1. There was a deliberate choice because of an
element’s favorable characteristic
2. There was a random selection from the alphabet
soup of elements present in the earth’s crust,
atmospheres, and universe.
So, which one is true??
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19. A comparison of the elemental composition of the earth’s crust and the universe with that
of living matter shown in Figure 1.4 refutes the second hypothesis.
Elemental composition of the universe (blue), the earth’s
crust (pink), and the human body (purple).
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20. Hypothesis 1
• We must conclude that elements were selected according to
their abilities to perform certain structural functions or to
provide specific reactivity.
• Example 1: Carbon forms multiple covalent bonds with other C
atoms as well as with other elements such as N, H, O or S. This
feature allows the construction of long carbon chains and rings
with the presence of reactive functional groups containing N, O
and S as in proteins, nucleic acids, lipids, and carbohydrates.
• Example 2: Iron was selected by evolutionary forces because it is
able to bind the oxygen molecule in a reversible fashion.
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21. Chemical Bonds In Biochemistry
• Biochemistry: chemistry that takes place within living systems.
• The strongest bonds in biochemicals: covalent bonds, eg C-C,
sharing of a pair of electrons between adjacent atoms. Because
this energy is relatively high, considerable energy must be
expended to break covalent bonds. More than one electron pair
can be shared between two atoms to form a multiple covalent
bond. For example, carbon–oxygen (C:O) double bonds. These
bonds are even stronger than C–C single bonds.
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22. Reversible Interactions of Biomolecules Are
Mediated by Three Kinds of Noncovalent Bonds
• Electrostatic interactions: An
electrostatic interaction depends on the
electric charges on atoms.
• Hydrogen bonds: relatively weak
interactions, which are crucial for
biological macromolecules such as DNA
and proteins.
• van der Waals interactions: the
distribution of electronic charge around
an atom changes with time.
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23. Combining elements into
compounds
23
• The combination of chemical elements into
biomolecules great variety in chemical
structure & reactivity
• Nature’s molecules: cations, anions, covalent
compounds, ionic compounds, metal ions,
coordination complexes, & polymers.
24. Combining elements into
compounds
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• Organic & organometallic chemicals: amino
acids, carbohydrates, lipids, vitamins
• Prominent among the natural
organometallic compounds: Heme &
chlorophyll consist of a substituted
porphyrin ring coordinated with metal ion.
25. (a) Heme: containing a porphyrin
ring & iron.
b) chlorophyll: containing a
porphyrin ring and Mg
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28. Biological Macromolecules
• 3 major classes of natural polymeric
macromolecule:
– Nucleic acids, proteins, & polysaccharides
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(Lipids are also considered a
major class of biomolecules, but
because they are not polymeric
macromolecules, they are not
described in this section)
29. Macromolecules
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Types of natural polymers.
(a) Cellulose, a homopolymer
formed by joining many identical
glucose units.
(b) Starch, a homopolymer formed
by joining many identical glucose
molecules. Note that different types
of bonding are used in starch and in
cellulose.
(c) Protein, a heteropolymer formed
by linking together amino acids.
(d) Nucleic acid, a heteropolymer
formed by combining different
nucleotides, A, G, C, and T or U.
30. Cellular reactions
This represents
the chemistry for
combining amino
acids to make
proteins.
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Chemical reaction that connects monomer units is
called condensation and results in the loss of a small
molecule (water).
The reverse process is called cleavage or hydrolysis
(if water is used).
31. Organelles, Cells, & Organisms
• Supermolecular assemblies (organized clusters of
macromolecules)
• i.e.: cell membranes, chromatin, ribosomes, cytoskeleton.
31
Molecules that are complementary
diffuse together to form a complex
that displays some biological activity.
The molecules are held together by
weak and reversible chemical forces.
32. Tree of
life
• Cell = fundamental
unit of life
• 2 basics classification
of organisms based
on morphological cell
structure & anatomy:
eukaryotes &
prokaryotes
• Classification based
on genetic analysis:
Bacteria, Archaea, &
Eukarya
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The
tree
of life
Nature Microbiology vol1: 16048
(2016)
33. Prokaryotic cells
• Most abundant & widespread of organisms
• Characteristics:
– Size range from 1-10μm in diameter
– Cellular components are encapsulated within a cell
membrane & rigid cell wall.
– Interior of the cell: cytoplasm; ribosomes
– chromosome
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38. Storage & Transfer of Biological
Information
• How biological information is transferred from 1
generation to another?
• The flow of info can be described using the basic
principles of chemistry.
• DNA, RNA, proteins are information-rich
molecules that carry instructions for cellular
processes.
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39. Biological information
• The total genetic info content of each cell
(genome) resides in the long, coiled,
macromolecules of DNA.
• 2 ways to express/process informational
message:
– Exact duplication of the DNA
– Expression of info to RNA and then manufacture
proteins
39
40. The storage and replication of
biological information in DNA
and its transfer via RNA to
synthesize proteins that direct
cellular structure and
function.
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41. DNA molecules
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• Long chain, unbranched heteropolymer,
constructed from 4 types of monomeric
nucleotide units.
• Each monomeric unit:
– An organic base containing N
– A carbohydrate
– A phosphate
42. Storage and transfer of Biological
information
DNA DNA
•Self-directed process
•Replication catalyzed by DNA polymerase
•Used as a template to produce a new complementary partner
strand
DNA RNA
•Transcription catalyzed by RNA polymerase
•Similar to DNA replication except that:
– Ribonucleotides (Deoxyribonucleotides)
•Result of the transcription: rRNA, mRNA, tRNA
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44. Storage and transfer of Biological
information
RNA Protein
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• Ultimate product: proteins
• Proteome: full array of proteins made from the
genomic DNA of an organism
• mRNA: intermediate carrier of the info
• DNA: A, T, G, C
• mRNA: A, U, G, C Translation
• Protein: amino acids
45. Synthesis of proteins on ribosomes. Each copy of mRNA may have several ribosomes moving along its length, each
synthesizing a molecule of the protein.
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47. Lecture plan
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Components Mark
Distribution
Quizzes (2) 10%
Tests (2) 20%
Practical 10%
Assignments 10%
Final Exam 50%
Subjected to modification
Quiz
2 quizzes (5%, total 10%)
•Quiz 1 – week 4 – Lecture 1-5
•Quiz 2 – week 11 – Lecture 14-20
Test
2 tests (10%, total 20%)
•Test 1 – week 7 – Lecture 1-13
•Test 2 – week 13 – Lecture 14-25
Tutorial: Tut1(Lec1-5,Week3), Tut2(Lec6-13,Week6), Tut3(Lec14-
20,week10), Tut4(Lec21-26,week13)
Assignment (10%): will be announced later.
Final exam (50%):
Short answer questions (5 questions)
Hinweis der Redaktion
1833 Robert Brown reported cell contain nucleus
1837 Cell theory by Theodor Schwann "All living things are composed of cells and cell products".[3] This became cell theory or cell doctrine
1933 Electron microscope invented
Cyclins are a family of proteins that control the progression of cells through the cell cycle by activating cyclin-dependent kinase (Cdk) enzymes.[1]
2003 Nobel prize in chemistry awarded jointly to Peter Agre for discovery of aquaporins
Aquaporins are integral membrane proteins from a larger family of major intrinsic proteins (MIP) that form pores in the membrane of biological cells.[1]
Olfactory receptors – odorant receptor – detection of odor molecules
Bioenergetics-the study of the transformation of energy in living organisms.
Bioenergetics is the part of biochemistry concerned with the energy involved in making and breaking of chemical bonds in the molecules found in biological organisms. It can also be defined as the study of energy relationships and energy transformations in living organisms.
Life is dependent on energy transformations; living organisms survive because of exchange of energy within and without.
Living organisms produce ATP from energy sources via oxidative phosphorylation
In photosynthesis, autotrophs can produce ATP using light energy.
Endergonic - anabolic
Exergonic- catabolic
polymers are made up of monomers, which lipids do not contain.
the basic units of lips are fatty acids and glycerol molecules that do not form repetitive chains. Instead, they form triglycerides from three fatty acids and one glycerol molecule.
The main difference between cellulose and starch is,
Cellulose is the polymeric form of glucose which has glucose units linked by glycoside linkage (beta 1, 4 linkages).
Starch is a polymeric form of glucose which is linked by alpha 1,4 linkage
Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication.
Chromosome, highly condensed DNA during metaphase
Cytoskeleton - complex network of interlinking filaments and tubules that extend throughout the cytoplasm, from the nucleus to the plasma membrane
-it gives the cell shape and mechanical resistance to deformation
-actively contract, thereby deforming the cell and the cell's environment and allowing cells to migrate
-uptake of extracellular material
-intracellular transport
template for the construction of a cell wall.[3]
Furthermore, it forms specialized structures, such as flagella, cilia, lamellipodia and podosomes.
Halophiles- high salt
Methanococcus- mesophile (moderate temperature)
-methanogens that produce methane (CH4)
Microsporidiae-fungi
Slime molds were formerly classified as fungi but are no longer considered part of that kingdom.[1] Although not related to one another, they are still sometimes grouped for convenience within the paraphyletic group referred to as kingdom Protista.
-found in forest, eat decaying things
Pili (pilus) for bacterial conjugation)
Shorter pili called fimbriae help bacteria attach to surfaces.
Flagella - Flagella are long, whip-like protrusion that aids in cellular locomotion.
Definition of mesosome. : an organelle of bacteria that appears as an invagination of the plasma membrane and functions either in DNA replication and cell division or excretion of exoenzymes.
