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Transcript of BCH 3000 - UPM EduTrain Interactive Learning · Kod/Nama Kursus BCM 3000 (4+0) (Prinsip Biokimia)...
Kod/Nama Kursus BCM 3000 (4+0) (Prinsip Biokimia)
Nama Pensyarah Prof. Dr. Mohd Arif Syed (MAS) (Penyelaras)
Dr. Syahida Binti Ahmad
Jabatan Biokimia
Jadual Kuliah ( Masa dan Tempat)
PENILAIAN Kerja Kursus = 60%
Peperiksaan Akhir = 40 %
2
1. Mid Term 40%
(20% + 20%)
2. SCL 20%
i. Model and presentation
ii. Assignment
15%
5%
3. Final Examination 40%
TOTAL 100%
Course Evaluation
3
Course Evaluation
Mid Term = 40% - October 2014 ????
Topics covered in test
1. Introduction-Biochemistry
2. Carbohydrates
3. Amino acid & protein
4. Lipid
5. Membrane
6. Nucleic acids
7. Enzymology
4
5
Course Evaluation
Mid Term = 40% - October 2014 ????
Types of Questions
1. Duration – 2 hours
2. Multiple choice – 60 questions (1 mark each)
3. Short Answers - Choose 8 out of 10 questions ; 5 marks each
5
Course EvaluationFinal Examination = 40%
Topics covered in exam
8. Carbohydrate metabolism
9. Photosynthesis
10. Lipid
11. Protein & amino acid metabolism
12. Nucleic acid metabolism
13. Hormones
14. Integration & control of metabolism
6
Course Evaluation
SCL (Student Centered Learning = 20%)
In this exercise, each student is required to produce a model of an oligopeptide using materials from the environment. The model should be able to demonstrate clearly the structural configuration of the oligopeptide . The student will be asked to present the model and explain the structural configuration
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Course EvaluationSCL (Student Centered Learning = 25%
Model Requirements
1. The student must design and produce a model of an oligopeptide
2. All amino acids must be different from one another and of different group
3. Materials used must be from the environment. No model kit will be allowed. This is also not computer modeling
4. The model should clearly show the structure of the amino acid
5. Student will be asked to explain their respective models
8
Course EvaluationSCL (Student Centered Learning = 25%
PRESENTATION
1. Week 14
2. Place – Biotek 1
3. Date – please inform when you are available
4. Evaluation by a panel
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Course Evaluation
ASSIGNMENT
1. TOPICS
2. Only 2 assignments are required
3. Assignments can be submitted any time but not later that week 12.
4. Assignments can be sent directly to me via e-mail, preferably in pdf formats
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TOPICS
1. Proteins are the most diverse category of biomolecules responsible for an array of biological functions. List the different classes of proteins and for each class, describe the functions of the proteins. Write short notes on the functions of the proteins in each class
2. Explain the biochemical background for the causes of diabetes
3. Explain how knowledge in biochemistry has been used in forensic sciences.
Figure 7.2 Outcome of twin
pregnancy in women
prescribed either
prophylactic
leave of absence from work
(treated) or not (controls).
Gestational duration did not
differ between the groups.
An illustrative example of a
legend including the message
alone is
presented in Figure 8.1.
Figure legends
How to design tables
(This course encompasses the main biomolecule
components in biochemistry. Metabolism
involving the anabolism and catabolism of
major biomolecules are also explained)
Sinopsis
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1. Membezakan struktur dan fungsi biomolekul yang terdapat dalam sistem biologi (C4)
2. Menyatakan pelbagai proses metabolisme yang utama (P2)
3. Menerangkan tindakbalas biokimia (A3)
4. Menyelesaikan masalah dalam metabolisme biomolekul dengan menggunakan maklumat dari pelbagai sumber (CTPS, LL)
Learning Outcome
14
1. Introduction-Biochemistry? Contributions? Important life components
2. Carbohydrates – Classification – mono, di polysaccharides – Structure –configuration & stereochemistry; reactions – glucose and other sugars
3. Amino acid & protein – biological roles, structure, classification, reactions, analysis. Peptides – primary, secondary, tertiary and quaternary structures
4. Lipid –functions & distribution, characteristics of fatty acids-saturated & unsaturated f/acids. Structures & characteristics of triacylglycerols, phospholipids, sphingolipids, terpenes & steroids
Brief Lecture Contents
15
5. Nucleic acids – components – purines, pyrimidines. Structure, reactions & importance of nucleosides, nucleotides & polynucleotides. DNA, RNA – structure, functions & types
6. Enzymology – Classification, naming, active sites. Enzyme kinetics. Factors affecting enzyme activity- enzyme & substrate concentration, pH, temperature . Substrate specificity – single & multiple substrate. Enzyme inhibitors – competitive, con-competitive, uncompetitive. Control of enzyme reactions – product inhibition, Isoenzymes, multienzyme system and allosteric enzymes
Brief Lecture Contents
16
7. Carbohydrate metabolism – Metabolic energy cycle –Bioenergetics: ATP other high energy compounds. Storage & energy transfer. Glycolysis & fermentation. Electron transport system. Compartmentation & mitochondria. Phosphorylation & production of ATP. Anaplerotic reactions. Glyoxylate cycle. Gluconeogenesis. Pentose phosphate pathway. Integration and control.
8. Photosynthesis – Fixation of CO2 during photosynthesis. Chlorophyll, components of photosynthesis. Photosystem I & II. Photophosphorylation. Calvin cycle. Hatch-Slack cycle.
Brief Lecture Contents
17
9. Lipid metabolism – Lipid oxidation- Enzymes involved, energy production. Oxidation of saturated & branched fatty acids. Formation of ketone bodies. Lipid biosynthesis –mitochondrial system and extra-mitochondrial. Cycle & enzymes involved. Synthesis of saturated & unsaturated fatty acids. Cholesterol synthesis & control.
10. Protein & amino acid metabolism – Degradation of amino acids- transamination, deamination, decarboxylation. Cycle involved- intermediates for the TCA cycle. Ammonia and urea metabolism. Biosynthesis of amino acids- role in the metabolism of porphyrin and nucleic acids. Nitrogen fixation.
Brief Lecture Contents
18
11. Nucleic acid metabolism – synthesis of mononucleotides – purines, pyrimidines – cycle and enzymes involved; control. Biosynthesis of ribo & deoxyribonucleotides. Characteristics of genetic materials – chromosomes. Genetic code, base sequence. DNA replication. DNA repair. Protein synthesis – ribosome, co-factor involved & phase of synthesis. Inhibition and control of synthesis.
12. Membrane Biochemistry – Modification & structure. Model for membrane structure. Transport mechanism across membrane – passive & active transport.
Brief Lecture Contents
19
13. Hormones- Introduction to plant & animal hormones. Reactions & control of endocrine hormones. Hormone reactions at the molecular level.
14. Integration & control o f metabolism. Relationship between carbohydrate, lipid and protein metabolism.
Brief Lecture Contents
20
● Part of curriculum
● Explain a lot of the controversies in the news at the moment.
Stem cell study
Cloning of the human being
Diseases (defect in metabolism)
GM food and organisms (genetically modified)
Why study biochemistry?
21
Biochemistry = the chemistry of life.
● bridges the gap between chemistry (the study of the structures and interactions of atoms and molecules) and biology (the study of the structures and interactions of cells and organisms).
● Since living things are composed of inanimate molecules, life, at its most basic level, is a biochemical phenomenon.
Inert; not living; not lively
BIOCHEMISTRY: A PROLOGUE
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● diverse in their macroscopic properties
● BUT remarkable similarity in their biochemistry that provides a unifying theme with which to study them.
◊ For example, hereditary information is encoded and expressed in an almost identical manner in all cellular life
◊ the series of biochemical reactions= metabolic pathways, as well as the structures of the enzymes that catalyze them are, for many basic processes, are nearly identical from organism to organism.
Living organisms
23
This strongly suggests that all known life forms are descended from a single primordial ancestor in which these biochemical features first developed
24
Although biochemistry is a highly diverse field, it is largely concerned with a limited number of interrelatedissues. These are
1. What are the chemical and three-dimensional structures of biological molecules and assemblies, how do they form these structures, and how do their properties vary with them?
2. How do proteins work?- what are the molecular mechanisms of enzymatic catalysis, how do receptors recognize and bind specific molecules, and what are the intramolecular and intermolecular mechanisms by which receptors transmit information concerning their binding states?
25
3. How is genetic information expressed and how is it transmitted to future cell generations?
4. How are biological molecules and assemblies synthesized?
5. What are the control mechanisms that coordinate the myriads of biochemical reactions that take place in cells and in organisms?
6. How do cells and organisms grow, differentiate, and reproduce?
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● fairly new field of science -the 20th century
● first landmark of biochemistry - Friedrich Wohler (1828) synthesized the organic compound urea from the inorganic compound ammonium cyanate
● building blocks of life were the same as those of non-living things
● The role of enzymes as catalyst - Buchner showed that a process of biochemistry, catalysis, could occur independently from living cells (enzymes in yeast extracts and fermentation)
History of Biochemistry
27
● Fischer developed the lock and key model (enzyme as rigid lock, substrate as key) A modified version of this model (induced fit) is still used today
● The second part of the 20th century saw advances in structural biology especially the structure of proteins
● The first protein structures were determined by John C. Kendrew and Max Perutz in the 1950s and 1960s.
● Now have determined the structures of more than 1000 proteins.
History of Biochemistry
28
● The role of nucleic acid as information molecules
In 1944 Oswald Avery et al extracted DNA from a toxic strain of a bacteria and when added to a nontoxic strain resulted in the bacteria being transformed into a virulent strain.
Watson and Crick (1950) deduced the 3D structure of DNA.
Crick predicted that information encoded in DNA is transcribed to ribonucleic acid and then translated to protein.
This unidirectional information flow is referred to as the central dogma of molecular biology
History of Biochemistry
30
Living things are enormously complex.
● simple E. coli cell contains some 3 to 6 thousand different compounds, most of which are unique to E. coli ; Homo sapiens (human beings), may contain 100,000 different types of molecules, although only aminor fraction of them have been characterized.
● biochemical understanding of any organism would be a hopelessly difficult task ??
No !!!! - Why ????
BIOLOGICAL STRUCTURES
31
Living things have an underlying regularity that derives from their being constructed in a hierarchical manner.
Multicellular organisms
Organizations of organs
Tissues
Cells
Subcellular organelles
Supramolecular assemblies of macromolecules 32
● Only six nonmetallic elements make up 97% of the weight of most organisms – carbon, oxygen, hydrogen, nitrogen, phosphorous and sulfur.
● All form stable covalent bonds.
● here are also 5 common ions found in all organisms: - Calcium (Ca2+), Potassium (K+) Sodium (Na+), Magnesium (Mg2+), Chloride (Cl-)
● Water is a major component of cells.
● Altogether, a total of 29 different elements are commonly found in living organisms.
The Chemical Elements of Life
35
Brown – important elementspurple – essential ionsdark blue – more common trace elementslight blue – less common trace elements
36
● Most of the solid material of cell consists of carbon-containing compounds (organic compounds).
● The organic compounds of interest is shown
Organic compounds
37
● The elements of life are assembled into molecules with common structures and patterns – how ?? –
via linkages (bonds)
39
● they are formed from smaller molecules called monomers that are linked together in a sequential way to form long chains
● After being joined together, the individual monomers in a chain are referred to as residues
● There are various levels in the hierarchy of life i.e. atoms, molecules, biopolymers, organelles, cells, tissues, organs and whole organisms
BIOPOLYMERS
41
An example of a biopolymer
● polymers formed from the condensation of individual monomers called amino acids
● Twenty amino acids are incorporated into proteins in all cells
● Each amino acid contains an amino group and a carboxylate group and a side chain (R group).
● The amino group from one amino acid reacts with the carboxylate group of the other to form an amide linkage that is referred to as a peptide bond
PROTEINS
42
● Many amino acids joined in this manner is called a polypeptide ( have N and C terminal
● The amino acids are combined in a specific sequence to produce proteins consisting of hundreds or thousands of amino acid residues
44
● A functional protein consist of one polypeptide or several different polypeptides tightly bound together.
● Proteins function as either enzymes or structural components of cells and organisms.
● The function of a protein depends on the 3D structure or conformation.
45
● Composed basically of carbon, oxygen and hydrogen.
● Monosaccharides – simple sugars, polysaccharides –polymers.
● Fischer projection – linear molecule.
● Haworth projection – ring form (usual biochemical form).
● Ribose – approx. 20 conformations
POLYSACCHARIDES
47
● Glucose –
o most abundant six-carbon sugar
o Monomer for cellulose, glycogen and starch
o Differ in bonding between C-1 of the monomer to the next
48
● Biopolymers of monomers called nucleotides.
● Nucleotides – five-carbon sugar, heterocyclic nitrogen base and at least one phosphate.
o Five – carbon sugar (ribose and deoxyribose).
o Base (purines and pyrimidines).
Purines – adenine (A) and guanine (G).
Pyrimidines (cytosine ( C), thymine (T) and Uracil (U)
Nucleic acids
50
Nucleic acids are polymers formed from monomers called nucleotides that are joined in a phosphodiester linkage
Polynucleotide-formed by linking phosphate group to C-3 oxygen atom of another nucleotide
51
1. DNA
● uses deoxyribose sugars
● Usually double stranded
2. RNA
● Uses ribose sugars
● Usually single stranded
● 4 types of RNA :
i. mRNAii. tRNAiii. rRNAiv. heterogenous RNA.
Examples of nucleic acids
52
● Diverse class of compounds rich in carbon and hydrogen (low in oxygen).
Fatty acids, glycerophospholipids, wax and beeswax.
● Most lipids not soluble in water.
● In membranes lipid are polar - hydrophilic water loving head and hydrophobic (water fearing) tail.
● Form bi-layer membrane system.
Lipids and Membranes
54
● Life requires input of energy – ultimately from the sun
● Metabolism
Describes the numerous reactions in which organic compounds are synthesized and degraded and useful energy is extracted, stored and used.
Bioenergetics
o The study of the changes in metabolic energy
The Energetics of Life
55
● DG – the free-energy change for a reaction is the difference between the free energy of the product and the free energy of the reactants.
DG = DH - T DS
where
DH is the change in heat content (enthalpy change)
DS is the change in randomness (entropy change)
T is the temperature in Kelvin.
DG < 0 reaction is spontaneous
DG > 0 reaction requires input of energy
DG = 0 reaction is at equilibrium.56
● Many many types of chemical reactions simultaneously occur in any living cell.
● Yet, these reactions follow a pattern that organizes
them into the coherent process we refer to as life.
o For instance, most biological reactions are members of a metabolic pathway - sequence of reactions that produce one or more specific products.
o Moreover, the rates of its reactions are so tightly regulated that there is rarely an unsatisfied need for a reactant in a metabolic pathway or an unnecessary buildup of some product.
Metabolic Processes
57
Metabolism - traditionally divided into two major
categories:
1. Catabolism or degradation, in which nutrients and cell constituents are broken down so as to salvage their components and/or to generate energy.
2. Anabolism or biosynthesis, in which biomolecules are synthesized from simpler components
The energy required by anabolic processes is provided by catabolic processes largely in the form of adenosine triphosphate (ATP).
58
● Deoxyribonucleic acid (DNA) is the cell's master repository of genetic information
● Genetic information is encoded in the sequence of these bases.
● The division of a cell must be accompanied by the replication of its DNA.
◊ each DNA strand acts as a template for the formation of its complementary strand
◊ every progeny cell contains a complete DNA molecule each of which consists of one parental strand and one daughter strand. Mutations arise when, through rare copying errors or damage
Expression and Transmission of Genetic Information
60
repository is a place where data or specimens are stored and maintained for future retrieval.
Encoded - prearranged; programmed, determined, set,preset
Replication - duplication,copying, reproduction
61
Cells are classified as eukaryotes or prokaryotes
1. Prokaryotes (bacteria)
Ubiquitous, no nucleus, only approx 1000 genes
2. Eukaryotes (plants, animals, fungi and protists)
Membrane bound nucleus, 1000 fold greater in volume.
The cell is the basic unit of life
62
● All living cells depend on water for their existence.
● Metabolic machinery of cells has to operate in an aqueous environment
● Water molecule – polar
● Water molecule is V-shaped with an angle of 104.5O
Properties
Water
66
There are 4 types of noncovalent interactions.
1. Charge-charge interactions
● Electrostatic interactions between two chargedparticles e.g. NaCl
● The strongest noncovalent forces
● Also responsible for mutual repulsion of similarly charged ionic groups
Noncovalent Interactions in Biomolecules
67
2. Hydrogen bonds
● A type of electrostatic interaction which occurs in many macromolecules
● Among the strongest noncovalent forces in biological systems
● Strong enough to confer structural stability but weak enough to be readily broken.
● Can form when a hydrogen covalently bonded to a strong electronegative atom, such as nitrogen, oxygen and sulfur
69
● Weak intermolecular forces produced between all neutral atoms by transient electrostatic interactions
● Have attractive and repulsive components
● forces that exist between MOLECULES of the same substance
3. Van der Waals Forces
72
● The association of a relatively nonpolar molecule or group in aqueous solution with other nonpolar molecules rather than with water
● The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other. Hydrocarbon alkyl groups on ala, val, leu, and ile interact in this way
4. Hydrophobic interactions
74
AIR – H2O
From the dissociation/ionization of water equation
pH = -log [H+]
ie. pH = negative log of hydrogen ion (H+) concentration
pOH = negative log of hydroxyl ion (OH-) concentration
78
= substance that donates proton
a substance which produces hydrogen ions (H+) by dissociation
For example
HCl H+ + Cl-
Hydrogen ions (H+) associate with water to form H3O+ (Hydronium ion)
ACID
79
= Substances that receive proton
= can associate with H+ (e.g. NH3)
= may produce hydroxide ions (OH- ) either by direct dissociation or subsequent to reaction with water
i. KOH K+ + OH-
NH3 + H2O NH4OH NH4+ + OH-
BASE
80
STRONG ACIDS are compounds that dissociate (ionize)
almost 100% in an aqueous solution.
HCl H+ + Cl-
81
The common acids that are almost one hundred percent ionized are:
HNO3 - nitric acid
HCl - hydrochloric acid
H2SO4 - sulfuric acid
HClO4 - perchloric acid
HBr - hydrobromic acid
HI - hydroiodic acid
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