LECTURE 8: CHEMISTRY OF LIFE. Simple to Complex – Life’s Levels of Organization Our journey begins here.

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1 LECTURE 8: CHEMISTRY OF LIFE

2 Simple to Complex – Life’s Levels of Organization Our journey begins here.

3 Chemistry and Life Apa perbedaan antara atom dan molekul? Apa yang membuat atom membentuk molekul? Does shape matter?

4 To Understand the Big, You’d Better Know the Small

5 Atoms and Atomic Structure Atom merupakan unit terkecil dari element kimia Elements merupakan substansi yang tidak dapat dipecah menjadi substansi yang lebih sederhama melalui reaksi-reaksi kimia.

6 INTRODUCTION Botany is the scientific study of plant life. It is also called plant science, phytology, or plant biology. Biology is the study of life. The word biology is composed of 2 Greek roots “bio” which mean “life” “logi” which mean “study of” Biology as a science is concerned with all life- plant and animal, but botany is interested in plant life in particular.

7 INTRODUCTION Plant life means Organization: Tersusun dari satu atau lebih sel, yang merupakan unit dasar dari kehidupan. Metabolism: Konsumsi energi melalui pengubahan non-living material menjadi cellular components (anabolism) dan mendekomposisinya menjadi bahan organik (catabolism) Growth: Mempertahankan laju synthesis lebih tinggi daripada catalysis

8 Cells are the basic and fundamental unit of structure, physiology, and organization of all living organisms. Mengetahui komposisi sel dan bagaimana sel bekerja merupakan fundamental bagi semua ilmu biologi (biological sciences)

9 Biology Systems Biology organizes living things along certain levels. That is living things can be viewed and organized at a chemical level, looking at the biochemistry of organisms, or at a cellular level where interest in the structure and functions of cells and cell physiology is considered, or at the levels of tissues or organs.

10 MOLECULAR PLANT COMPOSITION

11 Organic Compounds The major groups of organic compounds as far as life is concerned are: Carbohydrates Lipids Protiens Nucleic acids Hydrogen, oxygen and nitrogen are frequently found bonded to carbon. Organic compounds made up of carbon and hydrogen are known as hydrocarbons, this includes what common materials? All built around carbon atoms

12 Carbohydrates “Fuel molecules” consist of carbon, hydrogen and oxygen atoms (CH 2 O). Carbohydrates are further classified as Monosaccharides  Glucose Disaccharides Polysaccharides  starch dan chitin

13 Lignin The major noncarbohydrate, polyphenolic structural constituent of wood and other plant material that encrusts the cell walls and cements the cells together A highly polymeric substance, with a complex, cross-linked, highly aromatic structure of molecular weight about 10,000 derived principally from coniferyl alcohol (C 10 H 12 O 3 ) by extensive condensation polymerization

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15 Cellulose Tersusun dari rantai panjang ß-glucose yang berikatan satu sama lain (repeating unit C 6 H 10 O 4 ) Penyusun utama bagi kerangka struktural kayu dan sel-sel biomassa yang lain The  -linkages membentuk rantai linear yang sangat stabil dan resisten terhadap serangan bahan kimia karena tingkat ikatan hidrogen yang tinggi yang terjadi di antara rantai cellulose, menghambat peregangan molekul yang terjadi dalam perombakan hidrolisis adri iakatan glycosidic

16 Hydrolysis dapat mereduksi cellulose menjadi cellobiose (repeating unit C 12 H 22 O 11 ) dan akhirnya menjadi glucose, C 6 H 12 O 6

17 Hemicellulose Tersusun dari rantai gula yang berbeda, pendek dan bercabang Mengandung gula 5-C (biasanya D-xylose dan L-arabinose) dan gula 5-C (D-galactose, D-glucose, dan D-mannose) dan uronic acid Gula mudah disubstitusi dengan acetic acid Secara alami Hemicellulose tak berbentuk dan relatif mudah dihidrolisis menjadi gula dibandingkan dengan cellulose

18 Starch Tersusun dari rantai panjang molekul α-glucose yang saling berikatan (repeating unit C 12 H 16 O 5 ) Ikatan terjadi dalam rantai α-1,4 linkages dengan cabang yang terbentuk sebagai hasil dari α-1,6 linkages Distribusinya luas dan disimpan dalam semua biji dan umbi (tubers) Karena α linkages dalam starch, polymer ini sangat tidak berbentuk, dan lebih mudah dirombak oleh sistem enzim menjadi glucose

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20 Proteins Berperan utama dalam fungsi struktural dan pengaturan. Seperti: enzymes (mengatur ribuan rekasi kimia internal, enzim sebagai biologic catalyst), Proteins terdiri dari hydrogen, carbon, nitrogen, oxygen dan biasanya sulfur. Ini tergabung dalam cara yang berbeda untuk membentuk lebih dari 20 amino acids yang berbeda Tanaman dapat mensintesis semua asam amino yang dibutuhkan, tetapi hewan tidak dapat.

21 Nucleic Acids Large complex molecules. Two classes are ribonucleic acids (RNA) and deoxyribonucleic acid (DNA). Nucleic acids tersusun dari molecular units disebut nucleotides, setiap nucleotide terdiri dari: A 5 carbon sugar, apakah ribose atau deoxyribose, A phosphate group, A nitrogenous base yang mempunyai a double ringer purine atau a single ringed pyrimidine

22 Nucleic Acids DNA mengandung purine adenine (A), dan guanine(G) dan pyrimidines cytosine (C) dan thymine (T) bersama-sama dengan sugar deoxyribose dan phosphate RNA mengandung purines adenine dan guanine dan pyrimidines cytosine dan uracil (U) bersama- sama dengan sugar ribose and phosphate. Adenosine triphosphate (ATP) merupakan nucleic acid yang menyediakan energy secara teratur dalam semua cells, tersusun dari adenine, ribose dan tiga phosphates.

23 FORMATION OF MOLECULAR COMPOSITION OF PLANTS: ATOM

24 What causes atoms to form molecules? Basically, all things that happen spontaneously are energetically favorable (a book dropping)- You never see a book spontaneously rise Something must be energetically favorable about atoms coming together as molecules Molekul penyusun tanaman disintesis dari molekul yang sangat sederhana, yaitu inorganic molecules (CO 2, H 2 O and nutrient elements) Pembentukan hampir semua molekul kehidupan terjadi melalui reaksi yang dikatalissasi oleh enzymes dan berdasarkan karakteristik constituent dasar dari molecules (atom)

25 electron cloud Atomic Models

26 In a simplified yet useful view of an atom, electrons orbit a nucleus composed of protons and neutrons. Atoms and Atomic Structure

27 Atoms Come in Different Forms Called Isotopes 1. Isotopes of a given element have the same number of protons but different numbers of neutrons. 2. Many isotopes are unstable, making them radioactive. 3. Radioactive isotopes (radioisotopes) play an important role in health, medicine and biological research. Three isotopes of hydrogen.

28 Some Atoms are Sociable, Others Aren’t Atoms “want” (are most stable) to have a filled outer electron shell. Atoms without a filled outer shell will share electrons with other atoms to accomplish this “goal.” Filling outer electron shells controls which atom will pair with which others and in what combinations.

29 Filling Electron Shells An important rule: the innermost shell holds two electrons; subsequent shells hold 8 electrons.

30 Pairing for the Greater Good When atoms come together by sharing electrons the bond is a covalent bond. H2H2 A molecule is formed when two or more atoms are bound together covalently.

31 Drawing It Out The sharing of a pair of electrons between atoms (a covalent bond) is shown as: H-H (for H 2 ) or H-O-H (for H 2 O) or (for CH 4 )

32 Water - A Most Important Molecule Note how bonding fills all outer electron shells.

33 Valence Electrons The electrons found in the outer “shell” of an atom are known as valence electrons The valence of an atom is the number of electrons an atom must receive to become chemically stable (i.e., less reactive) For many atoms Valence = 8 - # valence electrons Oxygen: 6 valence electrons, valence = 2 Nitrogen: 5 valence electrons, valence = 3 Carbon: 4 valence electrons, valence = 4

34 Valence Electrons In Biology (even in chemistry) there are always exceptions: Hydrogen: 1 valence electron, valence = 1 Phosphorus: 5 valence electrons, valence = 5 These ideas of valence electrons and an atom’s valence will take on more meaning as we discuss chemical bonds and molecular structure

35 Valences of Various Elements 1 4 3 2 5 1

36 Polar and Non-Polar Covalent Bonding

37 A polar substance is one in which the molecule has a negative side and a positive side The covalent bonds of H 2 and CH 4 are non- polar and so are the molecules. Some atoms have an equal affinity for electrons. If so, the shared electrons spend equal amounts of time around each atom and the covalent bond is non-polar.

38 Polar and Non-Polar Covalent Bonding Therefore, the covalent bonds of H 2 O are highly polar and so is the molecule. Some atoms have an unequal affinity for electrons. If so, the shared electrons spend more time around one atom relative to another and the covalent bond is polar. Oxygen draws electrons to itself much more strongly than hydrogen. H2OH2O

39 Polar and Non-Polar Covalent Bonding

40 The polar versus non-polar distinction determines which molecules will dissolve in a particular solute. For example, sugar dissolves in water, but fat doesn’t. The general rule is like dissolves like. The familiar case of oil and water Water = polar molecule Fat = non-polar molecule Soap = polar and non-polar molecule

41 Some Atoms Do Almost Anything to Fill Electron Shells Sodium donates a lonely electron to chlorine to complete its outer electron shell. Chlorine is only too happy to accept. The result is ion formation. An ion is an atom or molecule with one or more full positive or negative charges.

42 Ions and Ion Formation

43 IONIC BONDING

44 Ionic Bonds Two oppositely charged ions bind together. This type of chemical bond is an ionic bond. Salts are solids held together by ionic bonds. Ionic bonds are common and important in biology.

45 Ionic bonding High electronegativity difference strips valence electrons away from another atom Electron transfer creates ions (charged atoms) Cation (positive ion); anion (negative ion) Ex: Salts (sodium chloride)

46 Ionic Bonds

47 Ionic Bonding Ionic bonds result from one atom essentially giving an electron to another atom  Ionic bonds represent an extreme of polarity and are represented in biological systems as the salt bridges within proteins

48 Ionic bonding Ionic bonding involves 3 steps (3 energies) 1) loss of an electron(s) by one element, 2) gain of electron(s) by a second element, 3) attraction between positive and negative

49 Ionic bonding: energies By convention, a requirement for energy is given a + sign (we have to put energy in) and is called endothermic, a release of energy is given a – sign and is called exothermic.

50 Strong Bonds in Solid In solid phase ionic bonds can be very strong But in aqueous phase ionic bonds tend to be weaker than covalent bonds

51 Hydrogen Bonding Oxygen and nitrogen are much more “hungry” for electrons than hydrogen. The result is a hydrogen bond. Bonds between nitrogen or oxygen and hydrogen are highly polar. This allows bonds to form between partially positive and partially negative atoms in different or (in large molecules) the same molecule.

52 Hydrogen Bonding Gives Water Unique Properties

53 Relative Bond Strengths Covalent Ionic Hydrogen >>

54 Molecular Shape Molecules have distinct shapes – and shape matters.

55 Molecular Shape A regulatory protein molecule (yellow) binding to DNA. Without complementary shapes, binding would not occur.

56 Molecular Shape Matters We perceive and distinguish odors because of the particular shape of the odorant (the molecule we smell) and receptor molecules on nose cells.

57 Biological Chemistry Takes Place in Solutions Molecules are often described as hydrophilic (water- loving) or hydrophobic (water-fearing) on the basis of their solubility in water.

58 The End