1. With thanks and respect to Dr. Khadijah Saeed Balamash
GENERAL BIOCHEMISTRY
Dr. Dina Abed Bakhotmah
With thanks and respect to
Dr. Khadijah Saeed Balamash

2. Textbook & References Textbook:
Voet & Voet: Biochemistry, Wiley & Sons Inc. New York
References:
Richard A. Harvey & Denise R. Ferrier : Biochemistry (Lippincott's Illustrated Reviews)

3. Content General Biochemistry (Bioc 201)
Contents
I-Introduction: 1- Definition 2- Biological Structures 3- Chemical bonds 4- Properties of water II- Carbohydrates 1- Monosaccharides 2- Disaccharides 3- Polysaccharides 4- Digestion of carbohydrates

4. III- Amino acids
1- Structures and general properties
2- Peptide bonds
3- Classifications and characteristics
4- Acidic basic properties
IV- Proteins
1- Primary structures
2- Secondary structures
3- Tertiary structures
4- Quaternary structures

5. V- Lipids and Membranes
1- Lipid classification
2- Properties of lipid aggregates
3- Biological membranes
4- Membrane assembly and protein targeting
5- Lipoproteins
VI- Nucleotides and Nucleosides and Bases
1- The chemical structures of DNA and RNA
VII- Introduction to
1- Enzymes
2- Hormones
3- Vitamins

6. Exams: First exam 15 marks Midterm Exam 20 marks Lab 25 marks
Final Exam 40

7. CHAPTER 1 Introduction: 1- Definition 2- Biological Structures
3- Chemical bonds
4- Properties of water

8. What is Biochemistry? -1
Biochemistry is the chemistry of the living organisms or life.
Biochemistry deals with: chemistry, structure, organization, and function of living matter.

9. Principle Areas of Biochemistry
Structure and function of biological macromolecules
Metabolism – anabolic and catabolic processes.
Molecular Genetics – How life is replicated. Regulation of protein synthesis

10. Origins of Biochemistry:
Famous Dead Biochemist!

11. Fallacy #1: Biochemicals can only be produced by living organisms
1828 Friedrich Wohler
Dead Biochemist #1

12. Glucose + Dead Yeast = Alcohol
Fallacy #2: Complex bioconversion of chemical substances require living matter
Dead Biochemists #2
1897 Eduard Buchner
Glucose + Dead Yeast = Alcohol

13. Fallacy #2: Complex bioconversion of chemical substances require living matter
Dead Biochemists #3
Emil Fischer

14. Cell Theory-1
Cell is the smallest unit of living matter. (Don’t confuse this with electrons, atoms, proteins, DNA, etc.,These are lifeless molecules)
Cell is the structural & functional unit of all organs and/or organisms made up of thousands of different types of molecules in highly organized self-assembled structures. .

15. Cell Theory-2
All organisms are composed of one or more types of cells.
All cells come from pre-existing cells by division.
Spontaneous generation does not occur.
Cell is capable of reproduction.

16. Cell Theory-3
Cells contains hereditary information which is passed from cell to cell during cell division.
Most biochemical reactions (but not all!) take place within cells

17. Typical Cells
Cells come in a variety of shapes, structures, and sizes.
They are usually divided into two broad groups: Eukaryotes and Prokaryotes.

18. Eukaryotic cells
(Eu = true; kary = nucleus): have a membranebound nucleus and a variety of organelles and internal membranes.

20. Prokaryotic cells
Prokaryotic cells (Pro = before) are smaller and lack much of the internal compart-mentalization and complexity of eukaryotic cells; No membrane-bound nucleus or other organelles.

21. Viruses
Viruses do not always conform to cell theory: one or more of the basic cell components is missing. Inside the host cell, viruses are living matters.

22. Sizes and Shapes of Cells

23. Organization of Life Elements (C, H, O, N)
Simple organic compounds (monomers)
Macromolecules (polymers)
Supramolecular structures (DNA, Lipids)
Organelles
Cells
Tissues (Epithelia, Connective, Muscle, Nerve Tissue)
Organs (Heart, skin, kidney, etc.)
Organisms (Human, bovine, etc)

25. Chemical Elements of Life
The cell is a COMPLEX
CHEMICAL FACTORY
containing some of the
same elements found in
the nonliving environment.
Chemical elements of a living cell are the same as in the Earth’s crust, but in different proportions.
CHNOPS: are the most abundant elements in cell.
They account for more than 99% of atoms in the human body

26. Chemical Elements of Life
H, O, N and C have common properties that are important to the chemistry of life. They all:
have relatively low atomic numbers.
capable of forming one, two, three and four bonds (for H, O, N and C , in order).
form the strongest covalent bonds in general.

27. Inorganic - usually "support" life - no specific ratio of C, H, and O
TWO TYPES OF COMPOUNDS
Organic - Contain C, H, and O in some ratio (usually referred to as chemicals of life)
Carbohydrates, Proteins, Lipids, Nucleic Acids
Inorganic - usually "support" life - no specific ratio of C, H, and O
Water (H2O), Carbon Dioxide (CO2)

28. Organic Chemistry
What makes Carbon Special? Why is Carbon so different from all the other elements on the periodic table?
The answer derives from the ability of Carbon atoms to bond together to form long chains and rings.

29. Organic Chemistry

30. Carbon can covalently bond with up to four other atoms.
Organic Chemistry
Carbon can covalently bond with up to four other atoms.

31. Carbon can form immensely diverse compounds, from simple to complex.
DNA with tens of Billions of Carbon atoms
Methane with 1 Carbon atom

32. Many Important Biomolecules are Polymers
Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)
Condensation reactions join monomers (H2O is removed in the process)
Residue - each monomer in a chain

33. Monomers form polymers through condensations
Common theme:
Monomers form polymers through condensations
Polymers are broken down through hydrolysis.

34. Many Important Biomolecules are Polymers
Carbo-
hydrades
lipids
proteins
nucleic acids
monomer
polymer
supramolecular
structure

35. There are relatively few species of monomeric units that occur in each class of biological macromolecule
Proteins
Are all synthesized from the same 20 species of amino acids
Nucleic acids
Are made from 8 types of nucleotides
4 each in DNA and RNA
Polysaccharides
are ~8 commonly occurring types of sugar in polysaccharides.

36. 1. Where in a eukaryotic cell, DNA can be found?
Nucleus
B. Mitochondrion
C. Vacuole
D. Both (a) and (b)

37. 2-The major elements in a human are C, H and Si
True
False

38. 3- In a human cell the nucleus and mitochondria and many other cell organelles have membranes surrounding them.
True
False

39. 4- Discribe the Cell Theory.
Cells are the smallest unit of life
All Cells come from previously existing cells
All living things are composed of cells

40. 5- Name an example of an organ. Heart kidney
6- Name several types of tissues
Muscle
Nerve Tissue

41. COVALENT BONDING IONIC BONDING
Chemical Bonds
COVALENT BONDING IONIC BONDING
non-polar covalent
And
polar covalent

42. Chemical Bonds
Covalent bonds
Strong
Hold the atoms in an individual molecule together
Noncovalent bonds
Determine the three-dimensional architecture of large biological molecules and molecular complexes
Weaker more easily broken
No one bond is strong, the effect of many weak bonds functioning together can be very powerful

43. COVALENT BONDING
SHARING IS CARING!

44. The outer electron shell of each atom has a characteristic number of electrons:
H C N P O S .
These atoms readily form covalent bonds with other atoms and rarely exist as isolated entities

45. As a rule:
Each type of atom forms a characteristic number of covalent bonds with other atoms.
A hydrogen atom: with one electron in its other shell, forms only one bond.
A carbon atom: with four electrons, generally forms four bonds, as in methane (CH4): H ..
H : C : H or

46. Nitrogen and phosphorus have five electrons in their outer shells.
These atoms can form either
Three covalent bonds, as in ammonia (NH3)
Five, as in phosphoric acid (H3PO4)

47. Oxygen and Sulphur contain six electrons in their outermost shells.
These atoms can forms only two covalent bonds
In molecular oxygen (O2)
Hydrogen sulphide (H2S)
O : : O or

48. Form as many as six covalent bonds Sulphur trioxide (SO3)
A sulphur atom can
Form as many as six covalent bonds
Sulphur trioxide (SO3)
Sulphuric acid (H2SO4)

49. Covalent bonds between different atoms are generally dipolar:
Because one of the atoms is usually more electronegative than the other.
When a dipolar bond breaks:
The bonding electrons often stay with the more electronegative atom, which then becomes a negatively charged ion, or an anion
The other part of the molecule becomes a positively charged ion, or a cation.

50. Electronegativity increases as you move from left to right.
Electronegativity decreases as you move down each column.

51. IONIC BONDS
Occur when 1 or more electrons are TRANSFERRED from one atom to another.
When an atom loses an electron it is a POSITIVE charge.
When an atom gains an electron it is a NEGATIVE charge
These newly charged atoms are now called IONS
Example: NaCl (SALT)

53. Ionic bonds
The ionic bonds result from the attraction of a positive charge for a negative charge.
Ionic bond do not have fixed or specific geometric orientations
Because the electrostatic field around an ion. Its attraction for an opposite charge. Is uniform in all directions.
Unlike covalent or hydrogen bonds

54. In some compounds the atoms are so different in electronegativity:
That the bonding electrons are always found around the more electronegative atom
That is, the electrons are never shared.
Because electrons are not shared,
The bonds in such compounds cannot be covalent
In sodium chloride (NaCl) for example:
The bonding electron contributed by the sodium atoms is completely transferred to the chlorine atoms
Even in solid crystals of NaCl, the sodium and chlorine atoms are ionized, so it is more accurate to write the formula for the compound as Na+ Cl-

56. The hydrogen bond
A hydrogen atom normally forms a covalent bond with only one other atom (D) at a time.
A covalently bonded hydrogen atom may form an additional bond with another atom (A):
A hydrogen bond:
Is a weak association between an electronegative atom (A) (the acceptor atom) and a hydrogen atom covalently bonded to another atom (D) (the donor atom).

57. Hydrogen Bonds
hydrogen bond donor :to which hydrogen is covalently bonded
hydrogen bond acceptor : with the nonbonded electron pair

58. The hydrogen bond in water is a classic example:
A hydrogen atom in one molecule is attracted to a pair of electrons in the outer shell of an oxygen atom in an adjacent water molecule.

59. Van der Waals Interactions
When two atoms approach one another closely, they create:
A nonspecific Weak attractive force that produces a van der Waals interaction
Named for Dutch physicist Johannes Diderik van der Waals ( ), who first described it.

60. Van der Waals Interactions
If two noncovalently bonded atoms are close enough together:
The transient dipole in one atom will perturb (disturb) the electron cloud of the other.
This perturbation generates a transient dipole in the second atom
The two dipoles will attract each other weakly.

61. Dipole – Induced Dipole (weak and short-lived)
Example e- H Cl d+ d- e- e- e- Ar e- e- d+ d- e- e- e- e- e- e- e- e- e- e- e- e-
non-polar
INDUCED
DIPOLE
A DIPOLE
(it’s polar)
Dipole – Induced Dipole
(weak and short-lived)

62. Van der Waals Interactions
All types of molecules, both polar and nonpolar exhibit van der Waals interactions
They are responsible for the cohesion (pulling together) among molecules of nonpolar liquids and solids:

63. Van der Waals Interactions
Attraction decreases rapidly with
Increasing distance and is effective only when atoms are quite close to one another.
If atoms get too close together:
They become repelled by the negative charges in their outer electron shells.
The van der Waals interaction is even weaker than the hydrogen bond

64. Properties of Water-1 Adhesion Cohesion high surface tension
holds heat to regulate temperature (High heat capacity)
less dense as a solid than a liquid

65. PRORERTIES OF WATER-2 The H2O molecule has a bent geometry
With an O — H bond distance of Å
An H — O — H bond angle of 104.5°.

66. PRORERTIES OF WATER-3 Water molecules Associate through Hydrogen bonds
The electrostatic attractions between the dipoles of two water molecules tend to orient them such that
The O — H bond on one water molecule points toward a lone-pair electron cloud on the oxygen atom of the other water molecule.
This results in a directional intermolecular association known as hydrogen bond:
An interaction that is crucial both to the properties of water itself and to its role as a biochemical solvent.

67. PRORERTIES OF WATER-4
The large electronegativity difference between H and O confers a 33 % ionic character on the O — H bond
As water is clearly a highly polar molecule, a phenomenon with enormous implications for living system.
The energy of a hydrogen bond (~ 20 kj. mol-1 in H2O) is small compared to Covalent bond energies (for instance, 460 kj. Mol-1 for an O — H covalent bond).

68. Properties of Water-5
Water is less dense as a solid! This is because the hydrogen bonds are stable in ice – each molecule of water is bound to four of it’s neighbors.

69. Water as a solvent
Solubility: depends on the ability of a solvent to interact with a solute more strongly than solute particles interact with each other.
Water is said to be the “universal solvent.”
The polar character of water makes it an:
Excellent solvent for polar and ionic materials, which are therefore said to be hydrophilic (Greek: hydor, water + philos, loving).

70. AQUEOUS SOLUTION
Life, as we know it, occurs in aqueous solution.
Water is a chemically reactive liquid with such extraordinary physical properties.
The structures of the molecules on which life is based (proteins, nucleic acids, lipids, and complex carbohydrates) Result directly from their interactions with their aqueous environment.

71. In aqueous solutions:
Simple ions of biological significance, such as Na+ , K+ , Ca2+ , Mg2+ , and Cl-:
Do not exist as free, isolated entities.
Instead, each is surrounded by a stable, tightly held shell of water molecules
Primary interaction occurs between the ion and the oppositely charged end of the water dipole

72. Ionic movements through membranes are Essential for the
Ions play an important biological role when they pass through:
Narrow pores
Channels
In membranes
Ionic movements through membranes are Essential for the
Conduction of nerve impulses
Stimulation of muscle contraction

73. Molecules with dipolar bonds also can attract water molecules, as can molecules that easily form hydrogen bonds
Such polar molecules can dissolve in water and are said to be hydrophilic (from the Greek for “water- loving”).

74. Typical chemical groups that interact well with water are:
Hydroxyl – OH
Amino – NH2
Peptide bond
Ester bond

75. Hydrophobic Interactions
Nonpolar molecules:
Contain neither ions nor dipolar bonds
Do not become hydrated. Because they are insoluble in water, they are said to be hydrophobic (from the Greek for “water-fearing”).
The covalent bonds between two carbon atoms and between carbon and hydrogen atoms
Are the most common nonpolar bonds in biological system.

76. Hydrophobic Interactions
Hydrocarbons – molecules made up only of carbon and hydrogen —are virtually insoluble in water.
The force that causes hydrophobic molecules or nonpolar portions of molecules to aggregate rather than to dissolve in water is called hydrophobic interaction.

77. Hydrophobic Interactions
A nonpolar molecule cannot form hydrogen bonds with water:
So it distorts the usual water structure
Forcing the water to make a cage of bonds around it, but not with it.
On the other hand, nonpolar molecules bond together comfortably through van der Waals interactions
The result is:
A very powerful tendency for hydrophobic molecules to bond together and
Not dissolve in water.

78. 1-butanol mixes completely with water in all proportions
Small hydrocarbons such as butane
CH3—CH2—CH2—CH3
Are slightly soluble in water:
Because they can dissolve without disrupting the water lattice (net) significantly.
1-butanol mixes completely with water in all proportions
CH3—CH2—CH2—CH2OH
Thus the replacement of just one hydrogen atom with the dipolar—OH group allows the molecule to form hydrogen bonds with water and greatly increases its solubility.

79. Multiple noncovalent bonds can contribute to the stability of large biological molecules
These interactions can also confer specificity by determining how molecules will fold or which regions of different molecules will bind together
Several different weak bonds and interactions can bind two protein chains together.

80. B. Water as a solvent
Solubility: depends on the ability of a solvent to interact with a solute more strongly than solute particles interact with each other.
Water is said to be the “universal solvent.”
The polar character of water makes it an:
Excellent solvent for polar and ionic materials, which are therefore said to be hydrophilic (Greek: hydor, water + philos, loving).

81. Nonpolar substances are
Insoluble in water (“oil and water don’t mix”) and are described as being hydrophobic (Greek: phobos, fear).
Soluble in nonpolar solvents such as
CCl4 or hexane.
This information is summarized by another maxim. “like dissolves like.”

82. 1- The formation of large molecules from small repeating units is accomplished by a(n) ______ reaction.
oxidation
reduction
dehydration
Hydrolysis
decarboxylation

83. 2- Which force is most important in allowing ammonia, NH3, to dissolve in water?
hydrogen bonding
dipole-induced dipole
ion-dipole
dipole-dipole
ionic

84. 3- Which one of the following species contains a polar covalent bond?
oxygen
carbon dioxide
sodium chloride
magnesium fluoride
helium

85. 4- What happens when a covalent bond is formed?
Electrons are transferred from one atom to another
Electrons are shared between two atoms
Protons are transferred from one atom to another
Protons are shared between two atoms

86. 5- Water (H2O) has a bent shape, resulting in an unequal distribution of the electrons. Oxygen, which is more electronegative than the hydrogens, has a greater pull on the electrons, giving the oxygen a partial negative charge and the hydrogens a partial positive charge. This unequal distribution is called a:
Covalent bond
Tail
Bent geometry
Dipole

87. 6-Which of the following BEST describes the “bonds” holding liquid water molecules together?
A. Ionic.
B. Covalent.
C. Adhesion.
D. Hydrogen.