Transcript Chapter 1

Part 1: Cell biology and
energetics
Chapter 1: Molecules of life
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Elements
•
•
H, O, N and C constitute 99 per cent of living parts
of organisms
12 to 14 other elements of importance to living
organisms
– P, S, Cl, Na, Mg, K, Ca
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Atoms
•
Each element is composed of one type of atom
• Atoms composed of subatomic particles, which
carry a charge
– proton (positive)
– neutron (neutral)
– electron (negative)
(cont.)
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Atoms (cont.)
•
Atomic structure
– nucleus composed of protons and neutrons
– electrons orbit nucleus
•
Atomic number
– number of protons in nucleus
•
Atomic mass
– number of protons + neutrons in nucleus
•
Isotopes of element have different numbers of
neutrons
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Electrons
•
Electrons move around the nucleus in orbitals
– zones of space in which electrons exist at any one
moment
•
Electrons in orbitals closest to the nucleus have
lowest energy levels
– those further away have successively higher energy
levels
– electrons can move between orbitals by gaining or losing
energy
(cont.)
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Electrons (cont.)
•
Each orbital contains no more than two electrons
• Single orbital at lowest energy level
– closest to the nucleus
•
At higher energy levels, more than one orbital
– electron shell
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Fig. 1.3a: Structure of carbon atom
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Fig. 1.3b: Structure of oxygen atom
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Fig. 1.3e: Structure of chlorine atom
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Bonds between atoms
•
Chemical properties of an element determined by
number and arrangement of electrons in outermost
shell
– atoms gain or share electrons to fill outermost shell
•
Outermost shell filled with
– two electrons in hydrogen (one shell)
– eight electrons in other elements (two or more shells)
•
Sharing electrons to fill outermost shell
– forms chemical bonds
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Covalent bonds
•
Sharing electrons creates covalent bonds
– atoms join to form molecules
•
Hydrogen atoms have one electron in outermost
shell
– two atoms form molecular hydrogen (H2) by sharing
electrons
•
Molecules formed by electron sharing between
atoms of C, O, H, N, P and S are basic
constituents of living systems
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Fig. 1.5a: Formation of covalent
compounds
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Fig. 1.5b: Formation of covalent
compounds
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Non-covalent bonds
•
Electrical charges bond atoms or molecules
– weaker than covalent bonds
•
Ionic bonds
– form between cations and anions
•
Van der Waals forces
– form between temporarily polarised atoms
•
Hydrogen bonds
– form between polar molecules of hydrogen and oxygen,
nitrogen or other electronegative atoms
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Ionic bonds
•
Atoms become charged when they lose or gain an
electron from the outer shell
– loss of electron creates a positively charged cation
(electrons < protons)
– gain of electron creates a negatively charged anion
(electrons > protons)
•
Cations and anions bond together by opposite
charges
– ionic bonds
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van der Waals forces
•
Charge on an atom is not uniformly distributed at
any instant
– one part may have slightly negative or positive charge
•
Attracts neighbouring atom with opposite charge
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Hydrogen bonds
•
•
Hydrogen and oxygen atoms bind covalently to
form water molecules
Electrons tend to stay closer to the oxygen atom,
resulting in polarisation of the molecule
– H end positive
– O end positive
•
Polar molecules form hydrogen bonds with similar
molecules
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Fig. 1.5c: Formation of covalent
compounds
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Water
•
Ionic compounds separate into constituent anions
and cations when dissolved in water
– polar molecules of water surround ions and shield them
from one another
– hydration
•
•
Water also forms hydrogen bonds with other polar
molecules
Non-polar molecules are repelled
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Acids
•
Acids are proton donors
– release H+ and an anion into solution
•
HCl
→
H+
+
acid
→
H+
+ anion
Cl-
pH of acid is < 7
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Bases
•
Bases are proton acceptors
– accept H+
H+
•
+
H2O
→
H3O+
pH of base is > 7
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Buffers
•
Substances that maintain stable internal pH
• Act as reservoir of H+
– release H+ when pH rises
– accept H+ when pH falls
CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3OH- + H2CO3 ↔ H2O + HCO3-
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Carbohydrates
•
Carbohydrates are the most abundant organic
molecules in living organisms
– chemical energy, structural components
– Cn(H2O)n
•
Monosaccharides
– single molecules with three to seven carbon atoms
(glucose, fructose, galactose)
•
Disaccharides
– formed by glycosidic linkages of monosaccharides
(lactose, sucrose, α, α′-trehalose)
•
Polysaccharides
– long chains of monosaccharides
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Structural polysaccharides
•
Cellulose (plant and algal cell walls)
– molecules group into microfibrils
– hydrogen bonds and van der Waals forces between
cellulose molecules prevent hydrogen bonding with water

•
insoluble
Pectins (component of plant cell wall matrix)
– galacturonic acid with side chains
– forms gels
•
Chitins (fungal walls, arthropod exoskeleton)
– forms microfibrils
– similar to cellulose
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Storage polysaccharides
•
Starch (plants)
– short-term storage in photosynthetic tissue
– long-term storage in tubers, seed endosperm and
cotyledons
– composed of amylopectin and amylose
•
Other plant storage polysaccharides
– inulins
– levans
•
Glycogen (animals)
– storage in all tissues, but most abundant in liver and
muscles
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Lipids
•
Water-soluble biomolecules
– structure

phospholipids, sterols
– energy storage and transport

triacylglycerols
– photoreceptors

carotenoids
– coverings

waxes
– chemical messengers

•
steroids, glycolipids. isoprenoids
Composed principally of C, H and O
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Simple lipids
•
Simple lipids are composed of
– fatty acids with long hydrocarbon chain
– alcohol
•
Triacylglycerols act as energy reserves
– calorific content 37.67 kJg-1

more than twice as much than that of carbohydrates and
proteins
– stored in adipose tissue (animals) and seeds and fruit
(plants)
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Biomembranes
•
Phospholipids
– amphipathic molecules

hydrophobic non-polar region (hydrocarbon chains)
 hydrophilic polar region (phosphate and nitrogen
compounds)
– form micelles and bilayers (basic structural units of all
biological membranes)
•
Glycolipids
– amphipathic molecules

hydrophobic non-polar region (hydrocarbon chains)
 hydrophilic polar region (monosaccharides)
– involved in cell–cell recognition
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Polyisoprenoid lipids
•
Steroids
– properties depend on degrees of unsaturation of steroid
structure and chemical groups at different positions
•
Cholesterol
– amphipathic sterol
– membranes, including myelin sheaths
– precursor of many hormones
•
Carotenoids
– long-chain polyisoprenoids
– photoreception in chloroplasts, animal eyes
– vitamins A, E, K
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Proteins
•
Proteins are the most functionally diverse
biomolecules
– enzymes
– structure

collagen, elastin, silk
– hormones

insulins, growth factors
– defence

immunoglobulins, fibrinogen
– haemproteins

haemoglobin, myoglobin, cytochromes
– membrane proteins
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Amino acids
•
Proteins are chains of amino acids
– components selected from set of twenty amino acids
•
All amino acids are composed of
– amino group (–NH2), which may gain a proton and
become –NH3+
– acidic carboxyl group (–COOH), which may donate a
proton and become –COO– various side-chain groups (denoted by R)
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Structure of proteins
•
Primary structure
– sequence of amino acids
•
Secondary structure
– determined by arrangement of R-groups: α-helix and βsheets
•
Tertiary structure
– final shape of protein: globular or extended rods
•
Quaternary structure
– association of several globular proteins to form a
functional protein
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Fig. 1.32: Secondary structure of protein
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Fibrous proteins
•
Keratin (hair, nails, feather, skin)
– α-helix, extensible, increasing proportion of cysteine
reduces extensibility
•
Silk
– β-sheet protein, strong and flexible, but low extensibility
•
Collagen (connective tissue, bone, cartilage, skin)
– α-helix, primary structure rich in glycine, proline, lysine
•
Elastin (arteries, skin, ligaments)
– α-helix, primary structure rich in glycine, proline, alanine,
lysine
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Nucleic acids
•
•
Nucleic acids carry genetic information in all living
cells
Composed of nucleotides
– nitrogenous base

pyrimidine (uracil, cytosine, thymine)
 purine (adenine, guanine)
– pentose sugar

ribose, deoxyribose
– phosphate group
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DNA
•
Deoxyribose nucleic acid
– double-stranded
– pentose sugar = 2-deoxyribose
– bases = A (adenine), T (thymine), G (guanine), C
(cytosine)
•
Two strands of DNA are joined by hydrogen bonds
between complementary bases
A — T (U in RNA)
G—C
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RNA
•
Ribose nucleic acid
– single-stranded
– pentose sugar = ribose
– bases = A (adenine), U (uracil), G (guanine), C (cytosine)
•
Types of RNA
– messenger RNA (mRNA)

specifies amino acid sequence for given polypeptide
– ribosomal RNA (rRNA)

major component of ribosomes
– transfer RNA (tRNA)

carries amino acids to ribosomes to add to polypeptides
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Fig. 1.40b: Structure of DNA
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