Transcript Chapter 2 - Simple Things of Life

CHAPTER 2
Basics of Life
Chemistry
INTRODUCTION
 All
living things are composed of matter
– Any substance that has mass and occupies space
 All
matter made up of chemicals
– O, C, H, N, C, etc
 Chemicals used for
– communication, defense, reproduction etc.
Features of matter
Energy:
all matter has
energy: Life uses energy
–Potential energy:
–Kinetic energy:
Composition of Matter
Atoms
(e.g. H, O)
–Smallest unit of matter/building
blocks
Form
elements
–Pure substances: one kind of atoms
Structure of an atom:
Bohr Model

Protons
 Neutrons
 Electrons: form chemical bonds
– Orbits/energy levels
– insignificant weight
– form chemical bonds
Elements vary in Neutrons but not
protons
 atomic
number -> # of protons ( = # electrons)
– Constant (unique for an element)
 Atomic
mass unit = mass of one proton
 Neutrons may vary for one element
– Isotope-Atoms of same element containing a different number of
neutrons
 Mass
number = # protons + # neutrons
 Atomic weight: average weight of all isotopes
Compound A
substance formed by chemical
union of atoms of 2 or more
different elements in a specific
ratio
–E.g water: H2O

molecule smallest
unit of a compound
–water - H2O
–sucrose – C12H22O11
some
are diatomic molecules
–H2, O2, N2
Periodic Table of the Elements  Provides
information about elements
– arrangement of elements by properties
– Name & chemical symbol for each element
– atomic number - # of protons (= # electrons)
– Atomic weight
What is a chemical bond?

Attractive force that holds atoms of molecules
together
ELECTRON DISTRIBUTION & chemical
bonds

modern theory recognizes e- in “clouds” or energy
levels
– The further from the nucleus, the more energy
e-’s have

Bohr model
–
# varies with shell
• 2 in the first
• 8 in the second
• 8 in the third (sometimes 18)
– generally 8 is the most stable configuration
ELECTRON DISTRIBUTION…cont’d
All atoms “want” 8 electrons in their outermost
shells and will interact with other atoms to the
end that all reach 8.
Basis for formation of molecules (compounds)
FORMATION OF MOLECULES



atoms interact such that both (all) have 8 electrons in
outermost orbit
thus, molecules are the most stable energy states for
atoms and their electrons
attractions between atoms in a molecule are
chemical bonds
– attractions result from distributing electrons so that each
atom in the molecule has 8 in its outermost shell, at least
part of the time
TYPES OF CHEMICAL BONDS

IONIC-one atom loses electrons, other gains electrons
– atom that loses electrons has a net positive charge
• cation
– atom that gains electrons has a net negative charge
• anion
– unlike charges attract
• molecules form

many elements in the body occur as ions (charged atom)
– called electrolytes
Sodium Chloride
–chlorine - 7 electrons in the outer
orbit
–sodium - 1 electron in the outer orbit
–Na+ + Cl- -> sodium chloride NaCl
TYPES OF CHEMICAL BONDS…cont’d)

COVALENT-two atoms share one or more pairs of

electrons
each has 8 electrons in its outermost orbit at least
part of the time
– non-polar covalent bond
• atoms share electrons equally
– methane
– polar covalent bond
• unequal sharing of electrons between atoms
– water
Covalent bonds (cont)form
proteins,
carbohydrate, lipids
(fats) and nucleic acids
hydrogen  atomic
number is 1
– has 1 proton & 1 electron
 energy
level 1 – needs 2 electrons
– forms 1 covalent bond
– only H2 exists naturally
• H-H -> structural formula
• H2 -> empirical
helium –
atomic
number is 2
–2 electrons
level 1 – filled
noble gas
energy
carbon –
 atomic
number is 6
– 6 electrons
level 1 – filled
 energy level 2 – has 4: Forms
 energy
• 4 covalent single bonds (formed by sharing a
electrons)
pair of
hydrogen bonds (not really)
Form mostly between molecules, do not bond
atoms
 Always between H & O; or H & N
 Each weak
 Many hydrogen bonds form very strong
structures
 water as an example

strength of bonds –
covalent > ionic >
hydrogen
IONIC COMPOUNDS
Acids
Bases
Salts
pH Scale  Measures
acidity /alkalinity or
– H ion conc.
 pH
Scale - ranges from 0 to 14
 pH 7 = neutral
pH Scale high
[H+] = low pH / acid
–< 7
low
–>7
[H+] = high pH / base
Summary: Define these terms
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–
–
–
–
–
–
–
–
–
–
–
Atom
Element
Molecule
Compound
Atomic mass unit
Atomic number
Chemical symbol
Atomic nucleus
Atomic weight
Acids
Bases
Salt

pH
 Proton
 Electron
 Neutron
 Ion
 Cation
 Anion
 Kinetic energy
 Chemical reaction
 Ionic Bond
 Covalent Bond
 Hydrogen Bond
Organic Chemistry, The Chemistry
of Life
Chapter 3
Inorganic molecules do
not contain carbon
linked to H
ex: water, salt, sodium
hydroxide
Organic molecules contain
carbon linked to H and oxygen (N,
S, P also, but not always)
– proteins
– lipids (fats)
– carbohydrates
– nucleic acids
Carbon / central atom
can
form 4 covalent bonds
bonds spaced evenly
|
-- C -|
Can form long chains
Can combine with many other atoms
All organic Molecules have a
Carbon skeleton / backbone

Linear or a ring (fig 3.3)
_________

Length & shape confers
uniqueness
 Functional groups attached
– determines the chemical
property of the molecules
–
Functional groups  Amino
group -
– -NH2
– found in amino acids and proteins
 Phosphate
group
– PO4
– found in phospholipids
 See
figure 3.7
Formation of organic
molecules Monomer
= single unit
– amino acid
– Glucose
 Polymer
/ macromolecules
–Starch:
• glu-glu-glu-glu…glu
Dehydration / Synthesis the
linking together of
monomers with covalent bonds
molecule of water removed
energy requiring
See
figure 3.8
Hydrolysisunlinking
of monomers
water molecule added
energy releasing
See figure 3.8
Carbohydrates - sugars and
starches 
function – provides energy
– support – cellulose
– component of other organic molecule • DNA-> deoxyribose sugar
• RNA -> ribose sugar
• ATP -> ribose sugar
Simple sugars: Monosaccharides
Form
complex CHO
–glucose – (dextrose)
–fructose –
–galactose-
Simple sugars: Disaccharides  lactose
(milk sugar) ->
– glucose + galactose
 sucrose
(table sugar) ->
– glucose + fructose
 Maltose
(malt sugar)
– Glucose + glucose
Polysaccharides - complex
carbohydrates -
Long
chains of
monosaccharides joined
together
Examples are:
Starch Polymer
of glucose
CHO/energy storage in plants
–amylopectin (trees shaped)
– amylose (straight)
–Figure 3.10
Glycogen “tree”
shaped polymer of glucose
energy storage in animals
–found in muscle and liver cells
–provides rapid bursts of energy
Cellulose Polysaccharide
Cell
walls of plant cellulose
Cannot be digested by humans : no
calories
Digested by ruminants
Lipids–
3
classes
–true fats –
–phospholipids –
–steroids –
fat
-> solid at room temperature
oil -> liquid at room temperature
Consist of C, H, & small amounts of
O large,
non-polar molecules
– can not dissolve in water
 formed
by dehydration /
synthesis
True (neutral) fats –
function  insulation
-
– prevents loss of body heat
 cushion
internal organs
 energy storage – fat -> 9 calories per gram
– sugar -> 4 calories per gram
Structure of true fats 1,
2, or 3 fatty acids
attached to glycerol
Fatty acidlong
carbon chain
carboxyl (-COOH)
group attached to the
end
FATTY ACID: Fig.
Saturated Fatty Acid
 no
double bonds / contains the
maximum # of hydrogen atoms
 from animal products
 Solid at room temp
– examples: butter, lard
Unsaturated Fatty Acid

contains C-C double bonds
 from plants
 liquid at room temperature
 polyunsaturated fatty acids: many double bonds
– Ex: olive oil, soybean oil

monounsaturated fatty acids: one double bond
– Ex: sunflower oil, corn oil
Glycerol –
3
C skeleton
3 alcohol groups attached
–See page 56
Structure of lipids
Triglycerides
–three fatty acids + one
glycerol
–most abundant true fat in the
body
Triglyceride: Fig. 3.21
Omega –3 & 6 fatty acids
Essential
fatty acids
Used for growth & hormone prdn
rd
double bond found after the 3 carbon
Abundant in fish oil, soybeans
Hydrogenation Adding
hydrogen to an unsaturated fat
solidifies the fat
ex: margarine
Phospholipids 1
Glycerol + 2 fatty
acids + Phosphate
cmpd
 function
component of cell
membranes
Steroids 
lipids without fatty acids
 interlocking rings
– cholesterol • component of cell membranes
• converted into bile salts (emulsify fat)
• vitamin D
– hormones • estrogen
• testosterone
Proteins 
function
–structural • cell membranes
• muscle cells
• Hemoglobin
Protein function (cont) regulation
-
–enzymes (organic catalysts)
–hormones- insulin, oxytocin
–antibodies - fight infection
Protein function (cont) carriers
-
–lipoproteins - transport fats
• cholesterol
• triglycerides
• Phospholipids
Consist of –
 Linked
amino
acids (AA)
 Peptide bonds
 Polypeptide
chain
 Only 20 AA
exist
Peptide bond: covalent bond
between amino acids
Protein structure &
Organization
Four levels of protein
organization  primary
- polypeptide chain
 secondary - polypeptide chain
twists– alpha helix (coil) - formed by
hydrogen bonds
– beta pleated sheet - formed by
hydrogen bonds
Protein organization (cont)  tertiary
–3D
– Folding of an
individual molecule
 quaternary
– 4D
– interactions of
individual 3D
molecules
Changes in protein structure sickle-cell
anemia-
–hemoglobin consist of 4
polypeptides
–change in one amino acid causes
the hemoglobin to fold poorly
–Forms a“sickle” shape under
increased oxygen demand
DenaturationChange
of a protein’s 3-D shape
Bonds broken by
– heat, light, or pH
not
reversible
–you can not unfry an egg!
Nucleic acidsfunction
- component of DNA &
RNA
–DNA - genetic code
–RNA - manufacturer of protein
Structure of nucleic acids made
up of nucleotides
Nucleotides – 5- carbon simple suger
• deoxyribose (DNA)
• ribose (RNA)
– phosphate group
– nitrogenous base
• Adenine
• Guanine
• Thymine
• Cytosine
• Uracil
NUCLEIC ACIDS
DNA
– Genetic material
– Nucleotides: building blocks
• 5-C sugar, deoxyribose
• Phosphate
• Nitrogenous Base
• Adenine,Guanine,Thymine, Cytosine
NUCLEIC ACIDS
DNA
– Double helix structure
– Sugar-phosphate backbone
– Bases complimentary paring
• A-T, C-G
– Coding strand
• Protein synthesis
NUCLEIC ACIDS
 RNA
– Protein synthesis
– Ribose sugar
– Uracil base and no Thymine
3
forms of RNA
– Messenger RNA : mRNA
– Transfer RNA : tRNA
– Ribosomal RNA : rRNA
SUMMARY

Chemistry of living things
– Based on Carbon

C atoms: all organic molecules
 Structure of OM related to function
 Common OM
– CHO, Pns, Lipids, Nucleic acids