Download Chapter 2 biochem

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Chemistry:
◦ Branch of science studying the composition of
matter and how it changes
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Biochemistry:
◦ Branch of science studying how chemistry affects
living organisms
◦ Focuses on carbon molecules called
macromolecules
◦ Ex: nucleic acids, lipids, proteins, carbohydrates
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Element:
◦ A chemical substance with only one type of atom
◦ Ex: oxygen, hydrogen, carbon, nitrogen
110+ known (92 naturally found)
 Usually combine to form compounds and
molecules
 Living organisms require about 20 elements
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◦ Ex: O, C, H, N (95% of biomass)
◦ Others: Ca, K, S, Cl, Na
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Atoms:
◦ Smallest particle of an element which still retains
properties of that element
◦ Made of subatomic particles:
 1) Proton: + charge, in nucleus (middle of atom)
 2) Neutron: neutral, in nucleus
 3) Electron: - charge, circles the nucleus in cloud/shells
◦ Atoms vary in weight, chemical properties and
physical properties
 Form attractions to other atoms (chemical bonds)
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Chemical bond:
◦ Def: an attraction between two or more atoms
◦ Will form between atoms of same element or atoms
of differing elements
 Same element: Example – Nitrogen gas (N2 – two
atoms of nitrogen)
 Different elements: Example – Water (H2O – two
atoms of hydrogen, one of oxygen)
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Bonding involves the sharing or transfer of
electrons
Atoms will bond to fill their electron shells
◦ 1st shell(closest to nucleus): 2 electrons needed to fill
 Ex: Hydrogen in water bond
◦ 2nd shell: 8
 Ex: Oxygen in water bond
(fills 1st level with 2, then fills
the 2nd level with 8)
◦ 3rd shell: 8
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Three types of bonds:
◦ 1) Ionic:
 Bond that forms between two charged atoms (ions)
 Atoms involved have transferred electrons – giving them
opposite charges
 Ex: NaCl (Na+ lost electron, attracted to Cl- (gained elec.))
 FORMS BETWEEN atoms of the SAME MOLECULE
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Three types of bonds:
◦ 2) Covalent:
 Bond that forms when two atoms SHARE electrons
 Polar: unequal sharing of electrons, ex: water
 Nonpolar: equal sharing of electrons, ex: N2, H2
 Forms BETWEEN atoms of the SAME MOLECULE
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Three types of bonds:
◦ 3) Hydrogen:
 Bond that forms between hydrogen atom and the negative
atom of another molecules
 Ex: between water molecules, connects two strands of
DNA, important in protein folding
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Chemical reactions:
◦ Reactants: Molecules/compounds which start a
reaction
◦ Products: Molecules/compounds which are formed
during a reaction
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Chemical reactions:
◦ Def: Form or break bonds between atoms, ions, or
molecules; generates new chemical combinations
◦ Ex: digestion, macromolecule synthesis, cellular
respiration, photosynthesis
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Types of chemical reactions:
 1) Synthesis:
 When two or more atoms bond to form a more complex
structure; requires energy input
 Ex: DNA replication, condensation reaction (formation of
macromolecules)
 2) Decomposition:
 When bonds within a reactant break to form simpler
molecules; energy is released
 Ex: Digestion
 3) Exchange reaction/double displacement:
 When two types of molecules trade atoms
 Ex: Acid/Base reactions form water and salts
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Many are reversible
◦ Shown with a doublearrow
◦ Reversible reactions
meant that the products of
the reaction can change
back into the reactants
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Chemical equilibrium:
◦ When the concentrations
of both reactants and
products do not change
◦ Reaction continues!
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Chemical reaction rates:
◦ Dependent upon a variety of environmental
variables
 Ex: pH, temperature, concentrations of
reactants/products, energy availability, salt/salinity
◦ Catalyst:
 Def: A molecule that can change the rate (usually
increase) of a chemical reaction
 Ex: enzymes
 Human body relies upon these to sustain life
 Ex: Enzymes involves in DNA replication (helicase, DNA
polymerase, ligase)
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Electrolyte:
◦ Substances that release ions in water
◦ The solution then can conduct electricity
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Acids:
◦ Def: An electrolyte that release hydrogen ions (H+) in water
◦ Ex: Hydrochloric acid (HCl) releases H+ and Cl- ions in water
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Base:
◦ Def: An electrolyte that release hydroxide ions (OH-) in
water
◦ Ex: Sodium hydroxide (NaOH) releases OH- in water
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Concentrations of H+ and OH- ions in body fluids
can greatly affect chemical reactions
◦ Ex: Blood pressure, breathing rate
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We measure these ion concentrations using pH scale
◦ pH scale: Measurement of H+ ion concentration
◦ Scale range: 0-14
◦ Each number represents 10-fold difference in H+ ions
 Ex: pH of 6 has 10X H+ ions than pH of 7
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pH of 7 means there is an equal concentration of H+
and OH- ions (neutral)
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Acid: pH = 0-7ish
◦ Ex: hydrochloric acid in stomach, battery acid, vinegar
◦ More H+ ions (than OH-) = lower number
 Ex: pH of 2 has MORE H+ than pH of 5
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Neutral: pH = 7ish (optimal for most life)
◦ Ex: Distilled water, cow’s milk (6.6), human blood (7.4)
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Base: pH = 7ish-14
◦ Ex: bleach, egg white, ammonia
◦ More OH- (than H+) = higher number
 Ex: pH of 14 has MORE OH-/less H+ than does 11
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Two groups of chemicals produced and used in
chemical reactions:
◦ 1) Organic:
 Def: those that contain both carbon and hydrogen atoms
 Ex: macromolecules, methane
 Nonelectrolytes (usually do NOT release ions in water)
◦ 2) Inorganic:
 Def: the remaining molecules
 Usually dissolve in water or react with water to form ions
 Electrolytes (Ex: acids, bases)
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Water (H2O):
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◦
◦
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Most abundant compound in living organisms
2/3 of the biomass of an adult human
Major component of blood and other body fluids
Important solvent (many substances dissolve easily within it)
Plays important role in moving chemicals (ex: oxygen, salts,
sugars, vitamins)
◦ Can absorb and transport heat
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Oxygen (O2):
◦ Enter body through respiratory organs and transported via
blood
◦ Organelles use oxygen to release energy from food
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Carbon dioxide (CO2):
◦ Produced as waste product during cellular respiration
(breakdown of food molecules to produce energy)
◦ Exhaled via lungs
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Salts:
◦
◦
◦
◦
Compound composed mainly of oppositely-charged ions
Ex: Na+ and Cl- = NaCl (table salt)
Abundant in cells and tissues
Provide necessary ions important to chemical/metabolic
processes
 Ex: nervous system action potential, muscle contraction
Made of monomers which combine to form
polymers
 4 macromolecule groups:
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◦ 1) Carbohydrates
 Ex: sugar, starch, cellulose
◦ 2) Proteins
 Ex: enzymes, antibodies, cell surface receptors
◦ 3) Lipids
 Ex: fats, steroids, phospholipids (cell membrane
component)
◦ 4) Nucleic acids
 Ex: DNA and RNA
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Made of C, H, and O (twice as many
hydrogen as oxygen)
◦ Ex: C6H12O6
Often involves chains or rings of carbon
atoms joined with atoms of hydrogen and
oxygen
 Functions:
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◦ Provide much of energy that cells require,
◦ Supply materials to build cell structures,
◦ Stored as energy reserves
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Monomers (ONE sugar)
◦ Monosaccharide
◦ Examples: glucose, fructose, galactose
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Dimers (TWO sugars)
◦ Disaccharides
◦ Examples: sucrose and lactose
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Polymers (MANT sugars)
◦ Polysaccharides
◦ Examples: starch, glycogen, chitin, and cellulose
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Dimers/Polymers are considered complex
carbohydrates
Chitin
Cellulose
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Made of C, H, and O (phospholipids have P)
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Do not dissolve in water
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Functions:
◦ Smaller proportion of Oxygen atoms than do carbs
◦ Ex: Fat tristearin (C57H110O6)
◦ Will dissolve in ether or chloroform
◦ Primary energy storage molecules (fats)
◦ Insulation (fats)
◦ Primary component of cell membrane
(phospholipids)
◦ Used to synthesize other fats (steroids)
◦ Important to development of gametes (steroids –
sex hormones)
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Parts of Fat molecule:
◦ 1) Glycerol molecule
◦ 2) Fatty acid chains
◦ Fatty acid chains are what
make fats diverse
 Differ in:
 # of chains
 Types of chains
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Triglyceride fats
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Phospholipid
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Steroid
◦ 1 Glycerol, 3 Fatty Acid Chains
◦ Examples: Fats found in adipose tissue
◦ 1 Glycerol, 2 Fatty Acid Chains
◦ Example: Molecules found in cell membrane
◦ 4 Carbon ring structure
◦ Example: cholesterol, testosterone, estrogen, and
other hormones
Phospholipid
Steroids
Cholesterol
Progesterone
Testosterone
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Made of C, H, O, N, S (not all)
Functions:
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◦
◦
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Structural materials
Energy sources
Hormones
Can combine with carbs to function as cell surface
receptors
◦ Detect foreign substances in body
◦ Catalysts to speed up chemical reactions
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Monomer
◦ Amino Acid (20 found in body)
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Polymer
◦ Polypeptide chain
◦ Amino acids are held together by peptide bond (covalent
bond)
◦ Polypeptide chain folds to become a functional protein
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Primary (simple chain of amino acids)
Secondary (forms alpha/beta chains)
Tertiary (alpha/beta chains fold up-on themselves)
Quaternary (more than one chain)
◦ Conformation (folding of protein) determines its function
Peptide bonds b/t
Amino acids
H
H3N+
C
R
H
COOH
H3N+
C
R
H
COOH
H 3 N+
C
R
H
COOH
H3N+
C
R
COOH
Made of C, H, O, N, and P
 Functions:
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◦ Energy source (molecule is broken apart to release
energy)
◦ Genetic source
Phosphate
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Monomer- Nucleotide
◦ Parts of a nucleotide:
Sugar
 1) 5-carbon sugar
 2) phosphate group
 3) nitrogenous base
Nitrogen Base
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DNA
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RNA
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ATP
◦ Sugar- Deoxyribose
◦ Nitrogen Bases- A, T, G, C
◦ Sugar- Ribose
◦ Nitrogen Bases- A, U, G, C
◦ Sugar- Ribose
◦ Nitrogen Base- A
◦ Contains three phosphate groups
Nucleic Acid - DNA
A=T
G=C
A
G
T
C
Nucleic Acid - RNA
•Single-stranded
Adenine
Adenosine
High Energy Bonds
Ribose
Phosphates