Download Chapter 2 Biochemistry Goux Guided Notes

Chapter 2- The Chemistry of Life
- Matter is anything that has mass and takes up space. The basic unit of matter is the atom.
Atoms:
- The study of chemistry begins with the basic unit of matter, the
______atom_____
- Atoms are incredibly ___small______________
- Despite its extremely small size, an atom contains subatomic particles that are
even smaller
- The subatomic particles that make up atoms are
protons
and electrons
- Protons and neutrons have about the same mass
- However, protons are __positively______charged particles and neutrons carry no charge
- Strong forces bind ____protons____and ___nuetrons__________together to form the nucleus, which is the
center of the atom
- The __electron_________is a negatively charged particle
- Electrons are in constant motion in the space surrounding the nucleus. They are attracted to the positively
charged nucleus but remain outside the nucleus because of the energy of their motion.
- Because atoms have equal numbers of electrons and protons, and because these subatomic particles have equal
but opposite charges, atoms are _nuetral______________
- Electrons are arranged in orbits around the nucleus
- Each ___orbital________, also called shells, can hold a maximum of _____8____ electrons
- The outer orbital is the ____valence________ shell. This is where bonding can occur.
Section 2.1 The Nature of Matter
Elements and Isotopes:
- A chemical ____element_____ is a pure substance that consists entirely of one type of atom
-The atomic number of an element is equal to the ___number of protons___ in its atoms.
- The atomic mass of an element is a _________sum of the protons and neutrons_____ in the nucleus of
the atoms of that element.
- Atoms of the same element can have different numbers of _________ neutrons________
- Atoms of the same element that differ in the number of neutrons they contain are known as
____isotopes______
- Because they have the same number of electrons, all isotopes of an element have the same chemical
properties.
- Some isotopes are radioactive, The radiation these isotopes give off can be dangerous, but radioactive
isotopes have a number of important scientific and practical uses; geologists can determine the ages of
rocks and fossils by analyzing the isotopes found in them. Radiation from certain isotopes can be used to
treat cancer and to kill bacteria that cause food to spoil. Radioactive isotopes can also be used as labels or
“tracers” to follow the movements of substances within organisms.
Chemical Compounds:
- Atoms are most stable when the outer electron shell, the ___valence_______ is filled. If this shell is not
filled then the atom will undergo bonding to form a compound.
- In nature, most elements are found combined with other elements in compounds
- A chemical __compound___________ is a substance composed of atoms of different elements that are
chemically combined. Ex. H2O
Characteristics of compounds
1) Proportions of atoms are fixed
H2O (water) = 2 hydrogen atoms: 1 oxygen atom
H2O2 (peroxide)= 2:2 ratio of atoms
2) Properties of compound differ from the elements that
compose it. Ex. NaCl – Sodium; Chlorine
Chemical Bonds:
- The atoms in compounds are held together by ________bonds ____________.
- The main types of chemical bonds are _______ covalent______ bonds ______ ionic______ bonds.
Covalent Bonds:
- Sometimes electrons are ___ shared ____by atoms instead of
being transferred
- A covalent bond forms when electrons are __equally
shared_____ between atoms
- When the atoms share two electrons, the bond is called a single __covalent__________
bond
- The structure that results when atoms are joined together by covalent bond is called a
___molecule____.
- The ____ molecule ____________ is the smallest unit of most compounds
Ionic Bonds
-An ionic bond is formed when one or
more electrons are __transferred
___________ from one atom to
another.
- An atom that loses electrons has a
____positive________
charge
- An atom that gains electrons has a _____negative_____________ charge
- These positively and negatively charged atoms are known as ___ions______________
Van der Waals Forces:
- When molecules are close together, a slight attraction can develop between the oppositely charged
regions of nearby molecules
- Chemists call such intermolecular forces of attraction __Van der Waals Forces___________
- Although these forces are not as strong as ionic bonds or covalent bonds, they can hold molecules
together, especially when the molecules are large.
Section 2.2 Properties of Water
- Like all molecules, a water molecule is ____polar ________
Polarity:
- A molecule in which the charges are unevenly distributed is called a __polar________ molecule because
the molecule is like a magnet with oppositely charged poles.
- A water molecule is_____polar___________ because there is an uneven distribution of electrons
between the ______oxygen________________ and _________hydrogen_________________ atoms .
-Because of their partial positive and negative charges, polar molecules such as water can
____attract_________ each other
Hydrogen Bonds:
- Hydrogen bonds are not as strong covalent of ionic bonds, but they are the
strongest of the bonds that can form between molecules
- The ability of water to form multiple hydrogen bonds is responsible for many
of the water's properties.
- __cohesion_______ is an attraction between molecules of the same
substance
- Because of hydrogen bonding, water is extremely ______cohesive____
- ____Adhesion_____ is the attraction between molecules different
substances
- _____Cohesion____is an attraction between molecules of the same substance. Water is extremely
cohesive. Water’s cohesion causes molecules on the surface of water to be drawn inward, which is why
drops of water form beads on a smooth surface.
- _____Adhesion____ is an attraction between molecules of different substances.
- The surface of the water in the graduated cylinder dips slightly in the center because the adhesion
between water molecules and glass molecules is stronger than the cohesion between water molecules.
- Adhesion between water and glass also causes water to rise in a narrow tube against the force of gravity.
This effect is called ___capillary action_______________________ .
. Capillary action is one of the forces that draw water out of the roots of a plant and up into its stems and
leaves.
- Cohesion and the adhesion of water molecules holds the column of water together as it rises.
Solutions and Suspensions:
- Water is not always pure; it is often found as part of a mixture
- A ___mixture_______ is a material composed of two or more elements or compounds that are physically
mixed together, but not chemically combined.
- The two types of mixtures that can be made with water are _____solutions_______ and
________suspensions__________________.
Solutions:
- The ions gradually become dispersed in the water, forming
a type of mixture called a _______solution______________
- All components of a solution are evenly distributed
throughout the solution
Figure 3 NaCl Dissolving in Water When an ionic compound such as
sodium chloride is placed in water, water molecules surround and
separate the positive and negative ions.
-In a salt-water solution, table salt is the ___solute_____, the substance that is dissolved
- Water is the ____solvent_____________________, the substance in which the solute dissolves
- Water's polarity gives it the ability to dissolve both ionic compounds and other polar molecules (like dissolves
like) such as salt and sugar molecules
- Water is often call the _____universal solvent_________________ due to its ability to dissolve both ionic
and polar compounds.
Suspensions:
- Some materials do not dissolve when placed in water but separate into pieces so small that they do not
settle out
- Such mixtures of water and non-dissolved material are known as ______suspensions_______
Acids, Bases, and pH
The pH Scale:
- Chemists derived a ____pH_scale ____________________ to indicate the concentration of H+ ions in
solution
- The pH scale ranges from ______0 to14_________________________
- At a pH of 7, the concentration of H+ ions and OH- ions is ___equal___ ______
- Pure water has a pH of ______7___________
- Solutions with a pH below 7 are called _____acids_____________ because they
have __more_____ H+ ions than OH- ions
- The lower the pH the greater the ______acidity ________
- Solutions with a pH above 7 are called _____basic_______________ solutions
because they have more OH- ions than H+ ions
- The higher the pH the more ____basic_____________the solution
Acids:
- An __acids_____________ is any compound that forms H ions in solution
- Acidic solutions contain higher concentrations of H+ ions than pure water
and have pH values _less than_____ 7
Bases:
- A ___base_____________
is a compound that produces OH- ions in solution
- Basic solutions contain lower concentrations of H+ ions than pure water have a pH __more than_7
Buffers:
- The pH fluids within most cells in the human body must generally be kept between ___7.35_____
and __7.45______
- The pH of human blood must be maintained between 7.35 and 7.45 by the lungs and kidneys.
- If the pH is lower or higher, it will affect the chemical reactions that take place within the cells.
- Thus, controlling pH is important for maintaining ___homeostasis ___
_ one of the ways that the body controls pH is through dissolved compounds called ___buffers___
- ___Buffers_______ are weak acids or bases that can react with strong acids or bases to prevent
sharp, sudden changes in pH
Section 2.3 Carbon Compounds
The Chemistry of Carbon:
- Carbon atoms have _____4_______valence electrons
- Each electron can join with an electron from another atom to form a strong
_covalent__ bond
- Carbon can bond with many elements, including _____hydrogen_______ ,
phosphorus, sulfur,
and nitrogen
- Even more important a carbon atom can bond to
other
____carbon________ atoms, which gives carbon
the ability to form
chains that are almost unlimited in length
- These carbon-carbon bonds can be ___single_________ , double, or triple covalent bonds
Macromolecules:
- Many of the molecules in living cells are so large that they are
known as ___macromolecules_________ , which means
"giant molecules"
- Macromolecules are formed by a process known as
___polyymerization_______
in which large compounds are built by joining smaller ones
together
- The smaller units, or ____monomers_____, join together to form __polymers________
- Four groups of organic compounds (have C and H) found in living things are
1)
__carbohydrates______
Organic
2)
__lipids______
Has both Carbon & Hydrogen
3)
__proteins_____
Inorganic
4)
__nucleic acids____
Does not have both Carbon & Hydrogen
1) Carbohydrates:
__Carbohydrates________ are compounds made up of carbon, hydrogen, and
oxygen atoms
- Living things use carbohydrates as their main source of ___energy_(glucose)____
- Plants and some animals also use carbohydrates for structural purposes.
- Living things store extra sugar as complex carbohydrates known as _____starches______________
- Single sugar molecules are also called ______monosaccharides______
- The large macromolecules formed from monosaccharides are known as _polysaccharides________
- Many animals store excess sugar in a polysaccharide called ___glycogen______ , or animal starch
- When the level of glucose in your blood runs low, ______glycogen_________________is released
from your __liver_______________
- Plants use a slightly different polysaccharide, called plant starch, to store excess ___glucose________
- Plants also make another important polysaccharide called ____cellulose_________
2) Lipids:
- Lipids are very large and varied group of biological molecules that are generally not soluble in water
- __Lipids____________ are made mostly from carbon and hydrogen atoms
- The common categories of lipids are ___fats______, oils, and _____waxes_____________
- Lipids can be used to store _____energy_______.
- Some lipids are important parts of biological membranes and waterproof coverings
- Many lipids are formed when a glycerol molecule combines with compounds
called ______steriods (hormones)_______________
- If each carbon atom in a lipid's fatty acid chains is joined to another carbon atom by
a single bond, the lipid is said to be ___ saturated_______________________
- The term ____saturated_________ is used because the fatty acids contain
maximum possible number of hydrogen atoms
- If there is at least one carbon-carbon double bond in a fatty acid, the fatty acid is said to
be __monounsaturated ___________
- Lipids whose fatty acids contain more than one double bond are said to be
polyunsaturated_____
3) Nucleic Acids:
- __Nucleic Acids_________ are macromolecules containing hydrogen, oxygen, nitrogen, carbon, and
phosphorus
- Nucleic acids are polymers assembled from individual monomers known as ___Nucleotides_____
- Nucleotides consist of three parts:
1. ___nitrogen base_______________________
2. ___sugar_____________________________
3. ___Phosphate group____________________
- Nucleic acids store and transmit _hereditary_, or genetic information
- There are two kinds of nucleic acids
1.___deoxyribonucleic acid (DNA)___________
2.________ribonucleic acid (RNA)___________
4) Proteins:
- _____Protiens________ are macromolecules that contain nitrogen as well as carbon, hydrogen, and oxygen
- Proteins are polymers of molecules called ___amino acids________
- The basic unit or building block of a protein are ____ amino acids _.
- More than ___20___different amino acids are found in nature.
-It is the ____sequence______ of amino acids that determine the
shape of the protein.
- Some proteins control the rate of reactions and regulate cell
processes. Some are used to form bones and muscles. Others
transport substances into or out of cells or help to fight diseases
Section 2-4 Chemical Reactions and Enzymes
Enzyme Action:
- A __chemical reaction_______
is a process that changes one set of chemicals
into another set of chemicals
- Chemical reactions that occur in organisms are known as metabolism. Ex)
digestion, cellular respiration, photosynthesis, etc.
- Some chemical reactions occur ______slowly______ , others occur ______quickly_______.
- The elements or compounds that enter into a chemical reaction are known as ____reactants______
- The elements or compounds produced by a chemical reaction are known as ___products_________
- Chemical reactions always involve the breaking of bonds in _______ reactants ______and
the formation of new bonds in ____products___.
-Chemical reactions are summarized using chemical equations that include the reactants and products.
Also chemical equations must be balanced due to the Law of Conservation of Matter.
Ex) 6CO2 + 6H2O
Reactants
C6H12O6 + 6O2
Products
-2 Types of reactions include:
1) Dehydration Synthesis – building new compounds, putting together by removing
water”.
2) Hydrolysis – aka decomposition – breaking down by adding water
Energy in Reactions:
- Energy is __released______or _____absorbded_________ whenever chemical bonds are formed or are
broken
- Because chemical reactions involve breaking and forming bonds, they involve changes ___in energy_______
Energy Changes:
- Some chemical reactions ____release___________ energy, and other reactions ____absorb_____ energy
- Chemical reactions that __release_____ energy often occur spontaneously
- Chemical reactions that absorb energy will not occur without a source of ____energy_______
- Chemists call the energy that is needed to get a reaction started the _____activation energy____
The peak of each graph represents the energy
needed for the reaction to go forward. The
the
energy.
difference between this required energy and
energy of the reactants is the activation
Enzymes:
- Enzymes are proteins that act as ___catalyst_____for chemical reactions
- A _______catalyst______ is a substance that speeds up the rate of a chemical reaction
- Catalysts work by lowering a reaction’s _____activation energy____
- ___Enzymes_____ are proteins that act as catalysts.
- The name of an enzyme is derived from the reaction it __catalyzes__
- Enzymes names end with ___ -ase____
Enzymes speed up chemical
reactions that take place in cells.
- The substance (reactant) that the enzyme changes during the reaction
Notice how the addition of an enzyme
is called a _____substrate_______
lowers the activation energy in this
reaction. This action speeds up the
- Enzymes are catalyst that are not changed or consumed during the reaction
reaction.
Enzyme Action:
- Enzymes provide a site where reactants can be brought together to __react____________
- The reactants of enzyme-catalyzed reactions are known as __substrates______
- The ____active site___________ is the place where the substrate fits into the enzyme and are
complimentary like a ______lock________ and ___key____________
- Binding of an enzyme and substrate is called an ___enzyme-subtrate complex____________
- Because they are catalysts for reactions, enzymes can be affected by any variable that influences a
chemical reaction.
-Enzymes, including those that help digest food, work best at certain __pH_____ values.
-Many enzymes are affected by changes in ___temperatures___________.
-Not surprisingly, those enzymes produced by human cells generally work best at temperatures close to 37°C,
the human body’s core temperature.
- Therefore, temperature and pH that are not ideal for a particular enzyme can change the __shape______ of the
enzyme, including the shape of its ______active site________.
- If the shape of the active site is altered, it may not work on its substate, as the exzyme-substrate do not fit in a
__lock____ and ___key_____ model.
-Cells can regulate enzyme activity using other
__proteins______ that help turn key enzymes on or off at
critical stages in the cell's life