Transcript File - knoxBioRocks

CHEMISTRY IN BIOLOGY
Biology Chapter 6
Chapter 6.1 – Essential Questions
What are atoms?
 How are the particles that make up atoms
diagrammed?
 What are the similarities and differences
between ionic and covalent bonds?
 What are van der Waals forces and why
are they important?

What are atoms?
Atoms
 (From the Greek for indivisible = “atomos”)
 The smallest unit of an element that still retains
the properties of that element.
Element
 A substance that cannot be broken chemically
into simpler substances.
 C, H, O, N, P & S make up more than 97% of
a human’s mass. (carbon, hydrogen, oxygen,
nitrogen, phosphorous and sulfur)
Compound
 a substance combined of two or
more different elements that are
chemically combined. (Ex: water =
H2O)
Molecule
 The smallest unit that can be
broken down and still retain the
properties of that compound.
 Can be compound or single
element.
What is the Structure of Atoms?
PARTS OF THE ATOM
Part
Charge
Mass
Location
Proton
+
1 a.m.u. Nucleus
Neutron
0
1 a.m.u. Nucleus
Electron
-
0 a.m.u. Orbits/Shells




The nucleus is the
center of the atom.
It has most of the
mass of an atom.
The shells or orbitals
are where the
electrons are.
The shells fill up with
2, 8, 8…
What is an Isotope?
Isotopes are atoms of the same element that
have a different number of NEUTRONS.
 One of the most known isotopes is Carbon-14

Carbon 14 & Radioactive Dating





Radioactive Isotope – an isotope that has an unstable
nucleus which emits radiation during its decay to a
stable form.
Cobalt-60 is used as a radiation source to stop the
development of cancer.
Other radioactive isotopes are used as tracers for
diagnostic purposes, as well as in research.
They can be traced with a Geiger counter or other
detection device.
Carbon-14 dating is used to determine the age of
artifacts and fossils up to about 50-80,000 years old.
Radioactive Dating with Carbon-14





It is used in dating things such as bone, cloth, wood and
plant fibers.
The ratio of normal carbon (carbon-12) to carbon-14 in
the air and in all living things at any given time is
nearly constant.
The carbon-14 atoms are always decaying, but they
are being replaced by new carbon-14 atoms.
As soon as a living organism dies, it stops taking in new
carbon. The ratio of carbon-12 to carbon-14 at the
moment of death is the same as every other living thing,
but the carbon-14 decays and is not replaced.
The carbon-14 decays in its half-life of 5,700 years,
Here’s a visual…
Here’s an example with U  Pb
Can you see the pattern?
Now, tell me who is missing!
What is the Periodic Table?
What info is on the Periodic Table?
5
Atomic Number
B
Element Symbol
Boron
10.81
Element Name
Atomic Mass
Atomic Number:
• Same as the number of protons.
• Defines what element it is.
• Also the number of electrons in a neutral
atom.
Element Symbol:
• one or two letters that represent
an element
("H" for "hydrogen," etc.).
• The first letter is always
capitalized
(Ca = Calcium; C = carbon).
5
B
Boron
10.81
Atomic Mass:
• The average mass of an element
in atomic mass units ("amu").
• It is the sum of protons and
neutrons – OR – the total mass of
the nucleus.
• It is stated as a decimal because
it is an average of the isotopes
of an element.
5
B
Boron
10.81
What are the 3 types of bonds?
Ion – an atom that has gained
or lost an electron; the atom
will be + or – charged after.
1) Ionic Bonding - In ionic
bonding, electrons are
transferred (given away).
 The oppositely (+/-)
charged ions are attracted
to each other.
 Occurs between metals and
non-metals.
CATION
ANION
Lithium loses an eand is now 1+
Fluorine gains an eand is now 1-


2) Covalent Bonding - The second major type of
atomic bonding occurs when atoms share electrons.
 This happens when two non-metals bond together.
 Both atoms share the stability of a full valence
shell.
3) Hydrogen Bonding – A
weak bond/attraction between
hydrogen and either oxygen,
nitrogen or fluorine atoms.
 This bond holds DNA strands
in a double-helix shape.
 It also is responsible for
water molecules sticking
together.
van der Waals bonds/forces




Molecules can attract each other
at moderate distances and repel
at close range.
The attractive forces are
collectively called "van der Waals
forces".
van der Waals forces are much
weaker than chemical bonds.
Geckos can stick to walls because
of Van der Waals forces.
Chapter 6.2 – Essential Questions
What are the parts of a chemical
reaction?
 How can energy changes be related
to chemical reactions?
 What is the importance of enzymes in
living organisms?

Chemical Reactions
Chemical Bonds – The attraction, sharing or
transfer of outer shell (valence) electrons.
 Chemical Reaction – involves the making and
breaking of chemical bonds to rearrange
atoms.
 Law of Conservation of Matter – Matter is
neither created nor destroyed in a chemical
reaction; it is just rearranged.

Chemical Reactions
WRITING CHEMICAL REACTIONS:
 Compounds & molecules are represented by their
symbol (H, Ca, N, O) and a subscript to show the
ratios of reactants.
 Ex: Water = H2O
 Reactant + Reactant → Product

hydrogen gas + oxygen gas → water
Activation Energy


Metabolism – All of the chemical reactions that
occur within an organism.
Activation Energy – the minimum energy needed to
start a chemical reaction.
Enzymes
Catalyst – a substance that lowers activation
energy. It speeds up chemical reactions without
getting involved or used up.
 Enzymes – proteins that act as biological
catalysts.
 Substrate – reactants that bind to the enzyme.
 Active site – the location where the substrate
attaches to the enzyme. It’s always a specific fit!

Enzymes
Chapter 6.3 - Essential Questions
How does the structure of water
make it a good solvent?
 What are the similarities and
differences between solutions and
suspensions?
 What are the differences between
acids and bases?

Special Properties of Water
Each hydrogen atom is covalently
bonded to the oxygen by a shared
pair of electrons.
Water is a "polar" molecule, meaning
that there is an uneven distribution of
electrons
 Water has a partial negative charge
near the oxygen atom due the
unshared pairs of electrons,
 It also has partial positive charges
near the hydrogen atoms.
There are other unique properties
of water due to the hydrogen
bonds…
 Ice floats because hydrogen
bonds hold water molecules
further apart in a solid than in a
liquid (i.e. – water expands when
it freezes).
 Water is the only substance to be
less dense as a solid.
Homogenous Mixture
Mixture – a combination of two
or more substances. Each
substance keeps its chemical
properties.
 Solution – a homogenous mixture.
 Solute – substance that is
dissolved. (Kool-Aid)
 Solvent – the substance that
dissolves the solute. (Water)

Heterogeneous Mixture
In a heterogeneous mixture, you can still tell each
individual part from each other; they can be
separated (Lucky Charms). There are 2 types:
 Suspension – a solution where the parts will
settle out over time.
 Colloid – a mixture where the parts do not
settle out. Ex: fog, smoke, butter, mayonnaise,
milk, paint, ink.
Acids and Bases
About pH and ACIDS/BASES…
 Scientists use the pH scale (“power
of hydrogen”) to measure how
acidic or basic something is.
 The scale goes from 0 to 14.
 Distilled water is 7 (right in the
middle).
 Acids are found between 0 and 7.
 Bases are from 7 to 14.
Acid:
+
 A solution that has an excess of H ions.
 It comes from the Latin word “acidus” that means "sharp".
 These are sour – lemon juice, vinegar, etc.
 HCl = 0; Gastric Juice = 2
Base:
 A solution that has an excess of OH ions.
 Another word for base is alkali.
 These taste bitter and feel slippery - baking soda, eggs.
 NaOH = 14; Hair Remover = 12.5; Bleach = 9
pH in Biology
Ionization is when a non-ionic compound separates
into ions. Examples:
 Sodium (Na+) – regulates fluid in and out of cells
 Potassium (K+) and Calcium (Ca+) – are involved in
many cell functions
Most of life needs a pH between 6.5 – 7.5
 Buffers are mixtures that can react with acids and
bases to keep a pH stable.
Neutralizing Acids and Bases
ACID + BASE = WATER + SALT
HCl + NaOH = H2O + NaCl
Chapter 6.4 – Essential Questions
What is the role of carbon in living
organisms?
 What are the four major families of
biological macromolecules?
 What are the functions of each
group of biological macromolecules?

Organic Compounds and Life
Organic Compounds contain carbon (+ H & O) and
play a role in living systems.
 Macromolecules are large molecules that are formed by
joining smaller organic molecules.
 Polymers are larger molecules made from repeating
subunits called monomers.
The 4 major groups of macromolecules are:

carbohydrates
 lipids
 proteins
 nucleic acids

Carbohydrates
1) Types:
monosaccharides - “sugars” – glucose & fructose
disaccharides - two single sugars linked together
 glucose + fructose = sucrose;
 glucose + galactose = lactose.
polysaccharides - many sugars linked together –
starch, glycogen and cellulose.
Carbohydrates
2) Structure: Carbohydrates are named (“a hydrated
carbon”) because the structural formula is typically (CH2O)n
 where “n” is an integer… 5 = C5H10O5 or 6 = C6H12O6
 this formula suggests that carbon atoms are joined to
water, the actual molecules are more complex.
Carbohydrates
3) Functions of Carbohydrates:
1. serving as building blocks for many
polymers
2. storing short-term energy (glycogen in
animals; starch/cellulose in plants)
3. providing structural building materials
4. serving as molecular "tags" to allow
recognition of specific cells and molecules
Lipids
1) TYPES - There are 3 types of LIPIDS
1. Neutral Fats & Oils
 Saturated
– no double carbon bonds, high melting point
& therefore solid at room temp, found in animals;
 Unsaturated – has double carbon bonds, liquid at room
temp, found in plants
 Partially Hydrogenated – (These are man-made). A
process takes plant oils & saturates the carbon bonds
with hydrogen to make them solid at room temperature
= MARGARINE.
Lipids
2. Phospholipids – an important part of cell
membranes.
3. Steroids - have two specific functions:
 hormones (i.e. - testosterone, estrogen,
progesterone, and cortisol)
 cholesterol (structural material) such as, an
important part of animal cell membranes.
Lipids
2) STRUCTURE
 Fats = 3 fatty acids + glycerol.
 Phospholipids = 2 fatty acids + glycerol + phosphate.
 Steroids = formed with 4 carbon rings.
3) FUNCTION - the most important is insolubility in water:
 helping form cell membranes (that enclose cells and cell
compartments).
 protection against drying out.
 storing long-term energy
 insulation
 absorbing shock
 regulating cell activities by acting as a hormone
Proteins
1) Type – proteins are the most abundant & diverse
molecules found in living cells.
2) Structure:
 Proteins range from simply large to enormous.
 Proteins make up about half the total weight of
biomolecules in a cell (excluding water).
 Are formed from amino acids using peptide bonds.
 Proteins are often called “polypeptides”.
Proteins
Ribonuclease
Collagen
Hemoglobin
Proteins
3) Function - Proteins play a wide variety of roles, including:
 Enzymes as catalysts that accelerate specific chemical reactions.
 Structural materials - keratin (the protein found in hair and nails)
and collagen (the protein found in connective tissue).
 Specific binding markers - such as antibodies that bind to foreign
substances to identify them to the body's immune system.
 Specific carriers - membrane transport proteins that move
substances across cell membranes, and blood proteins (such as
hemoglobin) that carry oxygen and iron through the body.
 Contraction - such as actin and myosin fibers that interact in
muscle tissue.
 Signaling - including hormones such as insulin that regulate sugar
levels in blood.
Nucleic Acids
1) Types - There are two types of nucleic acids:
• DNA – Deoxyribnucleic Acid (made with
deoxyribose)
• RNA – Ribonucleic Acid (made with ribose)
2) Structure - Nucleic acids are built
from subunits called nucleotides.
Each nucleotide has three parts:
 phosphate group
 5-carbon, or pentose, sugar
 nitrogen base (A,G,C,T,U)
Nucleic Acids
3) Function  DNA
serves stores information about all the
proteins (polypeptides) a cell can make.
 RNA is needed to convert DNA information into
protein and occurs in several different forms:
1.
2.
3.
messenger RNA (mRNA)
ribosomal RNA (rRNA)
transfer RNA (tRNA)