Download Unit 1 Biochemistry Presentation

Campbell Biology 9th Ed. Chapters 2, 3, 4 & 5
1. Describe the structure of an atom. State which
atomic feature determines the identity of the
element. Compare & contrast atoms vs. ions.
2. Explain covalent bonding.
3. Distinguish between polar and nonpolar
molecules. Give examples. Relate the polarity
of a molecule to its behavior in various
solutions.
4. Identify the characteristic behavior of water
molecules and discuss their significance to
living organisms (and the suitability of earth to
sustain life)
5. Define acid and base. Explain the relationship
between the pH scale and the concentration of
hydrogen ions.
6. Explain how carbon’s bonding arrangement
allows it to form a variety of structures
Note:
• Number and orientation of Covalent bonds
• Single, double and triple bonds
• Ring structures
7. Identify the characteristic functional groups of
organic molecules. Relate each functional
group to the type of organic molecules
possessing it.
8. Distinguish between carbohydrates, lipids,
proteins, and nucleic acids.
9. Match monomers with corresponding
polymers. Explain the chemical processes
which form and break apart polymers.
10. Distinguish between polypeptides and proteins.
Explain the four structural levels of proteins.
11. Describe the structure and explain the function
of nucleic acids. Distinguish between DNA and
RNA.
Atoms are the smallest
particles of elements, but
they consist of even
smaller “subatomic”
particles; Protons
Neutrons and Electrons
The number of protons
determines the element
Particle
Location
Charge
Mass
Proton
Nucleus
Positive
1 AMU
Neutron
Nucleus
Neutral
1 AMU
Electron
In constant motion
outside the
nucleus, in regions
referred to as
orbitals and energy
level
Negative
Negligible
(Small enough to
ignore relative to
the mass of the
whole atom)
Note the significance of charge. Charged particles will exert forces of attraction and
repulsion upon each other. Opposite charges attract. Similar charges repel.
Protons in the nucleus
are positively charged, so
they will repel each other
The only way to keep the
nucleus from exploding is
to keep protons
separated, which is
accomplished by
Neutrons
https://www.youtube.com/watch?v=SeDaOigLBTU
The number of neutrons
may vary for atoms of a
particular element.
This does not change the
identity of the element,
but it will affect the
stability of the nucleus.
Some combinations work
better than others
The different
combinations are called
Isotopes
https://www.youtube.com/watch?v=SeDaOigLBTU
The number of electrons may vary. We generally think of the
number of electrons as always being equal to the number of
protons, but that isn’t always true.
When the number of protons is equal to the number of electrons,
the particle is neutral and will be called an Atom.
When they aren’t equal, the particle is charged and is called an
Ion
https://www.youtube.com/watch?v=WWc3k2723IM
Because electrons repel each other, they tend to spread out in the space surrounding
the nucleus. At greater distances from the nucleus there is more space available.
This allows for both more movement and a greater number of electrons.
Electrons closer to the nucleus are said to be at “lower energy levels”. Electrons
further from the nucleus are at “higher energy levels”
http://www.middleschoolchemistry.com/multimedia/chapter4/lesson6
Regions in space where pairs of electrons are likely are
called Orbitals.
Higher energy levels, being larger, contain greater
numbers of orbitals
The pattern of orbitals filling is very distinct, and
described mathematically
In the diagram to the left
we see the shapes of the
different orbital types.
These figures are derived
from algebraic equations
We describe orbitals by type
(“s, p, d, and f”)
Each higher energy level
contains one additional type
of orbital
Each additional type has
space for more electron
pairs (following a pattern of
the next odd number; 1, 3,
5, 7 . . .)
So the first energy level
has only 1 orbital (an “s”
orbital). That means the
first energy level only
has room for 1 pair of
electrons
All the other energy
levels also have an “s”
orbital, but also 3 “p”
orbitals
Those 4 orbitals have
room for 4 pairs of
electrons (an “octet”)
Energy Orbital Number of
Level
Types
Orbitals
Max
number
of
electrons
1
s
1
2
2
sp
4
8
3
spd
9
16
4
spdf
16
32
Note that each higher energy level has
one more type of orbital than the level
before it. Each new type also has a
greater number of orbitals:
s = 1; p = 3, d = 5, f = 7
Note that the
periodic table is
organized to
demonstrate
electron
configuration
Electron
configuration
can be used to
predict the
chemical
behavior of
elements
Because electrons are attracted to the nucleus, they
tend to be close to it, at lower energy levels
Atoms with larger numbers of electrons will need to
have some electrons at higher levels as well
The highest energy level used is called the Valence level
It is the valence electrons that will form chemical bonds
In this Mg atom, the first 2 levels are full.
There are 2 electrons in the 3rd level. Those
2 electrons are the valence electrons.
When the atom reacts, those 2 valence
electrons are lost, leaving behind only the
electrons in the first 2 levels (which are
full to capacity).
It is the unpaired electrons that
will tend to be involved in
chemical reactions. They may
be lost, or the space may be
filled by gaining or sharing
electrons
Lewis Structures are
electron dot diagrams that
show the valence
electrons only
Note that the diagrams
show the electrons in
pairs, because orbitals are
electron pairs
There are spaces for 4
pairs because there is 1 s
orbital and 3 p orbitals
Examine each element in this chart and
predict the number of chemical bonds
that will be formed. Also predict
whether electrons will be gained, lost or
shared.
Note that Ne and Ar have
all 4 orbitals completed.
The valence level is full to
capacity so they are
chemically stable, no
reaction will occur
Li and Na each have only 1
valence electron. It will
usually be lost, forming a
positively charged ion
Ionic bonds happen
between ions (not atoms)
In this example, Na has lost
an electron (+ ion) which Cl
has gained (- ion)
Oppositely charged ions
attract each other
Look at the Lewis structures shown for these 2 elements. Na had 1 valence
electron. When that electron was lost, it left only the full energy levels behind.
The Cl atom had 3 of its 4 orbitals completed. Only 1 orbital contained an
unpaired electron. Gaining an electron filled that orbital and created a pair.
Covalent bonds are
formed when an
electron pair is
attracted by the
nuclei of 2 different
atoms simultaneously
They form when 2
atoms each have an
unpaired electron
The bond creates a
pair, filling an orbital
for both atoms
Electronegativity
is a number value
that describes the
relative strength
of attraction that
an atom will have
on a valence
electron
This helps us to
predict what will
happen when 2
atoms react
For example, if 2
atoms of H collide,
each of them will
attract a valence
electron from the
other atom with a
relative force of
2.1
Since the
attraction force is
equal for both
atoms, the
electron pair will
be shared equally
As a rule, if the difference between the 2 atoms
is 1.7 or greater the bond will be Ionic. If the
difference is less than 1.7 the bond will be
Covalent
If an atom of Na
collides with an
atom of Cl, the
electron pair will
be attracted by Na
with a force of .9,
but by Cl with a
force of 3.0.
Cl wins. It will
take the electron,
ionize both, and
form an ionic
bond
In this example, both atoms have an
unpaired valence electron. When they
collide a chemical bond will form
H has an electronegativity of 2.1 and C
has an electronegativity of 2.5.
Neither can exert a force strong
enough to ionize the other. The
difference is .4, far below the 1.7
needed to ionize, but not zero.
The bond will be covalent, but will
have a slight polarity in favor of the C
atom, represented by the “dipole”
shown
The H has a
partial + charge,
the C has a
partial - charge
Shape matters.
Both of the molecules shown have
3 atoms forming 2 covalent bonds
Both of the molecules have a
“dipole moment”, meaning the
bonds have a polarity
The bent shape of the first
molecule concentrates the
negative charge at one end, but
the linear shape of the second
molecule puts the polarities
directly opposite each other
Dipole moment is a
vector quantity, it has a
magnitude and a
direction
https://www.youtube.com/watch?v=PVL24HAesnc
Use the following
electonegativities:
H = 2.1, O = 3.5, C = 2.5
Determine the bond polarity for
each bond
Label each atom as d+ or d –
Draw the dipole moment for
each bond
Predict the polarity of the whole
molecule based on shape and
bond dipoles
Water is special for a number of reasons
The bond between H and O is extremely polar. It’s
right on the fringe between covalent and ionic
The oxygen atom has 2 pairs of unbonded
electrons, resulting in both a bent shape and a
concentration of negative charge on the oxygen
atom
The hydrogen has only 1 electron, and it is in the
bond between the H and O, leaving the H nucleus
exposed at the end of the molecule
https://www.youtube.com/watch?v=HVT3Y3_gHGg
In the diagrams given,
recognize the bent shape,
unbonded pairs of
electrons, and dipole
moment
Construct several water
molecules with your
modeling kit and predict
how they will behave
towards each other
Hydrophilic = Water Loving
Hydrophobic = Water Hating
Substances that are hydrophilic are
attracted to water, and usually
dissolved by water
Hydrophobic substances have no
attraction to water and will not
dissolve
https://www.youtube.com/watch?v=i3jA40arq9Y
Water molecules have strong attractions to each
other and to other polar substances
Water has a high “specific heat”, and resists
temperature change
Water absorbs significant amounts of heat
energy when it evaporates
Water expands when it freezes
Water is an excellent solvent of polar and ionic
solutes
Acid/Base chemistry is dependent upon water
https://www.youtube.com/watch?v=iOOvX0jmhJ4
Adhesion and
Cohesion both
refer to things
sticking together.
Adhesion
Water sticks to
something other
than water
Cohesion
Water sticks to
itself
Strong cohesion between water molecules at the surface can create unusual effects.
Note how the water beads up on the surface of the penny. The cohesion forces are
stronger than the force of gravity, so the water doesn’t fall off and drop to the table.
The insect shown should theoretically sink, but the surface tension is strong enough
to support its weight.
Watch the videos linked below. You’ll see some interesting effects.
https://www.youtube.com/watch?v=ntQ7qGilqZE
https://www.youtube.com/watch?v=ynk4vJa-VaQ
Compared to other substances, water requires a
huge amount of energy to change its
temperature.
That means that water tends to hold a steady
temperature. Consider a rain forest and a
desert. Both are hot, but one holds its heat and
the other varies temperature drastically from
day to night
It also means that water can store and move
energy very well. The oceans are a huge heat
sink
https://www.youtube.com/watch?v=dQk5yi05PIk
Consider Los Angeles and Phoenix. Almost
identical in latitude, but LA has a more
moderate climate because the ocean stabilizes
the temperature
How about Ireland. Further north than
Saskatoon, but with a moderate climate. The
gulf stream carries warm water from the
equator to the European coast and brings heat
energy to the British Isles
Evaporation is an
endothermic reaction. It
requires the input of a
significant amount of
heat energy
Sweating doesn’t cool you
off. It’s the evaporation
of the sweat. As it
evaporates it draws heat
energy from your body
MJ’s sweat isn’t really
orange
https://www.youtube.com/watch?v=vLfWnX0ahtc
The shape and polarity of water molecules cause them to form very distinct
arrangements when they crystallize. Note the difference between the
molecular arrangement of liquid water and ice. In ice the molecules are
closer together, but the crystals contain empty spaces in the hollow part of
the molecular bend.
Water is the only substance that expands when it freezes.
That expansion makes ice less dense than liquid water, causing it to float
https://www.youtube.com/watch?v=bzTZx1RDV3w
The polarity of water
creates a distinct + and –
end of the molecule.
Those charged regions
will pull apart crystals of
polar and ionic
substances, causing them
to dissolve.
Ionic substances will not
only dissolve, the ions will
“dissociate” from each
other
As the salt dissolves, the Na+
dissociates from the Cl-. Note the
orientation of the water molecules
relative to the ions in the hydration
shells
https://www.youtube.com/watch?v=0cPFx0wFuVs
The covalent bonds
between H and O are so
polar they are almost
ionic.
When water molecules
collide, especially when
the H from one collides
with the O from the
other, the H will ionize
forming H+ and OH-
https://www.youtube.com/watch?v=6gjZ88JbJas
On the average, every liter of water has 10-7
moles dissociated into H+ and OH- ions
The H+ ion is really a free
proton
H+ ions form Acids
OH- ions form Bases
In pure water there is
constant activity of the
molecules. Some
dissociate while others
form back in to H2O
https://www.youtube.com/watch?v=6gjZ88JbJas
Remember that H+ ions make
acids, so the greater the
concentration of H+ ions, the
stronger the acid
In pure water, the concentration
of H+ ions is 10-7 mol/L
The p in pH is a mathematical
function (-log). If I look at 10-7
and lose the base 10 and the –
sign, I end up with pH = 7
https://www.youtube.com/watch?v=LS67vS10O5Y
The word Organic comes from the word
Organism
Organic compounds are mostly compounds that
are formed by living organisms
Carbohydrates, Lipids, Proteins and DNA are all
organic compounds, but there are others
All organic compounds are structured around
Carbon
The diagram to the right
shows an apparatus used
for a famous experiment
to determine whether
organic compounds could
be produced from simple
inorganic substances
without living organisms
to direct the reaction
Watch the video and read
the text
Campbell Biology p58-59
https://www.youtube.com/watch?v=gWqJfBEzU98
Carbon has 4 valence electrons,
all unpaired, which allows it to
form 4 covalent bonds all equally
spaced around the carbon in 3
dimensions
It bonds readily with H, N, O, S, P
and with other C
It can form single, double and
triple bonds, and ring structures
It can form long, stable chains
when bonded with other C’s
https://www.youtube.com/watch?v=QnQe0xW_JY4
Using your molecular modeling
kit, construct 2 carbon
hydrocarbon molecules with
Only single bonds
One double bond
One triple bond
Note:
The number of hydrogens
The orientation of the bonds
Can the C-C bond rotate freely?
The simplest organic
compounds are saturated
hydrocarbons. Only H
and C, with only single
bonds
There is no limit to the
number of carbons in the
chain
The chart to the left
shows names, formulas
and structures of some
simple “alkanes”
https://www.youtube.com/watch?v=UloIw7dhnlQ
Because Carbon can form
covalent bonds with all
the other nonmetals, it
can easily bond to
something other than H
at a given position
In the Ethanol shown, an
oxygen atom has been
substituted on one of the
carbon atoms in Ethane
Any nonmetal atom or group of
nonmetal atoms can be
substituted an any position on the
chain.
The substitution may change the
shape, polarity, and behavior of
the resulting molecule
Using your molecular modeling kit, construct
A 2 carbon saturated hydrocarbon with a single
substitution
A 2 carbon unsaturated hydrocarbon with a single
substitution
A 2 carbon unsaturated hydrocarbon with 2
different substitutions
A 3 carbon saturated hydrocarbon with a single
substitution
A 4 carbon saturated hydrocarbon with no
substitutions
https://www.youtube.com/watch?v=22PkbCu3vYI
Using your molecular modeling kit, construct:
A 2 carbon saturated hydrocarbon (“ethane”)
The simplest molecule you can construct using only
Oxygen and hydrogen
Nitrogen and hydrogen
Carbon and oxygen
Identify the resulting simple molecules
Substitute each onto your ethane molecule (one at
a time, please)
Each of these functional
groups is a characteristic
structure that is commonly
found in organic molecules
Each is fundamentally a
simple, inorganic molecule
substituted onto the
hydrocarbon chain
Each will change the shape
and polarity of the
molecule, causing
characteristic chemical
behaviors
https://www.youtube.com/watch?v=OGD3q1eQ1TE
Mono = 1, Poly = many
Monomers are simple
organic molecules
Polymers are larger, more
complex molecules that
are formed by attaching
many monomers together
in a chain
https://www.youtube.com/watch?v=VigpwmH7E3M
Monomer
Polymer
Simple Sugar
Starch
Amino Acid
Protein
Nucleotide
DNA or RNA
Structures within organisms are built
from Carbohydrates (sugars and
starches), Proteins, Lipids (fats, oils,
waxes and cholesterol), and Nucleic
Acids (DNA and RNA)
https://www.youtube.com/watch?v=VigpwmH7E3M
Carbo = Carbon
Hydrate = water = H2O
Carbohydrate = CH2O
Glucose and Fructose are
simple sugars
(monosaccharides) consisting
of 6 carbon chains or rings
(CH2O)6 = C6H12O6
Use your modeling kit to make
6 units of CH2O and link them
together(C to C) forming a
chain
Sucrose is a disaccharide
formed by attaching the
two simple sugars, glucose
and fructose, together as
shown
Starches (polysaccharides) are
polymers formed from attaching
many simple sugars into a chain.
The chains may be straight or
branching, depending on the
organism that produces them
The diagrams above show some examples of plant and
animal starches and the variations in arrangement of the
polymer. Amylose, Amylopectin, and Cellulose are plant
starches. Glycogen is the main energy storage starch in
animal cells
Lipids are a large category of chemical
compounds with a wide variety of structures
and functions
In general lipids are categorized together
because they are largely hydrocarbons, so they
tend to be hydrophobic (not water soluble)
Types of Biological Lipids and their Functions:
Neutral Fats – Fats and Oils, Food fats
Cholesterol – A component of cell membranes and
steroid hormones
Waxes – form waterproof barriers
Phospholipids – largest component of cell
membranes
Neutral fats consist of fatty acids
attached to glycerol (shown at the
far left)
Since glycerol has only 3 carbons it
can only attach up to 3 fatty acids
The resulting molecule will be a
monoglyceride, diglyceride or
triglyceride
The fatty acids may be saturated or
unsaturated (one or more double
bonds)
Neutral fats are not technically
polymers, because the fatty acids are
attached to glycerol, not to each other
Cholesterol
Steroid
Testosterone
Cholesterol is a complex lipid
with a characteristic ring
structure as shown on the
diagram
Cholesterols vary greatly with
regard to the number and
position of functional groups
Different sterols will have
different effects and
behaviors depending upon
their structure
Waxes are long hydrocarbon
chains with few if any functional
groups
They tend to be solid at room
temperature because of their
high molecular weight, but melt
easily because of their low
polarity
They are hydrophobic, so they
are good at forming waterproof
barriers
Phospholipids are the main
component of cell membranes
Phospholipids are
diglycerides with a
phosphate group
attached at the 3rd
position on the
glycerol
The phosphate
“head” is
hydrophilic, while
the fatty acid
“tails” are
hydrophobic
Amino acids consist of 4
parts
A central carbon ( “alpha”) with
3 attachments
An amino group
A carboxyl group
A side chain (which is variable)
In the diagram:
a is alpha (note that it is basically a small a with a flourish)
R is the organic chemistry equivalent of the algebraic x. It represents a variable
There are more
than 20 amino
acids, but proteins
are made from
these 20
The shapes, sizes
and polarities of
the side chains
vary, which will
affect the function
of the protein they
form
Note that we can
categorize the 20
amino acids into
smaller groups
based on similar
structure
Amino Acid types:
Nonpolar
Polar uncharged
+ charged
- charged
Aromatic (ring)
Amino acids can bind
together, attaching
the amino group of
one to the carboxyl
group of the next
forming a “peptide”
bond
Polymer chains of
many amino acids are
called “polypeptides”
Polypeptides then
fold up into complex
functional shapes,
forming proteins
The first step in producing a
protein is to form the
polypeptide
There are 20 amino acids. Each
position in the polypeptide
could be any one of the 20
The sequence of the amino
acids is the 1st level, or
“primary” structure of the
protein
The sequence of amino acids is
controlled by genetics. A gene
is instructions for the AA
sequence in the polypeptide
Remember that each different
amino acid has a different side
chain, with a different shape,
size, and polarity
In the end, the shapes and
polarities will affect the overall
shape of the protein
Remember that the bond
angles between the atoms are
not nice straight lines, they are
bent
In a polymer, the bends can be
either in the same direction
(forming a spiral) or in the
opposite direction (forming a
zig-zag)
Secondary structure is the
bending or coiling of the
polypeptide
Secondary Structure:
Spiral = alpha (a) helix
ZigZag = beta (b) pleated sheet
OK, so some of the side
chains were polar, some
nonpolar, some +, some -,
some even contained
sulfur
Polar side chains will
attract other polar side
chains
Nonpolar side chains will
tend to be pushed away
from the water in the
cytoplasm
+ charged side chains will
form ionic bonds with –
charged side chains,
holding them together
more firmly than those
polar/nonpolar
interactions
Sulfur containing side
chains will form covalent
“disulfide bridges” which
will lock the fold in place
permanently
Of course these
interactions can be
affected by their
environment
Temperature can affect
flexibility
Moisture content affects
polar/nonpolar interaction
pH affects charged regions
Extreme heat and harsh
chemicals can break
disulfide bridges
Quaternary structure is
really a direct follow-up
of tertiary structure
The same forces that hold
parts of a polypeptide
folded together can also
hold two different
polypeptides together.
Many proteins consist of
several polypeptides
folded together to form a
larger structure
https://www.youtube.co
m/watch?v=zm3kovWpNQ
https://www.youtube.co
m/watch?v=nEHe3Aie9Ek
https://www.youtube.co
m/watch?v=yZ2aY5lxEGE
https://www.youtube.co
m/watch?v=cAJQbSLlonI
https://www.youtube.co
m/watch?v=Pjt1Q2ZZVjA
Please watch the videos and read about
protein folding and “chaperonins” on
page 85 in your textbook
Nucleic Acids are either
DNA or RNA
They are polymers
(generally found in the
nucleus) which consist of
“nucleotide” monomers
Nucleic Acids function for
genetic control, which will
be studied in far more
detail in another unit
Individual nucleotides
may also serve nongenetic functions
Nucleotides are
monomers, but are
complex molecules in and
of themselves
They have 3 parts:
A pentose sugar, which
may be ribose or
deoxyribose
A phosphate group,
actually phosphoric acid
A nitrogenous base, of
which there are 5 types
which fit into 2 categories
Ribose and
Deoxyribose are both
pentose (5 carbon)
sugars
As the name
suggests, deoxyribose
is simply ribose with
a missing oxygen
Deoxyribose is found
in DNA, whereas
Ribose is in RNA
Examine the
structures,
compare and
contrast shapes
and functional
groups to
clarify why
such similar
molecules
might behave
differently.
The nitrogenous bases are each either a purine or a
pyrimidine ring structure.
Adenine, Guanine, and Cytosine are found in both
DNA and RNA. Thymine in DNA only, Uracil in RNA.
The diagram to the left
shows DNA (how could you
tell?)
DNA consists of 2 strands of
nucleotide polymers
Note the orientation of the
strands in comparison to
each other
Note the nitrogen bases. Do
you see a pattern?
Note that in RNA, Uracil will take the place of
Thymine. Go back a few frames and see why this
works
In the DNA
polymer, Adenine
always pairs with
Thymine (A-T)
and Cytosine with
Guanine (G-C)
Note the
significance of
both shape
(purine vs
pyrimidine) and
attraction
between
functional groups
There are a lot of videos available on
macromolecules, some are linked below:
Khan Academy Playlist (macromolecules)
https://www.youtube.com/watch?v=-Aj5BTnzv0&list=PLh4gvBbNMoamw99TjjQCyXKqCsd2HV-k0&index=1
MIT Open Courseware
https://www.youtube.com/watch?v=1eGsdK1fPLM
Amoeba Sisters
https://www.youtube.com/watch?v=YO244P1e9QM
Crash Course
https://www.youtube.com/watch?v=H8WJ2KENlK0
Bozeman Biology
https://www.youtube.com/watch?v=QWf2jcznLsY