Download Biology 1020 – Unit 2

UNIT 2 – INTRO TO
BIOCHEMISTRY
Chapters 1 & 2 in text.
In this chapter, we will overview the foundational chemistry
of biology and how the chemical structure of biomolecules
determines their properties.
LEVELS OF BIOLOGY
Last time we mentioned that the smallest unit of life is the
cell.
However, there are many levels below this that are important
to biology even if they are not “alive” on their own.
The most basic unit of matter we will cover is the atom.
Atoms are the smallest unit of a element that still retains the
properties of the element.
THE ATOM
Atoms are very, very small. However, they are made up of
three still-smaller components – protons, electrons and
neutrons.
Atoms can be envisioned as a central core of the positivelycharged protons and neutral neutrons with the smaller and
lighter negatively-charged electrons flying around this core
in differing orbits.
This core is called the nucleus.
THE ATOM
This is what is known
as the planetary model
of the atom. The
electrons and nucleus
resemble planets
orbiting a star.
This model is a
simplification of how
atoms are structured
in reality, but is
accurate enough for
our purposes in
biology.
THE ATOM
In nature, positive and negative charges will move in such a
way to balance themselves out, if possible.
Positively-charged protons and negatively-charged electrons
will therefore work towards balancing each other out. Due to
this, standalone atoms will generally have a total net charge
of 0.
Electrons and protons have an equal yet opposite charge and
thus one electron cancels out the charge of one proton.
For atoms: # electrons = # protons
THE ATOM
Protons are what we use to define each element. If an atom
has 1 proton, regardless of what else it contains, it is some
form of hydrogen. Similarly, any atom with 8 protons, is some
form of oxygen.
The number of protons in an atom is called the Atomic
Number.
THE ATOM
Neutrons do not have a charge, and therefore having more or
less neutrons does not change its ability to react drastically.
More or less neutrons simply makes an atom slightly heavier
or lighter. This has a small effect on how a chemical behaves,
as heavier atoms take more energy to get moving, but also
have more momentum once going.
The mass number of an atom is the sum of the protons and
neutrons. Electrons are not counted as they have a mass
significantly much less than protons and neutrons.
IONS
The electrons of an atom determine how it will interact with
other atoms. This determines if it will form bonds, and how
strong they will be.
Electrons come in sets called shells. Atoms are most stable
when all their shells are full.
IONS
Atoms will give up or take up electrons so that all of their
occupied shells are all filled.
An atom that gains/loses electrons will now have a positive
or negative charge as the protons and electrons are unequal.
This is called an ion.
In general, only electrons are lost, gained, or shared. The
protons and neutrons are in the nucleus and thus not as
accessible.
IONS
As we have established, positive and negative charges will
try to balance each other out.
In the case of ions, this means that if an atom loses electrons
to become a positively-charged ion, a negatively-charged ion
will pair up with it making the set of the ions have a net total
charge of zero.
THE MOLECULE
When atoms group up due to positive-negative attraction,
this is called a molecule.
For example, table salt (sodium chloride) contains positivelycharged sodium ion and a negatively-charged chlorine ion
balancing each other out.
However, not all molecules are made by ion attraction.
THE MOLECULE
Atoms can also form by atoms sharing electrons.
In this case, two or more atoms form a tight bond by
collectively sharing electrons. Again, electron shells will be
filled, and positive and negative charges will zero out.
Carbon is exceedingly good at forming complex multi-atom
structures and makes up most biological molecules. Carbonbased compounds are called Organic Compounds. All other
compounds are called Inorganic.
ORGANIC VS.
BIOLOGICAL
What’s the difference between organic chemistry and
biochemistry?
Organic chemistry deals with carbon-containing compounds,
including many compounds that are not naturally occurring
such as plastics.
Organic compounds therefore do not have to have any
relation to living things.
ORGANIC VS.
BIOLOGICAL
Biochemistry covers the compounds that make up living
things. Life on Earth is carbon-based, so essentially most
biochemicals are also organic chemicals.
Biochemistry also covers some inorganic compounds
(compounds without carbon) that are used in life processes.
For a compound to be both an organic chemical and
biochemical, it must both contain carbon and be used by a
living creature.
BIOLOGICAL
MOLECULES
Four very important categories of biological molecules are:
1 – Carbohydrates – combinations of carbon, oxygen and
hydrogen atoms. Can be linked together to form long chains.
2 – Lipids – mostly carbon and hydrogen atoms. Do not
dissolve in water well (hydrophobic).
BIOLOGICAL
MOLECULES
3 – Protein – carbon and nitrogen based with other atoms.
Proteins are long chains of linked amino acids. Proteins are
very diverse and can perform many roles as enzymes.
4 – Nucleic Acids – very special molecules that are used by
cells to store information. The deoxyribonucleic acid (DNA)
of cells hold all the information a cell needs to function.
TYPES OF REACTIONS
Many reactions will either convert many small things into
large things or vice versa.
Anabolic reactions build larger molecules from smaller
reactants. (growth, repair, reproduction, etc)
Catabolic reactions break down larger molecules into smaller
ones. (digestion, shedding, etc)
WATER
Aside from organic compounds, water is the most important
ingredient for life as we know it.
Water can be formed in many ways from other elements and
compounds – the simplest is forming water from oxygen and
hydrogen.
Chemical Reaction Formula:
WATER
Chemical Reaction Formula:
In this reaction, hydrogen and oxygen are reactants and
water is the product.
Once made, water is not very reactive. For the most part it
acts as a solvent (things dissolve into it).
WATER
Water’s combination of atoms ends up creating a
molecule with a light positive and negative charge –
water is polar.
Polar molecules are great at interacting with charged
molecules. This is how salts, electrolytes, acids, bases
and some proteins and fats are able to dissolve in
water.
WATER
At the same time, water is not strongly polar. This lets
it be able to interact with neutral chemicals.
This is how sugars, some proteins, certain fats and
cholesterols, and other non-charged are able to also
be dissolved in water.
Most chemicals are either completely polar or nonpolar. By having a light polar charge, water is able to
dissolve a wider variety of chemicals than most other
chemicals.
WATER & LIFE
Liquid water is needed for all life as we know it.
Here are the four main traits of water that make it needed for life:
1 – Cohesion – water quite tightly sticks to itself. This allows
easier forming of ponds and oceans, and is important for the
continuous flow of liquids in systems like plant roots or animal
blood vessels.
2 – High Heat Capacity – water can hold a lot of heat per gram.
This allows water to stay at relatively stable temperatures easier,
making it more hospitable for life.
WATER & LIFE
3 – Density - Ice is less dense than Water. Most chemicals
become tighter-packed when they form into solids. Water’s shape
and polar charge prevent this. Ice being less dense if important
for aquatic life as ice will form on the top first rather than on the
seafloor first.
4 – Universal Solvent – water can dissolve a large variety of
substances due to being partially polar.
ACID/BASE/BUFFER
A combination of water and certain dissolved substances creates
an acid or base.
Acids donate extra hydrogen ions (H+) to the solution. Acids
have a sour taste, pH under 7, neutralize bases, give off hydrogen
gas when reacted with metals, conduct electricity, and turn
litmus paper red.
Bases accept H+, are often slippery, have a pH over 7 neutralize
acids, conduct electricity and turn litmus paper blue.
A Neutral solution is at pH=7.0 exactly. Perfectly pure water is
neutral.
ACID/BASE/BUFFER
Buffers are special compounds that help a system resist pH
change. In the event that a small amount of acid or base is added,
the system will not change pH radically. Buffers can be
overpowered by large amounts of acid/base.
Buffers are very important because most biochemicals are very
fragile and can be damaged or altered by slight changes in the
chemical environment.
POLYMERS
Many biological molecules are made from smaller units called
monomers. Monomers combine to make a polymer.
Linking monomers will result in a water molecule being released
so it is named dehydration synthesis.
POLYMERS
In the same way, to split a polymer into smaller units requires the
addition of water and is therefore called hydrolysis.
POLYMERS
Most polymers are recycled and rebuilt in new ways.
When animals eat another organism, they break down the
polymers in the food by hydrolysis into the base monomers.
These monomers are then rebuilt into parts of the animal. Protein
in food is used to build protein in the animal that ate it.
CARBOHYDRATES
Carbs are a family consisting of sugars.
Carbs are used for energy as well as structure and messaging.
Monosaccharides are a single lone sugar monomer (glucose,
fructose, etc).
Disaccharides are sugar polymers made of two monomers.
(maltose, etc).
CARBOHYDRATES
Polysaccharides consist of many sugar monomers linked
together. Up to as many as 3000. Most are either made of a single
monomer, or have a repeating pattern of monomers.
Three important polysaccharides:
Cellulose – important structural part of plants. It’s structure
makes it so that the human digestive system cannot break it
down easily so it passes through the body as fiber.
CARBOHYDRATES
Three important polysaccharides:
Glycogen – another all-glucose polymer found in the liver of
animals to store energy. This is how the body can fuel itself and
raise blood glucose levels easily during fasting.
Starch – long branched chains of glucose. Stores energy in
plants. Unlike cellulose, this can be digested and the glucose
used.
LIPIDS
Lipids, unlike most biomolecules, are hydrophobic and dislike
water (think of how oil and water do not mix).
Lipids is a large category, including vital molecules such as fats
and steroids.
Fats typically come in the form of triglycerides. These are made
of three fatty tails attached to a head. The tails can be taken off to
be broken down for energy.
LIPIDS
The fatty acid tails of lipids come in two forms:
Saturated fat – tails are simple carbon and hydrogen. Very flexible
and regular, so they stack together tightly. Found in animal fats.
Unsaturated fats – fats where the carbons are double or triple
bonded to each other, lowering the number of hydrogen atoms.
These bonds give the tails kinks and turns, making them pack
together much looser. Found in plant fats.
LIPIDS – STEROIDS
Steroids are another type of lipid but have a very different
structure than fats. Steroids are made up of rigid rings of atoms
and thus become stiff and flat, rather than the free-moving tails of
fats.
All steroids are not bad, nor are they all synthetic (human-made).
Normal substances like cholesterol, testosterone, estrogen and
other hormones are steroids.
Anabolic steroids are synthetic imitations of testosterone to gain
extra muscle-building potential. These are dangerous and
prohibited in professional sports.
LIPIDS – STEROIDS
FAT (TRIGLYCERIDE)
STEROID
(CHOLESTEROL)
PROTEIN
Amino acids are the monomers of protein.
Amino acids link together using a peptide bond and therefore
chains of amino acids are known as polypeptides.
Many proteins are hundreds and thousands of amino acids long,
these large structures preform chemical reactions (enzymes), can
carry other substances (hemoglobin) as well as can offer
structure (keratin). Short polypeptides are used for many roles
such as signalling (insulin).
PROTEIN
Amino acids come in a variety of shapes and sizes. Each one
effects how the final chain.
Bulky amino acids will cause the chain to be inflexible, smaller
amino acids allow more motion.
Some amino acids are charged positively or negatively, or are
neutral.
All of these will determine how that part of the chain will interact
with the rest of the chain, and with the environment.
PROTEIN
An important factor in determining a protein’s function is its final
three-dimensional shape.
Proteins begin to fold up as they are made because certain amino
acids will induce bends or attach to one another.
The basic sequence of the chain is called the primary structure.
This is just the order of amino acids in a line.
PROTEIN
Eventually small sections of the protein form small substructures such as sheets or helices. This is secondary structure.
Finally, all the sub-structures give a protein its characteristic
shape. This is tertiary structure.
Above that, many proteins will group together to form a working
complex. The interactions between each protein may alter the
proteins’ shape. This is known as quaternary structure.
PROTEIN
NUCLEIC ACIDS
Nucleic acids are complex polymers that all life forms use to
store information. The order of the monomers makes a code that
is used to tell a cell how to make certain proteins.
Two of the most important nucleic acids are deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA).
NUCLEIC ACIDS
The monomer of a nucleic
acid is called a nucleotide.
Nucleotides are made of
three parts:
A sugar (ribose in RNA,
deoxyribose in DNA)
A Phosphate group
A nitrogenous (nitrogencontaining) base. These
are the actual coding
pieces.
NUCLEIC ACIDS
The nitrogenous base actually determines the code of the
DNA. There are four bases possible in DNA and like letters,
they form “words” that code for specific amino acids in a
protein chain.
The bases are: Adenine (A), Guanine (G), Cytosine (C), and
Thymine (T). Each one is different structurally so that they
can be “read”.
NUCLEIC ACIDS
DNA is normally
found with two
stands locked
together. The bases
from one strand pair
up with bases from
the other to link the
strands.
The sugar-phosphate
backbone bends to
create a double helix.
NUCLEIC ACIDS
Due to their shape,
only C-G and A-T
bonds are possible.
This allows the cell
to know what
should be opposite
of any base if part
of the other strand
goes missing or is
damaged.
NUCLEIC ACIDS
The fact that G-C and A-T bonds are the only combination
possible allows for easy replication of the DNA.
During replication, the two original DNA strands are
separated, and each has a new second strand built upon
them. The cell knows what bases to use on the new strands
because there is only one base that could be across from
each base on the original strand.