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Topic 2 Molecular Biology
Biochemistry
Introduction
• Organic chemistry is the chemistry of carbon
compounds.
• Biochemistry is a branch of organic chemistry
dealing with living organisms.
• All living organisms are made of molecules
that can be classified into one of four types.
• Carbohydrates, lipids, proteins or nucleic acids
Metabolism
• Metabolism is all the enzyme catalyzed reactions
that take place in an organism.
• The four groups of molecules interact with each
other to carry out the reactions of metabolism.
• Example: Insulin (Protein) helps glucose
(carbohydrate) travel through the cell membrane
(lipid) and get into the cell. The insulin molecule
itself is created by DNA (nucleic acid)
Organic Chemistry
• Not all molecules that contain carbon are
considered organic, such as carbon dioxide.
• Carbohydrates, lipids, proteins and nucleic
acids are all organic and contain carbon.
• Live is sometimes referred to as carbon based
Carbon
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Atomic # 6, which means 6 protons.
Also normally has 6 electrons.
2 electrons form the stable inner shell.
4 electrons are found in the second, unfilled
shell.
• Carbon likes to “fill” this second shell by
sharing 4 electrons with other atoms. Each
“sharing” forms a covalent bond, so each
carbon atom can form 4 covalent bonds.
Common Atoms other than Carbon
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Hydrogen
Oxygen
Nitrogen
Phosphorus
Building Blocks
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Carbohydrates – Monosaccharides
Lipids – Glycerol and Fatty acids
Proteins (polypeptides)– Amino acids
Nucleic acids - Nucleotides
Carbohydrates
Monosaccharides Disaccharides Polysaccharides
Glucose (2)
Maltose
Starch
Galactose
Lactose
Glycogen
Fructose
Sucrose
Cellulose
Ribose
Chitin
PROTEINS
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Polypeptide Chains made from amino acids
Some types of proteins
Enzymes
Antibodies
Hormones
Lipids
• Triglyceride – Fat stored in adipose tissue
• Phospholipid – Form bilayer in cell membrane
• Steroid – A type of hormone
Nucleic Acids
• DNA – deoxyribonucleic acid
• RNA – ribonucleic acid
• ATP – adenosine triphosphate
Metabolism
• In a multicellular organism, all of the reactions
within all of the cells and fluids comprise the
metabolism of the organism.
• Reactions occur when certain molecules collide.
• Cells use enzymes to increase reaction rates.
• Enzymes are proteins with a very specific shape,
that very specific molecules can fit into.
• Area of enzyme that molecule fits into is called
the active site.
Enzyme at Work
Example reaction: ADP + Pi = ATP
Enzyme lowers the amount of energy needed
for the reaction to begin – activation energy
Metabolism = Catabolism + Anabolism
• Catabolism is breaking down large, complex
molecules (food) into smaller, simpler ones.
• Anabolism is converting small, simple
molecules into larger, more complex ones.
• Catabolism involves hydrolysis reactions and
hydrolytic enzymes
• Anabolism involves condensation reactions
Hydrolysis
• Hydrolysis reactions break things apart and
require a molecule of water to do so.
• Example: Lactose + water = glucose + galactose
Hydrolysis
• Example: Triglyceride + 3 waters = Glycerol + 3
fatty acids.
Condensation
• Condensation reactions combine smaller
molecules to create larger ones, and give off
water as a byproduct.
• Creating proteins from amino acids
• Creating triglycerides from glycerol and fatty
acids
• Creating di and polysaccharides from
monosaccharides.
2.2 Water
• Water is a good solvent – “solvent of life”
• Any solution where water is the solvent is
called an aqueous solution.
• To understand the properties of water, you
have to understand the structure.
Water molecular structure
• Bonds between the oxygen and the two
hydrogen atoms are polar covalent bonds.
Due to unequal sharing, the Oxygen end
is more negative and the hydrogen end is
more positive.
Hydrogen Bonding
•
Because of the polarity
of a water molecule, the
positive end of one
water is attracted to the
negative end of another
water molecule. This
attraction is called a
hydrogen bond
Cohesive property of water
• Cohesion is when molecules of the same type
are attracted to each other. So when one
water molecule is attracted to another water
molecule ( hydrogen bond) it’s called
cohesion.
• Explains water droplets, surface tension, how
water is able to move in plants.
Adhesive property of water
• Adhesion is when a molecule is attracted to a
different type of molecule. So if a water
molecule is attracted to a different kind of polar
molecule, it’s called adhesion.
• Water moves upward in plants using both
cohesion and adhesion.
• When the water is being pulled up, it moves due
to cohesion, when it isn’t being pulled, it remains
in place due to adhesion with the tube it is
traveling in.
Thermal properties of water
• Water has high specific heat – This means
water can absorb or give off a great deal of
heat with changing temperature very much.
• Water helps to stabilize our temperature.
• Water also has a high heat of vaporization,
meaning it absorbs a lot of heat when it
vaporizes.
• As sweat evaporates from our skin, it cools our
body.
Solvent properties of water
• Water is an excellent solvent of polar molecules.
The vast majority of biological molecules are
polar, including carbohydrates, proteins and
nucleic acids.
• Common aqueous solutions are cytoplasm,
nucleoplasm, stroma and plasma.
• Plants use water to transport material in xylem
and phloem. Animals use water in blood to
transport materials in arteries and veins
Hydrophilic and Hydrophobic
• Polar molecules, such as water, are “water
loving” or hydrophilic.
• Non-polar molecules are “water fearing” or
hydrophobic. Hydrophobic molecules are
usually made of large areas of only carbon and
hydrogen. Fatty acids are hydrophobic.
• Proteins can have areas that are hydrophobic
and areas that are hydrophilic
Solubility and Transport
• Glucose: polar, very soluble in plasma
• Amino acids: vary in polarity but all soluble in
plasma
• Cholesterol and fats: non-polar, low solubility,
transported in plasma by blood proteins that
have a polar area and a non-polar area.
• Oxygen: non-polar, low solubility. Carried in
plasma by hemoglobin of red blood cells.
• Salt: polar, very soluble in plasma
2.3 Carbohydrates and Lipids
• Most are very large molecules (polymers)
made of smaller repeating units (monomers).
• The monomers of carbohydrates are called
monosaccharides.
• These monosaccharides can be combined by
anabolic condensation reactions to form
larger molecules.
Monosaccharides
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Classified by how many carbons they contain.
Most common are:
Trioses (3) carbons – formula C3H6O3
Pentoses (5) carbons – formula C5H10O5
Hexoses (6) carbons – formula C6H12O6
• Notice the pattern for monosaccharides
• CnH2nOn
Monosaccharide Condensation
Reaction
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Two monosaccharides become a disaccharide.
Two glucose = maltose
Glucose + fructose = sucrose
Glucose + galactose = lactose
A water molecule is produced by this reaction.
An OH comes off of one of the sugars and an H
comes off of the other one.
• https://www.youtube.com/watch?list=PLvIduy9U
GVRXMUBXEEwQ0QxfceFYJiZY6&v=RwYobhHi1lE
Polysaccharides
• Repeatedly bonding glucose together creates
several polysaccharides.
• Cellulose: plant cell walls, rigidity/support
• Starch: Plants store glucose, product of
photosynthesis, as starch, in roots and
chlotoplasts.
• Glycogen: Animals store excess glucose as
glycogen, in liver and muscle tissue.
Fatty Acids
• All fatty acids have a carboxyl group (-COOH)
at one end, and a methyl group (CH3-) at the
other end.
• In between, what makes them different is a
chain of carbons and hydrogens that is usually
11-23 carbons long.
Saturated Fatty Acids
• Called saturated because all of the carbons
have as many hydrogens as possible, saturated
with hydrogens.
• Means there are no double bonds in the chain
• Mostly animal fat, solid at room temp, straight
chains.
Monounsaturated fatty acids
• Contain one double bond
• Double bond loses two hydrogen atoms, so no
longer saturated, also causes the chain to
bend at the bond.
Polyunsaturated fatty acids
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Have at least two double bonds.
Typically come from plants (olive oil example)
Usually liquids at room temp.
Very crooked, curves chains due to the double
bonds.
• Double bonds are usually cis, not trans
Cis vs Trans
Hydrogenation
• Food processors add hydrogen to remove
some or all of the double bonds.
• This straightens out the molecules.
• Naturally curved fatty acids are called cis fatty
acids, the processed straightened out ones are
called trans.
• Usually not all the double bonds are broken so
these fatty acids are called partially
hydrogenated.
Omega-3 fatty acids
• The last carbon in a fatty acid chain, the one in
the methyl group, is called the omega carbon
• Counting from that carbon, you can show
where a double bond is located in the chain.
• Omega-3 means there is a double bond on the
third carbon.
• Fish are a good source
Omega-3
Triglycerides
• Triglycerides are basically fats in animal cells
and oils in plant cells.
• The are made of one (1) glycerol molecule
with three fatty acid chains attached by
condensation reactions.
Energy storage
• Humans and many other organisms store
energy by using glucose to make glycogen,
and making triglycerides to store energy as
lipids.
• Triglycerides can be broken down (hydrolysis)
and used in the reactions of cellular
respiration to make ATP, just as glucose is.
• Triglycerides have twice the energy per gram
as carbohydrates and proteins.
• Triglycerides are also better for long term
storage of energy because they are non-polar
and not water soluble. They won’t cause
osmosis issues in cells they are stored in as
glucose will.
Body Mass Index
• Body mass index (BMI) is used as an indicator
of healthy weight.
• Uses both weight and height.
• Three methods:
• (1) Formula using weight and height
• (2) Using a graph called a nomogram
• (3) Using an on line calculator
BMI
• Use terms underweight, normal weight,
overweight, or obese.
• Should not be used with children or pregnant
women.
• Metric formula: weight (kg)/ height (m)2
• Imperial form: weight (lbs)/ height (in)2 x 703
BMI
2.4 Proteins
• Cells use 20 amino acids to create polypeptide
chains.
• Controlled by DNA, with each different chain
controlled by a specific piece of DNA called a
gene.
• Different types of cells use different genes to
make the polypeptides that are specific to them.
• Humans have between 20,000 and 25,000 genes
in each cell.
Amino Acids
• Virtually all organisms use the same genetic
code and the same 20 amino acids.
• All 20 amino acids have the same structure
except for one bonding location called the R or
variable group.
• In aqueous solutions (water) the OH of the
acid group will lose a H+ to the amine group.
• Polypeptide chains are made at the
Ribosomes using condensation reactions.
• The sequence of the amino acids is
determined by the gene controlling the
process.
Levels of polypept/protein structure
• Each polypeptide chain has its own 3D shape
which determines it’s function.
• Level 1 (primary) – order of the amino acids
• Level 2 (secondary) – repeating pattern, either
helix or pleated sheet. Example is spider silk
• Caused by hydrogen bonding within the main
chain, not the R groups.
• Usually structural
• Level 3 (tertiary) globular structure. Example:
enzymes. Bonding involving the R groups
• Level 4 (quaternary) 2 or more polypeptide
chains bonded together. Example:
hemoglobin.
• A good example of why not all polypeptide
chains are proteins.
• Everyone has unique DNA (genome), unique
proteins (proteome)
Denaturing of proteins
• The bonds that create secondary, tertiary and
quaternary structure are susceptible to
change due to heat and pH, which can change
the structure, therefor the function of
proteins.
• If temp is too high, hydrogen bonds break,
shape changes and protein wont function
properly (DENATURED)
• A change in pH causes the same thing
2.5 Enzymes
• Enzymes are proteins, a type of protein that
speeds up reactions. Anything that can speed
up a reaction is called a catalyst, so some
proteins (enzymes) are catalysts.
• Each specific enzyme has a specific shape.
• Within that shape is a certain area that
matches a specific molecule.
• The area is the active site of the enzyme, the
molecule it matches is called the substrate.
• A good analogy is lock and key.
• The lock is the enzymes active site and the key is
the substrate.
• A certain minimum rate of motion is needed by
the substrate when it enters the active site to
supply the energy needed for the reaction.
• This is called activation energy.
• Enzymes lower the activation energy needed for
a reaction to occur, they are not considered
reactants and are not used up
Factors affecting enzyme catalyzed
reactions
• Temp – cooler, slower – warmer, faster up to
the point where the enzyme becomes
denatured.
• pH – proteins (amino acids)have charges,
substrates have charges.
• If there are too many H+ (low pH), or –OH
(high pH) around the enzyme, they bond
instead of the substrate.
• Usually makes enzyme less efficient but can
completely denature it if sufficient change in
pH.
Substrate Concentration
• If there is constant amount of enzyme,
increasing the substrate increases the rate of
the reaction. (Increased collisions)
• There is a limit, enzymes can only work so
fast, there active sites can get full.
• Rate increases then levels off.
Immobilized enzymes
• Industry uses enzymes to make products but
enzymes are expensive.
• How can you use enzymes to make product
but keep the enzyme for future use and not
sent it out with the produce.
• Put the enzymes into calcium alginate beads
so the beads can be easily separated from the
product.
Lactose free milk
• Lactase is the enzyme that helps break lactose
into glucose/galactose.
• Some don’t have this enzyme.
• Bacteria take over the job which causes
problems
• Milk products are treated with lactase before
consumption.
2.6 Structure of DNA and RNA
• Nucleotides are the building blocks of nucleic
acids
• There are three types of nucleic acids,
adenosine triphosphate (ATP),
deoxyribonucleic acid (DNA), and ribonucleic
acid RNA)
• We are going to focus on DNA and RNA, the
genetic material of the cell.
DNA is a polymer
• DNA and RNA are polymers with the
monomer being nucleotides
• Each nucleotide consists of three parts: a
pentose (5 carbon) sugar, a phosphate group
and a single nitrogenous base.
• Chemical bonds at specific locations create
the appropriate structure.
Nucleotide structure
Nucleotide structure
• The bond between the phosphate group and
sugar, and the bond between sugar and base
are covalent bonds.
Nitrogenous bases
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The bases used in nucleotides are
DNA
RNA
Adenine
Adenine
Cytosine
Cytosine
Guanine
Guanine
Thymine
Uracil
Pentose Sugar
Making Polymers
• DNA and RNA Monomers (nucleotides) bond
together to form DNA and RNA polymers.
• The reaction bonding the nucleotides together
is a condensation reaction.
Strands
• RNA is composed of a single strand of
nucleotides while DNA is two strands
connected at the bases by hydrogen bonding
• Complementary base pairing involves Adenine
always attached to Thymine and Cytosine
always attached to Guanine.
• A=T
C=G
• 2 hydrogen bonds
3 hydrogen bonds
Antiparallel and direction
2.7 DNA Replication, transcription and
translation
• Cells make a copy of their DNA during the S
phase of their cell cycle.
• Molecules needed for the process include
enzymes and free nucleotides.
• The first step of replication involves the
separation of the double helix into two
strands using the enzyme helicase.
• Helicase separates the strands by breaking the
hydrogen bonds between the bases.
• Each strand is now used as a template to
create two identical DNA strands.
• The separation of the strands by helicase is
sometimes referred to as unzipping.
• Free nucleotides are added to the templates
by DNA polymerase which bonds them
together.
• One strand replicates in the direction that the
helicase is unzipping, while the other strand
replicates in the opposite direction.
• Called semi-conservative replication because
each new DNA molecule is half original and
half new.
Protein Synthesis
• DNA controls the proteins that are produced
by the cell.
• The sections of DNA that code for a certain
protein are called genes.
• Genes are specific codes for a specific protein
• Transcription makes mRNA
Transcription
• Transcription begins with the DNA of one gene
being unzipped by RNA Polymerase.
• Only one of the strands will be used as a
template – 3’ to 5’ in direction of unzipping
• RNA Polymerase adds RNA nucleotides to the
template.
• The order of the bases in the mRNA will
determine the order of the amino acids in the
polypeptide chain created at the ribosome.
• Every 3 bases is called a codon
• These groups of three bases that code for a
specific amino acid are called triplets.
• Some codons don’t specify an amino acid so
not all codons are triplets
Translation
• Summary of RNA:
• mRNA – copied from DNA and codes for a
polypeptide chain
• rRNA – what ribosomes are made out of
• tRNA – each type of tRNA transfers on of 20
amino acids to a ribosomes polypeptide chain.
tRNA
• mRNA will find a ribosome and align with it so
that the first two codon triplets are inside the
ribosome.
• A specific tRNA with the anti codon that is
complementary to the first mRNA codon attaches
to the mRNA.
• A second tRNA with the anticodon to the second
codon attaches.
• Now the two amino acids bond to each other
forming a peptide bond
• The first tRNA breaks loose from the amino
acid chain which is being held by the second
tRNA.
• The ribosome moves down the mRNA chain to
get to the next codon and the process repeats.
• The last codon is a stop code telling the
ribosome the polypeptide is finished.
Polymerase Chain Reaction PCR
• Developed in the 1970s
• Allows DNA replication to be carried out in the
lab.
• Used in forensic investigations where there is
only a small amount of DNA found.
• Uses an enzyme from a heat loving bacteria
called Taq polymerase.
2.8 Cellular Respiration
C6H12O6 + 6O2
6CO2 + 6H2O + 36 ATP
• Glucose, amino acids and fatty acids contain
energy within their bonds.
• Cells break down (metabolize) these molecules in
a series of enzyme catalyzed reactions called
cellular respiration.
• Each time a covalent bond is broken, a small
amount of energy is released.
• The goal is to trap/store this released energy as
ATP. Glucose is the molecule of choice but amino
acids and fatty acids will also work.
Glycolysis
• Glycolysis is the first step.
• Glucose enters the cells cytoplasm by
diffusion.
• A series of reactions breaks the 6 carbon
glucose into two 3 carbon molecules called
pyruvate.
• This process uses 2 ATPs in the first step and
creates 4 later for a net of 2 ATPs per glucose
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When ATP is used, it is changed into ADP
When it is created, ADT converts to ATP
Oxygen is not required for glycolysis
Some organisms, called anaerobes, can
survive on just these two ATPS per glucose so
they don’t need oxygen to survive.
• They do need to get rid of the pyruvate so
they undergo fermentation.
• Two types of fermentation, alcohol and lactic
acid.
• Alcohol fermentation (ex. Yeast) changes the 3
carbon pyruvates into a CO2 and a 2 carbon
ethanol molecule.
• Lactic acid fermentation changes the 3 carbon
pyruvates into 3 carbon lactic acid molecules.
• Reversible if oxygen shows up.
Aerobic respiration
• Begins with glycolysis and 2 ATPs being
produced.
• The pyruvates enter the mitochondria
• Each 3 carbon pyruvate releases a CO2 and
becomes a 2 carbon acetyl-CoA
• Each 2 carbon acetyl-CoA enters into a series
of reactions called the Kreb or citric acid cycle
• Each Acetyl CoA releases two CO2 molecules
• Each Acetyl CoA creates one ATP
• Molecules are also created that go one to a final
step where most of the ATP is formed.
• Review: for each glucose entering anaerobic
respiration, 2 ATPs are produced from glycolysis.
• For each glucose entering aerobic respiration, 4
ATPs are produced, 2 from glycolysis and 2 from
the Kreb cycle. Another 32 are produced in a final
HL step
2.9 Photosynthesis
6CO2 + 6H2O
C6H12O6 + 6O2
• Converts light energy into chemical energy.
• The most common chemical produced by
photosynthesis is glucose.
• Plants use the pigment chlorophyll (green) to
absorb light energy.
• Chlorophyll is found in chloroplasts within
leaves.
• There are other pigments in leaves
• Photosynthesis uses visible light from the
electromagnetic spectrum.
• Different pigments use different wavelengths.
• Red and blue light are used the most, green is
used the least. Green is reflected away
• Photosynthesis occurs in two stages:
• Light-dependent stage and light-independent
Light-Dependent Reactions
• Chlorophyll ( and other pigments) absorbs
light energy and converts it to ATP.
• Light energy is also used to cause a reaction
called photolysis of water where water is split
into hydrogen and oxygen.
• The oxygen is released as a waste product.
(Yea, we can breath)
• The ATP and the hydrogen will be used later
Light-Independent Reactions
• ATP and Hydrogen are used as forms of
chemical energy to combine CO2 and H2O into
glucose.
• Glucose is an organic molecule, where CO2
and H2O are inorganic. This is called fixation
• So: Photosynthesis can be described as a
series of reactions in which CO2 and H2O are
fixed into glucose and O2 is produced as a
waste product.
Light-Dependent Reactions
• The fixing of the CO2 and H2O require energy
which is supplied by the ATP created during
the light-dependent reactions.
• Plants perform cellular respiration year round
at a constant but low level.
• Photosynthesis rates vary drastically,
depending on intensity of light, air temp and
CO2 levels.
Rate of Photosynthesis
• A direct way is to measure rate of CO2 usage
or O2 production.
• An indirect method involves measuring the
biomass of the plant.
• Light intensity: increasing light intensity will
increase photosynthesis to a certain point
where it will level off due to the enzymes
being maxed out.
• Increasing the CO2 levels increases the rate of
photosynthesis to a certain point where it will
level off due to the enzymes being maxed out.
• Increasing temperature: As the temperature
increases, the rate of photosynthesis increases
to a point where it suddenly falls due to
denaturing of the enzymes.