Download Topic 2 Molecular Biology

Topic 2 Molecular Biology
Biochemistry
Introduction
• Organic chemistry is the chemistry of _______
compounds.
• Biochemistry is a branch of organic chemistry
dealing with _________ ___________.
• 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 __________ ___________
reactions that take place in an organism.
• The four groups of molecules interact with each
other to carry out the reactions of metabolism.
• Example: _________ (Protein) helps glucose
(carbohydrate) travel through the cell membrane
(lipid) and get into the cell. The insulin molecule
itself is created by ________ (nucleic acid)
Organic Chemistry
• Not all molecules that contain carbon are
considered organic, such as ________
__________.
• Carbohydrates, lipids, proteins and nucleic
acids are all _______ and contain _________.
• Life 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
_______ 4 electrons with other atoms. Each
“sharing” forms a bond, so each carbon atom
can form 4 covalent bonds.
Common Atoms other than Carbon
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Building Blocks
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Carbohydrates – _________________
Lipids – ___________ and _____________
Proteins (polypeptides)– _____________
Nucleic acids - ______________
Carbohydrates
Monosaccharides Disaccharides Polysaccharides
Glucose (2)
________
Starch
Galactose
_________
Glycogen
Fructose
_________
Cellulose
Ribose
Chitin
PROTEINS
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Polypeptide Chains made from _____ ______
Some types of proteins
____________
____________
____________
Lipids
• _____________ – Fat stored in adipose tissue
• _______________ – Form bilayer in cell
membrane
• ___________ – 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 _________ 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 ____________ reactions
and hydrolytic enzymes
• Anabolism involves _____________ reactions
Hydrolysis
• Hydrolysis reactions break things apart and
require a molecule of ________ to do so.
• Example: Lactose + water = glucose + galactose
Hydrolysis
• Example: Triglyceride + 3 waters = Glycerol + 3
fatty acids.
Condensation
• Condensation reactions _________ smaller
molecules to create larger ones, and give off
__________ as a byproduct.
• Creating __________ from amino acids
• Creating triglycerides from _____________
and fatty acids
• Creating di and polysaccharides from
___________________.
2.2 Water
• Water is a good solvent – “solvent of life”
• Any solution where water is the solvent is
called an ___________ solution.
• To understand the properties of water, you
have to understand the ___________.
Water molecular structure
• Bonds between the oxygen and the two
hydrogen atoms are _______ ________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
_________ end of one
water is attracted to the
_______ end of another
water molecule. This
attraction is called a
hydrogen bond
Cohesive property of water
• Cohesion is when molecules of the _______
_________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 _______ in plants.
Adhesive property of water
• Adhesion is when a molecule is attracted to a
__________ 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 ________, when it isn’t being pulled, it
remains in place due to ________ 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
without changing __________ very much.
• Water helps to stabilize our temperature.
• Water also has a high heat of_____________,
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 ______
molecules. The vast majority of biological
molecules are polar, including carbohydrates,
proteins and nucleic acids.
• Common aqueous solutions are __________,
_________,________and _________.
• Plants use water to transport material in _____
and ________. Animals use water in blood to
transport materials in arteries and veins
Hydrophilic and Hydrophobic
• Polar molecules, such as water, are “water
loving” or_____________.
• Non-polar molecules are “water fearing” or
hydrophobic. Hydrophobic molecules are
usually made of large areas of only ________
and __________. ______ ______are
hydrophobic.
• ___________ can have areas that are
hydrophobic and areas that are hydrophilic
Solubility and Transport
• Glucose: ______, very soluble in plasma
• Amino acids: _____ in polarity but all soluble
in plasma
• Cholesterol and fats:________, low solubility,
transported in plasma by blood __________
that have a polar area and a non-polar area.
• Oxygen: __________, low solubility. Carried
in plasma by hemoglobin of red blood cells.
• Salt: ________, very soluble in plasma
2.3 Carbohydrates and Lipids
• Most are very large molecules (___________)
made of smaller repeating units
(__________).
• The monomers of carbohydrates are called
________________.
• These monosaccharides can be combined by
__________ _____________ reactions to
form larger molecules.
Monosaccharides
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Classified by how many _______ they contain.
Most common are:
________ (3) carbons – formula C3H6O3
_________ (5) carbons – formula C5H10O5
_________ (6) carbons – formula C6H12O6
• Notice the pattern for monosaccharides
• _____________
Monosaccharide Condensation
Reaction
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Two monosaccharides become a disaccharide.
Two glucose = __________
Glucose + fructose = __________
Glucose + galactose = __________
A ______ 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 _______ together creates
several polysaccharides.
• _________: plant cell walls, rigidity/support
• ________: Plants store glucose, product of
photosynthesis, as starch, in roots and
chlotoplasts.
• __________: Animals store excess glucose as
glycogen, in liver and muscle tissue.
Fatty Acids
• All fatty acids have a ________ group (-COOH)
at one end, and a ________ group (CH3-) at
the other end.
• In between, what makes them different is a
chain of carbons and ___________ that is
usually 11-23 carbons long.
Saturated Fatty Acids
• Called saturated because all of the carbons
have as many __________ as possible,
saturated with hydrogens.
• Means there are no ______ _____in the chain
• Mostly _______ fat, _____ at room temp,
straight chains.
Monounsaturated fatty acids
• Contain _____ double bond
• Double bond loses two hydrogen atoms, so no
longer saturated, also causes the chain to
______ at the bond.
Polyunsaturated fatty acids
• Have at least _____ double bonds.
• Typically come from ______ (olive oil
example)
• Usually ________ at room temp.
• Very crooked, curves chains due to the double
bonds.
• Double bonds are usually____, not ______
Cis vs Trans
Hydrogenation
• Food processors add hydrogen to remove
some or all of the double bonds.
• This __________ 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 _________
hydrogenated.
Omega-3 fatty acids
• The last carbon in a fatty acid chain, the one in
the methyl group, is called the ______ 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.
• ______ are a good source
Omega-3
Triglycerides
• Triglycerides are basically ____ in animal cells
and _____ in plant cells.
• The are made of one (1) _______ molecule
with _______ fatty acid chains attached by
condensation reactions.
Energy storage
• Humans and many other organisms store
energy by using glucose to make_______, and
making triglycerides to store energy as______.
• Triglycerides can be broken down (hydrolysis)
and used in the reactions of cellular
respiration to make ____, just as glucose is.
• Triglycerides have ______ 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 ________.
• Uses both _______ and _________.
• Three methods:
• (1) __________ using weight and height
• (2) Using a graph called a ____________
• (3) Using an on line ___________
BMI
• Uses terms _____________, normal weight,
overweight, or ________.
• Should not be used with children or
___________ women.
• ________ formula: weight (kg)/ height (m)2
• ________ form: weight (lbs)/ height (in)2 x 703
BMI
2.4 Proteins
• Cells use ___ amino acids to create
polypeptide chains.
• Controlled by DNA, with each different chain
controlled by a specific piece of DNA called a
______.
• Different types of cells use different genes to
make the _________ that are specific to them.
• Humans have between __________ and
_________ 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
________ group.
• In ________ solutions (water) the OH of the
acid group will lose a H+ to the amine group.
• Polypeptide chains are made at the
____________ using condensation reactions.
• The sequence of the amino acids is
determined by the _____ controlling the
process.
Levels of polypept/protein structure
• Each polypeptide chain has its own 3D shape
which determines it’s function.
• Level 1 (primary) – ______ of the amino acids
• Level 2 (secondary) – repeating pattern, either
_____ or ______ sheet. Example is spider silk
• Caused by _________ bonding within the
main chain, not the R groups.
• Usually structural
• Level 3 (tertiary) ________ structure.
Example: enzymes. Bonding involving the R
groups
• Level 4 (quaternary) 2 or more polypeptide
chains bonded together. Example: _________.
• A good example of why not all polypeptide
chains are proteins.
• Everyone has unique DNA (________), unique
proteins (___________)
Denaturing of proteins
• The bonds that create secondary, tertiary and
quaternary structure are susceptible to
change due to _____ and ___, which can
change the structure, therefor the _________
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 a type of _______ 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 _______.
• Within that shape is a certain area that matches a
specific molecule.
• The area is the ______ ____of the enzyme, the
molecule it matches is called the ________.
• A good analogy is lock and key.
• The lock is the enzymes active site and the key is
the substrate.
• A certain minimum _________________is
needed by the substrate when it enters the active
site to supply the energy needed for the reaction.
• This is called ___________ ________.
• Enzymes ________ 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 __________ 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
• ______________ are the building blocks of
nucleic acids
• There are three types of nucleic acids,
adenosine triphosphate (____),
deoxyribonucleic acid (_____), and ribonucleic
acid _____)
• We are going to focus on DNA and RNA, the
____________ material of the cell.
DNA is a polymer
• DNA and RNA are __________ with the
___________ being nucleotides
• Each nucleotide consists of three parts: a
_________ (5 carbon) sugar, a __________
group and a single nitrogenous ______.
• _________ ______ at specific locations create
the appropriate structure.
Nucleotide structure
Nucleotide structure
• The bond between the __________ group and
sugar, and the bond between _______ and
base are ____________ bonds.
Nitrogenous bases
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The bases used in nucleotides are
DNA
RNA
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_________
________
_________
Pentose Sugar
Making Polymers
• DNA and RNA _________ (nucleotides) bond
together to form DNA and RNA ___________.
• The reaction bonding the nucleotides together
is a _______________ reaction.
Strands
• RNA is composed of a _______ strand of
nucleotides while DNA is _____ strands
connected at the bases by ________ bonding
• Complementary base pairing involves Adenine
always attached to _________ and Cytosine
always attached to ____________.
• 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
_____phase of their cell cycle.
• Molecules needed for the process include
enzymes and free _______________
• The first step of replication involves the
separation of the double helix into two
strands using the enzyme ____________.
• Helicase separates the strands by breaking the
___________ ______between the bases.
• Each strand is now used as a __________ to
create two identical DNA strands.
• The separation of the strands by helicase is
sometimes referred to as_____________.
• Free nucleotides are added to the templates
by ___ _________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 _____________________ replication
because each new DNA molecule is half
original and half new.
Protein Synthesis
• DNA controls the ___________ that are
produced by the cell.
• The sections of DNA that code for a certain
protein are called _________.
• Genes are specific codes for a specific
_______
• Transcription makes __________
Transcription
• Transcription begins with the DNA of one gene
being unzipped by ____ ___________.
• Only one of the strands will be used as a template
– _________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 ________ _____ in
the polypeptide chain created at the ribosome.
• Every 3 bases is called a _______
• These groups of three bases that code for a
specific amino acid are called _________.
• 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 ____________ 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 _____ _________are inside the
ribosome.
• A specific tRNA with the ____ ________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 __________ bond
• The first tRNA breaks loose from the amino
acid chain which is being held by the
________________.
• The ribosome moves down the mRNA chain to
get to the next codon and the process repeats.
• The last codon is a _____ _____telling the
ribosome the polypeptide is finished.
Polymerase Chain Reaction PCR
• Developed in the ________
• Allows DNA replication to be carried out in the
____.
• Used in ___________ investigations where
there is only a small amount of DNA found.
• Uses an enzyme from a heat loving bacteria
called ____ ______________.
2.8 Cellular Respiration
C6H12O6 + 6O2
6CO2 + 6H2O + 36 ATP
• ________, ________ and fatty acids contain
energy within their bonds.
• Cells break down (metabolize) these molecules in
a series of _________ catalyzed reactions called
cellular respiration.
• Each time a covalent bond is broken, a small
amount of __________ is released.
• The goal is to trap/store this released energy as
____. 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 __________ by
diffusion.
• A series of reactions breaks the 6 carbon
glucose into two 3 carbon molecules called
___________.
• This process uses ___ ATPs in the first step and
creates ____ later for a net of 2 ATPs per
glucose
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When ATP is used, it is changed into _____
When it is created, ADT converts to ATP
_________ is not required for glycolysis
Some organisms, called __________, 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 ______________.
• Two types of fermentation, ________ and
__________.
• Alcohol fermentation (ex. ________) changes
the 3 carbon pyruvates into a CO2 and a 2
carbon _________ molecule.
• Lactic acid fermentation changes the 3 carbon
pyruvates into 3 carbon lactic acid molecules.
• ______________ if oxygen shows up.
Aerobic respiration
• Begins with glycolysis and 2 ATPs being
produced.
• The pyruvates enter the ______________
• Each 3 carbon pyruvate releases a CO2 and
becomes a 2 carbon _____________
• Each 2 carbon acetyl-CoA enters into a series
of reactions called the _______ or citric acid
cycle
• Each Acetyl CoA releases two _____ molecules
• Each Acetyl CoA creates one ______
• Molecules are also created that go on 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 ___ are produced in a
final HL step
2.9 Photosynthesis
6CO2 + 6H2O
C6H12O6 + 6O2
• Converts ______ energy into chemical energy.
• The most common chemical produced by
photosynthesis is _________.
• Plants use the pigment ___________ (green)
to absorb light energy.
• Chlorophyll is found in ____________ within
leaves.
• There are other ___________ in leaves
• Photosynthesis uses _________ light from the
electromagnetic spectrum.
• Different pigments use different
___________.
• ____ and _____ light are used the most, green
is used the least. Green is reflected away
• Photosynthesis occurs in two stages:
• ______________ stage and _______________
Light-Dependent Reactions
• Chlorophyll ( and other pigments) absorbs
light energy and converts it to ___.
• Light energy is also used to cause a reaction
called __________ of water where water is
split into hydrogen and oxygen.
• The oxygen is released as a ________ product.
(Yea, we can breath)
• The ____ and the _____________ will be used
later
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
__________at a constant but low level.
• Photosynthesis rates vary drastically,
depending on ____________, _________and
CO2 levels.
Rate of Photosynthesis
• A ________ way is to measure rate of CO2
usage or O2 production.
• An indirect method involves measuring the
____________ of the plant.
• Light intensity: increasing light intensity will
increase photosynthesis to a certain point
where it will ____________due to the
enzymes being maxed out.
• Increasing the CO2 levels _________ 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
_____________ of the enzymes.