Transcript IBbioch2molecularbioppt (Radolinski, Lorene)

IB Biology-Chapter 2 –Molecular
Biology-Notes
A.Molecules to Metabolism
• Molecular Bio is the chemistry of organisms-Example
discussed of metabolism to show chemicals interact in
predictable ways in organisms:__________________=protein
hormone that FACILITATES the movement of glucose from
blood to inside of cells.It interacts with protein channels in
plasma membranes---opening channels to glucose(a
carb),…diffusion continues as long as concentration of glucose
is greater on outside of cell
Cell membrane composed of lipid-_________________Due to
molecule polarity differences,the phospholipids will not allow
glucose through w/o passing the protein channel .Insulin and
the channels are both proteins that must be coded for by the
DNA in cells involved.This serves as an example of each of 4
organic macromolecule classes working together to help an
organism function.
insulin
phospholipid
B. Carbon-based life-C is considered keystone element of life
(most all C compounds are organic.)
• Atomic #=6-inc. 6 p’s and 6 electrons-4 of
these e’s are valence electrons/shares
electrons forming ___________ bonds
• Many other elements in living things,inc.
H,O,N, and P-utilized in the 4 macromolecules
covalent
Biochemical compounds important to
organisms
D.Metabolism-Reactions controlled by enzymes
• Metabolism=interactions of molecules in organisms/all the
reactions within all the cells
• Molecules are naturally ,randomly moving and colliding with
some collisions with enough energy to produce products
• Factors affecting a reaction include 1-id of colliding
molecules 2-orientation of molecules 3-sped of molecules
when they collide
• Enzymes increase likelihood collision leads to product
• Enzymes –proteins with a specific shape into which a
reactant can fit-called____________________
•
Active site
• Example-ADP + Pi
ATP….reaction requires
energy,which may come from food or sunlight/odds on a
sufficient collision are small .Enzyme-being a ________-is not
used up and remains available.ADP fits into part of active site
and P group next to it and 2 reactants covalently bond—
reaction occurs at a much higher reaction rate and w/less
collision energy than w/o enzyme
catalyst
Most organism reactions catalyzed by enzymes
•
•
•
•
•
•
These reactions include:
DNA replication
Synthesis of RNA
synthesis of proteins-inc. bonding of amino acids
cell respiration-w/ultimate conversion of nutrients
into ATP
• photosynthesis
E.Metabolism=catabolism+anabolism
• Converts large molecules into smaller
molecules=_____________
• Example of catabolism is when animals eat food digested______________-into building blocks.Food chemically
digested in alimentary canal by hydrolyzing enzymes…Each
reaction is _________________ and requires a molecule of
water as reactant-water always split as part of reaction:
hydrolyzed
hydrolysis
catabolism
• Hydrolysis of a disaccharide to 2
monosaccharides
• Lactose + water
glucose+ galactose
Hydrolysis of a polysaccharide to many monosaccharides.
Starch+(many)water
(many) glucose
Hydrolysis of a triglyceride lipid to glycerol and fatty acids.
Triglyceride + 3 water
glycerol+ 3 fatty acids
Hydrolysis of a polypeptide to amino acids.
Protein+(many) water
(many) amino acids
• Anabolism=reverse of catabolism-converts
smaller molecules into larger,complex ones
• Example –when the building blocks produced
from food digestion are transported to body
cells and become bonded once again into
larger molecules
• Anabolism are condensation reactions…Noteany of the above 4 reactions –in reverse –are
catabolism-in which water molecules are
products
• Anabolism requires enzymes capable of
creating ,rather than breaking covalent bonds
• Therefore metabolism is actually the sum of
all the reactions that produce catabolism and
anabolism
• Practice drawing the following: alpha-Dglucose,beta-D-glucose,ribose,saturated fatty
acid,generalized amino acid-see p. 59
WATER
The Structure of water molecules and resulting polarity
• Solvent of life and most abundant molecule in
organisms
• Cytoplasm and intracellular fluid are
aqueous,water-based solutions-polar covalent
bonds-with unequal sharing of electrons
• Because of triangular shape of molecule ,2 ends
of each molecule have opposite charges-thus
_____________(different charges at each end
Polardipolarity
• This dipolarity creates unique properties
• Ephemeral H-bonds help explain properties
(see fig 2.11 on p. 62)
Cohesive Properties
• Highly cohesive• Water bonds to water easily due to polarity
• Ephemeral H-bonding in water –faster moving
liquid state –explains:
• Forming of droplets
• Surface tension allowing some organisms to
walk on water
• Capillary movement-in ‘column’-in vascular
tissues of plants
Adhesive Properties
• Adhesion=____________
• Example-column of water in a vascular plant- water attracted to cellulose(adhesion) and
water attracted to each other(cohesion)/
when column of water is moved up-cohesion
is causing movement/when column is not
pulled up-adhesion keeps entire column from
dropping down (~biological capillary tube)
Any attraction between 2 unlike molecules
Thermal Properties
• High specific heat(ie. Amount of heat per unit
mass required to raise the temperature of water
1 degree C)---absorbs or gives off heat w/o
changing temp much
• High heat of vaporization(ie. Amount heat
required to convert a unit mass of water into
vapor w/no increase in temp)-so water absorbs
a lot of heat when it evaporates-ie. cooling
mechanism-much of the heat that turns water
from liq to vapor came from body-thus lowering
body temperature
Solvent Properties
• Excellent solvent of other polar
molecules(like dissolves like)
• Most molecules inside and outside of cells
are polar(notable exception- most lipids)
• Thus water is the medium for the
biochemistry of a cell(aqueous solutions)
Examples of water as solvent in plants and animals
• Water’s properties make it an excellent transport medium
• _________carries water and dissolved minerals up from root
system to leaves
• ___________ carries dissolved sugars from leaves to
stems,roots,and flowers of a plant
Phloem
xylem
• ________________most common transport medium in
animals-mostly water(plasma)-solutes include:
• Glucose
• Amino acids
• _____________________(a protein involved in clotting)
• HCO3- ions(transports CO2)
blood
Fibrinogen
Water’loving’ or water ‘fearing’ substances
• Polar molecules,like water, are ______________________water-lover.This is a majority of important biochemical
substances-ex:carbs, due to multiple hydroxyl(alcohol)
functional groups
• Molecules nonpolar are ______________________-waterfearer/esp. organics w/just C’s and H’s-exampleCH4(methane)-will not dissolve in water
hydrophilic
hydrophobic
• Fatty acids in trigylcerides ( fatty acid has carboxyl
functional group at one end and a long chain of CH’s at
other end –so mostly nonpolar)and phospholipids
• Proteins polarity depends on arrangement of amino acidssome amino acids polar and some non-polar..The location
of each type of amino acid is important to the
_____________________________/example-proteins that
attaches to and goes down into membrane are hydrophobic
& easily mix w/hydrophobic tails of phospholipids/Portion
extending OUT of membrane is made of hydrophilic amino
acids that mix w/water environment in or outside cell
• See comparison of water and methane in figure 2.12,p.65
3-d structure of the
protein
How does the solubility in water affect the mode of transport
of molecules in organisms?
• Due to different polarities ,each substance has different
solubility in the aqueous environment. This can affect the
mode of transport:
• Polarity of different molecules: next frame
III.Carbohydrates and Lipids
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•
•
•
Monosaccharides:the building blocks of disaccharides
Monomer=monosaccharides
Condensation key to anabolism,making larger molecules
Monosaccharides classified by how many C-atoms
3 most common types of monosaccharides:
• __________-contain 3 C-atoms/C3H6O3
• _______________-contain 5 C-atoms/C5H10O5
• _______________--contain 6 C-atoms/C6H12O6
trioses
pentoses
hexoses
• CnH2nOn
• Condensation of glucose and fructose:
Condensation of 2 alpha-D-glucose molecules
:
Condensation between alpha-D-glucose and galactose:
• Glucose and fructose are isomers of each other because
they have the same chemical formula
• Water is always a product of a condensation reaction and 1
of the 2 monosaccharides donates a OH- ion and the other
donates H+ to make H2O/the bond that is freed up is used
to make covalent bond between 2 monosaccharides
Monosaccharides:the building blocks of polysaccharides
• Repeatedly bonding glucose monosaccharides produces
a variety of very large molecules or polymersex;cellulose,starch,and glycogen
• Use hotlinks to view and manipulate 3-D models of
cellulose,starch,and glycogen
• cellulose,starch,and glycogen are polysaccharides of
glucose
• bonding mentioned with each molecule refers to Cnumbers of glucose that create the covalent bond
• starch has 2 subcomponents-_____________________
• amylase is the only one of the 3 that is linear ,w/no side
branching
• all 3 polysaccharides can be composed of thousands of
glucoses
Amylopectin and
amylose
Fatty acids
• All fatty acids have a carboxyl group(-COOH) at one end and
a methyl group at other end(CH3-)
• In between is chain of hydrocarbons-usually 11-23 C’s
long(12-24-counting CH3)
• SATURATED FATTY ACIDS:
Notice methyl
omega
end,carboxyl
end,and
hydrocarbon
chain---3 main
sections of any
fatty acid
• Saturated fatty acids are called that because C-atoms are
bonded to as many H-atoms as possible-ie.saturated w/Hatoms
• Saturated fatty acids found in animal products like
butter,bacon,and meat fat
• Saturated fatty acids-usually solids @ rm temp
• No C-C double bonds
• Shape is straight-no bends or kinks
________________________-if there is one C-C double bond
Monounsaturated
•The absence of 2 H atoms causes
molecule to bend
Polyunsaturated fatty acids
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•
•
•
Have at least 2 double bonds in C chain
Typically come from plants-such as olive oil
Tend to be liquid @ rm temp
Molecule often has so many bends and kinks that it twists
around itself
Hydrogenation:cis and trans fatty acids
• In many processed foods,polyunsaturated are often
hydrogenated,or partially,as part of processing-double(and
kinks) are partially or totally eliminated by adding H-atoms
• Naturally curved fatty acids called_______________ fatty
acids
• Hydrogenated-straightened ones called _________fatty
acids-usually still contain 1 or more C-C double bonds
cis
trans
One type of Cis is
______________-the 1st C-C
double bond is @ 3rd C-atom
counting back from omega end
Omega
-3
• Fish good source of omega-3-fats
See summary of fatty acid
types fig 2.18-p.71
Condensation reactions result in the formation of triglyceride
lipids
• The component of triglyceride lipids(fats in animals and oils
in plants) are glycerol and 3 fatty acids
• The id and characteristics of the 3 fatty acids will determine
overall characteristics of the fat or oil
• Vary greatly,esp. in relative healthiness
• Condensation reaction showing 4 reactants needed to form
a triglyceride:
Energy storage solutions in humans
• Many organisms have developed chemical strategies to store
molecules in reserve for ATP during cell respiration
• Store glucose as glycogen in liver and muscle
• Store triglycerides within adipose
• Triglycerides,when needed ,can be hydrolyzed into 2 C
segments that go into cell respiration ,at a point efficient for
ATP production….THEREFORE lipids have 2x energy content
per gram than other molecules
• Lipids also are_________________________ and do not
upset osmotic balance of solutions(whereas so much glucose
store would cause cells to swell since it attracts water)…thus
an advantage of lipids
Insoluble in
water
Calculating BMI
• BMI reflects both weight and height
• 3 ways:
• Use a formula-1)
metric,BMI=weight(kg)/[height(m)xheight(m])
•
2) imperical units,BMI=
weight(lb)/[height(in)xheight(in)]x703
• Nomogram from central intersection point between
weight and height
• Online calculator
• Must be correlated w/info showing
underweight,overweight,or obese
IV.Proteins
Formation of polypeptides
• Under the control of DNA cells use the 20
_________________ to make proteins-ea. Polypeptide under
control of specific gene
• In multicellular organisms,every cell has same set of
chromosomes,thus same DNA,each cell uses the genes
needed for that cell only
• Some of the genes almost universal(eg. Protein in
ribosomes)
• Eg. Pancreas cells would turn on genes for making insulin
• Current estimate for number of genes in our cells
=__________________in each of our cells
• # genes= organism complexity-see table 2.7 p.75
Amino
acids
20,000-25,000
• All genes are the genetic code for possible polypeptides
and all are synthesized from same monomers
• w/few exceptions, all organisms use the same genetic
code
• ea of the 20 amino acids differ in 1 bonding location
around central C-atom=___________or variable
group/memorize generalized structure applicable to all
amino acids(do not need to remember R grps)
• when amino acids are in aqueous solns-eg.cytoplasm or
blood plasma-The ________________ionize-does not
alter covalent bonding pattern, but makes functional
grps look different(ea. Carboxyl grp has lost a H ion and
ea. Amine has gained a H ion)
• synthesis of proteins is a ________reaction
•
variable
Amine and
carboxyl
grps
condensation
• Label all the R-grps in the amino acids below:
Polypeptides are highly variable
• Condensation rxns not random but dictated by triplets of
_____________on DNA and RNA and directed by ribosome
• Each polypeptide has unique pattern of amino acids and its
own__________-which influences its function/one small
changes dramatically affects function
nucleotides
3-D
shape
Levels of polypeptide and protein structure
examples of some proteins and their functions
4 levels of organization to protein structure:
• Primary-sequence of amino acids-determines 3D shape
• Secondary-repetitive shapes of either a _____________ or a
pleated sheet-eg spider silk
• Tertiary-globular-eg.enzymes
helix
Some proteins are more than 1 polypeptide
• Terms polypeptide and protein ALMOST
interchangeable
• Actual chemical difference:-Protein consists of
covalently bonded amino acids and ready to carry out
function-while a polypeptide might not be ready
• Polypeptide is _______________________________It
has a single c-terminal and a single n-terminal end-if its
ready to function,then considered a protein
• Some polypeptides cannot function until they combine
1 or more peptides(ie.quaternary)---when bondedready to function-then is a protein
A single amino
acid chain
w/its own
Primary
structure
Your unique proteome
• Each individual has unique genome
and__________________-unique set of proteins capable of
synthesizing for that organism( note- a protein composed of
more than 1 polypeptide will have a gene for synthesizing
each polypeptide)
proteome
Proteins can be denatured by heat alteration of pH
environment
• Intra-molecular bonds of proteins that hold
together their secondary,tertiary,and
quaternary structures susceptible to temp and
pH-ie. Bonds can be disrupted(its 3-d shape
comes from interactions of amino acids w/ea.
Other
When temp higher than optimum,___________________puts
stress on the relatively weak intra-molecular bonds
• Primary structure may remain intact but
_______________may not stay in place under stress of
movement
• Function depends on shape so may not function-but if
covalent bonds(like peptide bonds)-stay intact,will return to
normal shape and function
H-bonds
Increased
molecular motion
When not optimal pH,loses 3-d shape and functionality
• The extra charges from H+ or OH- prevents
normal bonding-will not take normal shape
nor function
Quaternary-2 or more polypeptides combined
into 1 protein-eg.hemoglobin
V.Enzymes
• Enzymes are organic molecules that act as catalysts
• Complex globular proteins-shape specific and not random
• Molecule has________________ that matches substrate
specifically(analogy-glove(active site) fits hand(substrate)
• Lock and key analogy(lock-active site)
• Substrate must not only enter active site but must also
__________________that provides energy for reaction to
occur=____________
• Enzymes lower activation energy
• Enzymes not used up and can repeatedly be used
• Does not force rxn that normally would not happen but
makes a rxn more likely because activation energy lowered
Enter w/ minimum
range of motion that
will provide energy
Activation
necessary for rxn to
energy
Active site
occur
Factors affecting enzyme-catalyzed rxns
• All chemical rxns are molecules colliding
• Effect of temperature
• Temp increase increases speed of molecules and
likelihood for rxn
• Rxns w/enzymes have upper limits of temp___________
• When an enzyme loses shape the shape of active
site is changed-thus denatured-which is frequently
temporary as intra-molecular bonds re-form as
temp restored
Based on temp@which the enzyme
begins to lose its 3-D shape
because intra-molecular bonds
stressed and broken
Effect of pH
• The active site of an enzyme typically includes many
amino acids-some amino acids have areas that are
charged + or –must match opposite charge when
substrate is in active site,in order to have catalytic
activity
• When a soln has become too acidic,relative large # of
H+ ions can bond w/- charges of enzyme or substratePREVENTS PROPER CHARGE MATCHING BETWEEN
THE TWO
• If soln has become too basic -large amt OH- can bond
w/+ of substrate or enzyme-again preventing proper
charge matching
• Either scenario can render enzyme less affective or not
active at all
• Also numerous extra + or –‘s can result in enzyme losing
shape and thus denatured
• Many enzymes in our body are active near pH 7,but
exceptions-eg.pepsin active at low pH
For
Effect of substrate concentration
• w/ a constant amount of enzyme, as substrate concentration
increases ,the rxn rate increases-due to increased molecular
collisions-more reactant molecules to collide
• there is however a maximum rate
Use of immobilized enzymes in industry
• in last 50 yrs. industrial application
• major problems to overcome-if you want to catalyze 1
certain rxn,you want pure enzyme and not a mixture as
found in cells-extraction is expensive/enzymes need to
be reused but difficult to remove to reuse-difficult to
remove enzymes from liquid products
• an answer to this would be to trap enzymes in place
and prevent from getting washed out w/product
• researchers found that an enzyme could be held in
place in tiny pores on beads of a substance_________________________-they are called
immobilized
Calcium
alginate
Use of immobilized lactase to produce lactose-free milk
• lactase digests lactose into galactose and glucose,which are
more readily absorbed into blood
• many people lose ability to produce lactase as they age-so
normal milk and milk products enter digestive tract and are
not digested-thus normal bacterial colonies in intestines
feed directly on lactose-then they are overfedcramping,gas,diarrhea
• these people can eat milk products treated w/lactasedisaccharide pre-digested so they can absorb
monosaccharide sugars
• lactase enzyme molecules are trapped in the small pores of
alginate beads and then milk and its products are exposed to
beads long enough for pre-digestion to occur
VI. The Structure of DNA and RNA
•
•
•
•
Nucleotides are the building blocks of nucleic acids
3 examples in nature=__________________________
ATP( adenosine triphosphate)-energy storage molecule
Both DNA and RNA are polymers of
________________________
• Nucleotides contain 1)a phosphate grp 2) a 5 Cmonosaccharide 3) a nitrogenous base/Chemical bonds at
specific locations to produce a functional unit
ATP,DNA,RNA
nucleotides
*** Note-This uses symbols suggested by the
IB
All the bonds w/in the
nucleotide involve the sharing of
electrons-covalent/Phosphate
same in DNA and RNA/5
possible bases
Uracil only occurs in RNA and Thymine
occurs in DNA(Capital letters may be used
inside rectangle)
Pentose, deoxyribose and ribose very
similar in structure
Monomers into polymers
Look at page 87 to
see what color
each base is--(T=orange,A=blue,
C=yellow,G=green)
…Notice sugar/
phosphate
backbone remains
the same
result of condensation rxn
Single strand or double strand
• RNA is a single strand and DNA double strand
connected by H-bonds
• may involve a large # of nucleotides
• imagine the DNA double strand as a ladder with the
rungs made up of N-bases
• the 2 bases on each rung are complementary(A-T/C-G)
• Be sure to read p.88 and include the work of the
following:Watson & Crick,Chargaff,Rosalind
Franklin,and Maurice Wilkins
• The 2 strands of DNA are
______________________________ to one another
antiparallel
Notice in the diagram above the 3- or 3’
carbon is unattached .In the opposite
strand the 3’ C is at the top and the 5’ at
the bottom showing how it is antiparallel
electrical charges related to the 2
strands cause a twisting action to
produce the double helix