Hemoglobin, Trypsin, Insulin, Immunoglobulin (antibodies), Myosin, Keratin and Opsin.
Hemoglobin is the main protein found in
RBCs.
Hemoglobin's function is to
bind oxygen and helps blood carry oxygen from your lungs to your tissues.
The type of function that hemoglobin does is
transportation.
Trypsin is an enzyme secreted from
the pancreas into your small intestine.
Trypsin is a type of
enzyme
The function of trypsin is to
digest food proteins.
Insulin is a hormone secreted from
the pancreas into your blood stream.
Insulin is secreted when you eat a meal, shortly after a meal, when
blood glucose levels are high.
The function of insulin is to
stimulate cells to convert excess glucose into energy storage molecules such as glycogen.
Immunoglobulin are proteins which bind to the surfaces of
foreign objects such as viruses or bacteria.
Immunoglobulin are used for
defense
The function of the immunoglobulin is to
identify foreign objects as targets for attack by the immune system.
Myosin is one of the major proteins involved in
muscle contraction.
Myosin is involved with
motility
Keratin provides
structure
Keratin forms
fibers in hair.
Opsin is one of your
optical (vision) proteins
The function of Opsin is to
bind the pigment named retinal which is derived from vitamin A
When the retinal pigment is struck by a photon, it changes its own shape and the shape of the protein opsin which binds it, ultimately
triggering a nerve impulse to the vision processing portion of your brain.
Many different kinds of functions can be achieved by proteins because we have
many different chemical types of amino acids for construction of proteins AND because we have many different folded three-dimensional geometries for proteins.
Proteins are constructed by
linking amino acids into long chains.
There are ___ different types of amino acids used to construct proteins.
20
19 of the amino acids have the structure consisting
of a central carbon atom attached to four groups.
The four groups that are attached to the central carbon in the amino acids are
an NH2 amino group, a COOH carboxylic acid group, a hydrogen atom and an additional group called the sidechain of the amino acid.
The _______ group and ___________ group of the amino acid structure, give the amino acid its name.
amino and carboxylic acid
The amino acid sidechain varies in _________ from one type of amino acid to another.
Structure
The structure of the 1 amino acid that is different from the 19 amino acids is that
the sidechain forms two chemical bonds to the rest of the molecule, attaching both to the central carbon and to the N of the amino group.
The side chains in the figure extend towards the
right side of each structure.
The amino acid side chains can have something as simple as __________ or as complex as a _____________.
a simple hydrogen or functional group.
Proteins chains are created by joining
amino acids to each other.
The word "condensation" means
two objects are coming together to from one object; Two objects are condensing to a smaller space.
In many condensation reactions, _____________ is also produced
a molecule of water
"R" is a symbol used to denote
any sidechain
In the condensation reaction, the carboxyl group of one amino acid joins with
the amino group of another amino acid
In the condensation reaction, the carboxyl group of one amino acid joins with the amino group of another amino acid to form
a substituted amide group.
Carboxylic acid + amine =
amide
The condensation reaction produces an amide where one of the H's on the N is substituted by
a carbon going to another part of the molecule.
The resulting chain of a condensation reaction retains
one NH3+ amino end and one COO- carboxyl end.
The direction of the sequence is standardly written beginning at
the NH3+ end.
A longer chain of amino acids is constructed by
further condensation reactions.
Individual amino acids are called
monomers
A chain of amino acids are called
polymers
Proteins are called heteropolymers because they
are constructed from different types of amino acids
Starch is a homopolymer because
all the units used to construct it are the same.
A homopolymer is a polymer in which all the units used to construct it are the
same
A heteropolymer is a polymer in which all the units used to construct it are
different
Proteins are long chains that can contain up to several hundred
amino acids.
The amino acid groups in proteins occur in a specific sequence dictated by
information encoded in the genes of the organism producing protein.
Proteins are originally synthesized as
linear chains.
Proteins do not remain in linear chains in
solution .
Proteins are capable of folding themselves into
elegant, 3-d shapes without external help.
Proteins can fold into (2 types)
helices or sheets
Proteins that are folded into helices are usually aligned
in an antiparallel manner
The components that make up a sheet of proteins are called
strands of sheet.
A protein can mix helices and sheets
interchangeably
The two major uses of nucleic acid is that of
storing genetic information and storing chemical energy.
DNA is a type of polymer that stores genetic information in the form of
a double helix
The information the DNA stores is replicated when
cells divide
The process of using DNA information to synthesize proteins includes an intermediate step in which
a single polymeric strand of messenger RNA (mRNA) is produced.
RNA stands for
ribonucleic acid
The function type of mRNA is that of
genetics
DNA stands for
deoxyribonucleic acid
The individual monomer units of nucleic acids are called
nucleotides
ATP stands for
adenosine triphosphate
ATP is a small monomer (nucleotide) that releases a lot of
energy.
ATP releases a lot of energy when
one of the three phosphate groups is cleaved away from it.
Nucleic acid polymers are constructed from monomeric units called
nucleotides.
A ribonucleotide consists of
a 5 carbon sugar ribose, a phosphate group attached to carbon 5' of the sugar and a base attached at the 1' carbon.
Ribonucleotides are joined together to make
RNA
Deoxyribonucleotides have the same structure as Ribonucleotides except
an oxygen atom at the 2' position.
Deoxyribonucleotides are used to construct
DNA.
There are four different types of ________ which make up RNA polymers.
nucleotides
The bases that are attached to the C1 on the ribonucleotides are analogous to
the sidechains in amino acids and differ in each of the four types of nucleotides.
Nucleotides A and G have _______________ sidechains
large double ring groups
Nucleotides U and C have __________ sidechains
small one-ring
Numbered positions in the sugar ring are marked by
primes (')
Numbered positions in _____ have no primes
bases
All ___________ will either have a :N (a nitrogen w/ 3 bonds and a lone pair) or NH.
nucleotides
NH in nucleotides is a hydrogen bond
donor
:N in nucleotides is a hydrogen bond
acceptor
In DNA, the sidechains of A, G and C are the same as found in
RNA
The fourth type of sidechain in DNA is
T
T is like U in RNA with the exception that
there is an extra methyl group at position 5.
The direction to the RNA polymer is from the
5' end of the nucleotide to the 3' end of the nucleotide.
Nucleotides are joined together by a
condensation reaction to form polynucleotide chains
Polynucleotide polymers are
heteropolymers
There are four different type of monomers of DNA, they are
(dA, dC, dT and dG)
Ignoring the sidechains of the nucleotide leaves the rest of the polymer, called
the backbone.
____________are like ribs sticking out of a spine, and the spine is the backbone
sidechains
_________ nucleotides are not polymers (it's units are different)
individual
A polymer is a chain of units with
identical or very similar structures.
DNA is a polymer because
it is a chain of nucleotides
A and T pair together for DNA by
a bond between :N and NH and a bond between :O and NH (two hydrogen bonds)
G and C pair together for DNA by
two bonds between :N and NH and a bond between :O and NH (three hydrogen bonds)
The A and T pair cannot have a third hydrogen bond between the third hydrogen and the carbonyl
because they are too far apart.
The third hydrogen of the AT pair is considered to be part of a nonpolar C-H bond thus lacking
a positive charge.
The third hydrogen of the AT pair is not likely to donate a hydrogen because
it lacks a positive charge.
A complements
T
C complements
G
A (in RNA) complements
U
The primary function of DNA is to provide a mechanism for duplicating genetic information when a cell divides so
a copy can be incorporated into each of the resultant daughter cells.
During replication, the two strands of the original DNA molecule
separate.
During replication, two new strands are synthesized to
complement the two old strands from the original DNA molecule.
During transcription, DNA partially unwinds to
expose the sidechains of each DNA strand.
In transcription the lower DNA strand functions as a temporary template (blueprint) for
constructing a complementary RNA strand called messenger RNA.
The newly synthesized mRNA from the transcription is single
stranded.
The newly synthesized mRNA from the transcription has the same sequence as the top DNA from the original except
the T is replaced with U.
When U replaces the T after transcription this means that
the ribonucleotides replace the deoxyribonucleotides.
The mRNA eventually binds to
ribosomes.
When mRNA binds to ribosomes, the information in mRNA is used to make
a protein during translation.
Each group of three nucleotides on mRNA codes for
one amino acid in the protein being synthesized by the ribosome.
The correspondence between the nucleic acid triplet and its corresponding amino acid is called
the genetic code.
tRNA are attached to amino acids and bind to the mRNA in the ribosome during translation of the mRNA sequence.
Genetically coded biopolymers are heteropolymers of
long specific sequences and well-defined lengths.
Most industrial polymers are simple homopolymers of random variable length or are heteropolymers comprised of a small variety of types of monomeric units that join together in relatively
random sequences and lengths.
The primary energy storage molecule in cells is
ATP
Energy storage means
when a molecule can undergo an extremely favorable reaction characterized by a large negative change in Gibbs free energy (delta-G),
For ATP, cleavage of the molecule into phosphate and adenosine -diphosphate (ADP) is
extremely favorable.
It would be unfavorable and relatively unlikely for the negative phosphate ion in ATP cleavage to
diffuse back towards the negatively charged ADP molecule to remake ATP.
The equilibrium for ATP hydrolysis lies in the direction of
the cleaved products.
The two most popular carbohydrates are
glucose and starch.
Two examples where carbohydrates play a structural role are
cellulose and chitin.
Cellulose structural role is that of
forming the walls of plant cells
Chitin's structural role is that of
forming the exoskeleton of insects and crustaceans
Another function of ____________ is exhibited by the blood group markers.
carbohydrates
The blood group markers are
type A, type B, type O
Blood group markers are attached to
the exteriors of red blood cells in humans.
The monomeric units in carbohydrates are called
monosaccharides
The first carbon (upper carbon) in aldoses are
an aldehyde group (CHO)
At any given row the aldose structures differ in their
configurations (R or S forms) at the chiral carbons in the middle of the chain.
The forms that monosaccharides can have are
linear forms and cyclic forms
In aldoses the linear form has a carbonyl group (C=O) at the carbon at the top of the molecule whereas the other carbons are attached to
OH groups (alcohol groups).
In aldoses the linear form has a ____________ at the carbon at the top of the molecule
carbonyl group (C=O)
Ketoses get their name because they
contain a ketone group with the C=O positioned at the second carbon from the top.
All other carbon (w/o the C=O) in the ketoses have
alcohol oxygens (including the carbon at the top)
Carbohydrates derive their name from their overall formula
(CH2O)
The representing atoms (carbohydrates) are in a ratio of
one water per carbon
The "carbo" in carbohydrate stands for
carbon
The "Hydrate" in carbohydrate stands for
water
Glucose's carbon are attached to a _________ and a _________ group which makes it a carbohydrate.
hydrogen and hydroxyl
The OH group makes small carbohydrates very soluble in water because it is
polar.
The human blood groups (A,B,O) consist of
short polymers of sugars, arranged in a specific sequence and attached to lipids or proteins in the surface of cells.
Human blood groups are attached to
lipids or proteins in the surface of cells.
The specific sequences of the human blood groups are synthesized by
a series of enzymes.
The specific sequences of the human blood groups are synthesized by a series of enzymes, each catalyzing one reaction joining
two specific types of carbohydrate units.
Each of the blood types contains the core sequence
Fuc-Gal-Glc
the core sequence Fuc-Gal-Glc is found in the blood of the
type O person. (universal)
The type-A person has an additional gene
not found in the type-O person which codes for an enzyme.
The type-A extra gene codes for an enzyme which adds
an extra sugar GalNAc (N-acetylgalactosamine) at the left end of the H antigen core.
The type B person has a different supplementary gene from type A and O whose corresponding enzyme adds
a galactose (Gal) at that position.
An AB person has inherited both of those enzymes from
type A and B .
An AB person has inherited both (type A and B) of those enzymes and therefore has some polymers that are
fully synthesized as the type-A structure, some that are fully synthesized as the type-B structure, and some that have not yet developed beyond the type-O core structure.
Type A can accept from
type O and type A
Type B can accept from
type O and type B
Type O can accept from
type O
Type AB can accept from
type A, type B, type AB and type O
Starch is a homopolymer of
glucose
Starch is a homopolymer because
only one type of monomer, namely glucose, is used in its construction.
random variations make starch more similar to
industrial chemical polymers than to genetically coded biopolymers like DNA and proteins.
________________ form both homopolymers(starch) and heteropolymers (blood groups).
carbohydrates
Cellulose is a homopolymer of
glucose.
The meshwork of H-bonds in cellulose provides
rigidity, generating a rigid cell wall in plants.
Lipids are nonpolar molecules which are
insoluble or only slightly soluble in water
There are ___ major classes of lipids
two
The two major classes of lipids are
fatty acids and isoprenes
Two examples of fatty acids is the
phospholipids used to form the outer membranes of cells and the waxes of honeycombs in beehives.
Examples of lipids from the isoprene class are
the male sex hormone called testosterone, and the light-absorbing pigment called retinal.
Both the lipid, testosterone and the protein, insulin are
hormones.
Carbon and hydrogen atoms have similar
electronegativities.
C-H bonds are non polar
(not polar).
C-C bonds are nonpolar since
the connected atoms are both the same type (C).
Organic chemicals containing mostly hydrogen and carbon atoms are called
"hydrocarbons".
Fatty acids resemble
hydrocarbon fuels.
words ending in "ate"indicate the
negative deprotonated form of an acid.
The negative COO- form of the carboxylic acid group in organic compounds also may be given a name ending in
"ate."
Combustion of natural gas (methane)takes place by reaction
with oxygen produces water and carbon dioxide.
In water and carbon dioxide , oxygens are able to steal electron density away from the neighboring carbon or hydrogen atoms.
If you wanted to convert water and CO2 back into oxygen and methane, which is the reverse reaction, you would have to
add energy to the system.
If you wanted to convert water and CO2 back into oxygen and methane, which is the reverse reaction, you would have to add energy to the system because
that energy would have to do the work of taking away the extra electron density on the partially negative oxygens (oxygens hug onto electrons) in order to restore all the atoms back into neutral nonpolar forms.
The general structure of a phospholipid is generated by starting with
glycerol
The three carbon triple alcohol is
glycerol
To make a phospholipid first
Two fatty acids (R1-COOH and R2 COOH) form esters with two of the alcohol groups in glycerol. The third glycerol OH group then forms an ester to phosphoric acid, which in turn forms another ester bond to an alcohol (X). The final structure has a polar end (the negative phosphate group) and also has two long nonpolar tails (R1 and R2 extending from it.
In an aqueous solution, phospholipids aggregate to form
lipid bilayers.
A bilayer contains two (bi) layers of
lipid molecules
lipids do not form homopolymers or heteropolymers because
the individual lipid molecules are not chemically bonded to each other by covalent bonds
The bilayer in the lipid membrane is better described as
noncovalent aggregate
The bilayer exists in a fluid state where individual lipids molecules are free to diffuse past other lipid molecules.
The dual polar-nonpolar structure of phospholipids generates
the biological function of forming membranes to separate solutions and construct cellular and subcellular compartments
Retinal is derived from vitamin A, which in turn is derived from
the orange-colored pigment beta-carotene found in foods such as carrots.
Retinal is bound to the protein
opsin.
This lipid-protein complex of retinal and opsin is called
rhodopsin.
When light is absorbed by the retinal,
it switches back and forth between the cis and trans configurations at one of its double bonds. (triggers the sensation of vision)
An aldose with three carbons is called
aldotriose
An aldose with four carbons is called
aldotetrose
An aldose with five carbons is called
aldopentose
An aldose with six carbons is called
aldohexose
Constitutional isomers are
isomers that differ in their bonding sequence
Conformations of a molecule involves a rotation of
the single C-C bond.
When dealing with conformations a molecule can take two forms,
either staggered or eclipsed
Configurations at the double bond means the molecule is
cis/trans
Configurations at a chiral carbon means the molecule is
R,S
Two kinds of stereoisomers are
Chiral Carbons (R,S) and double bond (cis/trans)
In the staggered conformation of the atom the elements are apart visually at _______ increments
60 angle increments.
Rotation around a cis/trans molecule is not possible due to
the double bond.
Rotations around a double bond is not possible because
the pi cloud formed by overlap of p orbitals would break.
The cis isomer cannot be converted to the trans isomer unless
covalent bonds are broken and atoms are reattached in new locations.
A chiral carbon (asymmetric) is a carbon with
four different groups attached to it.
The two systems for naming a pair of enantiomers is the
R,S system names or the D,L system names.
The R,S system is more _____ than the D, L system
modern
Priorities of chiral carbon groups are ranked by
atomic weight (Highest weight gets first priority)
The only amino acid where the sidechain has a higher group priority than the backbone carboxyl group is
cysteine.
If 1->2->3-> is clockwise and group 4 is in the back, the configuration is
R
If 1->2->3-> is counterclockwise and Group 4 is in the back, the configuration is
S
If 1->2->3 is clockwise and group 4 is in the front, the configuration is
S
If 1->2->3-> is counterclockwise and group 4 is in the front, the configuration is
R
A polarimeter is a device for
analyzing rotation of plane-polarized light by asymmetric molecules.
The polarizer only transmits those waves whose planes are
oriented in a particular direction
The light leaving the polarizer is called
plane-polarized light
Plane polarized light can be rotated by
molecules containing one or more chiral carbons.
Molecules causing rotation in the direction marked "+" are called
dextrorotatory (d) (to the right)
Molecules causing rotation in the "-" direction are called
levorotatory (l) (to the left)
R and S enantiomers have _____________ effects.
equal but opposite
d and l actually describe
one whole molecule
Glyceraldehyde is a
carbohydrate
The molecular of formula of glyceraldehyde is
(C3H6O3)
Before the R,S system was developed, biochemists compared chiral carbons to the carbon found in the center of glyceraldehyde.
The enantiomeric form of glyceraldehyde which rotates light to the left is called
l
The arrangement of four groups in d-glyceraldehyde was arbitrarily called
the capital D arrangement
There are two main classes of sugars,called
aldoses and ketoses
A sugar with an aldehyde is called
an aldose
A sugar with a ketone is called
a ketose
Biochemists do not apply the D,L naming system to the asymmetric carbons in sugars, in the extra H-C-OH units.
The D,L system is applied only to the asymmetric carbon that is
furthest from the carbonyl group.
The asymmetric carbon in biological sugars always resembles the corresponding carbon in
D-glyceraldehyde.
During photosynthesis, D-glyceraldehyde is the starting compound for
synthesis of longer sugars.
All biologically occurring aldoses resemble
D-glyceraldehyde
the shortest biological ketose containing an asymmetric carbon is
D-erythrulose.
All other biological ketoses resemble D-erythrulose by
inserting a variable number of H-COH units between the D-carbon and the carbonyl group.
for biological sugars, both the aldoses and the ketoses have one particular carbon resembling the
D-carbon of D-glyceraldehyde.
To find out the total number of forms a compound can have, use the equation
2^n in which n is the number of chiral carbons.
The first carbon at the top of each aldose structure is not chiral because
it has only three groups attached.
The last carbon at the bottom of each aldose structure is not chiral because
it has two identical atoms (H) attached.
Aldotriose has ___ chiral carbon
1
Aldotetroses has ___ chiral carbon
2
Aldopentose has ____ chiral carbon
3
Aldohexoses has ____ chiral carbon
4
L sugars do not occur
in biology
In each aldose group there are only ____ non chiral carbon
2
In each ketose structure there are ____ non chiral carbons
3
There is one fewer chiral carbon in ketoses than
aldoses
There are non-chiral ______ groups at the ends of a ketose
-CH2-OH
A ketotriose has ____ chiral carbon
0
A ketotetrose has ___ chiral carbon
1
A ketopentose has ___ chiral carbon
2
A ketohexose has ____ chiral carbon
3
The D,L system is used for naming the chiral carbon occurring in
the backbone of amino acids.
The D,L system is based on the series
L-glyceraldehyde -> L-serine -> any other L-amino acid
In going from L-glyceraldehyde to the amino acid called L-serine, three groups are in the same position.
They are -H, -CH2OH, and C=O
The aldehyde C=O in the L-glycaraldehyde changes to a
carboxyl group C=O in the amino acid
The glyceraldehyde OH group changes to
an NH2 group in serine.
Glycine lacks an
asymmetric carbon
The central C in glycine has two identical groups
(H) attached to it.
Serine has one asymmetric carbon in
the backbone
The one asymmetric carbon in serine is attached to
an amino group, a carboxylic acid group, an H, and a sidechain
The naturally occurring form of serine in proteins is
L.
All of the remaining 18 types of amino acids found in proteins in biological organisms have the same configuration in the backbone carbon that is found in serine, so they are also called
L amino acids.
In going from L-serine to any other L-amino acid, three groups remain the same, but ________ changes to a different sidechain.
the sidechain -CH2-OH group of serine
The D,L system is only applied to the
chiral backbone carbon of amino acids.
biological amino acids are ___ at the backbone carbon
L
biological sugars are ____ at the asymmetric carbon farthest away from the C=O group.
Glycine is neither D nor L, since its backbone carbon has
two identical H's attached to it.
Cysteine is the one example of an L amino acid which is
R.
Cysteine's sidechain contains a
sulfur atom with a high atomic Weight
The reason why the older D,L system has persisted in biochemistry is because
the naturally occurring chiral amino acids are consistently L but are not consistently S.
In helices, the H-bonds join the backbone NH groups to the
backbone C=O groups.
The configuration of the carbon in the center of the backbone of one amino acid in biologically occurring proteins is
L
In each amino acid, the spiral generates
two pairs of eclipsed atoms
The D configuration would not work in amino acids because
eclipsing two large atoms will lead to unfavorable repulsion between their electron clouds.
In proteins it is important that all amino acids have the same configuration, so these helices can
form in a stable manner.
the efficient formation of hydrogen bonds (NH to O=C) in the repetitively twisting alpha helix stabilizes
the folding of many proteins.
The "substrate" is
the material upon which the enzyme is acting
three points of binding to the enzyme provide
the minimum requirement for specific discrimination between mirror images
For a chiral substrate molecule having two forms (R and S), only one of those forms will be able to
make all three potential contacts with the enzyme surface.
The compound containing the L form of phenylalanine tastes
sweet
the D amino acid tastes
bitter
Aspartame is the active ingredient in the commercial artificial sweetener called
"Equal."
Thalidomide caused birth defects via
the mirror image.
Most seashells are
right-handed
All biological enzymes' catalysts are
asymmetric
Since all biological enzymes' catalysts are asymmetric ________ is possible
stereospecificity
Aconitase is an asymmetric catalyst which acts upon a symmetric substrate (citrate) and converts it into a
specific diastereomer.
an enzyme or hormone receptor can distinguish between R and S forms
of asymmetric organic molecules
an asymmetric enzyme surface can convert a symmetric reactant into
a specific asymmetric product
In an XYZZ molecule one of the Z groups can join with X and Y to give three-point attachment to an enzyme surface, but the other Z group can not reach its
complementary site on the enzyme surface when X and Y are bound to the protein.
S (symmetric) + E (asymmetric) =
ES (asymmetric)
In the asymmetric ES complex, the Z group which points towards the ceiling could be chemically converted into something else (W), giving a
specific WXYZ' enantiomer
the Z' group could be modified to generate
an asymmetric product.
In the actual enzyme-citrate complex, All four chemical groups attached to the central C
are bound by the enzyme, so the protein can act differently on the two CH2-COO- groups
pH =
-log [H+]
[H+] =
10^-pH
A relationship linking [H+] and [OH-] is
[ H+] x [ OH- ] = 10^-14 M2
-pH =
log10[H+]
10-pH=
[H+]
Strong acids and bases completely
dissociate in aqueous solution.
Weak acids and bases only partially
dissociate
there is an equilibrium between the
protonated and the deprotonated forms.
The protonated form, which can donate an H+ to solution, is called the
conjugate acid
The deprotonated form, which can bind an H+ and thereby lower the [H+] in solution, is called the
conjugate base.
The equilibrium reactions, written from left to right, represent
dissociation of H+ from the molecule.
the equilibrium constant is given by
the ratio of products divided by reactants.
a large Ka means strong net dissociation producing
lots of H+ and therefore a large numerator.
Further to the right =
more dissociation
pKa =
-log10Ka
Ka =
10^-pKa
The minus sign causes a large Ka to correlate with a
small pKa.
The strongest acids have the largest ___ and the smallest ___.
largest ka - smallest pKa
Hydrogen is in column
1
Carbon is in column
4
Nitrogen is in column
5
Phosphorus is in column
5
Oxygen is in column
6
Sulfur is in column
6
The three ionized atoms in bio-organic molecules are
N+, O- and S-
S appears directly below O in the periodic table so it
behaves similar in a manner to O
Positive N has __ electrons
4
Neutral N has ___ electrons
5
Neutral O (or S) has ___ electrons
6
Negative O (or S) has ___ electrons
7
low pH = mostly _______ form
protonated
scientist = the cause, molecule =
the effect
The henderson-hasselbalch equation is
pKa= log(prot.)/(deprot) + pH
"low pH" means a number that is lower than
the pKa
the difference term is given by
(pKa - pH).
Acetic acid has the simplest
titration curve
To titrate is to cause
one H+ ion to dissociate
The pKa is the pH at the
midpoint of a titration curve
the slightest creation or consumption of H+ or OH- by biomolecules or living cells can easily
alter the pH of that water
We use buffered solutions in the laboratory to maintain
reactions at a relatively constant pH
The pKa value of acetic acid is
4.76
The titration curve of phosphoric acid is like three of
the acetic acid titration curves strung together in a row.
The three phosphoric acid midpoints occur at
.5, 1.5 and 2.5
The three pKa values for the phosphorus acid titration is
2.1, 6.9 and 12.4
Titrations go from fully protonated, to
fully deprotonated
Glycine is the smallest
amino acid
The sidechain of glycine is
a single H atom
Glycine has two titratable groups,
one of which is negatively charged under certain condition and one of which may be positively charged.
the low pH form at the extreme left side is the
fully protonated form
The fully protonated forms of amino and carboxyl groups are positive ___ and neutral ____
NH3+ and COOH
Glycine is net +1 at
low pH
The fully deprotonated form of glycine occurs
at the right
The deprotonated form of glycine includes deprotonated neutral ___ and deprotonated negative ____
NH2 and COO-
The charge of the glycine molecule changes from net ___ on the left, to net __ in the middle, to net __ on the right.
+1, 0, -1
it is favorable for COOH to deprotonate in the glycine titration because
The COO- form is resonance stabilized
In the glycine titration, the COO- form deprotonates before the
NH3+ group deprotonates
The isoelectric point is the point in when a molecule's net charge
is zero.
You have poor buffering when the molecule is
isoelectric (net charge = 0)
Good buffering corresponds to a
small slope which represents a small change in pH
Bad buffering corresponds to a
large slope which represents a large change in pH
Adding H+ on a titration chart is the equivalent to
moving from left to right in the chart
When CO2 dissolves in water, it combines with H2O to form
carbonic acid (H2CO3)
Carbonic acid dissociates into
bicarbonate (HCO3-) and H+
Any process which adds CO2 to the system or removes CO2 from the system causes
a shift in the equilibrium in the direction consistent with Le Chatelier's principle.
For the lungs, Depleting CO2 at the right of the diagram causes the series of reactions to shift towards the right to replenish the lost CO2. (lowers the H+ concentration)
In the lungs, the pH of the blood rises
In the muscles, metabolism converts glucose (C6 H12 O6) into
CO2 and H2O.
In the muscles, Adding CO2 to the right of the diagram causes
a shift in the series of reactions towards the other end, the left of the diagram.
In the muscles, the pH is
lowered
Lung blood pH =
7.4
Muscle blood pH =
6.8
the "large" muscles or lungs are the cause, and the molecules experience the
effect.
The enzyme that converts one isomer into another isomer is called
isomerase.
The active site of the isomerase enzyme includes a
carboxylate anion on the left side and an NH+ group on the right side
A catalyst is neither consumed nor created by the
overall reaction in which it takes part.
anion exchange chromatography is a procedure used for
separating molecules having different net negative charges
In anion exchange chromatography, the column contains
functional groups which are positive. (column binds negative anions)
In anion exchange chromatography, A mixture of biological anions is loaded onto the top of the column where they are bound by
the positively charged resin.
In anion exchange chromatography, The column is rinsed with
a NaCl (salt) solution, starting with dilute salt and gradually progressing to concentrated salt.
In anion exchange chromatography, The Cl- in the NaCl solution starts binding to the column, competing with the negative biolo
gical anions for the positive sites on the resin.
In anion exchange chromatography, The Cl- anion and the biological anion then
exchange positions.
In anion exchange chromatography, the excess Cl- sticks to the column and the biological molecule
reenters the solution
In anion exchange chromatography, The most weakly bound biological anion, having the smallest net negative charge, will be competed
by dilute Cl- and will elute (exit) first from the column.
In anion exchange chromatography, The most strongly bound biological anion, having the largest net negative charge, will require
high competing [Cl-] to loosen up from the column.
In anion exchange chromatography, The most negatively charged biological anion will elute
last.
The forms of nucleic acids which occur in biological samples have different numbers of
negative phosphate groups attached
AMP =
adenomonophosphate (1 phosphate group)
ADP =
adenodiphosphate (2 phosphate group)
ATP =
adenotriphosphate (3 phosphate group)
The order of elution of adenosine, AMP, ADP, and ATP is in the order of their
net negative charge
The order of elution of adenosine is in the order of their net negative charge because
the more negative molecules bind more tightly to the positive column and require higher concentrations of negative Cl- to compete with them for the positive sites on the column.
A phosphate OH group deprotonates to O- at pH
7
The "acid" in a nucleic acid nucleotide is a
phosphate group
dATP is an energy storage molecule because it contains
mutually repelling charged groups
The three phosphate groups in deoxy ATP are
connected to each other
Base pairing in DNA employs a strategy of complementary
sizes and H-bond properties
Large double rings pair with
small single rings
NH donors pair with with
N: or O: acceptors.
The type of biomolecule with naturally occuring examples of both homopolymers and heteropolymers is
carbohydrates
A class of structures where we have NOT seen examples of a network of H-bonds within the biomolecule itself is
lipids
Lipids are mostly nonpolar
hydrocarbons
Lipids are nonpolar and aggregate in
H2O.
Phospholipids form
membrane bilayers
Of the four types of biomolecules, one of them does not form polymers. This type is
lipids
Conversion of mRNA into a protein is called
translation
Formula is mostly CH2 = nonpolar hydrocarbon chain makes it a
fatty acid
Myosin is a
protein
Mysoin is a homo/hetero polymer?
heteropolymer
Oxidation of a fatty acid during metabolism converts
nonpolar bonds to polar bonds, and releases heat
Phosphates are components of
membrane lipids and nucleic acids
A reaction joining two amino acids together creates
an amide plus water
Colored pigments frequently have conjugated
pi cloud systems
The effect of absorption of light on the pigment retinal is
a change in configuration at a C=C double bond
The structural origin of the rigidity of cellulose is
hydrogen bonding
Every nucleotide in RNA contains a ___ component
ribose
The term which describes the reaction given below : amino acid + amino acid -> polymer + water
condensation
A linear aldose begins with an aldehyde group, ends with a -CH2-OH group, and has H-C-OH carbons in between. The chiral carbon(s) include the
H-C-OH carbons
When citric acid is bound to the enzyme aconitase, the two -CH2-COOH groups attached to the central carbon atom have ___ probabilities of interacting with groups on the enzyme.
different
The term configuration applies to ___ .
R vs. S ; and cis vs. trans
The naming system which is based on a comparison to the standard, glyceraldehyde, is the ___ system.
D vs. L
D-glyceraldehyde , a 3 carbon sugar with one chiral center, is the building block for longer sugars, so
its chiral center appears in other biological sugars.
Glycerol and glyceraldehyde each have
3 carbons
Ibuprofen has one chiral carbon. The most inexpensive way to synthesize it is as a racemic mixture of R and S forms. The % of the ibuprofen molecules in the pill you buy which are physiologically active is
50%
Racemic mixture are always 50/50 because
Only one of the two enantiomers is physiologically active.
Levo is the root word for
left
Linear aldose sugars have their aldose group at C-1. The D carbon is always ___ .
the highest numbered chiral carbon
In chiral amino acids,the L carbon is in the
backbone (HN-C-carbonyl)
Spark =
symmetric catalyst
a symmetric catalyst exerts no chiral forces on the reactants, so it
can't force a specific chiral product.
Except for glycine (which is neither D nor L), the amino acid products produced by passing a spark thru a mixture of NH3, CH4, H2O and H2 are ___ .
50% L and 50% D
The designations which are based on the rotation of plane-polarized light of a particular wavelength are ___ .
d and l
A surface marked T-F-M clockwise (thumb/forefinger/middle-finger) would bind the right hand
better than the left hand (3 contacts vs 2).
The stereospecificity of biological reactions can be demonstrated by considering a model requiring attachment of a substrate to an enzyme at a minimum of ___ points.
3
If a D amino acid is incorporated into the normal right-handed alpha helix of a protein, then there will be steric conflicts between the ___ .
sidechain R group and backbone carbonyl O atom
The "a" is for the equilibrium written in the direction of acid dissociation as in
HA -> H+ plus A-
When describing acid-base equilibria, we speak of the pKa. The "a" stands for
acid dissociation
The active site of triose phosphate isomerase contains a glutamic acid (Glu) sidechain (HOOC/COO- , pKa=5) and a histidine sidechain (HN+/N:). At pH 7, the glu sidechain initially acts to
revmove an H+ from the substrate
A molecule of the type (HA -> A- and H+) is best able to resist changes in pH due to either incoming H+ or incoming OH- when
pH=pKa
Buffers are composed of ___
weak acids or bases
An underwater swimmer holds his breath. CO2 from metabolism builds up in the blood. The [H+] ___ during the swim.
rises
H2PO4- can be what in water?
a conjugate acid or a conjugate base
The sidechain of cysteine exists as SH -> S:- plus H+ , with a pKa of 9. The dominant forms at pH 2 and pH 8 are
SH (pH 2) ; SH (pH 8)
One "equivalent" of NaOH is
the amount of NaOH needed to fully titrate one functional group
For the reaction HA -> A- + H+, Ka equals
Ka = dissociated products/reactants = ([A-]x[H+])/[HA]
One form of the Henderson Hasselbalch equation is (pKa-pH) = log (protonated/deprotonated). True or false : Another form is (pH-pKa) = log (deprotonated/protonated).
true
The "p" in pH and pKa means
-log (base 10)
The pH of blood is 7.4, and the pH of stomach gastric juice is 1.4. The blood [H+] is ____ than the gastric juice.
a million times lower (7.4 - 1.4 = 6 ... 10^6 = a million)
The titration curve for phosphoric acid exhibits three S-shaped curves. The first midpoint (pKa 2.15) corresponds to the reaction
H3PO4 <=> H2PO4(-1) + H+
A small pKa means a ___ Ka.
large
In the titration curve for glycine, the simplest amino acid, the structure in the middle of the curve is
-OOC-CH2-NH3+
The midpoint of a titration curve (reaction HA -> H+ and A-) has HA = A- = 50% of each. This occurs when
pH = pKa
At pH 4, what are the concentrations of [H+] and [OH-]? 10^-3 M is the notation for 1 mM.
