biochem lecture 3 Flashcards
reciprocal control
how are two opposing pathways regulated and under what conditions? can’t have them going simultaneously, so how do you see one pathway vs. another?
what is a strong component that controls regulation
hormones
how do hormones control metabolic activities
through activation/regulation of specific pathways
polysaccharides
sugar residues linked into a polymer
what are monomers of polysaccharides
monosaccharides
examples of monosaccharides
glucose, fructose, galactose
most abundant biomolecules in nature
cellulose
were is cellulose synthesized from
plants mainly
what are 2 main functions of polysaccharides
structure, energy/food source
describe the structural function of polysaccharide
polysaccharides (cellulose) make up cell wall in plants and some eukaryotes
describe the energy/food storage function of polysaccharides
serve as energy reservoirs/stores that can be tapped into and broken down to generate ATP
what types of polysaccharides are involved in energy/food storage
starches and glycogen
where is starch found
plant cells
where is glycogen found
animal cells
what are other uses for polysaccharides
proteins and lipids have carb units/polysaccharides attached to them
glycoproteins
proteins with carbs attached to them
glycolipids
lipids w/ carbs attached
where are glycoproteins/lipids found
cell surfaces (cell surface receptors, adhesion molecules, other cell surface proteins)
what is another function of polysaccharides
the heterogeneous array of polysaccharide containing components that make up the ECM
what is the ECM
holds us, our tissues, organs together; serves as a barrier and structure
what is a prime example of a structural polysaccharide
cellulose
what is the most abundant macro/biomolecule in nature
cellulose
where does the majority of cellulose come from
plants
where does a small portion of cellulose come from
algae, other eukaryotes w/ a cell wall
what is the equivalent of peptide bond for polysaccharides
glycosidic bond
what is a glycosidic bond
covalent bond that links together sugars
what are disaccharides
two sugars joined together via a glycosidic bond
sucrose
1,2 linked alpha glucose and beta fructose
what two monosaccharides make up sucrose
glucose and fructose
what kind of glycosidic linkage is found in sucrose
alpha-1,2-glycosidic linkage
what are sources of sucrose
sugar cane, sugar beet (common table sugar)
lactose
1,4 linked beta galactose and alpha glucose
what two monosaccharides make up lactose
glucose and galactose
what kind of glycosidic linkage is found in lactose
beta-1,4-glycosidic linkage
what are sources of lactose
milk
maltose
1,4 linked alpha glucose and alpha glucose
what two monosaccharides make up maltose
glucose and another glucose (2 glucoses)
what kind of glycosidic linkage is found in maltose
alpha-1,4-glycosidic linkage
what are sources of maltose
hydrolyzed starch
what is fructose
isomer of glucose
what does the alpha and beta designation have to do with
the orientation of the glycosidic bond
what is alpha configuration
cis configuration
what do the numbers in (alpha-1,2-glycosidic bond) mean
the specific carbons involved/linked together via this oxygen
describe a glycosidic bond
gonna have the carbon from one sugar, an oxygen, and the carbon from the linked sugar
describe the glycosidic bond on sucrose
C1 carbon of glucose and C2 carbon of fructose are linked together via the glycosidic bond –> alpha-1,2-glycosidic linkage
where is the beta configuration found on
lactose
where else do we see a beta-1,4-glycosidic linkage (besides lactose)
cellulose
lactose vs. cellulose
lactose is a disaccharide, cellulose is a polysaccharide
what is cellulose made up of
glucose units
most diverse biomolecules in nature
polysaccharides
why are polysaccharides the most diverse biomolecules in nature?
because they have 6 chiral centers —> potential for many isomeric forms
why are polysaccharides more diverse/abundant than proteins?
amino acids only have 1 chiral center, so its more restricted in terms of isomeric forms of those building blocks [basically due to 1 vs. 6 chiral centers, AAs can’t have as many isomeric forms]
what is cellulose
massive polymer of glucose units linked together via a beta-1,4-glycosidic bond
what is cellulose basically
structural polysaccharide from glucose
where is cellulose found
plant cell walls (primarily), but also bacteria, algae, fungi, seed hairs, animals
why can’t we digest cellulose?
humans don’t have enzymes that can break down the beta-1,4-glycosidic bonds found in cellulose
who does have enzymes that can break down the beta-1,4-glycosidic bonds
certain bacteria, fungi, protozoa, etc.
what is cellulose made of
glucose units linked together via beta-1,4-glycosidic bonds
who is an exception to this enzyme thing
ruminants; certain livestock like cows sheep have microorganisms in their gut that have enzymes
what enzyme breaks down beta-1,4-glycosidic bond in cellulose
cellulase
what is interesting about this situation
we have lactase, capable of breaking down the beta-1,4-glycosidic bond in lactose
why can’t lactase break down cellulose?
lactase is a disaccharide which lactase can easily accommodate; cellulose is WAYYY too large, can’t be broken down easily
what is cellulose an abundant source of
abundant energy source
can cellulose be metabolized by humans?
no
what can be metabolized by humans unlike cellulose
starch
what do starches provide
bulk of the energy we get from grains, potatoes etc.
why can we utilize starch as an energy source and not cellulose
unlike cellulose, we possess the enzymes capable of breaking the glycosidic bonds in starches
what is starch
major energy source form of polysaccharides in plants
what serves a parallel function as starches in animals
glycogen
what are 2 types of starches
amylose, amylopectin
what are both amylopectin and amylose made up of
glucose monosaccharide units linked together via alpha-1,4-glycosidic bonds
what is the primary difference between these 2 forms of starch
branch points/ amount of branching
what do alpha-1,4-glycosidic bonds generate
linear chains of glucose polymers (unbranched)
are alpha-1,4-glycosidic linkages branched or unbranched
unbranched glucose chains
how does a branch point occur
alpha-1,6-glycosidic bond
what does an alpha-1,6- bond do vs. alpha-1,4
positions the adjoining glucosyl units in a different orientation/position
how does this branching occur from the different types of bonds
the linkage occurs between diff carbons (1,4 vs. 1,6)
are alpha 1,4 and alpha-1,6 linkages also found in glycogen
yes
what does amylose tend to be
straight, linear, unbranched
what does amylopectin tend to have
more branching, because of its alpha-1,6 linkage
what delineates the amylose and amylopectin?
this alpha-1,6 linkage which causes branching
describe amylose
straight chain
describe amylopectin
branch point; alpha-1,6
what does a-1,6 give rise to in amylopectin
these branch points
what emanates from these branch points
more linear chains
how are reducing and non-reducing ends oriented
on opposite sides
how do you induce branch points vs. straight chains
when you form a 1,4-alpha linkage vs. an alpha-1,6, you can see that there’s a diff positioning of one sugar relative to others
what occurs at non-reducing end
enzymes that break down glycogen work at the non-reducing end
what are enzymes that break down glycogen
glycogen phosphorylase, debranching enzymes, etc.
what are major sites of glycogen storage (glycogen stores)
liver and muscle
what is the major energy storage form of polysaccharides in animals
glycogen
what is glycogen
polymer, polysaccharide
how is glycogen stored
glycogen granules; glucose units are linked together to form glycogen, concentrations are so high that they form a granule
why do we store glucose in polymeric form (glycogen granules) and not as glucose monmers
glucose is soluble; if there’s to much it can swell and cause cell to burst
polymers of glucose
glycogen
describe solubility of glycogen (glucose polymers)
insoluble
what does this insolubility mean
will have minimal effects on the osmotic state of the cell
what does glucose’s solubility (in monomeric form) mean
can affect the osmotic state of the cell; high solute concentration inside the cell vs. outside the cell means more water outside the cell than inside the cell…. water would flow from outside to inside, cause the cell to swell up and burst
glycogen
stored form of glucose
glycogenin
enzyme that initiates the formation of glycogen from glucose through synthesizing the primer
what protein serves as a mean to initiate glycogen protein formation
glycogenin
what is glycogenin important for
synthesis of a short piece of glucose polymer, eight glucosyl residue know as the primer
besides the primer, is the rest of this particle made by glycogenin?
no; made by 2 other enzymes: glycogen synthase and branching enzyme
how does glycogenin form the primer
2 steps; first reaction involves transfer of UDP-glucose to glycogenin (glucosyl transferase reaction); second reaction is series of attachments of additional UDP glucose residues, up to 8 glucosyl residues
describe the first step of glycogenin forming the primer
attachment/transfer ofa UDP-glucose to glycogenin protein
how does this attachment of UDP-glucose to glycogenin occur
glycogenin is going to cleave UDP from glucose, and at the same time links the glucose to the glycogen and tyrosine residue
what happens to the UDP
it’s eliminated; goes away
what serves as a link/tether between UDP-glucose and glycogenin
tyrosine–194
what happens when you attach a UDP molecule to glucose
glucose has been biochemically activated; enables it to participate in some biochemical reaction
what is UDP glucose going to be acted on
by glycogenin
what is the 2nd reaction
transfer of glucosyl residues to existing glucose(n)-glycogenin (attachments of additional UDP glucose residues)
when is the primer formed
when you get up to 8 glucosyl residues, that forms the 8 glucosyl primer
how are these glucosyl residues linked
via alpha-1,4-glycosidic bonds; once you reach 8, that forms primer
what does primer serve as
scaffold/starting point for building the rest of the polymer
what is the synthesis of the primer due to the actions of
protein glycogenin
is glycogenin involved in any other parts of the particle
no, just in synthesis of initial primer
how many chains of glycogen exist in tiers
glycogen chains of 12-14 residues exist in tiers
describe inner chains
at least 2 apha-1,6 branches / branch points
describe outer chains
unbranched
how many tiers in mature particles
12
how are the 12-14 glucosyl residues subdivided
inner and outer tiers
what does it mean whenever you see a branch
it’s an alpha-1,6 glycosidic bond
what color is the linear chain
purple
what is emanating off of linear chains
the primer w/ branch point
describe outer and inner tiers
inner tiers have branch points, outer tiers are unbranched
describe a mature glycogen particle
upwards of 12 tiers, 55,000 individual glycogen residues; huge
how many individual glycogen residues in a mature glycogen particle
upwards of 55,000
what is the primer made up of
8 glucose units linked via 1,4-glycosidic bonds
describe structure of glycogen particle
glycogenin-glucose chain in the center
what is primer important for
formation of the particle; can’t build particle w/o primer
what are the 2 catabolic pathways
glycogenolysis and glycolysis
what is glycogenolysis
breakdown of glycogen into individual units in form of glucose-6-phosphoate units (glycogen –> glu-6-p)
what is glycolysis
breakdown of glucose (glu-6-p) into pyruvate (glu-6-p –> pyruvate)
what are the anabolic pathways
gluconeogenesis and glycogenesis
what is gluconeogenesis
synthesis of glucose from pyruvate/lactate
what is glycogenesis
synthesis of glycogen from glucose
what enzymes are involved in glycogen breakdown (glycogenolysis)
glycogen phosphorylase, phosphoglucomutase, glucose-6-phosphatase
what enzyme carries out the breakdown of glycogen
glycogen phosphorylase
what is phosphorylase gonna do
acts on glycogen, removes glucose units one at a time
how does phosphorylase work
takes a phosphate group, transfer that phosphate group to the glucose units that its releasing
what two reactions does phosphorylase do simultaneously
removes glucose units from glycogen AND simultaneously phosphorylates that glucose
what do you end up with after phosphorylase does its job
glucose-1-phosphate monomers AND ALSO glycogen has been shortened by one glucose unit
what does phosphoglucomutase do
takes glucose-1-phosphate monomers (released from glycogen) and isomerizes G-1-P to G-6-P
why does phosphoglucomutase isomerize G1P to G6P
G6P is the first intermediate in glycolysis; G-1-P can’t be directly fed into glycolysis, needs to undergo isomeization to go thru it
what happens to glucose-6-phosphate once it’s formed
it will either go through glycolysis or released into the blood stream
what happens to glucose-6-phosphate in the muscle
G6P is fed into glycolysis, gets oxidized to generate ATP in the muscle
what happens to glucose in the muscle
stays in the muscle; like vegas
what happens to glucose in the liver
released into the bloodstream
what helps release glucose in liver into the bloodstream
glucose-6-phosphatase
why do we phosphorylate glucose (G1P)
keeps the glucose trapped inside the cell, less likely for glucose to be transported out of the cell (what happens in vegas stays in vegas)
are there situations where you wanna transport glucose out of the cell
yes, especially if it’s in the liver (glucose-6-phosphatase helps with that)
what does glucose-6-phosphatase do
removes the phosphate group from G6P to form glucose and inorganic phosphoate
is glucose-6-phosphatase in muscle or liver
liver, not found in muscle
does muscle have glucose-6-phosphatase
no
why does it make sense for liver to have glucose-6-phosphatase
because glycogen in liver is gonna serve as an energy reservoir for entire body
where does glucose used in the brain or other tissues come from
glucose from diet or glucose synthesized (via gluconeogenesis) or glucose released from liver [unless we’re talking about muscle]
what does it mean in terms of transport if glucose is phosphorylated
it’s trapped, can’t really transport to different parts of the body
if you want to release glucose from liver into bloodstream what do you need to do
need to dephosphorylate it (cuz if it’s phosphorylated it’s trapped)
why is phosphatase so important
glucose in the liver is all about its distribution to other parts of the body; can’t do that unless you dephosphorylate glucose first
describe steps of glycogen breakdown
glucose that’s released from glycogen via glycogen phosphorylase produces glucose-1-phosphate.
glucose-1-phosphate gets isomerized into glucose-6-phosphate
in muscle, G6P gets directed to glycolysis
in liver, G6P gets dephosphorylated by phosphatase, glucose is released into bloodstream (to other tissues and organs)
what’s another enzyme involved in glycogen breakdown
debranching enzyme
what are the two activities associated w/ debranching enzyme
debranching activity and alpha-1,6 glucosidase activity
describe the debranching activities of the enzyme
it helps remove the branch points when glycogen is being broken down.
what kinds of linkages are in glycogen
alpha-1,4 linked glucose units (straight chains) AND alpha-1,6 branch points
what breaks down glycogen
glycogen phosphorylase
is glycogen phosphorylase able to break down a branch point
no; that’s where debranching enzyme comes in
what does the debranching enzyme do (1st function)
transfers 3 of the 4 terminal glucosyl residues at the branch point to the adjacent straight chain
what is still remaining after the transfer of 3 of the residues
there is still one remaining glucosyl residue at the alpha-1,6 branch point
what is the other activity of the debranching enzyme
alpha-1,6 glucosidase activity
describe the alpha-1,6-glucosidase activity
removes the 4th residue at the branch point, removing the branch point entirely
what is the debranching enzyme known as
a tandem enzyme
what is a tandem enzyme
enzyme that possesses 2 activities within the same polypeptide
how are these two functions carried out
in sequence
why do you need a debranching enzyme
phosphorylase is only able to act on straight chain polymers of glucose, not at a branch point
what enzymes are involved in glycogen breakdown
glycogen phosphorylase, phosphoglucomutase, glucose-6-phosphatase, debranching enzyme
what is glycogen phosphorylase
releases glucose monomers from glycogen in the form of glucose 1-P
what is phosphoglucomutase
converts glucose 1-P into glucose 6-P which can feed into glycolysis
what is glucose-6-phosphatase
converts glucose 6-P to glucose, allows glucose release into the bloodstream
what is debranching enzyme
removes a-1,6 branch points and ‘linearizes’ glucose chain (2 activities in 1 enzyme)
does phosphorylase act on straight or branched chains
straight chains; linear chains
describe how phosphorylase and debranching enzymes work together
imagine phosphorylase chews on linear chain indefinitely until it hits a branch point, at which point the debranching enzyme acts on it
what happens after the debranching enzyme transfers
the straight chain has been lengthened by 3 residues
at when end do enzymes that break down glycogen work at
non-reducing ends
what kind of sugar is glucose
a reducing sugar
how do you define one end of glycogen molecule vs. another
glycogen phosphorylase acts at the non-reducing end
what are reducing sugars
sugars that reduce mild oxidizing agents
examples of mild oxidizing agents
ferric (Fe2+) or cupric (Cu2+) ions
what kind of functional group is formed when sugars reduce mild oxidizing agents
aldehyde is oxidized to form a carboxyl group
what is Fehling’s reaction
and old test trying to test for the presence of glucose in urine of patients (test for diabetes or high glucose levels in urine)
how does Fehling’s reaction work
if glucose is present in a specimen, mix it w/ Fehling’s reagent (iron or copper ions) –> it will reduce those copper ions
what would be reduced to what
Cu2+ is reduced to Cu+ (for example)
how can you tell that the reaction has occurred
a color change
why is glucose able to do this?
it can cycle from this cyclical form to a linear form
what happens to glucose in this reaction
by virtue of the fact that it reduces the copper ion, glucose becomes oxidized from glucose into D-gluconate
basically what ends up happening
goes from aldehyde to a carboxyl group (results from oxidation reaction)
what is necessary in sugars for this reaction to happen
sugars able to do this have a free/accessible C1 carbon
what sugars can’t participate in this reaction
sugars that have C1 carbons tied up in some way
what does phosphoglucomutase act on
acts on glucose-1-phosphate monomers generated from the glycogen phosphorylase
how are the glucose units released from glycogen released as
glucose-1-phosphate
what does phoshporylase transfer
transfers an inorganic phosphate to each of the glucose/glucosyl residues that are released/cleaved from glycogen
phosphoglucomutase
converts glucose-1-phosphate to glucose-6-phoshpate
are mutases the same as isomerases
no, their catalytic mechanisms are kinda different than isomerase reactions
what is interesting about phosphoglucomutase
in its active site it has a catalytically relevant serine residue that undergoes phosphorylation
why is the phosphorylation of the serine within the active site of the enzyme significant
essential for enabling the isomerization of glucose-1-phosphate to glucose-6-phosphate
how is the serine phosphorylation relevant
catalytic action of mutase is a 2 step rpocess
what is the 1st step in catalytic action of mutase
transfer of phosphate group from serine of active site to G1P, produces di-phosphorylated intermediate glucose-1,6 bisphosphate
what is the intermediate
glucose-1,6-bisphosphate
what is the 2nd step in catalytic action of mutase
generate the glucose-6-phosphate product AND regenerate phosphorylated serine
how is the phosphorylated serine regenerated
there’s going to be a second phosphoryl group transfer reaction here carried out within enzyme’s active site; phosphate at C1 position of glucose is transferred to serine
what phosphate is transferred where
phosphate at C1 position of glucose is transferred to serine
what does this process do
regenerates the enzyme, so that once it encounters the second G-1P molecule it can carry out the same reaction again
what would happen without the regeneration of phosphorylated serine within the active site of enzyme
it wouldn’t be able to perform another round of catalysis
what is the significance of G6P
it’s a usable form of glucose that can be fed into glycolysis
can G1P be directly used in glycolysis
no; has to go through an isomerization reaction
what is another significance of the phosphorylation of glucose
it traps the glucose inside the cell
when would the glucose not want to be trapped
glucose in the liver; it wants to be released to the bloodstream and spread to other tissues/organs
what has to happen for the glucose to be released
phosphorylated glucose has to undergo a round of dephosphorylation
