Biochemistry Exam 3
hexokinase
adds phosphate groups to 6-carbon sugars
Glyoxyate cycle
allows plants to use acetate as fuel isocitrate goes through the citric acid cycle or gets converted to succinate and ultimately produces glucose
Gluconeogenesis
generates glucose in reverse to glycolysis and catalyzes irreversible reactions it requires cleavage of 6 phosphoanhydride bonds to synthesize one molecule of glucose from pyruvate 4 from ATP and 2 from GTP
Fate of Pyruvate
gets oxidized to acetyl CoA and enters the citric acid cycle (matrix) and oxidative phosphorylation
Monosaccharides
galactose, glucose, fructose
Functions of Carbohydrates
-serve as energy sources -serves as supporting structures in plant cell walls in the outer -covering of bacterial cells, cartilage, and in exoskeletons in arthropods -serves as components of nucleic acids DNA and RNA -play a role in the immune system Oligosaccharides modifies cell surface proteins to identify native versus foreign cells -has carbohydrate side groups in cell surface receptor proteins that play a role in signal ransduction systems
Glycolysis Investment stages
2 ATP consumed in first 5 steps
products of glycolysis
2 pyruvate per molecule of glucose, ATP, NADH
a. What type of reaction is D-glucose + ATP glucose-1-phosphate + ADP? What type of enzyme catalyzes it? b. What type of reaction is glucose-1-phosphate glucose-6-phosphate? What type of enzyme catalyzes it?
9a. This is an example of a group transfer reaction, catalyzed by a kinase. 9b. This is an isomerization, catalyzed by an isomerase, specifically phosphoglucomutase
What molecules regulate the balance between glycolysis and gluconeogenesis? Which enzymes represent the key steps at which the balance is regulated? Why is this a sensible arrangement?
AMP and ADP stimulate glycolysis, while citrate and ATP inhibit it. The critical enzymes are phosphofructokinase and fructose-1,6-bisphosphatase. This is sensible, because a high AMP or ADP level indicates that you have used a lot of your ATP up, so it makes sense that it would stimulate glycolysis and the production of new ATP. High levels of ATP should obviously be a good signal to inhibit glycolysis, and the resultant production of more ATP. Citrate is produced by the commitment step in the citric acid cycle, so if citrate levels are high, you are already putting plenty of stuff into the citric acid cycle, which will produce ATP, so you don't need to do more.
inhibitors of citric acid cycle
ATP, NADH, citrate and succinyl-CoA are the major inhibitor ADP stimulates
Explain the difference in structure between an aldose and a ketose. What structural feature is required for a sugar to be a reducing sugar
An aldose has an aldehyde structure--H-C = O O || A ketose has a ketone structure--R-C-R In order to be a reducing sugar, the sugar must have an aldehyde group on the end. The ketose, having a C=O, is as oxidized as it can get, so it can't reduce anything
What processes are used to metabolize glucose in aerobic versus anaerobic organisms? How many ATP are generated per molecule of glucose in an aerobic organism? At what stages of glucose metabolism are they generated?
Anaerobic and aerobic organisms all use glycolysis to oxidize glucose to pyruvate. Anaerobic organisms use fermentation to reduce the pyruvate to lactate or ethanol. Aerobic organisms oxidize the pyruvate to acetyl-CoA, then put the acetyl-CoA into the citric acid cycle, and the reduced electron carriers that are produced by the citric acid cycle into the electron transport chain. Anaerobic organisms generate 2 ATP from a molecule of glucose, both through glycolysis, while aerobic organisms generate 36 or 38 ATP per molecule of glucose, depending on the tissue in question. Two ATP are produced by glycolysis, 2 ATP are produced in the citric acid cycle, and 32 or 34 ATP are produced by the electron transport chain.
Please explain how electron transport is coupled to ATP synthesis in the mitochondrion. Name the specific places where the important events happen
As the electrons get passed down the electron transport chain (in the inner mitochondrial membrane), energy is given off at each step. This energy is used to pump protons across the inner mitochondrial membrane, from the mitochondrial matrix into the intermembrane space. The proton gradient that results is a high-energy force, and once it builds up to a certain level, the protons pass back into the mitochondrial matrix through the ATP synthase complex. The ATP synthase complex includes a proton channel and the protein complex ATP synthase. Movement of protons through the channel causes the catalysis of ADP ATP by the ATP synthase complex.
What is the difference in the processes whereby glucose gets harvested and activated for glycolysis from dietary glycogen versus stored glycogen?
Glucose is harvested from dietary glycogen by salivary amylase, which hydrolyzes the alpha 1 4 O-glycosidic bonds holding the glucoses together. The glucose is then phosphorylated to glucose-6-phosphate by hexokinase. Stored glycogen is harvested by phosphorolytic cleavage by glycogen phosphorylase, in which the glucose is released as glucose-1-phosphate, and then converted to glucose-6-phosphate by phosphoglucomutase.
Please describe the structure of a glycoprotein, and name one function of glycoproteins.
Glycoproteins have short oligosaccharide chains (usually less than 15 sugars), bonded to an OH-containing amino acid by an O-glycosidic bond or an NH2-containing amino acid by an N-glycosidic bond. Glycoproteins mediate self versus other recognition, to direct the immune system to kill the foreign cells and spare the native ones. They also can tell the protein degradation system which proteins are old enough to be turned over. They also help prevent certain animals from freezing in cold environments.
How does brown fat help hibernating mammals keep warm during the winter
In brown fat, the protein thermogenin provides a proton channel that is not coupled to the ATP synthase complex. Thermogenin allows the protons to pass back into the mitochondrial matrix without their movement causing the synthesis of ATP, so that all it generates is heat.
What two pathways carry cytoplasmic NADH into the mitochondrion, so it can feed into the electron transport chain? What tissues do the two different pathways work in?
In the liver and heart, it is the malate-aspartate shuttle that brings the electrons from cytoplasmic NADH into the electron transport chain. In skeletal muscle and brain, it is the glycerol-3-phosphate shuttle
More reactions of Monosaccharides
O-glycosidic bonds between OH group and the anomeric carbon link monosaccharides together N-glycosidic bonds between an NH group and the anomeric carbon linking monosaccharides together with bases in nucleotides
alpha vs. Beta
OH groups below the plane are alpha OH groups above the plane are beta
Why does drinking alcohol shift your metabolism toward fatty acid synthesis? (Hint--you oxidize the ethanol, using NAD+).
Oxidizing the ethanol produces the reduced carrier NADH. High NADH levels inhibit the citric acid cycle, and shift your metabolism from putting acetyl-CoA into the citric acid cycle to using it to synthesize fatty acids.
Which two enzymes represent the primary control point by which the balance between glycolysis and gluconeogenesis is maintained? How are these enzymes affected by NAD+, ADP and AMP?
Phosphofructokinase and fructose-1,6-bisphosphatase. Phosphofructokinase is stimulated and fructose-1,6-bisphosphatase is inhibited by NAD+, ADP and AMP. NADH and ATP have the opposite effect.
Please give me one important function of phosphorylated sugars, and one important function of amino sugars
Phosphorylated sugars--activates glucose from glycogen for glycolysis, used to build nucleotides Amino sugars--chitin in exoskeletons, cartilage in joints
How many phosphoanhydride bonds must be cleaved in order to synthesize one molecule of glucose from pyruvate? What molecules are used as source of phosphoanhydride bond energy?
Six phosphoanhydride bonds are cleaved to make one molecule of glucose: 4 from ATP, 2 from GTP
Please describe the structure of glycogen and starch. What is the advantage inherent in them being so extensively branched?
Starch contains the linear glucose polymer amylose and the highly branched amylopectin. Amylose is a linear polymer of glucoses held together by an alpha 14 linkage. Amylopectin has a backbone of glucoses held together by alpha 14 O-glycosidic bonds, and also branches that are attached to the backbone by alpha 1 6 O-glycosidic bonds. Glycogen is similar to amylopectin. The advantages to the branched structure are: 1) they provide several ends from which glucoses can be harvested, making a lot of glucose available quickly when needed. 2) they fit more polysaccharide into the small space that is available when they are branched.
Why does hydrolysis of starch by the salivary enzyme α-amylase produce maltose as one of its products?
Starch contains the linear polymer amylose, and the branched polymer amylopectin. Amylose and the backbone of amylopectin both consist of glucose residues joined by an alpha 1 4 O-glycosidic bond. Maltose is two glucoses joined by the same alpha 1 4 O-glycosidic bond. As the polysaccharides get broken down, oligosaccharides and disaccharides get formed. The disaccharide that gets formed from amylose and the backbone of amylopectin is maltose.
Please describe the difference between O-glycosidic bonds and N-glycosidic bonds, and give an example of where you find each one.
The O-glycosidic bond involves a carbohydrate that gets linked at an OH group (which supplies the O). These are used to link monosaccharides together into oligosaccharides or polysaccharides. The N-glycosidic bond involves a carbohydrate that is linked to an amino group (which supplies the N). These hold sugars and nitrogenous bases together to form nucleotides.
Why can you digest maltose but not cellobiose? They are both two glucoses held together by a 1,4 glycosidic bond
The enzymes that degrade disaccharides are very specific, and will only cleave one type of bond. For example, humans can digest maltose, in which two glucoses are held together by alpha 1 4 bonds, but do not have the enzymes required to cleave the beta 1 4 bonds that join two glucoses to make cellobiose.
Why are the first five steps of glycolysis called the investment stage? What is the overall yield of ATP in glycolysis? What else, other than pyruvate and ATP, is produced by glycolysis that can be used to generate cellular energy? How is this other product of glycolysis used to produce energy?
The first five steps of glycolysis consume 2 ATP. The next five steps yield 4 ATP, so the overall yield is 2 ATP. NADH is also produced, which can yield ATP if it feeds into the electron transport chain. The malate-aspartate shuttle (in liver and heart) and the glyceraldehyde-3-phosphate shuttle (skeletal muscle and brain) bring the electrons from the cytoplasmic NADH into the mitochondria so they can be used to produce ATP
. What advantage does the glyoxylate cycle provide for the plants and microbes that use it? What does it enable them to use, and what does it generate from that molecule
The glyoxylate cycle allows plants and microbes to use acetate. The acetate is converted to acetyl-CoA, which can be put into the citric acid cycle or, at the isocitrate point, be converted to succinate, which can be used to synthesize glucose
How are monosaccharides tagged and activated for polysaccharide synthesis? What enzyme builds glycogen from glucose in the human body?
They get linked to diphosphonucleotides--UDP, ADP or GDP. Glycogen synthetase catalyzes the building of glycogen from these diphosphonucleotide-linked glucoses.
Why is the synthesis of glucose not accomplished merely by running the glycolysis reactions in reverse? Be as specific as you can in your answer
Three of the glycolysis reactions are not reversible due to thermodynamic considerations. Other reactions must be used to bypass these steps.
Please name two amino acids which could serve as the site where a protein gets modified by addition of an oligosaccharide unit, attached by an O-glycosidic bond? What structural/chemical feature must these amino acids have to form O-glycosidic bonds with a sugar?
Tyrosine, serine and threonine--they all have the reactive OH residue in their "R" group.
oligosaccharides
are composed of between 3 to 20 sugars makes up side chains that give the protein its characteristic structure and function often called glycoprotein is usually attached to an OH containing amino acid by an O-glycosidic linkage or and N-glycosidic linkage
NADH
can produce extra energy for the cell by entering electrons into the electron transport chain in the mitochondria this is done via a shuttle of glycerol 3 phosphate or malate-aspartate shuttle
anomeric carbon
carbon 1
Glycogen
composed of thousands of glucose sugars held together by glycosidic linkages O-glycosidic bonds
Electron Transport Chain
consists of four large protein complexes in the inner membrane of the mitochondria consists of coenzyme Q and cytochrome C reductase which helps generate energy NADH to produce 2.5-3 ATP FADH2 produces 2 ATP
functions of glycoprotein
contact inhibition protein turnover antifreeze allows fish to live in cold water hiding viruses viruses can mimic glycoproteins thus allowing them to hide from the host immune system
products of fermentation
ethyl alcohol and lactate
yield for citric acid cylce
for each molecule of pyruvate 1 ATP, 3 NADH, and 1 FADH2 per cycle
Carbon five and carbon six sugars produce what
furanoses, and pyranoses
Brown FAt
in hibernating animal and infants contains the protein thermogenin instead of the proton channel/ATP synthase complex that the white fat has thermogenin contains the proton channel found in the white fat protein but it does not have the ATP synthase complex the transfer of electrons generate a lot of energy the energy can't be captured so it gets released as heat
Glucose
is an essential fuel for the brain and red blood cells if the brain is unable to get glucose the brain will use ketone bodies and if this becomes hard to do the brain will use amino acids to make glucose depriving the body of amino acids the body needs to build proteins
Glycolysis
is increased by ADP, NAD+, stimulates phosphofructokinase but can be inhibited by ATP and NADH, Citrate decreasing glycolysis
gluconeogenesis
is increased by ATP, NADH, and citrate stimulates fructose 1-6 bisphosphate but can be inhibited by ADP and NAD+ decreasing gluconeogenesis
Pyruvate
is produced from lactate, amino acid breakdown, and glycerol from triglyceride breakdown
What is the fate of glucose once absorbed
it gets carried to the liver via the hepatic portal vein where the liver can either make ATP, store it as glycogen, break it down to acetyl-CoA then use acetyl-CoA ot make fatty acids and triglycerides the liver can release the glucose into the circulation where it can go to tissues like neurons and red blood cells which use it as their primary fuel it can go to skeletal muscle cells which will either make ATP o store it as glycogen it can go to adipose tissue
Glycoprotein
mediate cell recognition blood type is determined by what sugars you have in particular oligosaccharide side chains on one of the proteins that lies on the surface of your red blood cells
ETC and ATP Synthesis
movement of electrons through the ETC causes protons to be pumped from the mitochondrial matrix to the intermembrane space the protons flow back into the mitochondrial matrix through the ATP synthase complex F0 subunit is a proton channel F1 subunit is ATP synthase
Aerobic respiration
produces 36 or 38 ATP per glucose ETC yields 32 or 34 ATP per glucose 16 0r 17 per pyruvate
Glycolysis 6-10
produces 4 ATP per molecule of glucose
pentose phosphate pathway
produces ribose-5-phosphate a precursor for nucleotides, nucleic acids and cofactors such as NADH and NADPH makes electron carriers
peptidoglycan
provides support for bacterial cell walls alternates N-acetylgucosamine and N-acetylmuramic acid residues
Reactions of Monosaccharides
reducing sugars have a free aldehyde group that can be oxidize to carboxylic acid to reduce the metal ions in solution They can undergo phosphorylation to begin the process of glycolysis by transferring a phosphate group from ATP to glucose forming glucose 6 phosphate which begins the process of glycolysis this reaction is catalyzed by kinase the enzyme phosphatases removes the phosphate group to stop or reverse the pathway Monosaccharides also make amino sugars by replacing of of the hydroxyl groups with an amino group this is catalyzed by aminotransferase
The Cori Cycle
replenishes glucose after anaerobic metabolism
polysaccharides
starch serves as energy supply in plants has linear unbranched amylose alpha 1-4 O-glycosidic bonds and branched amylopectin alpha1-6 o-glycosidic bonds glycogen serves as energy supply for animals has highly branched glucose polymers with alpha 1-4 linkages in the backbone and alpha 1-6 linkages attaching the branches to the backbone cellulose provides cell structural support in plants has beta 1-4 linkages Chitin(animal exoskeleton) contains beta 1-4 linkages
Trace Digestion
starts in mouth with chewing and enzymes salivory amylase starts breaking the food down the food then enters the stomach denaturing salivory amylase- then goes in to the duodenum the 1st stage of the intestine where the pancreas injects pancreatic alpha amulase- then it goes to the brush border where the remaining polysaccharide is broken down dissacharides are oligosaccharides are digested into glucose by the intestinal mucosa's brush border cells that contain disaccharides and oligosaccharides-glucose is then absorbed by the intestinal mucosal cells using an active transport process- the hepatic portal vein carries all products of digestion into the liver first
Glycogenesis
stores energy monosaccharides are activated by linking them to diphosphonucleotides which make up the backbone of glycogen by glycogen synthase which makes alpha 1-4 o-glycosidic bonds glycogen is highly branched due to the alpha 1-6 linkages
storage vs dietary polysaccharides
the way glucose is released phosphorolytic cleavage by glcogen phosphorylase versus hydrolysis by amylase both are converted from glucose 1-phosphate to glucose-6 phosphate
Anaerobic Respiration
undergoes glycolysis producing 4 ATP per molecule of glucose then undergoes fermentation that produces no net ATP but oxidizes NADH to NAD+ so that glycolysis can begin again occurs in red blood cells and hardworking skeletal muscles to produce lactate which is then sent to the liver which oxidizes it to pyruvate which uses it for gluconeogenesis glucose then gets sent back to the red blood cells and teh skeletal muscle