![\frac{d[P]}{dt} = k_2[E_0]\frac{[S]}{K_m + [S]} = V_{max}\frac{[S]}{K_m + [S]}](announcements_clip_image001.gif)
Special Announcements:
Winter 2008
FINAL EXAM AND GRADES
A copy of the final exam with answers is available on line.
The highest score was 189.5. The raw scores were normalized to 185 = 100% (several students obtained this score or better).
As announced, the midterm counts 40% and the final counts 60%. Students who improved noticeably in the final received extra consideration.
NOTE:
You should carefully compare your exam with the answers. The TAs have been carefully instructed on how to grade, and I generally consider their judgement to be final. We make a distinction between excellent, very good, good, etc. Any requests for re-grades must be submitted in writing with the blue book and left at my office before Friday, April 4.
Clerical errors such as addition mistakes should also be noted (and there will be no arguments about making the correction).
I will not discuss any exam until after I have looked at all of them at a time to be set aside for this review.
Jennifer, Jackie and Lauren Mack have a review session on Wed, from 11:30 - 1:20 in CSB 001
Ronnie will hold a problem solving session at 1 PM, Friday, in 3010A YORK.
The Review Session with the Instructor is on Monday, March 17, from 3:30 - 4:50 PM in York 2622
The Final Exam will be held in YORK 2722 (i.e. the normal class room)
Several TAs have scheduled a review session on Sunday, March 16, from 5 - 7 PM in York 2622
Preparation for the FINAL EXAM (Winter 2008 )
Remember: to get 100% you should remember all pathways and structural formulae, but you still get an A if you get 85% of the answers. To get a C ("SATISFACTORY") you need to know only 60%.
Consider seeking advice from a professional in the future, knowing they they know only 60% of what you want to know.
Chapter 14.5 ... the pentose phosphate pathway, but not the non-oxidative pathways that follows
Chapter 16, the TCA cycle; you should be able to relate it to the glyoxylate cycle ( how does it differ from the TCA cycle) and the urea cycle
Chapter 17, oxidation of fatty acids; the physiology is interesting, but we really start on p. 634 with activation and transport into mitochondria (know the role of carnitine, but not its structural formula)
know some general principles about complete oxidation of poly-unsaturated fatty acids and odd-number fatty acids, but not the detailed reactions (isomerizatins to move double bonds around, reductions to change two double bonds into one)
dealing with propionyl-CoA requires cobalamin (containing cobalt) as a co-factor; vitamin B12
very long chain fatty acid degradation in peroxisomes (generation of hydrogen peroxide)
p. 650 ketone bodies (structure and formation/reactions); under what conditions are they particularly relevant?
Chapter 18
transaminations and the role of pyridoxal phosphate
ammonia from glutamate in the liver
the urea cycle (p. 666)
Chapter 19 inhibitors , proton pumps, structure of ubiquinone)
no need to memorize the Q cycle
know the complexes and what each of them does
oxidative phosphorylation
chemiosmotic hypothesis
understand the meaning of P/O ratio
uncouplers and thermoregulation (thermogenin/UCP)
ATP synthase (overall structure, orientation in the membrane)
from Table 19-4 you should understand the following inhibitors (their targets and their effect on electron transport and OXPHOS):
cyanide, malonate, antimycin A, rotenone, dinitrophenol (DNP), atractyloside, oligomycin
Photosynthesis
light reactions; recognize chlorophyll or other pigments, but no need to memorize structural formulae
skip sections on bacteria, but concentrate on the "Z-scheme" in higher plants; know the components (general names) of the electron pathway in photosystems I and II (where are the quinones, where are the chlorophylls, the Fe-S centers, the heme/cytochrome, the ferredoxin, plastocyanin, flavin-containing oxidoreductase, oxygen evolving complex, why manganese ion,.... )
compartmentalization of the chloroplast and its significance
comparison of ATP synthesis in chloroplasts and mitochondria
cyclic photophosphorylation
Chapter 15
gluconeogenesis: what is common and what is different from reverse of glycolysis (see Fig. 14.16 and 15.15) ; start at chapter 14.4 and continue with regulation in 15. 3
the by-pass reactions
the regulation of the PFK-1 and FBPase-1 by Fru 2,6-bisphosphate and the regulation of PFK-2 and FBPase-2 (Figs. 15-22 and 15-23_
Chapter 20
dark reactions in photosynthesis p. 751 - 770
understand the Calvin cycle with intermediates and utilization of ATP and NADPH
simplified form of aldolase and transketolase reactions (as shown in class) with no need to memorize the precise structural formulae of 4 carbon or 7 carbon intermediates (i.e. the correct stereochemical position of OH and H in the linear representation of the sugar intermediates) or the various isomers of the pentoses (except ribulose 1,5 bisphosphate)
net reactions
some general ideas about coordination/control of light and dark reactions (what does thioredoxin do?)
photorespiration and the glycolate pathway: no detailed pathway, but understand that three subcellular organelles are involved; what is the net reaction?
C3 vs C4 plants: how to increase the CO2 concentration in bundle sheath cells; role of mesophyll cell; the C4 pathway and its costs (ATP, NADPH).
Chapter 21
synthesis of fatty acids
the general role of biotin in acetyl-CoA carboxylase
the reactions of fatty acid synthase (the distinction between the two important SH groups in the enzyme
up to p. 797 (with no details on further elongation or desaturase reactions )
p. 782: biosynthesis of cholesterol
know the steps to HMG-CoA and the choice between making ketone bodies with the lyase (p. 650-51: Fig. 17.18) and mevalonate with the dehydrogenase
from acetyl-CoA to mevalonate; skip the details to activated isoprenes
but, know the importance of isoprenes in the formation of various biologically important compounds:
cholesterol, steroid hormones, ubiquinone, dolichol, various vitamins, carotenoids, rubber
structures to recognize: thiamine pyrophosphate, NADPH, ubiquinone, FAD, biotin, pyridoxal phosphate, CoA, schematic of acyl carrier protein, vit. B12, ubiquinone
structures to remember: most of the molecules in the various cycles and pathways (except the disposal of glycolate);
no need to remember intermediates/transition states in the enzyme catalysis in most reactions;
remember cholesterol and esters of fatty acids and cholesterol, pyridoxal phosphate
THAT'S ALL
March 4, 2008
Apparently not all of you discussed the problem assigned on February 22 in the sections. The answer is provided by this link.
March 2, 2008
Sorry about being late for the assignments for the Section in the following week:
Review light and dark reactions of photosynthesis;.Chapter 20: look at problems 2, 3, 4, 10,
February 22, 2008
For the sections next week :
Chapter 19, problems #: 19, 26
try the following problem:
We turn over the equivalent of our body weight in ATP per day. The ATP synthase (complex V) operates at 120 rpm, and each revolution is capable of converting three ADP and Pi to 3ATP. How many molecules of ATPsynthase do we need to achieve the required daily turnover? How many moles does that correspond to? What would be the total mass of ATP synthases in our body (the Molec. Mass of complex V is 212 kD).
Assume that we make 2.5 ATP molecules for each NADH oxidized, or 5 ATPs for each oxygen molecule converted to water. How many liters of oxygen do we need every day?
February 21, 2008
the following is a link to an essay by two local experts in the SD Union about biofuels
February 19, 2008
An alert student asked me today about the physiological effect of glucagon :
in an earlier lecture we had discussed how glucagon activates glycogen breakdown in liver (see Lehninger Fig. 15.25)
today we discussed how glucagon causes a decrease in Fru2,6 bisphosphate (F2,6P) and thus stimulates gluconeogenesis (Lehninger Fig. 15.23)
these statements appear to be incompatible, if glycogen breakdown is stimulated to provide glucose for glycolysis.
The explanation would require a long lecture, but I refer the interested students to chapter 23, section 2: TISSUE SPECIFIC METABOLISM
some material from this chapter will be discussed in a later lecture on Diabetes Type II
a more specific explanation can be found in the textbook by Voet, Voet and Pratt (3rd edition): there are different isozymes of the PFK-2/FBPase-2 enzyme, and the muscle F2,6P control system functions quite differently. In heart muscle, phosphorylation of this enzyme activates rather than inhibits the PFK-2, and in skeletal muscle the phosphorylation site is lacking altogether and there is no cAMP-dependent control.
February 15
For sections next week
1) understand the information in Tables 16.1 and 19.5 (yield of ATP from various pathways)
2) chapter 19: problems 6, 7, 12, 13, 14 and 18
February 14
FINAL Application Deadline for TEACH FOR AMERICA
Friday, February 15, 2008
You can aplly ONLINE at www.teachforamerica.org/online/info/index.jsp
February 11, 2008
The answers for the midterm and the curve are given by the following link: MIDTERM
The maximum number of points is 124
divide your raw score in the blue book by 124 to get the normalized score (%);
>85% ==> A
>72% ==> B
>60% ==> C
>50% ==> D
Because of the preoccupation with the midterm I failed to announce new problems to be covered in Sections this week. SORRY.
You should go over your midterms and consult wit the TAs about any concerns you have with the grading.
New Problems to be covered:
Chapter 16: #s 6, 8, 9, 12, 13, 20
Chapter 19: #s 4, 5,
February 7, 2008 (Thursday)
MIDTERM TONIGHT
6:30 - 8:30 PETERSON 108
WE WILL PROVIDE THE BLUE BOOKS
February 1, 2008
Several TAs have scheduled extra time for review:
1) Ed Chen will meet (next week only) with anyone from 9-11
on the first floor of the Biomed Library
2) Jacqueline and Jennifer will hold a review session on Tuesday night (5:30 - 7:00 in U413)
3) Several TAs will be at Revelle Plaza (inside?) from 5 - 7 PM on Wednesday)
4)
Rona will be available from 6-8:30P.M., Monday, at Cafe Roma.
5) Lauren (Mack) will be at CLICS from 3 - 5 PM on Wednesday.
February 1, 2008
The Midterm exam is next week (Thu, Feb. 7, 6:30 - 8:30)
Coverage: up tp lecture 8, including pyruvate dehydrogenase, but not the Krebs cycle;
- proteins, enzymes, enzyme kinetics, inhibitors
- bioenergetics (chapter 13)
- glycolysis
- glycogen synthesis and degradation
- disaccharides, galactose metabolism
Structures you should know: NAD, ATP, cAMP, UDP-Glu, intermediates in the pathways listed above
Sections next week may focus on exam preparation; look at problems
# 3, 7, 8, and 11 in chapter 15
January 25, 2008
For the Sections next week you should prepare the following:
Chapter 13: problem #19 and 22
Chapter 14: problem #s 3, 4, 5, 6, 9, 10, 11
NOTE: on the website the dates and times for the MIDTERM and FINAL EXAMS had been left from the previous quarter (as one student finally pointed out). They were given correctly in the UCSD Class Schedule . They have now ben corrected on the website.
January 17, 2008
There has been a confusion created by the webmaster in Biology because there are two Metabolic Biochem courses offered in the same quarter, and some usernames and passwords were mixed up. This is now cleared up, and for the time being you do not need any username/password to get at the site and to the slides
Later next week the whole site will be protected and you should use the following:
USERNAME: bibc102-2wi08 (small letters)
PASSWORD: glucose6P
For the Sections next week you should look at the following problems in chapter 13: #s 4, 9, 11, 13, 14 . Since Monday is a holiday, students in Monday's section can go to any of the others during the week.
January 2, 2008
Sheets for signing up for the sections can be found outside of my office in BH.
SECTIONS will start Monday, January 14
for the sections in week 2 you should prepare with solving problems in Chapter 6:
Question #s 5, 6, 7, 8, 9, 15 (you may not be able to do some of these until we have covered more material in the lectures this week)
December 13, 2008
These announcements will be updated as we go along.
There will be no Sections during the first week of classes. In the first week the lectures will be given by Dr. Dennis Otero. IES will be back for the rest of the quarter starting January 14, 2008.
If you look at the slides, you will find the slides for Fall 2007; they will be re-packaged for 80 min Lectures as we go along.
Happy Holidays.
December 5, 2007
Farnaz and Shibani will hold extra office hours on Tues, Dec. 11, from 2 - 4 PM in the Geisel Library (Science and Engineering)
December 1, 2007
For the Sections next week consider the following problems:
Chapter 17 (Fatty acid oxidation): #s 11, 14, 16, 17, 1920
Chapter 21 (Fatty acid synthesis): #'s 1, 2, 3, 4, 7
Students in sections scheduled for Friday should attend sections earlier in the week; note the review session scheduled below.
More announcements about exam coverage of the material presented next week will follow.
November 28, 2007
A review session with the instructor has been scheduled for Friday, Dec. 7, from 3 - 5:00 PM in PCYNH 109
November 21, 2007
The gut microbiota of termites can theoretically
convert a sheet of A4 paper into two
litres of hydrogen. Figures such as this have
focused attention on termite guts as a source
of microorganisms and enzyme systems for the
production of biofuels. The biotechnological
challenges in this process are getting a grip on
the initial step — the breakdown of the highly
stable polymers of lignocellulose to microbial
substrates — and redirecting the carbon and
electron flow in the metabolic fermentations
to useful products (such as ethanol or hydrogen).
Read more about this (Nature 450: 487-488 (2007) Termites and Cellulose
For the Sections next week you should consider some problems from
chapter 16: #s 8, 9b, 12, 13, 14 (difficult), 20,
chapter 19: #s 23, 31, 32, [and 30 for someone who wants to be challenged!)
More entertainment for the long weekend http://www.faseb.org/asbmb/media/media.asp
November 18, 2007
Monday is the final day for returning midterm tests with any problems related to the grade. Leave blue books at my office with a note inside. [This is not a wholesale invitation for regrades, since the TAs did a very thorough job in grading everyone fairly and consistently].
For the sections this week review oxidative phosphorylation in mitochondria and photophosphorylation in chlorplasts.
Problems:
Chapter 14: problems # 16, 17, 19.
Chapter 19: problems # 1, 4, 6, 12
November 9, 2007
No Sections today, Friday
Next week:
1) discuss your exam with the TAs and clarify any problems. The answers for the exam questions are provided at the following link:
MIDTERM FA07
2) there are two slides on today's lecture that will not be explained explicitly: you are to discuss those in the sections (Table 16.1 and 19.5)
3) review the Krebs cycle and the glyxylate cycle and Mitchell's Chemiosmotic hypothesis
4) review two slides at the end of today's lecture (not shown in class) explaining the difference between substrate level phosphorylation and oxidative phosphorylation
Since Monday is a holiday, students should either go to other sections later in the week, or arrange with their TAs for an alternate date to meet.
November 6, 2007
Room assignments for the midterm:
Last names starting with A - G go to CENTR 115
Last nmes starting with H - Z go to CENTR 101
November 1, 2007
The midterm will cover material including the pyruvate dehydrogenase reaction. Your are responsible for material covered in the lectures from chapters 6, 13, 14, and 15 and the beginning of 16.
To prepare, you can do problems 3, 7, 8, and 11 from chapter 15
Sections next week will be used to prepare for the midterm (Monday), and I will hold a review session from 3-5 in PCYNH 109.
Sections later in the week will be devoted to discuss the midterm and material from chapter 16
October 29, 2007
The midterm has now been rescheduled for Tuesday, Nov. 6, from 7 - 9 PM in CENTR 101 and 115. Another announcement will direct you to the appropriate room depending on your last name.
The review session with IES will be held on Monday, Nov. 5, in 119 Pepper Canyon Hall from 3 - 5 PM
October 25, 2007
The faculty has received a letter from our Academic Senate leaders with instructions on how to procede during the remainder of the quarter. Excerpts can be found at the following link: Fire 2007.
We will continue from where we stopped at the last lecture and go through the material as indicated in the syllabus until we run out of time in the last week of the quarter.
The MIDTERM will be scheduled one week later than initially scheduled, but I still have to get a room reservation. This may not happen for a few days.
I hope that nobody was affected personally by the fire; if anyone suffered personal losses, please feel free to come to talk to me about your situation.
October 24, 2007
The midterm will definitely be postponed by at least a week; a new date will be announced when I can get a room assignment.
The University is considering at a higher level what to do about the whole week of lost classes, and I will be informed as soon as a decision has been reached. In the meantime, do not e-mail me, but keep an eye on this page.
October 23, 2007
The University will be closed tomorrow (Wednesday). At the moment I am waiting for the situation to normalize. I have requested rooms for the midterm to be held a week later (but at this time no one is around to deal with this). If facilities are available, the midterm will be postponed by a week. Stay tuned to this web site; I cannot answer dozens of individual e-mails (I had to move out of my house).
October 19, 2007
For the Sections next week : Chapter 14, Problems # 3, 4, 5, 6, 7,8,9,10,11
The Midterm Exam is on October 30; there will be a Review Session with the instructor (IES) from 4 - 5:50 on Monday, October 29, in CENTR 119.
October 9, 2007
For the Sections next week you should be sure to cover problem #6 in chapter 6, if you have not already done so;
in addition, do problems # 4, 9, 13, 14, 19, and 21 in chapter 13
I will not be available for office hours for the rest of this week, but will be back next Monday.
October 1, 2007
Wait-listed students:
Attend the first lectures; I cannot sign up anyone, but experience shows that quite a few students will drop during the first week, and students can sign up in the Biology Student Affairs Office in Pacific Hall as slots become available
Those of you who wish to to download POWER POINT SLIDES need a username and a password. These will be given out in the first lecture.
The following material is from last year and should be ignored for the moment. There will be regular updates as we get into the course.
Preparation for the FINAL EXAM (FA 2007)
Chapter 14.5 ... the pentose phosphate pathway, but not the non-oxidative pathways that follows
Chapter 16, the TCA cycle; you should be able to relate it to the glyoxylate cycle ( how does it differ from the TCA cycle) and the urea cycle
Chapter 17, oxidation of fatty acids; the physiology is interesting, but we really start on p. 634 with activation and transport into mitochondria (know the role of carnitine, but not its structural formula)
know some general principles about complete oxidation of poly-unsaturated fatty acids and odd-number fatty acids, but not the detailed reactions (isomerizatins to move double bonds around, reductions to change two double bonds into one)
dealing with propionyl-CoA requires cobalamin (containing cobalt) as a co-factor
very long chain fatty acid degradation in peroxisomes (generation of hydrogen peroxide)
p. 650 ketone bodies (structure and formation/reactions); under what conditions are they particularly relevant?
Chapter 18
transaminations and the role of pyridoxal phosphate
ammonia from glutamate in the liver
the urea cycle (p. 666)
Chapter 19 inhibitors , proton pumps, structure of ubiquinone)
no need to memorize the Q cycle
know the complexes and what each of them does
oxidative phosphorylation
chemiosmotic hypothesis
understand the meaning of P/O ratio
uncouplers and thermoregulation (thermogenin/UCP)
ATP synthase (overall structure, orientation in the membrane)
from Table 19-4 you should understand the following inhibitors (their targets and their effect on electron transport and OXPHOS):
cyanide, malonate, antimycin A, rotenone, dinitrophenol (DNP), atractyloside, oligomycin
Photosynthesis
light reactions; recognize chlorophyll or other pigments, but no need to memorize structural formulae
skip sections on bacteria, but concentrate on the "Z-scheme" in higher plants; know the components (general names) of the electron pathway in photosystems I and II (where are the quinones, where are the chlorophylls, the Fe-S centers, the heme/cytochrome, the ferredoxin, plastocyanin, flavin-containing oxidoreductase, oxygen evolving complex, why manganese ion,.... )
compartmentalization of the chloroplast and its significance
comparison of ATP synthesis in chloroplasts and mitochondria
cyclic photophosphorylation
Chapter 15
gluconeogenesis: what is common and what is different from reverse of glycolysis (see Fig. 14.16 and 15.15) ; start at chapter 14.4 and continue with regulation in 15. 3
the by-pass reactions
the regulation of the PFK-1 and FBPase-1 by Fru 2,6-bisphosphate and the regulation of PFK-2 and FBPase-2 (Figs. 15-22 and 15-23_
Chapter 20
dark reactions in photosynthesis p. 751 - 770
understand the Calvin cycle with intermediates and utilization of ATP and NADPH
simplified form of aldolase and transketolase reactions (as shown in class) with no need to memorize the precise structural formulae of 4 carbon or 7 carbon intermediates (i.e. the correct stereochemical position of OH and H in the linear representation of the sugar intermediates) or the various isomers of the pentoses (except ribulose 1,5 bisphosphate)
net reactions
some general ideas about coordination/control of light and dark reactions (what does thioredoxin do?)
photorespiration and the glycolate pathway: no detailed pathway, but understand that three subcellular organelles are involved; what is the net reaction?
C3 vs C4 plants: how to increase the CO2 concentration in bundle sheath cells; role of mesophyll cell; the C4 pathway and its costs (ATP, NADPH).
Chapter 21
synthesis of fatty acids
the general role of biotin in acetyl-CoA carboxylase
the reactions of fatty acid synthase (the distinction between the two important SH groups in the enzyme
up to p. 797 (with no details on further elongation or desaturase reactions )
p. 782: biosynthesis of cholesterol
know the steps to HMG-CoA and the choice between making ketone bodies with the lyase (p. 650-51: Fig. 17.18) and mevalonate with the dehydrogenase
from acetyl-CoA to mevalonate; skip the details to activated isoprenes
but, know the importance of isoprenes in the formation of various biologically important compounds:
cholesterol, steroid hormones, ubiquinone, dolichol, various vitamins, carotenoids, rubber
structures to recognize: thiamine pyrophosphate, NADPH, ubiquinone, FAD, biotin, pyridoxal phosphate, CoA, schematic of acyl carrier protein, vit. B12, ubiquinone
structures to remember: most of the molecules in the various cycles and pathways (except the disposal of glycolate);
no need to remember intermediates/transition states in the enzyme catalysis in most reactions;
remember cholesterol and esters of fatty acids and cholesterol, pyridoxal phosphate
THAT'S ALL
The following are some clarifying statements about electron transport and oxidative phosphorylation.
In your textbook, Fig. 19-15 shows four protons pumped by complex I, four protons pumped by complex III (the Q-cycle), and two electrons pumped by complex IV (total of ten). Most other textbooks agree with these numbers, but Fig. 19-14 shows four protons being pumped by complex IV. There appears to be some discrepancy. However, in one figure a molecule of oxygen is used, while the other uses 1/2 molecule of O2. Even the experts still argue about the exact number of protons pumped by the individual complexes or by the whole electron transport chain. It is a number that is very difficult to measure experimentally. The following are some numbers to consider:
2 moleculaes of NADH have to be oxidized to form two molecules of water from one molecule of oxygen. In this process a total of 4 electrons (from 2 NADHs) are sent through the electron transport chain. These are all exact numbers.
There are some numbers that are not yet exactly measured (or known):
the (H+/2e-) ratio: how many protons are pumped out of the matrix for two electrons passed through complexes I, III, IV? the book gives a number 10 (see above), but even the experts are still arguing about that, since experimental measurements are very challenging, and there are theoretical predictions only for the Q-cycle in complex IV. For purposes of this class the number is 10, but this is a soft number as long as we do not fully understand the mechanism of proton pumping by complexes I and IV. One possibility is that there is "slippage".
the P/O ratio: how many ATPs are produced per oxygen atom converted to water?
the H+/P ratio: how many protons pass through complex V for each ATP synthesized?
Again, for this class we take H+/P to be 3, but it need not be an integer (depending on the structure of the Fo subcomplex and the precise mechanism by which protons return to the matrix through complex V)
if H+/P = 3, then we can calculate that P/O = 3 (10/3) (for NADH oxidized), but since protons can return to the matrix through other channels, and are even needed for uptake of phosphate (and other ions), this is a maximum estimate; we assume P/O = 2.5, but this is also a soft number. As uncoupling increases (by artificial uncouplers or natural uncouplers like UCP-1) the P/O ratio drops towards ZERO.
The point is not to memorize an exact number, but to understand why these numbers are still somewhat uncertain, AND to understand why they do not have to be integers (whole numbers).
The midterm will cover material up to the beginning of chapter 16 (section 16.1 covering pyruvate dehydrogenase).
Complete structural formulae are to be known for : ATP, NAD+/NADH, UDP-Glu, cAMP, intermediates in glycolysis,
you should recognize certain co-factors and know what the functional groups are : CoA, lipoic acid, thiamine pyrophosphate, FAD/FADH2,
Major topics to be covered on the midterm are:
Chapter 6: Enzymes, enzyme kinetics (Michaelis Menten), inhibitors, the distinction between allosteric enzymes and enzymes obeying M&M kinetics
Chapter 13: Bioenergetics, "high energy" phosphate in group transfer reactions, free energy of hydrolysis, coupled endergonic and exergonic reactions, free energy change and equilibrium constants;
biological redox reactions, standard reduction potentials, relationship between DG and DE; oxidation stat of carbon in various carbon compounds, the role of NAD+/NADH and FAD/FADH2 in redox reactions
Chapter 14: Glycolysis (omit gluconeogenesis, pentose shunt); feeder pathways from disaccharides and glycogen ; fate of pyruvate under anaerobic conditions
Chapter 15: glycogen synthesis and breakdown; regulation of glycogen phosphorylase and glycogen synthase; feeder pathways of glycolysis (metabolism of galactose)
Chapter 16: pyruvate dehydrogenase
Lactose tolerance in East Africa points to a surprisingly recent moment in human evolution By Nicholas Wade
The ability to digest milk in adulthood was conferred by genetic changes that occurred as recently as 3,000 years ago, a team of geneticists has found.
http://www.iht.com/articles/2006/12/11/news/milk.php
some intersting reading from the NY Times
January 12:
Because of the holiday on Monday, we will miss a lecture. To gain a little time, I will start on Wednesday with the Michaelis Menten Equation (Equation 6.20 and 6.9 in the 4th edition of Lehninger, and 8.9 and 8.20 in the 3rd edition, and see below) without deriving it in class. You can follow the derivation in the textbook, or you can find another version of the derivation from a page on the internet: enzyme kinetics. You are not required to derive the equation for an exam, but you should memorize it. The important thing is to understand the meaning of this equation, and this is what I will present in the lecture on Wednesday.
Message received from a student :
"hello professor, i was about 20 minutes late to the 8am BIBC 102 lecture today and i was just wondering if anything important was discussed during the first 20 mintues of lecture...such as info regarding course syllabus, class web page, how to add discussion sections. thank you for your time "....
the Metabolic Chart can be found at the following web site
unfortunately I do not have a source where you can buy it (ask at the bookstore?)
This is an important message for those of you who want to access some of the recommended websites related to Structural Biochemistry Review:
To display the structures, some plug-ins are required: RASMOL, or CHIME. The computers in the CLICS (previous Undergrad Library) do not have these plug-ins (to my surprise, and I am trying to do something about this).
On your home computers you can download CHIME quite easily; it is free. Follow the instructions from the Macromolecular Museum Web Site.
*****************************************************************************************************************************************************************************************
the following announcements/information is from previous years and will not be relevant until later in the course
There is a potential for confusion (even in my own lectures?) about the nomeclature for various enzymes; here is a paragraph from the textbook by Voet and Voet (p. 419)
"Racemization is an isomerization reaction in which a hydrogen shifts its stereochemical position at a molecule's only chiral center so as to invert that chiral center. Such an isomerization is called an epimerization in a molecule with more than one chiral center."
Thus, methylmalonyl-CoA has only one chiral center and its interconversion is a reaction involving a racemase (in V&V, p.673), but in LNC it is called an epimerase (p. 609).
I also found that V&V refer to (S)-methylmalonyl-CoA and (R)-methylmalonyl-CoA (as I did in class), but LNC refer to D- and L-methylmalonyl-CoA.
Take your pick on the exam.
Note that an enzyme called a mutase actually changes one chemical compound into another (glucose to fructose, methylmalonyl to succinyl, etc.), without a change in overall chemical composition.
The following figures will be shown in class and they are not in the textbook
in exactly the same form. Consult your notes for the context and explanation.
********************************************************************************************
There will be no official sections during the first week, but all students
are urged to read Chapter 6 in "Lehninger", especially those who have not taken
Structural Biochemistry.
I can also strongly recommend a visit to the following web site:
Macromolecular
Museum
Go in and have some fun; pick Catalase from
the Hall of Oxidoreductases and start clicking:
clicking on the MDL in the lower right corner opens a window with more options
for different displays. By clicking on various items in the description on the
right side, different aspects of the enzyme and its structure and function are
emphasized. ( I will be happy to give a demonstration in my office for those
who need help).
You should sign up for the sections on the sheets outside of my office.
"Everything should be made as simple as possible
but not simpler" (A. Einstein)
I must stress repeatedly that the amount
of material in either text is too voluminous to cover in a single course/quarter.
Thus, I am somewhat selective, and the only way to find out what is covered
(and what is not) from each chapter is to pay attention in class
.
check out the following:
Animation Movies of ATP Synthase
rotation of F1-ATPase
A. typical trace of the remaining oxygen in a suspension of mitochondria when various substrates and inhibitors are added in succession.
B. In tightly coupled mitochondria the above experiment may not yield the predicted results, unless ADP and Pi are present in the solution.
