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Module 2 - General Biochemistry (Chem.2)
Module 2 - General Biochemistry (Chem.2)
MODULE 2
in
GENERAL
BIOCHEMISTRY
(CHEM. 2)
NAME : ————————————————
INSTRUCTOR : ————————————————
SEMESTER : ————————————————
SCHOOL YEAR : ————————————————
Compiled by:
DEMEIAPE V. BAGALAY
Course Instructor
Republic of the Philippines
VISION
A leading ―Glocal‖ University with widened academic perspectives that focus on attaining
food security, supporting poverty alleviation, developing renewable energy, and conserving
natural environment
MISSION
SDSSU shall provide competency based higher education and training driven by relevant
and responsive instruction, research, extension and sustainable resource management.
PROGRAM GOALS:
Course Overview
Hello and welcome to Biochemistry! This course covers the fundamental aspects
of biochemistry and the structure and dynamics of important cellular components. It
deals with the properties and metabolism of carbohydrates, lipids, proteins and other im-
portant biochemical compounds. This course is also designed to develop techniques and
skills in qualitative and quantitative tests on carbohydrates, proteins, lipids and nucleic
acids.
Biochemistry is an intensive, challenging course as it encompasses many areas
of chemistry and biology. Hence, you are assumed to have prior knowledge in biology,
general chemistry and organic chemistry to better grasp the concepts presented in the
following four (4) modules covered in this course, namely;
Module 1: Fundamentals of Biochemistry
Module 2: Carbohydrates
Module 3: Lipids
Module 4: Proteins and Nucleic acids
The lessons in each module are brief but packed with figures, short activities
and assessments to supplement and evaluate learning. Each lesson has the following
parts and corresponding icons:
This will give you an idea of what you need to acquire
after completing each lesson.
This task is given before starting each lesson. It aims
to test what you knew about the topic.
This can be a question or two that serves as motivation
to build up your interest on the lesson.
This section provides the discussion of the lessons
and aims to help you discover and comprehend the
concepts you have to learn.
This provides you the link to additional readings or
video clips to learn more about the topics.
This task will help you transfer or apply your new
knowledge or skill.
This is an assessment of your level of mastery in
achieving the intended learning outcomes
INTRODUCTION
From the given figure, encircle all the foods which you think contain carbohydrates. Then,
list down in the table provided on the right the 10 foods which are very rich in carbohydrates.
1.
2.
3.
4.
5.
6
7.
8.
9.
Figure 1. Carbohydrates from variety of foods. © 2017 Denniston, 10.
et al. McGraw-Hill Education.
It is possible for any organism not to need carbohydrates? Why or why not?
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All monosaccharides are colorless, crystalline solids. They are all soluble in water because
hydrogen bonding is possible between their polar -OH groups and water. They are slightly soluble in
ethanol and insoluble in non-polar solvents such as benzene, diethyl ether, and dichloromethane.
Monosaccharides are the simplest type of carbohydrates. They are composed of
carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 as shown the generalized formula C nH2nOn,
where n is at least 3. Each monosaccharide contains a single polyhydroxy aldehyde or polyhydroxy
ketone unit (figure 3).
A monosaccharide can be an aldose or a
ketose on the basis of functional group it contains.
Aldoses are families of monosaccharides that
contain aldehyde functional group, where carbonyl
(C=O) is at carbon-1, while ketoses are mono-
saccharides that contain ketone functional group
where carbonyl (C=O) is at carbon-2 (figure 3). Figure 3. The carbonyl group in aldose and ketose.
© 2017 Denniston, et al. McGraw-Hill Education.
Monosaccharides are also classified and named using the suffix -ose to indicate that a
molecule is carbohydrate, and the prefixes tri-, tetr-, pent, and so forth to indicate the number of
carbon atoms in the chain (table 1).
Table 1. Some monosaccharides based on number of carbon atoms
Number of carbons Generic name examples
3 triose glyceraldehyde, dihydroxyacetone
4 tetrose erythrose, threose
5 pentose ribose, deoxyribose
6 hexose glucose, fructose, galactose
7 heptose sedoheptulose
9 nanose Numaminic acid
These simple sugars are also classified and named based on configuration using the D, L
system proposed by the German Chemist Hermann Emil Fischer in 1891. When written in Fischer
projection, D – monosaccharide has the -OH group on the right side of the penultimate carbon,
while L – monosaccharide has the -OH group on the left side of the penultimate carbon or the
carbon that is next to the last carbon on the chain.
Combining the three systems of classifying and naming gives even more information about
the structure and composition of a sugar especially monosaccharides that often have
stereoisomers (figure 4).
Figure 4. Naming sugar. (a) D-glyceraldehyde is
an aldotriose, a three-carbon sugar that contains
an aldehyde group, and with D- configuration
because the -OH is on the right side of the
penultimate carbon. (b). D-glucose is an
aldohexose, meaning it is an aldose with 6 carbon
penultimate carbon atoms. The name also indicates that it has an -OH
on the right of its penultimate carbon. (c) D- fruc-
tose is a ketohexose because it is a six-carbon
(a) (b) (c) sugar with ketone group and -OH on the right side
of its penultimate carbon. © 2017 Denniston, et
al. McGraw-Hill Education.
convert to
Fischer projection
(a) Ball -and-stick models (b) Perspective formulas (c) Fischer Projection formulas
Figure 5. Writing Fischer projections. © 2013 W.H. Freeman Company. Lehninger Principles of Biochemistry, 6th ed.
Figure 7. Haworth Projections of fructose and galactose. (a) fructose also called levulose and fruit sugar, is the
sweetest of all sugars. It is found in large amounts in honey, corn syrup, and sweet fruits. Unlike glucose, it forms
a five-membered cyclic hemiacetals with anomeric carbon at carbon 2. (b) galactose is a component of lactose,
or milk sugar. This is the principal sugar found in the milk of most mammals. It is diastereomer of glucose and it
forms a six-membered cyclic hemiacetals with anomeric carbon at carbon 1. © 2017 Denniston, et al.
McGraw-Hill Education.
In the linear forms of monosaccharide, which is in equilibrium with the cyclic forms, the
anomeric carbon is easily oxidized, making the compound a reducing sugar.
(b)
(c)
(d)
Figure 8. Disaccharide formation. (a) formula for disaccharide (b) Maltose is formed when two glucose molecules
are linked by glycosidic bond. (c) Lactose is formed when galactose is linked to a glucose molecule. (d) A sucrose is
formed when glucose is linked to a fructose . All these three disaccharides are formed through dehydration synthesis/
condensation process where water molecule is removed thus glycosidic bond between the two monosaccharides is
formed. As a result, water molecule is also release when a disaccharide is formed. © 2017 Denniston, et al. McGraw
-Hill Education.
Disaccharides that do not contain a hemiacetal group on carbon 1(C-1) just like sucrose,
are called non-reducing sugars and they do not react with Benedict’s reagent.
Figure 9. Homopolysaccharide and heteopolysaccharide linear and branched structure.© 2015 Stoker, S. H.
General, Organic and Biological Chemistry. 6th ed. Cengage Learning, Inc
Homopolysaccharides that serve as structural elements in plant cell walls and in animal
exoskeletons:
Cellulose is an un-branched A. cellulose
Figure 12. Sections of polymeric structures of hylarunic acid (a) and heparin (b).© 2015 Stoker, S. H. General,
Organic and Biological Chemistry. 6th ed. Cengage Learning, Inc.
Introduction:
Carbohydrates are polyhydroxycarbonyl compounds (aldehydes or ketones) or their
derivatives with a general formula (CH2O)n. They are most abundant constituents of plants and
animals. In some plants, sugar is usually stored in the roots as polysaccharide starch.
Starch is one of the main ingredients of human food. It consists of two fractions: amylose
and amylopectin. Amylose is a linear unbranched polymer of glucose residues combined with α-1,4
-glycosidic bonds. Amylopectin contains additional branches, where there are α-1,6 bonds.
Objective: This activity aims to isolate and test the presence of starch from different plant extracts.
Materials:
Glass containers stirring rod medicine dropper knife basin
stove spatula cheesecloth grater pan
Cassava or sweet potato (crop root) distilled water IKI / betadine solution
Activity No. 2
THREE- DIMENSIONAL MODEL OF A SIMPLE SUGAR
Direction: Form a group of four within your class. With your group mates, construct a three-
dimensional (3D) model (Fischer or Haworth projections) of glucose or fructose. Components of the
sugar must be distinguishable from one another. Show creativity and care to nature by using only
biodegradable materials. Your model will be graded using the following criteria:
Correctness of the model - 50%
Workmanship (beauty, creativity, durability) - 30%
Materials used - 10%
Participation of group members - 10%
100%
Note: Take a two -minute video of your group making the model. Each member must be present in
the video. The video must also include brief description of the model and its make-up. Send the
recorded video to your instructor through FB messenger.
ACTIVITY 1
ISOLATION OF STARCH FROM PLANT EXTRACT
ACTIVITY 1
ISOLATION OF STARCH FROM PLANT EXTRACT
ANALYSIS:
1. Why do you think starch are abundantly present in the crop roots?
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3. Is starch present in fruits and vegetables? How about in meat? Why or why not?
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CONCLUSION:
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Name: Rating:
Section: Date:
Subject Instructor:
2. Make a Haworth projections of the first and third sugars in item number 1. Then, name the
anomers of each sugar.
2. Describe three functions of carbohydrates that explain why they are the most abundant
biomolecules in nature.
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3. Do you agree that carbohydrates are important to organisms? Why or why not?
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Using boxes and arrows, diagram the carbohydrate digestion in the human body.
In your previous subjects, you have surely learned about metabolism. In both aerobic and
anaerobic cellular metabolism, glycolysis is the first stage. Can you remember what is primarily
needed for glycolysis to occur? Yes, glucose!. This simple carbohydrate is the prime substrate
readily converted into ATP, the energy currency in cells. So, let’s start carbohydrate metabolism
with glycolysis. You will learn in the next topics the anabolic pathways in metabolism of
carbohydrates.
2.1. Glycolysis
Glycolysis, from Greek word glykys meaning sweet or sugar, and lysis or splitting, is
anaerobic pathway that takes place in a cell cytoplasm of all types of cells, prokaryote or eukaryote.
This pathway is also called Embden-Meyerhof Pathway. This metabolic pathway breaks down
1 glucose molecule into 2 pyruvate molecules and yields 2 ATP and 2 NADH. It has two halves with
five steps in each half. The first half is called ―energy-requiring‖ steps . This half uses 2 ATP
molecules to split glucose into 2, three-carbon molecules which will proceed to the next half of the
pathway, the ―energy-releasing‖ steps. In this half, 4 molecules of ATP, 2 molecules of NADH are
released. Since 2 ATP are used in the first half, glycolysis then has a net gain of 2 ATP molecules,
2 NADH and 2 pyruvate molecules.
Figure 14. Steps in the first half of Glycolysis. Glucose is split into two three-carbon containing molecules,
dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate. Two ATP molecules are used and notice the enzymes
involved in every step. Source: https://tinyurl.com/yx9d7qa7 .
Figure 15. Steps in the second half of Glycolysis. Glyceraldehyde-3-phosphate undergoes phosphorylation without using
ATP and a series of reaction that results in the production of 2 NADH and 4 ATP molecules. After this half, the pathway pro-
duces 2 molecules of pyruvate from a glucose molecule. Image obtained from https://tinyurl.com/yx9d7qa7.
2. Lactate through lactate fermentation, the enzymatic anaerobic reduction of pyruvate to lactate.
The only purpose of this process is to convert NADH to NAD+. The lactate so formed is
converted back to pyruvate when aerobic conditions are again established in a cell.
Figure 17. Lactate fermentation. © 2015 Stoker, S. H. General, Organic and Biological Chemistry. 6th ed. Cengage Learning, Inc.
Figure 18. Alcohol fermentation. © 2015 Stoker, S. H. General, Organic and Biological Chemistry. 6th ed. Cengage Learning, Inc.
After you have learned the fate of breaking down of glucose molecules, let’s find out how
glucose is synthesize through different metabolic pathways.
2.2. Pentose Phosphate Pathway
Pentose phosphate pathway is also known as the hexose monophosphate shunt or the
phosphogluconate pathway. It occurs entirely within the cytoplasm. It is an alternative pathway for
glucose oxidation. It provides the cell with energy in the form of NADPH, which is the reducing agent
required for many biosynthetic pathways. This pathway involves both oxidative and non-oxidative
pathways (figure 19).
Figure 19. The pentose phosphate pathway generates NADPH for biosynthetic pathways and ribose-5-P for nucleotide
synthesis. Flux through the pentosephosphate pathway is modulated in response to the metabolic needs of the cell. The
conversion of glucose-6-P to ribulose-5-P is the oxidative phase of the pathway, whereas the conversion of ribulose-5-P
to glyceraldehyde-3-phosphate (glyceraldehyde-3-P) and fructose-6-phosphate (fructose-6-P) is the non-oxidative phase
of the pathway. The key enzymes in the pentose phosphate pathway are glucose-6-phosphate dehydrogenase,
transketolase, and transaldolase. © 2017 Meisfeld, et al. W. W. Norton & Company, Inc.
Figure 19. Reduction of NADP+ to NADPH. Reduction of NADP+ into NADPH involves the
transfer of two electrons in the form of a hydride ion (:H−) and the release of a proton (H+). © 2017
Meisfeld, et al. W. W. Norton & Company, Inc .
At first glance (figure 21), the processes of gluconeogenesis, which is from pyruvate to
glucose appears to be simply the reverse of glycolysis, which is from glucose to pyruvate. But,
these two processes are not exact opposites. Why? Because steps 1, 3, and 10 of glycolysis are
irreversible hence, the reverse reactions must be carried out by other enzymes (figure 20).
In step 1 of glycolysis, hexokinase catalyzes the phosphorylation of glucose. In gluconeo-
genesis, the dephosphorylation of glucose-6-phosphate is catalyzed by glucose-6-phosphatase,
which is found in the liver but not in muscle. In reaction 3, the phosphorylation of fructose-6-
phosphate catalyzed by phosphofructokinase, is irreversible. That step is bypassed in gluconeo-
genesis using the fructose-1,6-bisphosphatase. Finally, in step 10 of glycolysis, the phosphorylation
of ADP catalyzed by pyruvate kinase cannot be reversed. In gluconeogenesis, the conversion of
pyruvate to phosphoenolpyruvate involves two enzymes and some unusual reactions. First, the
enzyme pyruvate carboxylase adds CO2 to pyruvate to produce the four-carbon compound oxalo-
acetate. The enzyme phosphoenolpyruvate carboxykinase then removes the CO2 and adds a
phosphoryl group. The donor of the phosphoryl group in this reaction is guanosine triphosphate
(GTP), a nucleotide like ATP, except that the nitrogenous base is guanine.
Figure 21 shows most obvious difference of the two processes. There are 11 compounds
involved in gluconeogenesis and only 10 in glycolysis. Why? The last step of glycolysis is the
conversion of the high-energy molecule phosphoenolpyruvate to pyruvate. The reverse of this
process is the beginning of gluconeogenesis which cannot be accomplished in a single step only
because it requires two enzymes to catalyze the reactions. So, in gluconeogenesis pathway, a two-
step process by way of oxaloacetate is required to effect the conversion of pyruvate to phospho-
enolpyruvate. Both ATP and GTP molecules are needed to drive this two-step process.
(a) (b)
Figure 24.Glycogen degradation and synthesis involves three key reactions catalyzed by (1) glycogen phosphorylase,
(2) glycogen synthase, and (3) the glycogen branching and debranching enzymes. Glycogen phosphorylase removes
glucose from the non-reducing ends of glycogen through a phosphorolysis reaction that generates glucose-1-P. The
enzyme phosphoglucomutase converts glucose-1-P to glucose-6-P, which is either used by muscle cells in glycolysis or
dephosphorylated in liver cells and exported. The glycogen synthase enzyme catalyzes a reaction that links glucose to
nonreducing ends of glycogen, using UDP-glucose as the substrate. Generation of UDP-glucose requires the enzymes
UDP-glucose pyrophosphorylase and nucleotide diphosphate kinase. The branching and debranching enzymes are
responsible for modifying the glycogen polymer to maximize the number of reducing ends available during glycogen
degradation and synthesis. Hormonal signaling is the primary regulatory mechanism in controlling glycogen degradation
(epinephrine, glucagon) and synthesis (insulin). © 2017 Meisfeld, et al. W. W. Norton & Company, Inc.
Watch:
Carbohydrate metabolism @ https://tinyurl.com/10gnzabm
Glycolysis @ https://www.youtube.com/watch?v=SUPQVg1vO0Q
Krebs cycle @ https://tinyurl.com/kx3gvmh1
Oxidative phosphorylation @ https://tinyurl.com/eg5xyh6y
PPP @ https://tinyurl.com/ymqsdkt3
Cori cycle @ https://tinyurl.com/y4z5pp8m
Glycogen synthesis @ https://tinyurl.com/5e4brzkg
Glycogen Synthesis and Degradation @ https://tinyurl.com/zvrx6swh
Glycogenolysis @ https://tinyurl.com/yescn3sq
Read: Carbohydrate metabolism @ https://tinyurl.com/1qz1hk59
Activity 3
CONCEPT MAP
Direction: Create a concept map that summarizes and correlates the different chemical pathways
in carbohydrate metabolism. Please include the starting materials and products of each metabolic
pathway. Be guided of the terms and phrases in the box below. You can use a term or a phrase
more than one time. You can also add terms or processes not written in the box.
Carbohydrate metabolism pyruvate Cori cycle glycogenesis glycolysis
Pentose Phosphate Pathway lactate gluconeogenesis glycogenolysis glucose
Acetyl CoA NADH NADPH liver muscle
Name: Rating:
Section: Date:
Subject Instructor:
2. What are the major differences between gluconeogenesis and glycolysis? What about
glycogenesis and glycogenolysis?
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Denniston, K. J., Topping, et al. (2017). General, Organic, and Biochemistry. 9th ed. New
York, USA: McGraw-Hill Education.
Meisfeld, R. L., McEvoy, M. M. (2017). Biochemistry. New York, USA : W. W. Norton &
Company, Inc.
Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry. 7th ed.. New York,
USA: W.H. Freeman and Company.
Stoker, S. H. (2015). General, Organic and Biological Chemistry. 6th ed.. Pasig City,
Philippines: Cengage Learning Asia Pte Ltd.
Yutimco, Mac Gerald A. (2021). Chem 14: Biochemistry. Compostela Valley State University.
(Unpublished Course Pack)
Online references:
https://www.youtube.com/watch?v=wFYsufJ9XMM
https://www.youtube.com/watch?v=FILqt0nSiRo
https://courses.lumenlearning.com/wm-biology1/
https://byjus.com/chemistry/classification-of-carbohydrates-and-its-structure/
https://courses.lumenlearning.com/suny-ap2/chapter/carbohydrate-metabolism-no-content/
https://www.coursera.org/lecture/science-exercise/5-carbohydrate-metabolism-during-exercise-
crzgf
https://www.youtube.com/watch?v=SUPQVg1vO0Q
https://www.youtube.com/watch?v=FmEm0CgHGdA
https://www.youtube.com/watch?v=VxCdheLvrx4
https://www.khanacademy.org/test-prep/mcat/biomolecules/carbohydrate-metabolism/v/pentose
-phosphate-pathway
https://www.youtube.com/watch?v=LSIIxX1Fa2E
https://www.youtube.com/watch?v=P_5ubq6MikQ
https://www.youtube.com/watch?v=rqDGlChGZPk
https://www.youtube.com/watch?v=VCFAGNb5exk