PCAT Biochemistry: A Biology and Chemical Cocktail
In this section you will learn about:
- The basics behind biochemistry
- Important biochemicals
- Synthesis of important biochemicals
- Introducing polymerisation
Biochemistry is a relatively new science which concerns itself with the study of biologically created molecules. The main focus of biochemistry is to delve deep into how biological molecules give rise to the processes that occur within organisms which in turn relates to the study of the whole organism.
Biomolecules are biological molecular entities, there are 92 distinct essential naturally occurring natural elements the most important of which include macromolecules such as proteins, nucleic acids, carbohydrates and lipids. These molecules often form the structures that are found in every living cell on this planet. This section delves deeper into how these molecules are created and what an organism does with them.
Carbohydrates are the most important type of biomolecules and represent the major energy source for most living cells. Carbohydrates are used in the anabolic processes of making proteins and lipids. They are made of three key elements which actually make up 99% of elements in the body these are carbon, hydrogen and oxygen and have an empirical formula of (CH2O)n. Each sugar unit that makes up a carbohydrate is characterized by having many hydroxyl groups in addition to either a keto group (C= O)-, named in such a case ketose, or an aldehyde group (CH=O)-, named aldose.
Monosaccharides - these are single unit sugars and hence the term monosaccharides (single sugars). An example of an aldose monosaccharide is glucose as shown in Figure 13-1 :
Figure 13-1: Aldose monosaccharide - Glucose.
Glucose exists in several different structures, but all of these structures can be divided into two families of mirror-images called stereoisomers. Only one set of these isomers exists in nature, those derived from the "right-handed form" of glucose, denoted D-glucose. Another important monosaccharide is the ketose monosaccharide fructose, which is shown below:
Figure 13-2: Ketose monosaccharide.
Monosaccharides can have 3, 4, 5 or 6 carbons, which are named trioses, tetroses, pentoses and hexoses, respectively. Both glucose and fructose are hexoses. Both fructose and glucose have the same formula C6H12O6. They are isomers, as they have the same molecular formula but different structures, one has an aldehyde group (glucose) and the other a ketone group (fructose). An example of a triose sugar is glyceraldehyde. Another important example is that of pentose that constitutes the RNA and DNA; these are the ribose and deoxyribose ( a deoxy derivative of the ribose monosaccharide) sugars.
Disaccharides - are formed of two monosaccharide units like glucose shown above. Two monosaccharides are linked together through a glycosidic linkage. One of the simplest disaccharides is maltose, a reducing disaccharide, is made up of 2 glucose units linked by α (1-4) glycosidic linkage, like so:
Figure 13-3: Maltose disaccharide.
You can see that the two glucose molecules are chemically bonded making a larger polymer, this glycosidic link can be broken via hydrolysis to yield the original two molecules of glucose.
A "reducing sugar” is any sugar that either has an aldehyde group or is capable of forming one in solution through isomerism.
Lactose, also a reducing disaccharide, made up of one glucose and one galactose, linked by β (1-4) glycosidic linkage. It is the popular sugar present in milk.
Figure 13-4: Lactose disaccharide.
Sucrose is a non-reducing sugar. It is composed of one glucose and one fructose linked by α1- β2 glycosidic linkage.
Figure 13-5: Sucrose, an important disaccharide.
Oligosaccharides and Polysaccharides - can be seen as more complex disaccharides and have more than two monosaccharides attached to one another (3-6 is a oligosaccharide and 6+ is a polysaccharide) linked together again by glycosidic bonds. They are classified into homopolysaccharides and heteropolysaccharides (see figure 13-6).
- Homopolysaccharidesare composed of repeating identical same monosaccharide units eg. Starch, glycogen, cellulose. Starch is found in cereals, legumes, potatoes. Here, glucose is the monosaccharide unit. Starch is a complex polysaccharide, it is formed of two large polysaccharides linked together. A linear polysaccharide called amylase and a branched amylopectin polysaccharide as shown in fig (3). Glycogen is made of a very branched amylopectin polysaccharide. Glycogen is stored in the liver and muscles.
- Heteropolysaccharidesare composed of different types of monosaccharides or their derivatives. Examples are the mucopolysaccharides, glycoproteins and proteoglycans.
Figure 13-6: Homopolysaccharides Vs Heterosaccharides.
There are two super important polysaccharides, which you must know the first is glycogen, which is a storage energy source in humans and cellulose which is found in plant cell walls. The latter, cellulose, is made by plants and has completely no use in humans as they cannot digest it and therefore use it as fiber in their diet although it is a polysaccharide made of glucose, shown in Figure 13-7:
Figure 13-7: Cellulose and important plant polysaccharide.
The next super important long chain sugar is glycogen which serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue in the form of fat. Primarily glycogen is biosynthesized by the muscles and the liver, but can also be made by glycogenesis within the brain and stomach.
Figure 13-8: Starch.
As seen in figure 13-8 above, glycogen, which is an analogue of starch (a glucose polymer in plants) and is sometimes referred to as "the animal starch”. Glycogen forms an energy reserve that can be quickly mobilized to meet an immediate need for glucose, but one that is less compact than the less immediately available energy reserves of triglycerides (lipids).
Lipids comprise of a wide range of molecules which are water-insoluble or nonpolar compounds of a biological origin. There are more familiar to you as waxes, phospholipids, glycolipids, fatty acids and the vitamins A, D, E and K. Their main biological function is to act as an energy store, in cellular signaling and a structural component of cell membranes. A common misconception is that lipids are used interchangeably with fats, however, fats are subgroup of lipids called triglycerides. Although the majority of lipids can be obtained from a mixed diet some lipids can only beast synthesized within the cell, and therefore they need could be biochemically created.
Lipids are synthesized by chain elongations in a process known as fatty acid synthesis. This puts a hydrocarbon chain together with a carboxylic acid termination group. These chains can either be saturated or unsaturated. This process is diagrammatically shown below, it looks a little complicated but it is basically a polymerization of fatty acid chains using NADPH as an energy source.
Figure 13-9: A simplified view of fatty acid synthesis.
Proteins usually perform structural roles within the cell, we have already visited the role that proteins such as actin and myosin play within muscle contraction and antibodies play in binding to antigens. Proteins are macromolecules made up of smaller molecules called amino acids. There are over 20 different amino acids, they are similar in that there is a standard central carbon atom but the variation comes in what is attached to this atom, there are four other functional groups, which could be included, these include:
- A simple hydrogen atom
- A carboxylic group - COOH
- A denoted group -R (i.e. this could contain anything)
- An amino group - NH2
Amino acids can join together via a peptide bond, by dehydration synthesis to form long, polymerized chains. When two amino acids get together like this it is deemed a dipeptide (in a similar nomenclature to disaccharides). If this chain grows to above two but less that thirty this is called a polypeptide, if this chain gets any bigger it is called a protein.
|Amino acid à Dipeptide à Polypeptide à Protein|
The final structure of proteins is classified as either:
- Primary- the linear sequence of combined amino acids.
- Secondary- has a structure such as a helix and can contain additional nucleic acids to make larger biopolymers. This structure does not,describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
- Tertiary- is an even more 3 dimensional structure
- Quaternary- is the most complex type of protein, which consists of multiple peptide sub units.
A nucleic acid or polynuleotide, is a ubiquitous, high molecular weight molecule which is composed of nucleotides that store genetic information. Probably you know this already as either deoxyribonucleic acid (DNA) or its precursor Ribonucleic acid (RNA), which store and convey all of the genetic material within your cells. Nucleic acids are linear polymerised chains of nucleotides. Each nucleotide consists of three components: a purine or pyrimidine nucleobase sometimes termed nitrogenous base or simply base, a pentose sugar, and a phosphate group.
PCAT Practice Biochemistry Questions
1. Hydrolysis of a molecule of maltose yields:
A. glucose + glucose
B. glucose + galactose
C. glucose + fructose
D. fructose + lactose
2. What type of sugar is composed of repeating identical same monosaccharide units?
3. Sucrose is:
a. Hydrolyzed by lactase enzyme
b. Hydrolyzed into fructose and glucose
c. A polysaccharide
A. Uses up 3ATP molecules
B. Produces 6 ATP molecules
D. Occurs in aerobic organisms only
5.Cellulose is characterized by which of the following options?
A. It makes up the cell membrane of eukaryotic cells
B. It is a homopolysaccharide
C. It is a disaccharide hydrolyzed to fructose units
D. It contains an amino group
6. Mucopolysaccharides can be defined as which as the following?
A. Are homopolysaccharides
B. Contain an amino group
C. Are found in plant cell walls
D. An example of which is maltose
7. Which of the following is NOT a lipid soluble vitamin?
8. An protein which has an alpha helical structure is consdered to have which of the following structures?
9. What is the relationship between the two chemical structures show below?
A. A is maltose and B is glucose
B. A is dextrose and B is glucose
C. A is sucrose and B is maltose
D. They are the same molecular entity
10. A polymer chain of sugars which contains 5 monosacharides is catergorised as which of the following?
Answers and Explanations
Homopolysaccharidesare polysaccharides which have the same monosaccharide repeating units. Heteropolysaccharides are those which have differing repeating units.
When a molecule of glucose is completely oxidized to CO2 and O2, it yields 38 ATP molecules. Complete oxidation of glucose involves three processes: glycolysis , krebs cycle and electron transport chain. Glycolysis produces 4 ATPs but it uses up 2 in the process, making a net product of 2. The krebs or citric acid cycle doesn't produce ATP but the electron transport chain produces 36 ATPs.
Explanation: Sucrose is a disaccharide formed from glucose and fructose joined together by an α, β(1→2) glycosidic linkage. Lactase is an enzyme that hydrolyzes the disaccharide lactose to glucose and galactose.
Glycolysis uses up 2 ATP molecules and produces 4 ATP molecules (a net of 2 ATP molecules) and produces pyruvate. It doesn't require oxygen so it is utilized in both aerobic and anaerobic conditions. In anaerobic conditions the pyruvate is converted to lactate.
Cellulose is a homopolysaccharide composed of many glucose units linked together through β(1→4) glycosidic linkages. Cellulose is not present in a eukaryotic cell membrane; it makes the cell walls of plant cells.
Mucopolysaccharides are heteropolysaccharides cause they are made up of different monosaccharide derivatives. They are formed of an amino sugar (N-acetylglucose amine or N-acetylgalactose amine) and a uronic sugar (glucuronic acid or iduronic acid). They are also called glycosaminoglycans due to the presence of amino groups. They are found in fungal cell walls.
Vitamin C, otherwise known as L-Ascorbic acid (don't get confused with citric acid) is not lipid soluble, unlike A, D, E and K.
A protein secondary structure is the general three-dimensional form of local segments of biopolymers such as an alpha helix.
The two molecules shown A and B have the same chemical formula however, they are stereoisomers of one another. Molecule A is an example of D-glucose and the molecule on the right, B is L- glucose.
Any sugar which contains between 3-6 monosaccharide is called an oligosaccharide.