BIO 202_ General Physiology I (FULOKOJA).docx

**BIO 202: GENERAL PHYSIOLOGY (2 UNITS)** **PHOTOSYNTHESIS** Literally photosynthesis is synthesis with the help of light. It can also be defined as the process by which the green plants synthesis organic matter in the presence of light. It is represented by this equation: 6CO2 + 6H2O → C6H12O6 +...

**BIO 202: GENERAL PHYSIOLOGY (2 UNITS)** **PHOTOSYNTHESIS** Literally photosynthesis is synthesis with the help of light. It can also be defined as the process by which the green plants synthesis organic matter in the presence of light. It is represented by this equation: 6CO2 + 6H2O → C6H12O6 + 6O2 During the process of photosynthesis, light energy is converted into chemical energy and is stored as organic matter (carbohydrate) along with O2 as the end product of photosynthesis. CO2 and H2O constitute the raw material for the process and it is an anabolic process. **History of Photosynthesis** a\. Van Helmont (1648) proposed that increase in weight of willow tree come from water alone. b\. Stephan Hales (1727) pointed out that plants obtained a part of their nutrition from the air and that sunlight plays a role. c\. Priestley (1772) proposed that plants might restore the air laden with CO2 by the burning of candles d\. Ingen Houz (1779) noticed that only the green parts of plant can purify the air in the presence of sulight. e\. Jean Senebier (1783) observed that the air-purifying activities of plants depend on the presence of CO2. f\. Nicolas Theodore de Saussure (1804) concluded that CO2 and water must constitute the raw material for this process. g\. Meyer (1845) recognized the role of light as a source of energy for the process. h\. Julius Sachs (1862) proved that the process of photosynthesis takes place in the chloroplasts and result in the production of organic matter. **Importance of Photosynthesis to Man** a\. It provides food directly to man and indirectly as meat or milk of animal. b\. It maintains equilibrium of O2 in the atmosphere. c\. It provides least resources of energy to man as fuel such as coal, oil, wood and dung. ***Questions:*** ***Mention four scientists that worked on photosynthesis*** ***What are the four conditions necessary for photosynthesis?*** **Photosynthetic Pigments** There are three types of photosynthetic pigments: a\. Chlorophylls b\. Carotenoids c\. Phycobillins i. Chlorophylls and carotenoids are insoluble in water and can be extracted only with organic solvents. ii. Phycobillins are soluble in water. iii. Carotenoids include carotenes and Tanthophylls (carotenols). iv. Different pigment absorbs light of different wavelength and show characteristics absorption peak in vivo and in vitro. v. Pigments also show florescence property. **Absorption and Utilization of Light Energy By Photosynthetic Pigments** Sun is the chief source of light energy for photosynthesis. The plant receives only 40% of the total solar energy, the rest is either absorbed by the atmosphere or is scattered into the space. Not all the light energy falling on green parts of plants is absorbed and utilized by pigments. Some of the light is reflected, some is transmitted through the plants while only a small portion is absorbed by the pigments. Photosynthetic pigment absorb light energy only in the visible part of the spectrum ranging usually between 400-700mμ (nm). Such radiations are called Photosynthetically Active Radiations (PAR). Only about 1% of the total solar energy received by the earth is absorbed by the pigments and is utilized in photosynthesis. There is very weak absorption by pigments in green part of the spectrum, thus, the chloroplast appears green in green plants. Q: *What is the main source of energy in photosynthesis?* **Mechanisms of Photosynthesis** The process of photosynthesis is the oxidation of water and reduction of CO2. The mechanism of photosynthesis consists of two parts: 1\) Primary photochemical reaction or light reaction or Hill's reaction. 2\) Dark reaction or black man's reaction or part of carbon in photosynthesis. **A. Light reaction or Hill's reaction** Light reaction which is faster than the dark reaction takes place only in the presence of lipids in the grains portion of the chloroplasts. The reaction follows these steps: i\. Different chloroplast pigments absorb light in different regions of the visible part of the spectrum. ii\. The light energy absorbed by the pigments is transferred by resonance to chlorophyll-a which alone takes place in the light reaction. iii\. The chlorophyll becomes an excited molecule having more energy than the ground state energy. It is this excited form of Chlorophyll-a that takes part in the light reaction. It expels its energy along with an electron and a positive charge comes on the chlorophyll-a which is now oxidized. iv\. When pigment system II is active, that is, it receives light, the water molecules split into OH- and H+ ions (photolysis of water). The OH- ions unite to form some water molecules again and release O2 electrons 4H2O → 4H^-^ + 4(OH^-^) 4(OH) → 2H2O + O2 + 4^e-^ 2H2O → 4H^+^ + O2 + 4^e-^ v\. The electron released by the excited chlorophyll-a travels through a number of electron carrier system where it is either recycled or consumed in reducing NADP to NADPS + H+. The extra light energy carried by the electron is utilized in the formation ATP molecules at certain places during its transport. This process of the formation of ATP from ADP and inorganic phosphate (Pi) in photosynthesis is called PHOSPHORYLATION or PHOTOPHORYLATION. **Dark reaction / Black man's reaction** The dark reaction of photosynthesis is purely enzymatic and slower than the light reaction or primary photochemical reaction. It takes place in stroma portion of the chloroplast and is independent of light, that is, it can place either in presence or absence of light provided the assimilatory power is available. It involves the conversion of CO2 to carbohydrate with the help of assimilatory power (NADPH + H+ and ATP) in dark reaction. By using ^14^C labeled carbon(IV)oxide (^14^CO2) in photosynthesis and observing the appearance of characteristics radiation in different reaction intermediates and products, Calvin Melvin and others formulated the complete pathways of carbon assimilation in the form of a cycle called Calvin cycle. *Q: Mechanism of photosynthesis involves what two reactions?* **Summary** Photosynthesis is the process by which green plants synthesize organic matter in presence of sunlight. During the process, the light energy is converted to chemical energy and is stored in organic matter which is usually carbohydrate and oxygen. **The Calvin Cycle (C3 Pathway)** The following steps are followed in Calvin cycle: a\. Carboxylation- the CO2 is accepted by ribulose 1,5-biphospahte (RUBP) already present in the cells and an unstable 6-carbon addition is formed. The 6-carbon compound is hydrolysed into 2 molecules of 3-phosphoglyceric acid (3PGA). b\. Reduction- 3PGA is reduced to 3-phosphoglyceraldehyde by the assimilatory power in the presence of triose phosphate dehydrogenate. c\. Formation of hexose sugar and regeneration of RUBP- some molecules of 3-phosphoglyceraldehyde isomerise into dihydroxyacetone phosphate, which unite in the presence of aldolase to form fructose 1,6-biphosphate. d\. Fructose 1, 6-biphosphate is converted into fructose 6-phospahte in the presence of phosphatase. e\. The fructose 6-phosphate (Hexose sugar) is taken off the Calvin cycle and is converted into glucose, sucrose of starch. f\. Some of the molecules of 3-phosphoglyceraldehyde produced in step (b) are diverted ton regenerate ribulose 1,3-biphosphate. The first visible product of Calvin cycle is 3-phosphoglyceride acid which is a 3-C compound. Hence it is also called C3 pathway or PCR (photosynthetic carbon reduction) pathway. Calvin cycle is also known as Reductive Pentose Phosphate (RPP) cycle. *Q: What is the first product of the Calvin Cycle?* **C4 --Dicarboxylic Acid Pathway (Hatch-Slack Pathway)** For many years the Calvin cycle was thought to be the only photosynthetic reaction sequence operating in higher plants and algae. But in 1965 Kortschak, Hartt and Burr reported that 4-C containing dicarboxylic acids, malate and aspertase where major labeled products when sugarcane leaves were allowed to photosynthesize for short period of time in ^14^CO2. It was thus established that CO2 reduction has another pathway which is called Hatch-Slack pathway and because C4 dicarboxylic acids are the earliest product, it is also called C4 dicarboxylic acid pathway. Plants using this pathway (c4 plants) are sugarcane, maize, sorghum, amaranthus. These plants are different from other plants by i\. Absence of photo-respiration ii\. Anatomical similarities of the leaves (cane type) The anatomy of the C4 plants is also called Krantz' anatomy because of the presence of partially arranged cells of bundle sheath around their vascular bundle which look like a ring or wreath. Steps in Hatch-Slack pathway involves 2 carboxylation reactions, one taking place in chloroplasts of mesophyll cells and another in chloroplast of bundle sheath cells. Hatch-Slack pathway is significant in i\. It is a modification of Calvin cycle and beneficial for growing plants in tropical vegetation where Co2 concentration is reduced. ii\. It is adaptation to plants due to plants due to reduction in CO2 concentration in the atmosphere due to photosynthesis. iii\. It proves existence of alternative pathway to Calvin cycle. **Factors Affecting Photosynthesis** The rate of photosynthesis is affected by external and internal factors A. External factors i\. Light ii\. Temperature iii\. CO2 iv\. Water v\. O2 B. Internal factors i\. Chlorophyll content ii\. Protoplasmic factors iii\. Anatomy of leave iv\. Accumulation of end product of photosynthesis v\. Microstructure of chloroplasts. *Q: List three examples of C4 plants.* **Question**: *List five external factors affecting photosynthesis* **Answer**: *Light, temperature, oxygen, water, carbon (IV) oxide* **PROTEINS** **What are Proteins?** Proteins are known as the building blocks of life because they are the most abundant molecules present in the body and form about 60% of the dry weight of cells. They make up the majority of the cells in all living things. Aside from cells, proteins make up the majority of the body's structural, regulatory, and enzyme components. They are therefore crucial for an individual's [growth and development](https://byjus.com/biology/growth-development/). Food like eggs, pulses, milk and other milk products form the major high-protein foods for the body. **Composition of Proteins** Proteins are composed of: - Amino acids (building blocks of proteins) - Carbon - Hydrogen - Oxygen - Nitrogen - Sulfur (in some proteins) **Structure of Proteins** The structure of proteins is organized in a hierarchical manner: 1. **Primary Structure**: sequence of amino acids 2. **Secondary Structure**: local arrangements of amino acids (alpha helices, beta sheets) 3. **Tertiary Structure**: overall 3D shape of a single protein molecule 4. **Quaternary Structure**: arrangement of multiple protein molecules (subunits) A polymeric chain of amino acid residues constitutes proteins. A protein's structure is primarily made up of long chains of amino acids. The arrangement and placement of amino acids give proteins certain characteristics. All [amino acid](https://byjus.com/biology/amino-acids/) molecules contain an amino (-NH2) and a carboxyl (-COOH) functional group. Hence, the name "Amino-Acid". Polypeptide chains are synthesized by linking together amino acids. A protein is created when one or more of these chains fold in a specific way. Methane is substituted by amino acids, with hydrogen, amino groups, carboxyl groups, and a variable R- group filling the first three valencies of the -- alpha carbon.\ There are many sorts of amino acids depending on the R-group, and a polypeptide chain contains 20 of them. The final structure and purpose of proteins are determined by all these characteristics of amino acids. The structure of the protein is classified at 4 levels:- - **Primary** -- The primary structure of a protein is the linear polypeptide chain formed by the amino acids in a particular sequence. Changing the position of even a single amino acid will result in a different chain and hence a different protein. - **Secondary** -- The secondary structure of a protein is formed by hydrogen bonding in the polypeptide chain. These bonds cause the chain to fold and coil in two different conformations known as the α-helix or β-pleated sheets. The α-helix is like a single spiral and is formed by hydrogen bonding between every fourth amino acid. The β-pleated sheet is formed by hydrogen bonding between two or more adjacent polypeptide chains. - **Tertiary** -- The tertiary structure is the final 3-dimensional shape acquired by the polypeptide chains under the attractive and repulsive forces of the different R-groups of each amino acid. This is a coiled structure that is very necessary for protein functions. - **Quaternary** -- This structure is exhibited only by those proteins which have multiple polypeptide chains combined to form a large complex. The individual chains are then called subunits.  **Structure of Proteins** **Properties of Proteins** - **Solubility**: ability to dissolve in water or other solvents - **Viscosity**: thickness and flowability - **Conductivity**: ability to conduct electricity - **Optical activity**: ability to rotate plane-polarized light - **Stability**: resistance to changes in temperature, pH, and other environmental factors **Functions of Proteins** Proteins perform a wide range of functions in the body, including: - **Enzymes**: catalyze chemical reactions - **Structural proteins**: provide structure and support (e.g., collagen, keratin) - **Transport proteins**: carry molecules or ions across cell membranes (e.g., hemoglobin) - **Defense proteins**: help fight off pathogens (e.g., antibodies) - **Storage proteins**: store and release nutrients (e.g., casein in milk) - **Hormones**: regulate various bodily functions (e.g., insulin, growth hormone) - **Receptor proteins**: receive and respond to signals from other molecules - **Digestion** -- The digestive enzymes, which are primarily proteinaceous in origin, carry out digestion. - **Movement** -- Muscles include a protein called myosin, which helps muscles contract, allowing for movement. - **Structure and Support** -- The structural protein known as keratin is what gives humans and other animals hair, nails, and horns. - **Cellular communication** -- Through receptors on their surface, cells can communicate with other cells and the outside world. These receptors are made of proteins. - **Act as a messenger** -- These proteins serve as chemical messengers that facilitate communication among cells, tissues, and organs. The amino acids present in proteins differ from each other in the structure of their side (*R*) chains. The simplest amino acid is [glycine](https://www.britannica.com/science/glycine-amino-acid), in which *R* is a hydrogen atom. In a number of amino acids, *R* represents straight or branched [carbon](https://www.britannica.com/science/carbon-chemical-element) chains. One of these amino acids is [alanine](https://www.britannica.com/science/alanine), in which *R* is the [methyl group](https://www.britannica.com/science/methyl-group) (―CH~3~). [Valine](https://www.britannica.com/science/valine), [leucine](https://www.britannica.com/science/leucine), and [isoleucine](https://www.britannica.com/science/isoleucine), with longer *R* groups, complete the alkyl side-chain series. The alkyl side chains (*R* groups) of these amino acids are nonpolar; this means that they have no [affinity](https://www.merriam-webster.com/dictionary/affinity) for [water](https://www.britannica.com/science/water) but some affinity for each other. Although plants can form all of the alkyl amino acids, animals can synthesize only alanine and glycine; thus valine, leucine, and isoleucine must be supplied in the diet. Two amino acids, each containing three carbon atoms, are derived from alanine; they are [serine](https://www.britannica.com/science/serine) and [cysteine](https://www.britannica.com/science/cysteine). Serine contains an [alcohol](https://www.britannica.com/science/alcohol) group (―CH~2~OH) instead of the methyl group of alanine, and [cysteine](https://www.britannica.com/science/cysteine) contains a mercapto group (―CH~2~SH). Animals can synthesize serine but not cysteine or [cystine](https://www.britannica.com/science/cystine). Cysteine occurs in proteins predominantly in its oxidized form (oxidation in this sense meaning the removal of hydrogen atoms), called cystine. Cystine consists of two cysteine molecules linked by the disulfide bond (―S―S―) that results when a hydrogen atom is removed from the mercapto group of each of the cysteines. Disulfide bonds are important in protein structure because they allow the linkage of two different parts of a protein molecule to---and thus the formation of loops in---the otherwise straight chains. Some proteins contain small amounts of cysteine with free sulfhydryl (―SH) groups. Four amino acids, each consisting of four carbon atoms, occur in proteins; they are [aspartic acid](https://www.britannica.com/science/aspartic-acid), [asparagine](https://www.britannica.com/science/asparagine), [threonine](https://www.britannica.com/science/threonine), and [methionine](https://www.britannica.com/science/methionine). Aspartic [acid](https://www.britannica.com/science/acid) and asparagine, which occur in large amounts, can be [synthesized](https://www.britannica.com/dictionary/synthesized) by animals. [Threonine](https://www.britannica.com/science/threonine) and [methionine](https://www.britannica.com/science/methionine) cannot be synthesized and thus are essential amino acids; i.e., they must be supplied in the diet. Most proteins contain only small amounts of methionine. Proteins also contain an amino acid with five carbon atoms (glutamic acid) and a secondary amine (in [proline](https://www.britannica.com/science/proline)), which is a structure with the amino group (―NH~2~) bonded to the alkyl side chain, forming a ring. [Glutamic acid](https://www.britannica.com/science/glutamic-acid) and aspartic acid are dicarboxylic acids; that is, they have two carboxyl groups (―COOH).  [Glutamine](https://www.britannica.com/science/glutamine) is similar to asparagine in that both are the amides of their corresponding dicarboxylic acid forms; i.e., they have an amide group (―CONH~2~) in place of the carboxyl (―COOH) of the side chain. Glutamic acid and glutamine are abundant in most proteins; e.g., in plant proteins they sometimes [comprise](https://www.merriam-webster.com/dictionary/comprise) more than one-third of the amino acids present. Both glutamic acid and glutamine can be synthesized by animals.   The amino acids proline and [hydroxyproline](https://www.britannica.com/science/hydroxyproline) occur in large amounts in [collagen](https://www.britannica.com/science/collagen), the protein of the [connective tissue](https://www.britannica.com/science/connective-tissue) of animals. Proline and hydroxyproline lack free amino (―NH~2~) groups because the amino group is enclosed in a ring structure with the side chain; they thus cannot exist in a zwitterion form. Although the nitrogen-containing group (\>NH) of these amino acids can form a peptide bond with the carboxyl group of another amino acid, the bond so formed gives rise to a kink in the peptide chain; i.e., the ring structure alters the regular bond angle of normal peptide bonds. Proteins usually are almost neutral molecules; that is, they have neither acidic nor basic properties. This means that the acidic carboxyl ( ―COO^−^) groups of aspartic and glutamic acid are about equal in number to the amino acids with basic side chains. Three such basic amino acids, each containing six carbon atoms, occur in proteins. The one with the simplest structure, [lysine](https://www.britannica.com/science/lysine), is synthesized by plants but not by animals. Even some plants have a low lysine content. [Arginine](https://www.britannica.com/science/arginine) is found in all proteins; it occurs in particularly high amounts in the strongly basic protamines (simple proteins composed of relatively few amino acids) of fish sperm. The third basic amino acid is [histidine](https://www.britannica.com/science/histidine). Both arginine and histidine can be synthesized by animals. Histidine is a weaker base than either lysine or arginine. The imidazole ring, a five-membered ring structure containing two nitrogen atoms in the side chain of histidine, acts as a buffer (i.e., a stabilizer of hydrogen ion concentration) by binding hydrogen ions (H+) to the nitrogen atoms of the imidazole ring. The remaining amino acids---[phenylalanine](https://www.britannica.com/science/phenylalanine), [tyrosine](https://www.britannica.com/science/tyrosine), and [tryptophan](https://www.britannica.com/science/tryptophan)---have in common an aromatic structure; i.e., a [benzene](https://www.britannica.com/science/benzene) ring is present. These three amino acids are essential, and, while animals cannot synthesize the benzene ring itself, they can convert phenylalanine to tyrosine. Because these amino acids contain benzene rings, they can absorb [ultraviolet light](https://www.britannica.com/science/ultraviolet-radiation) at wavelengths between 270 and 290 nanometres (nm; 1 nanometre = 10^−9^ metre = 10 angstrom units). Phenylalanine absorbs very little ultraviolet light; tyrosine and tryptophan, however, absorb it strongly and are responsible for the absorption band most proteins exhibit at 280--290 nanometres. This absorption is often used to determine the quantity of protein present in protein samples. Most proteins contain only the amino acids described above; however, other amino acids occur in proteins in small amounts. For example, the collagen found in connective tissue contains, in addition to hydroxyproline, small amounts of [hydroxylysine](https://www.britannica.com/science/hydroxylysine). Other proteins contain some monomethyl-, dimethyl-, or trimethyllysine---i.e., lysine [derivatives](https://www.britannica.com/dictionary/derivatives) containing one, two, or three methyl groups (―CH~3~). The amount of these unusual amino acids in proteins, however, rarely exceeds 1 or 2 percent of the total amino acids. Physicochemical properties of the amino acids ============================================= The physicochemical properties of a protein are determined by the [analogous](https://www.merriam-webster.com/dictionary/analogous) properties of the amino acids in it. The α-carbon [atom](https://www.britannica.com/science/atom) of all amino acids, with the exception of glycine, is asymmetric; this means that four different chemical entities (atoms or groups of atoms) are attached to it. As a result, each of the amino acids, except glycine, can exist in two different spatial, or geometric, arrangements (i.e., [isomers](https://www.britannica.com/science/isomerism)), which are mirror images akin to right and left hands. These isomers exhibit the property of [optical](https://www.britannica.com/science/optical-activity) rotation. Optical rotation is the rotation of the plane of polarized light, which is composed of light waves that vibrate in one plane, or direction, only. Solutions of substances that rotate the plane of polarization are said to be optically active, and the degree of rotation is called the optical rotation of the [solution](https://www.britannica.com/science/solution-chemistry). The direction in which the light is rotated is generally designed as plus, or *d*, for dextrorotatory (to the right), or as minus, or *l*, for levorotatory (to the left). Some amino acids are dextrorotatory, others are levorotatory. With the exception of a few small proteins (peptides) that occur in [bacteria](https://www.britannica.com/science/bacteria), the amino acids that occur in proteins are l-amino acids.  In bacteria, d-alanine and some other d-amino acids have been found as components of gramicidin and bacitracin. These peptides are [toxic](https://www.britannica.com/dictionary/toxic) to other bacteria and are used in medicine as [antibiotics](https://www.britannica.com/science/antibiotic). The d-alanine has also been found in some peptides of bacterial membranes. **Amino Acid Sequence in Protein Molecules** Since each protein molecule consists of a long chain of amino acid residues, linked to each other by peptide bonds, the hydrolytic cleavage of all peptide bonds is a prerequisite for the quantitative determination of the amino acid residues. Hydrolysis is most frequently accomplished by boiling the protein with concentrated hydrochloric acid. The quantitative determination of the amino acids is based on the discovery that amino acids can be separated from each other by chromatography on filter paper and made visible by spraying the paper with ninhydrin. The amino acids of the protein hydrolysate are separated from each other by passing the hydrolysate through a column of adsorbents, which adsorb the amino acids with different affinities and, on washing the column with buffer solutions, release them in a definite order. The amount of each of the amino acids can be determined by the intensity of the color reaction with ninhydrin. To obtain information about the sequence of the amino acid residues in the protein, the protein is degraded stepwise, one amino acid being split off in each step. This is accomplished by coupling the free α-amino group (―NH2) of the N-terminal amino acid with phenyl isothiocyanate; subsequent mild hydrolysis does not affect the peptide bonds. The procedure, called the Edman degradation, can be applied repeatedly; it thus reveals the sequence of the amino acids in the peptide chain. Unavoidable small losses that occur during each step make it impossible to determine the sequence of more than about 30 to 50 amino acids by this procedure. For this reason the protein is usually first hydrolyzed by exposure to the enzyme trypsin, which cleaves only peptide bonds formed by the carboxyl groups of lysine and arginine. The Edman degradation is then applied to each of the few resulting peptides produced by the action of trypsin. Further information can be gained by hydrolyzing another portion of the protein with another enzyme, for instance with chymotrypsin, which splits predominantly peptide bonds formed by the amino acids tyrosine, phenylalanine, and tryptophan. The combination of results obtained with two or more different proteolytic (protein degrading) enzymes was first applied by English biochemist Frederick Sanger, and it enabled him to elucidate the amino acid sequence of insulin. The amino acid sequences of many other proteins subsequently were determined in the same manner. Protein Synthesis ----------------- Synthesis of proteins occurs in the ribosomes and proceeds by joining the carboxyl terminus of the first amino acid to the amino terminus of the next one. The end of the protein that has the free α-amino group is referred to as the amino terminus or N-terminus. The other end is called the carboxyl terminus or C-terminus , since it contains the only free α-carboxyl group. All of the other α-amino groups and α-carboxyl groups are tied up in forming peptide Linking of amino acids through peptide bond formation bonds that join adjacent amino acids together. Proteins are synthesized starting with the amino terminus and ending at the carboxyl terminus. Cis vs trans orientation of R-groups around peptide bond Image by Aleia Kim ### Primary Structure Primary structure is the ultimate determinant of the overall conformation of a protein. The primary structure of any protein arrived at its current state as a result of mutation and selection over evolutionary time. Primary structure of proteins is mandated by the sequence of DNA coding for it in the genome. Regions of DNA specifying proteins are known as coding regions (or genes). The base sequences of these regions directly specify the sequence of amino acids in proteins, with a one-to-one correspondence between the codons (groups of three consecutive bases) in the DNA and the amino acids in the encoded protein. The sequence of codons in DNA, copied into messenger RNA, specifies a sequence of amino acids in a protein. The order in which the amino acids are joined together in protein synthesis starts defining a set of interactions between amino acids even as the synthesis is occurring. That is, a polypeptide can fold even as it is being made. The order of the R-group structures and resulting interactions are very important because early interactions affect later interactions. This is because interactions start establishing structures - secondary and tertiary. If a helical structure (secondary structure), for example, starts to form, the possibilities for interaction of a particular amino acid R-group may be different than if the helix had not formed. R-group interactions can also cause bends in a polypeptide sequence (tertiary structure) and these bends can create (in some cases) opportunities for interactions that wouldn't have been possible without the bend or prevent (in other cases) similar interaction possibilities.    From RNA to amino acids - the genetic code **CARBOHYDRATES** Carbohydrates are a group of biomolecules that serve as the primary source of energy for the body. They are composed of carbon, hydrogen, and oxygen atoms, usually in a ratio of 1:2:1. Carbohydrates are the major components of plant tissue, making up to 60% to 90% of the dry matter (DM). Carbohydrates contain carbon, hydrogen, and oxygen in the proportion found in water (CH~2~O) and is hence hydrates of carbon. Carbohydrates are the basic energy source in animal cells. Dietary carbohydrates obtained from plant-based products serve as a major source of energy for the animal. The chlorophyll in plant cells traps solar energy and produces carbohydrates using carbon dioxide and water and gives off oxygen, as shown in the following equation: **Solar energy + 6 CO~2~ + 6 H~2~O → C6H~2~O + 6 O~2~** **Composition of Carbohydrates** Carbohydrates are composed of: - Carbon (40-45%) - Hydrogen (6-7%) - Oxygen (45-50%) - Sometimes, nitrogen, sulfur, or phosphorus **Structure of Carbohydrates** The structure of carbohydrates can be classified into: 1. **Monosaccharides** (simple sugars): single sugar unit (e.g., glucose, fructose) 2. **Disaccharides**: two sugar units bonded together (e.g., sucrose, lactose) 3. **Polysaccharides** (complex carbohydrates): long chains of sugar units (e.g., starch, cellulose, glycogen) **Structure and Classification** One method of classifying carbohydrates is based on the number of carbon atoms per each molecule of a carbohydrate and on the number of molecules of sugar in the compound. Based on the number of carbon atoms, a carbohydrate can be classified as triose (3 C), tetrose (4 C), pentose (5 C), and hexose (6 C). The suffix "*ose*" at the end of a biochemical name flags the molecule as a "sugar." Among these, pentoses (e.g., ribose in ribonucleic acid (RNA)) and hexoses (e.g., glucose, or blood sugar) are the most common sugars in animal tissues. Based on the number of molecules of sugar in the compound, carbohydrates can be classified as (1) monosaccharide, one unit of sugar; (2) disaccharide, two monosaccharides; (3) oligosaccharide, three to fifteen monosaccharides; and (4) polysaccharides, large polymers of simple sugars. **A. Monosaccharides** are often referred to as simple sugars (e.g., glucose) and cannot be hydrolyzed into simpler compounds. Monosaccharides can be subdivided based on the number of carbon (C) atoms. The following list shows the prefixes for numbers of carbons in a sugar. 1. Triose (3 C) 2. Tetrose (4 C) 3. Pentose (5 C; e.g., Xylose and Ribose) 4. Hexose (6 C; e.g., glucose, fructose, galactose, and mannose)Most monosaccharides in animal tissues are of 5 C and 6 C sugars. Simple sugars are also subdivided into aldose, a sugar that contains an aldehyde structure, or ketose, a sugar that contains a ketone group. Both glucose and fructose have the same molecular formula C6H12O6 and are hexoses (6 C). But glucose is an aldose (also called aldohexose) and fructose is a ketose, or a ketohexose. The three hexoses that are nutritionally and metabolically important are glucose, fructose, and galactose  Structure of simple sugars (Glucose) (Source: Wikipedia) The chemical structure of glucose can be represented as a straight chain form and in cyclic form (also shown in figures above). In a biological system, glucose exists primarily as a cyclic form and very rarely in a straight form (in aqueous solution). Glucose is the form of carbohydrates found in circulating blood (blood sugar) and is the primary carbohydrate used by the body for energy production. Fructose, or "fruit sugar," is found in ripened fruits and honey and is also formed by digestion of disaccharide sucrose. Galactose is found along with disaccharide lactose in mammalian milk and is released during digestion. **B. Disaccharides** are made up of two monosaccharides bonded together by a glycosidic (covalent) bond. The following are some of the common disaccharides: 1. Sucrose-glucose + fructose (e.g., table sugar) 2. Lactose-glucose + galactose (milk sugar) 3. Maltose-α-D-Glucose + β-D-Glucose (malt sugar) 4. Cellobiose-β-D-Glucose + β-D-Glucose (cellulose) Among the different disaccharides, lactose (milk sugar) is the only carbohydrate of animal origin. However, cellobiose as a component of cellulose is important in animal nutrition. Monogastric animals cannot digest cellulose because they do not produce the cellulase enzyme that can split β-D-Glucose. https://open.oregonstate.education/app/uploads/sites/85/2019/10/Untitled-1-02-1-scaled.jpg Important disaccharides in animal nutrition and feeding, lactose and cellobiose Source: Wikipedia **C. Oligosaccharide are made by bonding together three or more (3 to 15) monosaccharides bonded together.** 1. Raffinose (glucose + fructose + galactose; 3 sugars) 2. Stachyose (glucose + fructose + 2 galactose; 4 sugars) In animal diets, oligosaccharides are commonly found in beans and legumes. Some oligosaccharides are used as substances to enhance the growth of good microbes (prebiotics). Recently, there has been an increased interest in the use of different oligosaccharides as feed additives to enhance hindgut health (e.g., fructooligosaccharides, mannan oligosaccharides). **D. Polysaccharides, as their name implies, are made by joining together large polymers of simple sugars.** Polysaccharides are the most important carbohydrate in animal feed. Polysaccharides are composed of many single monosaccharide units linked together in long, complex chains. The functions of polysaccharides include energy storage in plant cells (e.g., seed starch in cereal grains) and animal cells (e.g., glycogen) or structural support (plant fiber). Components of cell wall structure are also called nonstarch polysaccharides, or resistant starch, in animal nutrition, as they cannot be digested by animal enzymes but are fermented by hindgut and rumen microbes. Polysaccharides can be homopolysaccharides or heteropolysaccharides. - a\. Homopolysaccharide - b\. Heteropolysaccharide a. **Homopolysaccharide:** Contains only one type of saccharide unit. Examples of homopolysaccharides that are important in animal nutrition include starch (nonstructural form), glycogen (animal form), and cellulose (plant structural form). 1. **Starch:** Principal sugar form of carbohydrate in cereal grains (seed energy storage). The basic unit is α-D-Glucose. Forms of starch in cereal grains include a. Amylose-α 1,4 linkage-straight chain, nonbranching, helical structure b. Amylopectin-α 1,4 linkage with alpha 1,6 linkage at branch points **Amylose** is the simplest of the polysaccharides, being comprised solely of glucose units joined in an alpha 1,4 linkage (Figure 3.4). Amylose is water soluble and constitutes 15% to 30% of total starch in most plants.    Figure 3.4. Amylose structure showing straight α 1,4 linkage  Source: Wikipedia **Properties of Carbohydrates** - **Solubility**: ability to dissolve in water - **Sweetness**: varying levels of sweetness - **Viscosity**: thickness and flowability - **Fermentability**: ability to be broken down by microorganisms - **Crystallinity**: ability to form crystals **Functions of Carbohydrates** Carbohydrates perform several functions in the body: - **Energy source**: primary source of energy for cells - **Structural components**: cell walls, exoskeletons, and connective tissue - **Storage molecules**: glycogen and starch store energy for later use - **Cell signaling**: involved in cell recognition and signaling - **Fiber**: indigestible carbohydrates promoting digestive health - **Nutrient absorption**: aid in absorption of other nutrients. **Importance of Carbohydrates:** 1. **Brain function**: carbohydrates are the primary energy source for the brain 2. **Physical performance**: carbohydrates provide energy for muscles 3. **Fiber**: indigestible carbohydrates promote digestive health **LIPIDS** Lipids are a group of biomolecules that are insoluble in water but soluble in organic solvents. They are an essential component of living organisms and serve various functions. Lipids are a diverse group of molecules that all share the characteristic that at least a portion of them is hydrophobic. Lipids play many roles in cells, including serving as energy storage (fats/oils), constituents of membranes (glycerophospholipids, sphingolipids, cholesterol), hormones (steroids), vitamins (fat soluble), oxygen/ electron carriers (heme), among others. **Composition of Lipids** Lipids are composed of: - Carbon (70-80%) - Hydrogen (10-15%) - Oxygen (5-15%) - Sometimes, phosphorus, nitrogen, or sulfur **Structure of Lipids** The structure of lipids can be classified into: 1. **Triglycerides** (fats and oils): glycerol backbone with three fatty acid chains 2. **Phospholipids**: glycerol backbone with two fatty acid chains and a phosphate group 3. **Steroids**: four fused carbon rings (e.g., cholesterol) 4. **Waxes**: long-chain fatty acids with a hydrocarbon chain ***Assignment: Draw the structure of a named triglycerides, phospholipids, and steroids.*** **Properties of Lipids** - **Hydrophobicity**: insoluble in water, soluble in organic solvents - **Viscosity**: varying levels of thickness and flowability - **Melting point**: varying levels of heat stability - **Saponification**: ability to react with alkali to form soap - **Emulsification**: ability to mix with water and other liquids **Functions of Lipids** Lipids perform several functions in the body: - **Energy storage**: stored energy source (triglycerides) - **Cell membrane structure**: phospholipids and cholesterol maintain membrane integrity - **Hormone regulation**: steroids regulate various bodily functions (e.g., cortisol, estrogen) - **Vitamin absorption**: aid in absorption of fat-soluble vitamins (A, D, E, K) - **Protection**: waxes and oils protect skin and hair - **Signaling**: involved in cell signaling and communication