Information

3: Biological Macromolecules - Biology

3: Biological Macromolecules - Biology



We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

  • 3.1: Prelude to Biological Macromolecules
    Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. These macromolecules (polymers) are built from different combinations of smaller organic molecules (monomers). What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, these questions will be explored.
  • 3.2: Synthesis of Biological Macromolecules
    Biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids); each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass).
  • 3.3: Importance of Carbohydrates
  • 3.4: Carbohydrates
  • 3.5: Lipids
  • 3.6: Proteins
  • 3.7: Nucleic Acids

3.1 – Synthesis of Biological Macromolecules

As you’ve learned, biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major biological macromolecule classes (carbohydrates, lipids, proteins, and nucleic acids). Each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass). Biological macromolecules are organic, meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements.


Ch. 3 Biological Macromolecules

 Biological macromolecules: large molecules made from smaller organic molecules necessary for life  Four macromolecules: carbohydrates, lipids, proteins, and nucleic acids  Make majority of cell’s dry mass, water majority of cell’s mass

A. Dehydration Synthesis

 Single building block of most molecules is a monomer  Monomers combine through a covalent bond to make polymers  Monomer-&gtpolymer=dehydration  A water molecule is released during dehydration synthesis  A hydrogen (H+) of one monomer combines with a hydroxyl group (OH-) of the other  Sharing electrons (covalent bond)  Formation of new bond requiring energy

B. Hydrolysis

 Water molecules are used to breakdown polymers to monomers  One part gains hydrogen atom (H+) and another gains a hydroxyl molecule (OH-)  Bond breaking releasing energy

II. Carbohydrates

 Provide energy to the body mainly through glucose  Glucose is a simple sugar of starch

A. Molecular Structures

 Can be represented by stoichiometric (CH 2 O)n n= the number of Carbon in a molecule  Ratio of carbon:hydrogen:oxygen is 1:2:  Carbohydrates= “carbo” = carbon ”hydrate”= water  Classified into three subtypes: monosaccharides, disaccharides, and polysaccharides

1. Monosaccharides

 Monosaccharides= “mono” = 1 “saccharides” = sweet  Most common simple sugar (a monosaccharide) is glucose  Normally 3-7 Carbons tend to end with –ose suffix  If sugar has. o an aldehyde group: functional group with structure R-CHO, it is known as aldose o a ketone group: functional group with structure RC(=O)R’ it is known as ketose o three carbons = triose o five carbons = pentose o six carbons = hexose  monosaccharides classified based on position of their carbonyl group and # of carbons in backbone  aldose have a carbonyl group is at the end of carbon chain  ketose have carbonyl group in the middle of the chain  triose, pentose, and hexose have three, five, and six carbon backbones  chemical formula for glucose = C 6 H 12 O 6  glucose is an important source of energy for humans, it releases energy during cellular respiration, that energy helps make adenosine triphosphate (ATP)  plants synthesize glucose using carbon dioxide and water, used for energy requirements for plants  excess glucose is stored as starch and catabolized (cell breaks down large molecules) by consumers  Galactose (part of lactose, or milk sugar)  Fructose (found in sucrose, in fruit)

 Glucose, galactose, and fructose all have same chemical formula C 6 H 12 O 6 BUT are different chemically and structurally which make them isomers  The arrangement of functional groups around the asymmetric carbon is different which also makes the isomers  More than one asymmetric carbon  They are all hexose but glucose and galactose are aldose while fructose is ketose  Monosaccharides can be a linear chain or ring-shaped molecules  In aqueous solutions they are found in ring forms  Glucose can have two different arrangements of hydroxyl group (OH-) around the anomeric carbon (carbon 1 that becomes asymmetric in ring formation)  If the hydroxyl group (OH) is below carbon number 1 in sugar it is in the alpha () position and in the beta () position above  Between linear and ring forms, five and six carbon monosaccharides exist  When the ring forms, the side change it closes on is locked into either an  or  positon  Ribose and fructose form 5 membered rings while glucose forms 6

2. Disaccharides

 Disaccharides= “di-“ = two two monosaccharides go through dehydration reaction (condensation reaction or dehydration synthesis)  Hydroxyl group of one monosaccharide combines with a hydrogen of another monosaccharide realizing a water molecule forming a covalent bond  The covalent bond formed between a carbohydrate molecule and another molecule (this case two monosaccharides) is a glycosidic bond (glycosidic linkages)  Can be  or  type  When a monomer of glucose and a monomer of fructose join in a dehydration reaction forming a glycosidic bond, sucrose is formed  Carbon atoms in a monosaccharide are numbered from terminal carbon closest to the carbonyl group  In sucrose, a glycosidic linkage forms between carbon 1 in glucose and carbon 2 in fructose  Common disaccharides are. o Lactose (found in milk) = glucose and galactose o Maltose (malt sugar) = glucose and glucose o Sucrose (table sugar) = glucose and fructose

3. Polysaccharides

 Long chain of monosaccharides formed by glycosidic bonds are polysaccharides = “poly-“ = many  Can be branched or unbranched and contain different types of monosaccharides  Molecular weight may be 100,00 daltons or more depending on the number of monomers joined  Primary polysaccharides are. o Starch: stored from sugars in plants (excess glucose) and is a mixture of amylose (polymer of glucose) and amylopectin (polymer of glucose)  Stored in different parts of the plant like the roots and seeds  Starch in seeds provides food for the embryo and can be food for consumers  The starch consumed is broken down by enzymes (salivary amylases) into smaller molecules (maltose and glucose) and then the glucose is absorbed by cells  Made up of glucose monomers joined by  1-4 or  1-6 glycosidic bounds  1-4 and 1-6 refer to carbon number of the two that joined from the bond  amylose is starch formed by unbranched chains of glucose monomers (only  1-4) linkages

o Saturated fat= Animal fat with stearic acid and palmitic acid (common in meat) and fat with butyric acid (common in butter)  Adipocytes store fat in animals  Unsaturated fat or oil is stored in many seeds  Cis and trans fat identify the configuration of the molecule around the double bond o Cis = hydrogens present in the same plane (cause double bond to bend or “kink”) preventing tight packing, liquid at room temperature o Trans = hydrogen atoms are on two different planes  Unsaturated fats consist of. o Olive oil o Corn oil o Cod liver oil o Canola oil  Unsaturated fats lower blood cholesterol levels  Saturated fats contribute to plaque formation in arteries  Saturated fatty acid: hydrocarbons connected by single bonds  Unsaturated fatty: one or more double bonds, each bond either cis or trans configuration o Cis configuration: both hydrogens on the same side of hydrogen chain and kink present o Trans configuration: hydrogens on opposite sides

1. Trans Fats

 Oils are hydrogenated to form semi-solids o Cis conformation in the hydrocarbon may be converted to double bonds in trans conformation o Some examples of artificially hydrogenated trans fats are margarine and some types of peanut butter  Increase of trans fat in diets can lead to increase in levels of low-density lipoproteins (LDL) also known as bad cholesterol o Lead to plaque deposition in arteries

2. Omega Fatty Acids

 Essential fatty acids required but not synthesized by the human body  Omega-3 polyunsaturated fatty acid because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by double bond  The furthest carbon from the carboxyl group is numbered as omega ()  Reduce risk of sudden heart attack, reduce triglycerides in the blood, lower blood pressure, prevent thrombosis, reduce inflammation, provide insulation to the body

B. Waxes

 Covers some aquatic birds and leaves of some plants  Hydrophobic nature cause water to just fall off  Made up of long fatty acid chains esterified to long-chain alcohols

C. Phospholipids

 Are major constituents of plasma membrane, outermost layer of animal cell  Composed of fatty acid chains attached to a glycerol or sphingosine backbone like fats instead of 3 fatty acids, there are 2 (diaclglycerol) and a modified phosphate group  Two important phospholipids are Phosphatidycholine and Phosphatidylserine:  A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone o Phosphate group may be modified by addition of charge or polar chemical groups  Choline:  Serine:  Phospholipids are amphipathic: has both a hydrophobic and hydrophilic part

 Fatty acids are hydrophobic  Phosphate-containing group is hydrophilic  Phospholipid bilayer is the major component of cell membranes, responsible for the dynamic nature of the plasma membrane  Forms micelle = hydrophilic phosphate heads face outside and fatty acids face inside

D. Steroids

 Unlike phospholipids and fats, steroids have a fused ring structure  Are hydrophobic and insoluble  have several 4 linked carbon rings, have a short tail and many have –OH functional group (sterols)  cholesterol and cortisol composed of four fused hydrocarbon rings  cholesterol = most common steroid o synthesized in the liver o precursor to many steroid hormones (testosterone and estradiol) and Vitamin o found in the phospholipid bilayer o responsible for transport of materials, cellular recognition, and cell-to-cell communication

IV. Proteins

 One of the most abundant organic molecules in the living system  Most diverse range of functions of all macromolecules  May be structural, regulatory, contractile, or protective  May be transportation, storage, or membranes  May be toxins or enzymes  Each cell contains thousands of proteins with unique functions and structures  They are polymers built from amino acids arranged in a linear sequence

A. Types and Functions of Proteins

 Enzymes: produced by living cells and catalyst in biomedical reactions like digestion  Specific for the substrate, may break down rearrange, synthesis reaction o Help break down: catabolic enzymes o Build more complex molecules: anabolic enzymes o Affect rate of reaction: catalytic enzymes (all enzymes do this . organic catalyst) o synthesis reactions  Hormones: chemical-signaling molecules, small proteins or steroids secreted by endocrine cells that control or regulate specific physiological processes o Growth o Development o Metabolism o Reproduction  Protein Types and Functions Type Examples Functions Digestive Enzymes Amylase, lipase, pepsin, trypsin

Help digestion of food by catabolizing nutrients into monomeric units Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones Insulin, thyroxine Coordinate the activity of different body systems


Hydrolysis

Polymers break down into monomers during hydrolysis. A chemical reaction occurs when inserting a water molecule across the bond. Breaking a covalent bond with this water molecule in the compound achieves this (Figure). During these reactions, the polymer breaks into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule.

In the hydrolysis reaction here, the disaccharide maltose breaks down to form two glucose monomers by adding a water molecule. Note that this reaction is the reverse of the synthesis reaction in Figure.

Dehydration and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, catalytic enzymes in the digestive system hydrolyze or break down the food we ingest into smaller molecules. This allows cells in our body to easily absorb nutrients in the intestine. A specific enzyme breaks down each macromolecule. For instance, amylase, sucrase, lactase, or maltase break down carbohydrates. Enzymes called proteases, such as pepsin and peptidase, and hydrochloric acid break down proteins. Lipases break down lipids. These broken down macromolecules provide energy for cellular activities.


Biological molecules

Before we begin, we assume that you know these basic chemical concepts:

  • Atoms and elements
  • Periodic table of the elements
  • Valence electrons
  • Electronegativity
  • Chemical bonds

If you are unfamiliar with them, you should review our web page: Chemical context for Biology. You can also read a fuller explanation in the OpenStax Biology textbook (free): 2.1 Atoms, Isotopes, Ions and Molecules: the Building Blocks

1. All living organisms are made of organic molecules.
One of the distinguishing features of life is that cells are made of organic compounds and large molecules constructed from simple organic compounds. Up to the early 19th century, scientists thought only living organisms could make organic compounds. Organic compounds are all built from carbon atoms, but not all molecules containing carbon are organic. So how do we recognize organic molecules?

  • Organic molecules must have C and H, and may have O, N, P, S (a handy mnemonic is CHNOPS for carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur)
  • Organic molecules have at least one covalent bond between C and H or between C and C. In chemistry parlance, the carbon atom in organic molecules must be reduced and not be fully oxidized (has covalent bonds only to oxygen atoms). Carbon dioxide (CO2 O=C=O) is an inorganic form of carbon because the carbon atom has bonds only to oxygen atoms, and is therefore completely oxidized.
  • (An exception to the above rules is urea, where carbon has bonds to 2 amino nitrogens and a double bond with oxygen – but we won’t ask you to remember this exception focus on the general rules above.)

Organic molecules can arise naturally from abiotic synthesis (see Miller-Urey expt), but in the biosphere, most organic molecules are synthesized by living organisms.
Synthesis of organic carbon molecules from inorganic CO2 requires energy and chemical reducing power, as the carbon atoms in organic molecules are in reduced form. For a review of oxidation-reduction (redox) reactions from a biology point of view, see this Khan Academy video. Briefly, atoms such as carbon or oxygen are said to be reduced if they form covalent bonds with an atom with lesser electronegativity, such as hydrogen. Conversely, carbon is oxidized when it forms a covalent bond with an atom with greater electronegativity, such as oxygen. Recall that a covalent bond is formed when two atoms share a pair of electrons. The reduced atom has gained a majority share of the electrons that form the covalent bond, and the oxidized atom has only a minority share.

2. The biomass of a cell (the organic contents, excluding water and inorganic salts) is composed of 3 types of macromolecules plus lipids.

The 3 types of macromolecules (very large molecules) are polysaccharides, nucleic acids (DNA and RNA), and proteins. Students should know how cells make these macromolecules, and their basic structures and functions.

3. Small organic molecules are covalently linked (polymerized) to form the 3 types of large biological macromolecules (polymers) lipid membranes self-assemble.

One recent study concluded that cells are composed of 68 distinct organic molecules (https://ucsdnews.ucsd.edu/newsrel/health/09-0868Molecules.asp) that are assembled into 3 biological polymers plus lipid structures (membranes).
Polymerization of monomers into polymers occurs by dehydration reactions – linking two subunits together via a covalent bond extracts an -OH and a H to create a molecule of water: H2O. So dehydration reactions remove a molecule of water from the starting molecules in the process of forming a covalent bond between the molecules.

Cleavage of polymers back to monomers occurs by hydrolysis reactions – a molecule of water is split (hydrolyzed) to -OH and H and used to break the bond linking two subunits. This is exactly the reverse of a dehydration reaction. See the diagrams below on glycosidic bonds and peptide bonds to see how water molecules are created or used in these reactions.

Lipids by definition are water-insoluble organic molecules. Lipids in water can spontaneously aggregate via hydrophobic interactions to form lipid bilayer membranes. Hydrophobic interactions arise from nonpolar molecules avoiding water – having all the nonpolar molecules associate together minimizes their interaction with water.

How can we predict whether an organic molecule will be hydrophobic (a lipid) or hydrophilic? If the molecule has negatively or positively charged atoms (is ionized), or has a high proportion of polar bonds (C-O or C-N), then the molecule is hydrophilic. If the molecules has mostly non-polar bonds (C-H or C-C), then it is hydrophobic.

Below are descriptions of the 3 types of macromolecules and lipid membranes:
a. Polysaccharides are polymers made by linking monosaccharides via glycosidic bonds (see figure below). Examples are starch, cellulose, and chitin. Monosaccharides are organic molecules with the composition [CH2O]n, where n is usually 3-6. Examples are 6-carbon sugars like glucose, and 5-carbon sugars like ribose. Carbohydrates may refer either to monosaccharides of the composition [CH2O]n, or to polysaccharides. Complex carbohydrates often have branched structures.

b. Nucleic acids (RNA and DNA) are polymers made by joining nucleotides (5-carbon sugar-phosphate + nitrogenous base) in a phosphodiester linkage. Hydrogen bonding between paired bases (A:T and G:C) stabilize DNA duplexes and RNA secondary structures that form by intra-molecular base pairing (A:U and G:C).

c. Polypeptides (proteins) are polymers of amino acids, joined together by peptide bonds. Peptide bonds are formed between the carboxyl group (carbon with 2 oxygen atoms bonded to it) of one amino acid and the amino group (nitrogen with 2 hydrogen atoms) of the next amino acid. All amino acids have a nitrogen, an alpha-carbon with a side chain (the R group in the diagram below – the 20 different amino acids differ in their R groups), and a carboxyl carbon. The nitrogen, alpha-carbon and carboxyl carbons form the peptide backbone of a polypeptide chain. Figures of protein structures often show only the peptide backbone, leaving out the side-chain R groups.

How proteins fold into their overall 3-dimensional structures, and interact with each other to form larger multi-protein complexes, are determined by various bonds and interactions, as described below (section #6).
Students should be able to distinguish among these macromolecules, and identify the monomers that build each type of macromolecule.

d. Living organisms also contain lipid bilayer membranes made of phospholipids. The phospholipids spontaneously self-assemble in water to form bilayer membranes, via hydrophobic interactions.

The phospholipid bilayers create boundaries and a hydrophobic environment that separates the internal aqueous environment of the cytosol from the outside of the cell, and also separates distinct intracellular organelle compartments in eukaryotic cells. Membranes make it possible for cells to create and maintain large differences in ion concentrations that drive cellular energy metabolism, to regulate transport of materials and water into and out of the cell, and to receive and sense extracellular signals.

4. Cells use the different classes of biological macromolecules in different ways.
a. Polysaccharides are used primarily for energy storage (glycogen, starch) and static structures (such as cellulose, chitin), but can also play important roles in cell-cell recognition/adhesion and signaling.

b. Proteins are used primarily for enzymatic activities, signaling, and dynamic structural components.

c. Nucleic acids are used for genetic information storage (DNA or RNA) and retrieval (mRNA). Some RNAs play key catalytic roles in information processing (RNA splicing, protein synthesis).

d. Lipids are used to define the cell’s boundary, compartmentalize the cell (in eukaryotes), for energy storage (triglycerides: fats and oils), and signaling (steroid and other lipid hormones).

5. Cells have two types of nucleic acids: DNA and RNA, that differ in key ways
DNA has bases A, C, G, and T , deoxyribose , and two strands that form a duplex via hydrogen bonds between the bases on one strand and the complementary bases on the partner strand. The primary function of DNA is storage and transmission of hereditary information

RNA has bases A, C, G and U , ribose , and one strand that may form internal duplexes (called RNA secondary structure) by folding upon itself. In cells, RNA functions in expression of genetic information in DNA to make proteins (mRNA, tRNAs, rRNAs, and other small RNA molecules), but may also serve for storage of hereditary information in many viruses (e.g., influenza, HIV, Ebola).

Summary table:

Major biomass components Subunits Primary elemental composition* Major Functions
Lipids hydrocarbons C, H membranes energy storage signaling
Carbohydrates monosaccharides C, H, O energy storage static structures cell adhesion
Proteins amino acids C, H, O, N, S enzymes dynamic structures signaling
Nucleic acids nucleotides C, H, O, N, P hereditary information storage and processing

*Any of these molecules may have modifications or be linked to other molecules that include O, N, P, or S – the elemental compositions are given for the basal molecule types.

6. Protein structures can be described at 4 levels
Among all the biological macromolecules, proteins have the most complex and dynamic structures. Many proteins consist of just a single polypeptide chain. Many other proteins consist of two or more polypeptide chains that must assemble properly to form a functional complex. The function of a protein is determined by its structure a change in the protein’s activity involves a change in some aspect of the protein’s structure. What, then, determines a protein’s structure?

Each polypeptide is assembled as a linear chain of amino acids covalently linked by peptide bonds. As this chain is being assembled (each subsequent amino acid is bonded onto the free carboxy- terminus of the nascent polypeptide chain), the polypeptide chain begins to fold.

Biologists distinguish 4 levels of protein structure. Students should be able to identify the four levels of protein structure, and the molecular forces or interactions responsible for stabilizing each level of structure.

Four levels of protein structure

Primary structure – the linear sequence of amino acids, held together by covalent peptide bonds.
Secondary structurealpha helices and beta sheets, stabilized by hydrogen bonds between peptide backbone amino groups and carboxyl groups of amino acids within the same polypeptide chain, but not immediately next to each other. Note that the side-chain R groups are not involved in bonds that stabilize secondary structures.

Tertiary structure – overall 3-D shape of the folded polypeptide chain, that can be described as the spatial relationships of the secondary structure elements linked by loops. Stabilized by various types of amino acid side chain (R-group) interactions, including: hydrophobic and van der Waals interactions, hydrogen bonds, ionic bonds, covalent disulfide bonds between cysteine residues, and interactions with solvent water molecules.

Quaternary structure – assemblage of two or more folded polypeptides into a functional protein unit. Stabilized by inter-chain hydrophobic and van der Waals interactions, hydrogen bonds, ionic bonds, and covalent disulfide bonds between cysteine residues on different polypeptide chains. Proteins that consist of a single polypeptide chain do not have quaternary structure only proteins that have two or more polypeptide chains have quaternary structure.

7. Changes in the amino acid sequence (primary structure) of a protein can change the structure of the protein and the way it functions.

Case examples:

Hemoglobin: The classic case exploring protein structure is hemoglobin. Functional hemoglobin is a tetramer, consisting of two alpha-globin and two beta-globin polypeptide chains. Hemoglobin also requires a cofactor, heme (also called a prosthetic group), containing an iron atom that binds oxygen.

Questions to be answered after watching the video above:

  1. What levels of protein structure does hemoglobin exhibit?
  2. The most common sickle-cell disease mutation changes a glutamic acid (a negatively charged amino acid) in beta-globin to valine (a hydrophobic amino acid). Where would you most commonly expect to find a charged amino acid like glutamic acid, in the interior of the folded protein, or on the surface, interacting with solvent water molecules?
  3. Which of the following changes do you think might also cause sickle-cell disease?
    1. the glutamic acid changes to an aspartic acid, a different negatively charged amino acid
    2. the glutamic acid changes to a lysine, a positively charged amino acid
    3. the glutamic acid changes to a tryptophan, a hydrophobic amino acid
    4. the glutamic acid changes to a serine, an uncharged, hydrophilic amino acid

    Cystic fibrosis: The most common mutation associated with cystic fibrosis causes a single amino acid, a phenylalanine, to be omitted from the protein called CFTR (cystic fibrosis transmembrane conductance regulator). The CFTR protein functions as a chloride channel in the membrane, formed as the single long CFTR polypeptide chain crosses the membrane back and forth several times. The absence of this phenylalanine, which has a large hydrophobic side chain, causes the protein to be mis-folded. Most of the mis-folded protein is recognized by the cellular quality control system and sent to the cellular recycling center (the proteasome) only about 1 percent of the mis-folded CFTR protein makes it to the proper destination, the plasma membrane. My case study is published as a blog post:
    Cystic Fibrosis: A Case Study for Membranes and Transport

    Extremophiles: Microbes that live in extreme environments of temperature, salt and pH have proteins that are adapted for structural stability in these extreme environments.

    Questions for review, further research and thought:

    1. Do all living organisms synthesize organic molecules from inorganic molecules?
    2. What processes created organic molecules before life arose? In what environments?
    3. Why do proteins have enzymatic activities, but generally not polysaccharides or nucleic acids?
    4. Carbon atoms are in their most reduced form in which type of organic molecules – carbohydrates, lipids, proteins or nucleic acids?
    5. Which macromolecules often have branching structures?
    6. If you heat a cell extract to near boiling for a few minutes, what will be the effect on the 3 types of biological polymers (polysaccharides, proteins and nucleic acids)? Think in terms of the bonds responsible for the structures of these molecules. This is what happens when cooking food!
    7. Expanding from Q#6 above, how will changes in pH or salt concentrations affect solutions of each type of macromolecule?

    People have preserved food in vinegar and salt before refrigeration became available.

    The Powerpoint slides for the videos on this page are in this file: B1510_module3_1a_biomolecules


    The Macromolecules of Life: Overview

    Learn about the basic molecular structures and primary functions of lipids with this interactive tutorial. This is part 3 in a five-part series.

    Primary Resource Type: Original Tutorial

    Learn about the basic molecular structures and primary functions of proteins with this interactive tutorial. This is part 4 in a five-part series.

    Primary Resource Type: Original Tutorial

    Learn to identify and describe the structural and functional features of nucleic acids, one of the 4 primary macromolecule groups in biological

    Primary Resource Type: Original Tutorial

    Attachments

    • SC.912.L.18.1: Describe the basic molecular structures and primary functions of the four major categories of biological macromolecules.

    Learn to identify the four basic biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids) by structure and function with this interactive tutorial.

    This is part 1 in a five-part series. Click below to explore other tutorials in the series.


    Biomolecules

    There are four basic kinds of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. These polymers are composed of different monomers and serve different functions.

    • Carbohydrates: molecules composed of sugar monomers. They are necessary for energy storage. Carbohydrates are also called saccharides and their monomers are called monosaccharides. Glucose is an important monosaccharide that is broken down during cellular respiration to be used as an energy source. Starch is an example of a polysaccharide (many saccharides linked together) and is a form of stored glucose in plants.
    • Lipids: water-insoluble molecules that can be classified as fats, phospholipids, waxes, and steroids. Fatty acids are lipid monomers that consist of a hydrocarbon chain with a carboxyl group attached at the end. Fatty acids form complex polymers such as triglycerides, phospholipids, and waxes. Steroids are not considered true lipid polymers because their molecules do not form a fatty acid chain. Instead, steroids are composed of four fused carbon ring-like structures. Lipids help to store energy, cushion and protect organs, insulate the body, and form cell membranes.
    • Proteins: biomolecules capable of forming complex structures. Proteins are composed of amino acid monomers and have a wide variety of functions including transportation of molecules and muscle movement. Collagen, hemoglobin, antibodies, and enzymes are examples of proteins.
    • Nucleic Acids: molecules consisting of nucleotide monomers linked together to form polynucleotide chains. DNA and RNA are examples of nucleic acids. These molecules contain instructions for protein synthesis and allow organisms to transfer genetic information from one generation to the next.

    The Role of Carbon in Living Things

    A carbon atom has four electrons in its valence shell. To become stable, carbon will form four covalent bonds to fill its outer valence shell. These bonds may be with other carbon atoms, or with other elements such as hydrogen and oxygen. When two carbon atoms form a covalent bond, each atom can share:

    • one electron to form a single bond,
    • two electrons to form a double bond or,
    • three electrons to form a triple bond.

    Carbon atoms bond to each other in different ways to form compounds of various shapes including, straight-chain, branched-chain, or ring compounds. These compounds can have any number of carbon atoms and will contain atoms of other elements, the most frequently occurring of which is hydrogen. This results in a huge number of carbon compounds being synthesized in living organisms.

    Monomers and Polymers

    Carbon compounds vary greatly in size from a single carbon like that seen in methane (CH4) to those which contain hundreds or thousands of atoms. The largest carbon-based molecule known to exist is called PG5 and contains around 15 million carbon atoms.

    Cells synthesize (make) macromolecules by joining smaller molecules called monomers together. These large macromolecules are called polymers are defined as a long chain of repeating subunits (monomers). An example of this is seen when amino acids are bonded together to form a polypeptide chain.

    Condensation reaction (dehydration synthesis)

    Polymers are made through a chemical reaction called condensation. In this reaction, the monomers which are being bonded together have a hydrogen atom (–H) on one end and a hydroxyl group (–OH) group on the other. When the molecules join, the hydrogen atom and hydroxyl group bond and are removed as a water molecule.

    The subunits are bonded together by a covalent bond, as the water molecule is released.

    The figure below shows the condensation of two glucose molecules to form a maltose molecule. The covalent bond forms between the glucose units.

    When these polymers break apart the reverse reaction called hydrolysis occurs.

    Carbohydrates

    Carbohydrates as their name suggest consist of carbon, hydrogen and oxygen. The ratio of these atoms is approximately two hydrogen atoms and one oxygen atom to one carbon atom. These macromolecules are the most abundant in the living cell and are used as the primary fuel source for all living cells.

    Carbohydrates have various chain lengths and can be divided into three categories: monosaccharides, disaccharides, and polysaccharides.

    Monosaccharides (mono- = “one” sacchar- = “sugar”) are the simplest type of carbohydrates and typically contain between 3 and 7 carbon atoms. The most common examples in this category are the compounds glucose and fructose.

    Disaccharides (di- = “two”) are two-sugar molecules that form when two monosaccharides join via a condensation reaction. For example, when glucose and fructose form a covalent bond, a molecule of sucrose commonly known as table sugar is produced.

    Polysaccharides (poly- = “many”) are the largest carbohydrate molecules. These are long chains of monosaccharides linked together by covalent bonds. Starch, glycogen, and cellulose are examples of polysaccharides that are essential in living organisms. Their structure is shown in the diagram below.

    • Starch consists of branched chains of glucose molecules and is utilized as energy storage by plants.
    • Glycogen is a highly branched glucose polymer that functions as an energy storage molecule found in the liver and muscle cells of mammals.
    • Cellulose is a glucose polymer that is typically found in the plant cell walls and serves as structural

    Lipids

    Lipids consist of carbon and hydrogen atoms bonded to a small number of oxygen atoms. Lipids are used to store energy, as insulation, form cell membranes, and provide the building blocks for hormones such as testosterone and estrogen. The most common examples of lipids are fats, oils, waxes, and steroids. Lipids are generally insoluble in water because they have a non polar region which is not attracted to water molecules.

    Lipids are made of glycerol, a three-carbon molecule that serves as the ‘backbone’ for the structure to which the fatty acids are attached. A fatty acid is a long chain of carbon and hydrogen. If the carbon atoms in the chain are bonded to other carbons with single bonds, the fatty acid is called a saturated fatty acid. When a double bond exists in the chain, the fatty acid is called an unsaturated fatty acid. Fatty acids which contain more than one double bond are called polyunsaturated fatty acids.

    Proteins

    Proteins are large, complex polymers which are made up of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.

    They are one of the most abundant macromolecules found in living systems. A single living cell contains thousands of proteins that perform unique functions such as the contraction of muscle tissue, transportation of oxygen in the bloodstream, immunity, control of other proteins, and speeding up chemical reactions.

    Amino acids are monomers that form the building blocks of a protein molecule. There are 20 naturally-occurring amino acids that, in various combinations produce thousands of proteins, each with their own unique function. An amino acid is composed of a central carbon atom which is bonded to a hydrogen atom, a carboxyl group (–COOH), an amine group (–NH2), and a variable group (–R) that makes each amino acid different.

    Amino acids are bonded together by covalent bonds called a peptide bond. The peptide bond is formed when the –H atom from the amine group of one amino acid and the –OH group from the carboxyl group of another amino acid are removed to release a water molecule as is seen in the reaction below.

    As the amino acids join together, they create a long chain known as a polypeptide shown in the diagram below.

    The different chemical properties of amino acids cause them to attract and repel each other in different ways. The attraction and repulsion of the amino acids cause the polypeptide chain to fold back and forth on itself into pleated sheets or coiled up helices. The folding is then stabilized by hydrogen bonds. As the side chains interact and continue to fold up, the polypeptide forms a three-dimensional structure. This structure then joins with other coiled up polypeptide chains into the final protein which has a specific role in the cell. This process is summarized in the diagram below.

    Two of the most common types of proteins which act in the human body are enzymes and hormones.

    1. Enzymes speed up the rate of a biochemical reaction — for example, salivary amylase acts on starch found in bread, pasta and rice to break it down into monosaccharides such as glucose.
    2. Hormones are biochemical messengers that are released by endocrine cells to control specific processes, such as growth, development, metabolism, and reproduction. The hormone insulin controls the amount of glucose present in the blood.

    Nucleic acids

    Nucleic acids are the genetic material that stores cellular information. These polymers are made up of small building blocks called nucleotides. Nucleotides are composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms arranged as three separate molecules (a nitrogenous base, a sugar, and a phosphate molecule) which have been bonded together. The structure of the nucleotide is shown below.

    The two naturally-occurring varieties of nucleic acid are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

    DNA (Deoxyribonucleic acid)

    DNA is a double-stranded molecule which is found in the nucleus of the cell. It is the main copy of an organism’s genetic code containing the instructions to create every protein required by the cell. These proteins are then expressed as characteristics or traits in the organism.

    RNA (Ribonucleic acid)

    RNA is the nucleic acid molecule which forms the copy of DNA that is used to make proteins. Unlike the DNA molecule, RNA is a single-stranded molecule. There are four types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and regulatory RNAs.


    3: Biological Macromolecules - Biology

    Listed below are links to pages containing 3-dimensional displays of models of molecules of Biological interest.
    These may be moved in an intuitive way using the computer mouse or touchscreen.
    In the explanatory text are links which highlight features of the molecule or give extra information.

    These units are now based on HTML5 and javascript, so they should be more accessible from most PCs and tablets, including iPads.
    These are mostly upgrades of my previous units on molecules which used applets based on Java .

    On Windows PCs, best results are obtained using Firefox or Chrome. Internet Explorer displays interaction in a rather slow and jerky way.

    Some files have been converted to be compatible with mobiles and tablets which have a narrower screen, incompatible with the display format used on desktop/laptop machine.
    But it is a tedious process, and the potential "responsive" template appears to work but breaks some rules about HTML5 formatting.

    CARBOHYDRATES - in Jsmol format
    Monosaccharides
    hexoses glucose alpha and beta glucose
    fructose glucose-galactose comparison
    pentoses ribose deoxyribose
    glucose derivatives glucosamine N acetyl glucosamine
    Disaccharides
    glucose dimers maltose cellobiose
    mixed dimers sucrose lactose
    Oligosaccharides
    fructo-oligosaccharides nystose inulin
    Polysaccharides
    storage compounds - animal glycogen
    storage compounds - plants amylose [another form of amylose] amylopectin
    structural compounds - plants cellulose
    starch-iodine test amylose-iodide complex
    AMINO ACIDS - in Jsmol format
    All shown on one page 20 amino acids
    Individual amino acids
    - seen a little larger
    glycine, alanine, valine, leucine, isoleucine, serine, threonine, lysine, histidine, arginine, phenylalanine, tyrosine, tryptophan, cysteine, methionine, aspartic acid, asparagine, glutamic acid, glutamine, proline
    DIPEPTIDE
    Special request Leucine-alanine
    PROTEINS- in Jsmol format
    Levels of protein structure General principles as shown by Insulin
    as shown by Glucagon, Fibroin as shown by hCG
    as shown by Haemoglobin as shown by Myoglobin
    Enzyme structure Amylase as an example
    Pepsin
    Pepsinogen
    More to be added soon
    Fibrous proteinsCollagen
    LIPIDS (FATS and OILS)
    Sub-units glycerol saturated and unsaturated fatty acids
    Polyunsaturated fatty acids alpha-linolenic acid gamma-linolenic acid
    More about functional foods plant sterols and stanols and their esters
    Neutral fats triglycerides monoglycerides and diglycerides
    phospholipids phospholipid bilayer
    cardiolipin
    Sterols and steroids cholesterol More to follow
    NUCLEIC ACIDS
    Section DNA
    nucleotidesAMP, TMP pair GMP, CMP pair
    bases DNA bases RNA bases
    co-enzymes ATP NAD and reduced NAD
    Nucleoside analogues Emtricitabine
    Tenofovir
    AZT
    Fialuridine XXX
    Non-nucleoside reverse transcriptase inhibitor ( NNRTI) Efavirenz
    Base analogues 5-FluoroUracil (5FU)
    Nucleotide analogues Remdesivir
    VITAMINS - in Jsmol format
    Fat Soluble Vitamin A Water Soluble Vitamin B1
    Retinal Vitamin B2
    Vitamin B3
    Vitamin D Vitamin B5
    Vitamin B6
    Vitamin E Vitamin B7
    Vitamin B9
    Vitamin K Vitamin B12
    Vitamin C

    Beta
    Lactams
    Examples
    Penicillins
    (Penems)
    Penicillin G
    Amoxicillin
    Ampicillin
    Methicillin
    Cephalosporins
    (Cephems)
    Cephalexin
    Monolactams

    Web references and useful websites

    The Protein Data Bank (PDB https://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules, now containing more than 100,000 structures.

    Structural View of Biology is a portion of the PDB, focusing on the biological function of the molecules.

    Orientations of Proteins in Membranes (OPM) database "provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer."

    FirstGlance in Jmol is a simple tool for macromolecular visualization.

    ChemInteractive is a free site designed to promote active learning of Chemistry. It is targeted at students learning Organic Chemistry in the early years of College or University programmes.

    The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

    ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry.


    Biological Macromolecules: Carbohydrates

    A biological macromolecule is defined as a large molecule made up of smaller organic molecules, known as monomers. There are four classes of biological macromolecules, one of them being carbohydrates. Carbohydrates are made of three base elements Carbon, Hydrogen, and Oxygen in a 1:2:1 ratio.

    There are three different classes of carbohydrates monosaccharides, disaccharides, and oligosaccharides. These three saccharides will be further looked into in terms of structure, bonds, and uses, along with the differences between the three.

    Monosaccharides, otherwise known as simple sugars, can be differentiated from di- and oligosaccharides because of their ringed structure. A monosaccharide is made up of a carbon backbone, with many hydroxyl groups (OH) attached to it. Depending on the number of carbons, a monosaccharide can be a trios (3 carbons), tetros (4), pentose (5), hexose (6), etc.

    It is monosaccharides that are covalently bonded together to make both disaccharides and oligosaccharides, making them the original structure for carbohydrates. Examples of monosaccharides include glucose, fructose, and galactose. These monosaccharides are most commonly seen in fruits, vegetables, honey, and dairy products.

    Disaccharides are sugars that are made up of two monosaccharides that are covalently bonded together. Examples and uses of disaccharides include lactose (milk sugar), maltose (involved with starch), cellobiose (product of cellulose), maltose (beer), and the most important disaccharide, sucrose. Sucrose is found most commonly in photosynthetic plants, where it is an easily transported energy source. Sucrose is also found in sugar cane and beet sugars.

    The most complicated carbohydrates are oligosaccharides, otherwise known as polysaccharides. These are carbohydrates that are composed of numerous covalently bonded monosaccharides. All common polysaccharides contain glucose as the main monosaccharide unit. The two polysaccharides that are most commonly known are starch and cellulose.

    Starch is a storage polysaccharide found in plants and is made of amylose and amylopectin. Cellulose is a major component in the cell wall of a plant and consists of long linear chains of glucose.

    Carbohydrates are the building blocks to both simple and complex sugars that we use in our everyday lives. Without carbohydrates, the majority of the food that we eat would not exist.

    Biological macromolecules, including carbohydrates, are components essential to the world components that will continue to be studied and investigated to find further uses for them.


    Watch the video: Biological Molecules. Cells. Biology. FuseSchool (August 2022).