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Bio.203-5.BMolecules
Molecular Biology Ch. 5 - Structure and Function of Biological Molecules
| Question | Answer |
|---|---|
| Important large molecules (i.e. macromolecules) of all living things fall into four main classes | Carbohydrates, lipids, proteins, and nucleic acids |
| Polymers | A long molecule consisting of many similar or identical building blocks linked by covalent bonds, like a train consists of a chain of cars. All macromolecules are polymers |
| Monomers | Repeating units that server as the building blocks of polymers |
| Enzymes | Specialized macromolecules that speed up chemical reactions. E.g. enzymes are responsible for making and breaking down polymers |
| Dehydration reaction | A chemical reaction in which two molecules become covalently bonded to each other with the removal of a water molecule. Monomers are connected via this reaction. |
| Describe the synthesis of a polymer | When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction. One provides a hydroxyl group, and the other, a hydrogen. The reaction is repeated. |
| Hydrolysis | The reverse of the dehydration reaction: breaking the bond using water. |
| How many molecules of water are needed to completely hydrolyze a polymer that is 10 monomers long? | Nine; one of each bond |
| During digestion, what must occur for amino acids being consumed to be converted to new proteins? | Hydrolysis to separate the amino acids, then a dehydration reaction to synthesize them into new polymers |
| Carbohydrates; simplest kind? The other kinds? | Includes both sugars and polymers of sugars. Simplest: monosaccharide (i.e. simple sugars) are the monomers of more complex sugars. Other: disaccharides (2 monosaccharides) and polysaccharides (>2 monosaccharides) |
| Monosaccharide | Generally has a molecule formula that’s some multiple of the unit CH2O, e.g. the most common monosaccharide glucose: C6H12O6. |
| Minimum # of carbons for a sugar | Three: C3H6O3 |
| Difference between glucose and galactose? | Both are C6H12O6. Difference in spatial arrangements of their parts around asymmetric carbons. I.e. they’re enantiomers. |
| Why use fructose in food/drinks? | In the 70s a process was developed that converts the glucose in corn syrup (a syrup made from corn starch) to its sweeter structural isomer, fructose. |
| Why are sugar molecules important for organisms? | Monosaccharides, especially glucose, are major nutrients for cells. They’re used in cellular respiration. Their carbon skeletons are also used for amino acids and fatty acids. If not used immediately, they’re stored as polysaccharides. |
| Depending on the location of the carbonyl group, a sugar is either a _____ or a _____ | Aldose (aldehyde sugar, e.g. glucose. Carbonyl group is at end of skeleton) or ketose (ketone sugar, e.g. fructose. Carbonyl group is within skeleton.) |
| Arranging types of sugars by size of carbon skeleton | 3-carbon triose=aldose: glyceraldehyde, ketose: dihydroxyacetone. 5-carbon pentose=aldose: ribose, ketose: ribulose. 6-carbon hexose=aldose: glucose/galactose, ketose: fructose |
| All simple sugars are of ____ form of enantiomer, except ____. Why? | D (dextro-, or right as opposed to left). Except dihydroxyacetone. Why? Because it doesn’t have a chiral carbon. |
| Disaccharide | To monosaccharides joined by a glycosidic linkage. |
| Glycosidic linkage | A covalent bond formed between two monosaccharides by a dehydration reaction. |
| Common disaccharides | Glucose+glucose = maltose. Glucose+fructose = sucrose (table sugar). Gluctose+galactose = lactose (milk sugar). |
| Polysaccharides | Macromolecules. Polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. |
| 2 examples of general functions of polysaccharides | 1. Storage material: hydrolyzed as needed to provide sugar for cells. 2. Building material: to protect cell or organism. |
| Starch | Both plants/animals store sugars for later use in the form of storage polysaccharides. Plants store starch, a polymer of glucose monomers, as granules within cellular structures known as plastids, which include chloroplasts. |
| Two forms of starch | Amylose: unbranched; simplest form of starch. Amylopectin: more complex; branched with 1-6 linkages at branch points. |
| Most of the glucose monomers are joined by _____ linkages | 1-4 linkages |
| Glycogen | While plants store sugars as starch, animals store sugars as glycogen, a polymer of glucose that is like amylopectin but more extensively branched. Stored in liver and muscle cells. Hydrolyzed when needed. |
| Review: amylase vs. amylopectin vs. glycogen | Amylase: simple unbranched starch; amylase: complex branched starch; glycogen: not a starch, has most complex branches. All of the above are storage polysaccharides as opposed to structural polysaccharides |
| Cellulose | A major component of the tough walls that enclose plant cells. Cellulose is a structural polysaccharide. |
| Two slightly different ring structures for glucose | The hydroxyl group attached to the #1 carbon is either positioned below or above the plane of the ring. If below it’s “alpha”, if above it’s “beta” |
| Difference between starch and cellulose | The glycosidic linkages differ. Starch has an alpha configuration. All monomers of starch are in the same configuration. Cellulose has a beta configuration. Each monomer is upside down with respect to its neighbor. |
| How do the differing glycosidic linkages affect the shape/appearance of starch vs. cellulose? | Starch = largely helical and also digestible by human enzymes. Cellulose = linear, never branched. Cellulose can hydrogen-bond to parallel cellulose molecules which allows them to reinforce each other. |
| Microfibrils | Cable-like microfibrils are strong building material for plants. About 80 cellulose molecules associate to form a microfibril (e.g. wood, plant walls, etc). Parallel cellulose molecules are held together by hydrogen bonds. |
| Can starch and cellulose be digested? | Enzymes that digest starch by hydrolyzing its alpha linkages are unable to hydrolyze beta linkages of cellulose. |
| Examples of organisms that can digest cellulose | Cows harbor cellulose-digesting prokaryotes and protists in their stomachs which hydrolyze hay and grass. Termites do as well. |
| Although cellulose is not a nutrient for humans, it is an important component of a healthful diet; why is that? | As it passes through the intestines it abrades the wall of the digestive tract and stimulates the lining to secrete mucus which aids in the smooth passage of food. “Insoluble fiber” in nutrition data refers mainly to cellulose. |
| Chitin | An important structural polysaccharide used by arthropods (insects, spiders, crustaceans, etc) to build their exoskeletons. Pure chitin is leathery and flexible but it becomes hardened when encrusted with CaCO3. |
| Difference between chitin and cellulose? | Both are comprised of beta linkages so they are the same except that the glucose monomer of chitin also has a nitrogen-containing appendage. |
| Use of chitin in medicine | Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. |
| Lipids | Lipids are not true polymers and are not big enough to be considered macromolecules. The reason lipids are grouped together is because they share one important train: they mix poorly, if at all, with water. |
| What is the cause of lipids’ hydrophobic behavior? | Lipids consist mostly of hydro-carbon regions. These are nonpolar covalent bonds. |
| The most biologically important types of lipids | Fats, phospholipids, and steroids |
| Fat | A fat is not a polymer, it is a large molecule assembled from smaller molecules by dehydration reactions. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. |
| Fatty acid | Has a long carbon skeleton usually 16 or 18 carbon atoms in length. The carbon at one end is part of a carboxyl group, the functional group that gives these molecules the name fatty ACID. The rest of the skeleton = hydrocarbon chain. |
| How to make a fat; i.e. triacylglycerol | Three fatty acid molecules are each joined to glycerol by an ester linkage. The resulting fat, called a triacylglycerol, consists of three fatty acids linked to one glycerol molecule. AKA: triglyceride |
| Ester linkage | A bond between hydroxyl group and carboxyl group |
| Saturated fatty acid | If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton, thus “saturating” it. |
| Unsaturated fatty acids | Has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. This causes the chain to kink and thus NOT BE PACKED DENSELY with the other fats. |
| Examples of saturated fats and unsaturated fats | Saturated: animal fats, butter, lard, hydrogenated oils. Unsaturated: fish, plants, etc. |
| Trans fats | Like unsaturated fats, they have double bonds except they don’t kink because of the hydrogen placement (cis-isomer hydrocarbons will kink, but not trans-isomer hydrocarbons) |
| Why are certain unsaturated fats necessary? | Because they can’t be synthesized in the body, e.g. OMEGA-3 FATTY ACIDS! |
| Major functions of fats? | Energy storage. A gram of fat contains twice as much energy as a gram of a polysaccharide such as starch or glycogen. Also, for insulating a protecting the body. |
| Phospholipids | They make up cell membranes. They have similar structure to fats except they have two fatty acids attached to a glycerol rather than three. The third hydroxyl group in the glycerol has a phosphate group giving it a negative charge |
| How do phospholipids interact with water? | The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate groups and their attachments form hydrophilic heads. When phospholipids are added to water they self-assemble into bilayers |
| Steroids | Lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids, such as cholesterol, are distinguished by the particular chemical groups attached to its rings. |
| What is cholesterol’s function and where is it synthesized | It is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. In humans, cholesterol is synthesized in the liver and obtained from the diet. |
| Are steroids polar or nonpolar? | They’re amphipathic |
| What are proteins comprised of? | They are all unbranched polymers constructed from the same set of 20 amino acids. Technically, a protein is a molecule that consists of one or more polypeptides; each folded and coiled into a specific 3D structure. |
| Polypeptides | Polymers of amino acids |
| List of protein types | Enzymatic, transport, hormonal, receptor, contractile/motor, defensive, structural, and storage proteins. |
| Storage proteins: function and examples | Stores amino acids. E.g. casein (milk); egg whites; and storage proteins in seeds |
| Structural proteins: function and examples | Structural support. E.g. silk fibers (spider webs); collagen and elastin; keratin (hair, horns, feathers), etc. |
| Defensive proteins: function and examples | Protection against disease. E.g. antibodies. |
| Enzymatic proteins: function and examples | Selective acceleration of chemical reactions. E.g. digestive enzymes |
| Transport proteins: function and examples | Transport of other substances. E.g. hemoglobin (blood); proteins and transport molecules across cell membranes, etc. |
| Contractile and motor proteins: function and examples | Movement. E.g. Actin and myosin (muscles); and proteins responsible for undulations of cilia and flagella |
| Hormonal proteins: function and examples | Coordination of an organism’s activities. E.g. insulin |
| Receptor proteins: function and examples | Response of cell to chemical stimuli. E.g. Nerve cell receptors which detect chemical signals released by other nerve cells |
| Enzymes | Proteins that regulate metabolism by acting as catalysts: chemical agents that specifically speed up chemical reactions without being consumed by the reaction. They’re like workhorses that keep working. |
| Amino acid | An organic molecule possessing both an amino group and carboxyl group. At the center of the amino acid is a chiral carbon called the alpha carbon. Its four different partners are 1. Amino group, 2. Carboxyl group, 3. H, 4. Side chain (R). |
| Significance of the side chain? | The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid, affecting its functional role in a polypeptide. |
| Acidic amino acids are those with _____. Basic amino acids are those with _____ | Acidic: side chains that are generally negative in charge, owing to the presence of a carboxyl group which is usually dissociated (ionized) at cellular pH. Basic: positively charged side chains |
| How many amino acids are there? What type of enantiomers are they? Examples of 5 amino acids: | Twenty. L enantiomers. E.g.: Alanine, phenylalanine, serine, aspartic acid, and lysine |
| What is the affect of the pH of the solution on the amino acid’s backbone? | If pH is low, carboxyl group will be normal (COOH) and an H would be added to the amino group (NH3+). if pH is neutral/high the H will detached from the carboxyl group (COO-) and the amino group will be normal (NH2) |
| Peptide bond | When two amino acids are positioned so that the carboxyl group of one is adjusted to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. |
| Polypeptide | When peptide bonds are repeated over and over. A polymer of many amino acids linked by a peptide bonds results. |
| Polypeptide backbone | The polypeptide bonds, ignoring the R-group portion. |
| N-terminus and C-terminus | One end of a polypeptide backbone will have a free amino group (N-terminus) and the other will have a free carboxyl group (c-terminus) |
| Why are side chains (R-groups) important in polypeptide chains? | The side chains far outnumber the terminal groups, so the chemical nature as a whole is determined by the kind and sequence of the side chains |
| A protein is not only a polypeptide chain, but… | …one or more polypeptides precisely folded/twisted/coiled into a unique shape. |
| What determined the 3D structure of a protein? | The amino acid sequence of each polypeptide. The folding is driven and reinforced by the formation of a variety of bonds between parts of the chain, which in turn depends on the sequence of amino acids. |
| Examples of diseases caused by misfolded polypeptides | Alzheimer’s, Parkinson’s, mad cow disease, sickle cell |
| Two types of computerized models of proteins | 1. Ribbon model: only shows the polypeptide chain, looks less globular without R-groups. 2. Includes side—chains, looks globular. |
| Globular proteins vs. fibrous proteins | Globular = spherical. Fibrous = shaped like fibers |
| Four levels of protein structure | 1. Primary, 2. Secondary, 3. Tertiary, 4. Quaternary |
| Primary structure | Linear chain of amino acids. The primary structure is like the order of letters in a very long word. The precise primary structure is determined by inherited genetic information. |
| Secondary structure | Dictated by the primary structure. The coiled and folded patters of proteins represent the secondary structure and are the result of hydrogen bonds between repeating constituents of the polypeptide backbone (not side chains) |
| Alpha helix | One main type of secondary structure. It is a delicate coil held together by hydrogen bonding between every fourth amino acid. Example, alpha-keratin, the structural protein of hair. |
| Beta-pleated sheet | The other main type of secondary structure. Two or more strands of the polypeptide chain lying side by side (called beta-strands) are connected by hydrogen bonds between parts of the parallel backbones. E.g. spider web |
| Tertiary structure | Superimposed on the patterns of secondary structure. Results from interactions between the side chains (R-groups). One type of interaction: hydrophobic interaction; where nonpolar side chains cluster within the protein. |
| Quaternary structure | The overall protein structure that results from the aggregation of two or more polypeptide chains into one functional macromolecule. E.g. hemoglobin: made up of 4 polypeptide subunits. |
| Disulfide bridges | Form where two cysteine-monomers, which have SH groups on their side chains are brought closed together by the folding of the protein. A disulfide bridge (-S-S-) is formed which rivets part of the protein together. |
| Sickle-cell anemia | Caused by the substitution of just one amino acid in the primary structure: glutamic acid swapped with valine. This results in a domino effect up through quaternary structure giving RBCs weird angular shapes that clog vessels. |
| Denaturation | High temperatures, radical pH levels, chemicals, etc. will denature proteins, causing them to lose shape. It can often renature if the environment returns to normal. |
| Chaperonins | Proteins that assist in the proper folding of other proteins. They don’t specify final structure; instead they keep the new polypeptide segregated from “bad influences” in the cytoplasmic environment while it folds. |
| X-ray crystallography | A technique used to study the 3D structures of molecules. It depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule |
| Gene | The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. Genes consist of DNA, which belongs to a class of compounds called nucleic acids. |
| Nucleic acids | Macromolecules. Polymers made of monomers called nucleotides |
| The two types of nucleic acids | 1. Deoxyribonucleic acid (DNA) and 2. Ribonucleic acid (RNA) |
| DNA | A double-stranded, helical nucleic acid molecule consisting of nucleotide monomers with bases Adenine (A), Cytosine (C), Guanine (G), and Thymine (T); capable of being replicated and determining protein structure |
| RNA | Made up of nucleotide monomers with a ribose sugar and A, C, G, and U (Uracil instead of T); usually single-stranded and functions in protein synthesis, gene regulation, and as the genome of some viruses. |
| mRNA | Messenger RNA, a type of RNA responsible for conveying genetic instructions for building proteins from the nucleus to the cytoplasm. |
| Short overview of gene expression | mRNA is synthesized in the nucleus. It leaves the nucleus, meets up with ribosomes in the cytoplasm. Proteins are generated from the mRNA according to the code. |
| mRNA in prokaryotes | Prokaryotes lack nuclei but still use mRNA to convey a message from DNA to ribosomes and other cellular equipment that translated coded info into amino acid sequences. |
| Polynucleotides | A polymer consisting of monomers called nucleotides. It’s comprised of three parts: a nitrogen-containing (nitrogenous) base, a five-carbon sugar (pentose), and one or more phosphate groups |
| Nitrogenous base | Each nitrogenous base has one or two rings that include nitrogen atoms. (They are called nitrogenous *BASES* because the nitrogen atoms tend to take up H+). |
| Two families of nitrogenous bases: | Pyrimidines and purines |
| Pyrimidine family | Has one six-membered ring of carbon/nitrogen atoms. The members of the Pyrimidine family are: (C) cytosine, (T) thymine, (U) uracil |
| Purine family | Larger than pyrimidines. Six-member ring fused to a five-membered ring. The purines are: (A) adenine and (G) guanine |
| Nitrogenous bases only found in DNA and RNA | DNA: T, RNA: U |
| In DNA the sugar is a _____, in RNA the sugar is a _____ | DNA: deoxyribose, RNA: ribose |
| Deoxyribose means… | The sugar lacks an O atom in the second carbon in the ring. |
| Notation to distinguish the numbers of the sugar carbons from those used for the nitrogenous bases | Sugar carbon numbers of a nucleoside have a prime (‘) after them. E.g., in a nucleotide, the nitrogenous base is connected to 1’, the phosphates to 3’ and 5’ |
| Nucleoside | The portion of the nucleotide, not including the phosphate group (i.e. nitrogenous base + sugar) |
| Adjacent nucleotides in a polynucleotide (nucleic acid) are joined by _____. This results in… | Phosphodiester linkages, consisting of a phosphate group that links the sugars of two nucleotides. The resulting chain is known as the sugar-phosphate backbone. |
| The phosphate group in a polynucleotide is attached to what two primes? | 3’ and 5’ |
| What does 5’-AGGTAACTT-3’ mean? | 5’ refers to the location of the starting point. 3’ refers to the ending point. Between them is the order of nitrogenous bases. |
| The linear order of bases in a gene specifies… | The amino acid sequence (the primary structure of the protein), which is turn specifies the protein’s 3D structure and function |
| Difference between RNA and DNA with regard to macromolecular structure | RNA = single-stranded, DNA = double-stranded double-helix consisting of two polynucleotides running antiparallel to each other. |
| Antiparallel | The two sugar-phosphate backbones of DNA run in opposite 5’->3’ directions; this arrangement is referred to as antiparallel, somewhat like a divided highway |
| How are nitrogenous bases held together within the center of the double helix of DNA? | H-bonds |
| Base pairs in DNA and RNA | DNA: AT, CG. RNA: AU, CG. Mnemonic: “all tigers can growl”. Remember to turn T to U for RNA |
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