module 1 chapter 2: chemical basis of life

what are primary, secondary, tertiary and quaternary levels of proteins structure? what is the nature of interactions and bonds responsible at each level? NOT FINISHEDDDDDDD

1. primary (1°) structure: concerns the amino acid sequence of a protein; all levels of structure are ultimately determined by the primary level 2. secondary (2°) structure: describes polypeptide conformation (spatial organization) chain portions; preferred ones provide maximum possible number of H bonds between neighboring amino acids 3. tertiary (3°) structure: the level above secondary structure, is the conformation of the entire protein 4. quaternary (4°) structure: the linking of polypeptide chains to form multisubunit functional protein via intermolecular R group interactions

define functional groups

functional groups are particular atom groupings that behave as unit. they give organic molecules their physical properties, chemical reactivity & solubility in aqueous solutions

describe the structure and biological functions of glycogen.

glycogen is a nutritional polysaccharide, a storehouse for extra chemical energy in most animals, and typically ranges in molecular weight from ~1 - 4 million daltons. structure: branched glucose polymer mostly joined by alpha (1—> 4) bonds (only one kind of monomer) and sugar at branch point is joined to 3 neighboring units instead of 2 ex: human skeletal muscles have enough glycogen to fuel about 30 min of moderate activity

what are glycosaminoglycans and give some examples of their functions?

glycosaminoglycans (GAGs)=group of polysaccharides with a more complex structure. unlike other polysaccharides, they have the structure of repeating disaccharides (2 different sugars in a repeating pattern). most occur in spaces surrounding cells examples: heparin (the most researched, and is usually extracted from pig tissue), which is secreted by cells in the lungs & other tissues in response to tissue injury. heparin inhibits blood coagulation and prevents the formation of clots that can block the flow of blood to the heart or lungs in plant cell walls-glycosaminoglycans are extremely important in development and structure

what is ionic interaction? ionic interactions are pretty strong in crystal form, in vacuum or in the absence of water? what happens to them in water?

ionic bonds (or salt bridges) are noncovalent bonds. crystal of table salt is held together by an electrostatic attraction between positively charged Na+ & negatively charged Cl- ions ionic bonds within a salt crystal may be quite strong however, if salt crystal is dissolved in water, each of individual ions is surrounded by water molecules, which inhibit oppositely charged ions from approaching one another closely enough to form ionic bonds because cells are made primarily of water, bonds between free ions are of little importance ionic bond strength in a cell is generally weak (~3 kcal/mole) due to the presence of water

identify ring or linear forms of glucose.

linear: each sugar molecule consists of carbon atom backbone linked together in a linear array by single bonds. each carbon of backbone is linked to single OH group except for one bearing a carbonyl (C=O) group. linear form is important because the aldehyde group at the end of the chain can react with proteins, notably hemoglobin but the vast majority of sugars is found in ring form; it is in this form that they are used as building blocks to build other types of carbohydrates ring form: usually depicted as flat (planar) structures lying perpendicular. the H & OH groups lie parallel.

what is a protocell? what are the components that are widely believed to make a protocell?

protocells=the earliest cells (very simple, made up of just nucleic acids, such as DNA or RNA, surrounded by a membrane)

identify the nitrogenous bases as purines or pyrimidines.

purines in RNA & DNA= adenine & guanine; they are larger structures, consisting of 2 rings pyrimidines in RNA= cytosine & uracil; in DNA, uracil is replaced by thymine, a pyrimidine with an extra methyl group attached to the ring; they are smaller, single ring structures

describe the structure and biological functions of starch.

starch is a nutritional polysaccharide and a glucose polymer. most plants get chemical energy in the form of starch. in plant cells, it gets stored as densely packed granules (called starch grains), which are enclosed in membrane-bound (plastids). structure: starch is made of a mixture of 2 different polymers: 1. amylose- unbranched, helical molecule, whose sugars are joined by alpha (1—> 4) linkages and 2. amylopectin-branched (it differs from glycogen in being much less branched & has an irregular branching pattern); alpha (1—> 6) bonds at branch) ex: potatoes & cereals are primarily starch. animals also possess the enzyme (amylase) to hydrolyze starch, even though they don't synthesize it

what are the constituent monosaccharides of sucrose and lactose?

sucrose (table sugar): glucose and fructose lactose (milk sugar): galactose and glucose

what is stereoisomerism?

the arrangement of groups around a carbon atom is depicted with the carbon in the center of a tetrahedron & the bonded groups projecting into its 4 corners; carbon can bond with 4 other atoms

identify and state properties of 7 common functional groups found in biological molecules.

1. hydroxyl group: —OH (polar, hydrophilic) 2. carboxyl group: —COOH; acquires charge —COO- (charged, ionized to release H+, considered acidic) 3. sulfhydryl group: —SH; react to form disulfide bonds in polypeptides (polar) 4. amino group:—NH2; acquires charge —NH3+ (charged, accepts H+ to form NH3+. considered basic) 5. phosphate group: —PO3H22- (charged, ionizes to release H+, considered acidic). 6. carbonyl group: C=O (polar) 7. methyl group: —CH3 (non polar)

describe some technical methods used to determine the tertiary structure of a protein.

1. x-ray crystallography can be used to determine detailed tertiary structure; ~20,000 3D structures have already been reported. in x-ray crystallography, a protein crystal is bombarded by a thin x-ray beam, the radiation scatters (diffracted) by the electrons of the protein's atoms, then strikes the radiation- sensitive detector. this forms an image of spots, the patterns of which do not directly show the protein structure, but computer programs based on the mathematics of diffraction can derive the structure responsible for producing the pattern. they can provide higher resolution structures for larger proteins but limited by the ability to get any given protein to form pure crystal 2. nuclear magnetic resonance (NMR) spectroscopy, a method in which proteins in solution are placed in a powerful magnetic field, then probed with radio waves to produce a spectrum, providing information about the distances between atoms. the spectrum itself does not directly show protein structure, but computer programs can derive the structures most likely to give the observed spectrum. it does not require crystallization , but it becomes increasingly difficult to apply as the protein gets bigger

describe the structure and biological functions of cellulose.

cellulose is a structural polysaccharide that solely contains glucose monomers (like glycogen and starch). it is the most abundant organic material on earth & is rich in chemical energy, and an important component of dietary fiber, however almost all multicellular animals lack enzymes needed (cellulase) to degrade cellulose cellulose is the major plant cell wall component. it is also an important component in cotton & linen production, due to the durability of the long, unbranched cellulose molecules. cellulose can be ordered into side-by-side aggregates to form molecular cables that are able to resist pulling (tensile) forces it is different from many other polysaccharides because it is bonded with beta (1—> 4) bonds rather than alpha (1—> 4) bonds. some animals live by digesting cellulose (ex: termites, sheep) by harboring bacteria & protozoa that make cellulase

what is the role of cellulose as a dietary fiber?

cellulose is an important component of dietary fiber= includes all the polysaccharides humans eat that cannot be digested by human enzymes

describe the structure and biological functions of chitin.

chitin is a structural polysaccharide. it is an unbranched polymer of the sugar N-acetylglucosamine (similar in structure to glucose, but with an acetyl amino group, instead of an OH, bonded to second carbon atom of glucose ring) used as a structural material among invertebrates (ex: insects, spiders, crustaceans) it is a tough, resilient, yet flexible material, similar to certain plastics.

describe the formation of a covalent bond. how many bonds can a given element such as C, H, O, N, form and what is it determined by?

covalent bonds=pairs of electrons are shared between pairs of atoms. the formation of a covalent bond: an atom is most stable when its outermost electron shell is filled so the number of bonds an atom can form depends on the number of electrons needed to fill the outer shell. H: 1 covalent bonds O: 2 covalent bonds N: 3 covalent bonds C: 4 covalent bonds it is determined by how many electrons are needed to fill its outer shell

what are general properties of lipids? describe the three major classes of lipids and their associated functions. (general overview)

lipids= diverse nonpolar biological molecules. common properties: solubility in organic solvents (benzene, chloroform) & insolubility in H2O (explains many of their varied biological functions) 1. triglycerides (fats)=serve as lipid storage form for fuel (stored in adipocytes). fatty acids are long, unbranched hydrocarbon chains with a single carboxyl group at one end. fatty acids are amphipathic. 2. phospholipids= structure is glycerol + 2 fatty acids + phosphate group on third hydroxyl. one end containing the phosphate group is hydrophilic. the other end is hydrophobic. present in membranes (properties of which depend on phospholipids) 3. sterols=complex & built around a 4-ringed hydrocarbon. most common: cholesterol, a precursor for the synthesis of many steroid hormones (testosterone, progesterone, estrogen)

what are macromolecules and what are different kinds? which of the above are usually polymers?

macromolecules form the structure & carry out the activities of cells. they are huge & highly organized molecules (can perform complex tasks) and contain from dozens to millions of carbon atoms. 4 major categories: proteins, nucleic acids, polysaccharides, certain lipids - first 3 types are polymers; made of large number of building blocks (monomers) these macromolecules are constructed from monomers by a process called polymerization

name various kinds of monomers present in cells that are used to build polymers

monomers (building blocks of macromolecules) sugars/polysaccharides amino acids/proteins, nucleotides/nucleic acids fatty acids & glycerol/lipids

what are monosaccharides, disaccharides, oligosaccharides and polysaccharides?

monosaccharides:the simplest form of sugar and the most basic units of carbohydrates (ex: glucose, fructose, galactose, etc). disaccharides: made of monosaccharides covalently bonded together; serve primarily as readily available energy stores (ex: sucrose and lactose) oligosaccharides: can link together small chains of sugars; usually, they are covalently attached to lipids & proteins, converting them to glycolipids & glycoproteins (ex: raffinose and stachyose) polysaccharides: a polymer of sugar units joined by glycosidic bonds; they are very large molecules (ex: glycogen, starch, cellulose, etc).

what is the role of nucleoside triphosphates in cellular functions?

overall: important as the building blocks of nucleic acids adenosine triphosphate (ATP): produces most of the energy used by a living organism guanosine triphosphate (GTP): very important in cellular activities, GTP binds to a variety of proteins (called G proteins) & acts as a switch to turn on their activities