Chapter 5 (5.1-5.4): The Structure and Function of Large Biological Molecules

Collagen

40% of the protein in the human body. Consists of four polypeptide subunits, two of one kind and two of another, both kinds are mostly helical secondary structure. These structures combine and make a quaternary structure

Glycosidic Linkages "carbohydrate link"

A covalent bond between monosaccharides by a dehydration reaction. The HO in one monosaccharide and HO in the other create a molecule of water leaving the one oxygen atom shared between the monosaccharides.

Saturated Fatty Acid

A fatty acid with no double bonds between carbon atoms allowing as many hydrogen atoms as possible to be bonded to the carbon skeleton. Saturated fats are usually solid at room temperature because the hydrocarbon chains on their fatty acids lack double bonds allowing them to pack closely together.

a Helix

A secondary structure. It is a coil held together by hydrogen bonding between every fourth amino acid

B Pleated Sheet

A secondary structure. two or more segments of the chain that lie side by side connect with hydrogen bonds between parts of the parallel sides

Chitin

A structural polysaccharide. Chitin is the carbohydrate that arthropods (insects, spiders, crustaceans and related animals) use to build their exoskeletons. (a hard case that surrounds the soft part of an animal) The exoskeleton is made of chitin embedded in a protein layer, it is leathery and flexible at first but hardens when proteins chemically link to each other (in insects) or are encrusted with calcium carbonate (in crabs). Chitin is also in fungi, they use chitin instead of cellulose to build their cell walls. It has beta glucose linkages except the glucose monomer of chitin has a nitrogen-containing appendage

Hormonal Proteins

Coordinate an organism's activities. ( insulin, causes other tissues to take up glucose, regulating blood sugar concentration)

Unsaturated Fatty Acid

Has one or more double bonds, with one fewer hydrogen atom at each double bonded carbon Nearly all double bonds in naturally occurring fatty acids are cis double bonds, which cause a kink in the chain where they occur. Unsaturated fats are usually liquid at room temperature because the cis double bonds prevent the molecules form packing together closely enough to solidify. referred to as oils. "hydrogenated vegetable oil" means that they have converted unsaturated fat to saturated fat by adding hydrogen. They add hydrogen to peanut butter, margarine and many other products to prevent lipids from separating out in liquid form. -CIS bonds are natural

Secondary Structure

Structure that is the result of the coiling and folding patterns in the polypeptide chains. These folds and coils are caused by hydrogen bonds between the constituents of the polypeptide backbone. The oxygen in the backbone have a partial negative charge and the hydrogen attached to the nitrogens have a partial positive charge; hydrogen bonds form between them. Although individually hydrogen bonds are weak, because of the amount over a long region they can support the shape for their specific part of the protein

Polysaccharide

THE POLYMERS OF SUGARS, have storage and structural roles. macromolecules. Polymers with hundreds to thousands of monosaccharides joined by glycosidic linkages. some polysaccharides serve as storage material, some as building material, determined by its sugar monomers and the positions of its glycosidic linkages.

Proteins

a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three dimensional structure. their name comes from the greek word proteios which means "first" or "primary." They account for over 50% of the dry mass of most cells. The most structurally sophisticated molecules known. There are 10s of thousands of different proteins, each with a specific structure and function. But they are all constructed from the same set of 20 amino acids linked in unbranched polymers with peptide bonds. A protein is made up of one or more polypeptides precisely twisted and folded into a molecule of its own unique shape. Many proteins are spherical (globular proteins) and some are shaped like long fibers (fibrous proteins). There are countless variations within these broad categories

Sickle-Cell Disease

a blood disorder caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) in the primary structure of hemoglobin (an oxygen carrying protein). Hydrophobic interactions cause the sickle-cell hemoglobin to aggregate into a fiber reducing its capacity to carry oxygen.

Polymer

a long chainlike molecule made up of many similar or identical building blocks linked by covalent bonds. Polymers are macromolecules with a repeating subunit called monomers. -Carbohydrates -Proteins -Nucleic Acids

X-Ray Crystallography

a method used to determine the 3-d structure of proteins. Other methods for finding the 3-d structure are nuclear magnetic resonance (NMR) spectroscopy and bioinformatics.

Carbohydrates

include sugars and polymers of sugars. the simplest carbohydrate are the monosaccharides, or simple sugars: these are the MONOMERS from which more complex carbohydrates are built. Carbohydrates macromolecules are polymers called polysaccharides, made of many sugar building blocks.

Steroids

lipids with a carbon skeleton including four fused rings. Different steroids are characterized by the chemical groups that are attached to their rings.

Beta glucose ring

the hydroxyl group is above the plane of the glucose ring. All of the glucose that makes up cellulose are beta rings -Linkages are opposite of each other and harder to break down: cellulous

Alpha glucose ring

the hydroxyl group is below the plane of glucose ring. All of the glucose monomers in starch are alpha rings -easily broken because of their shape: starch and glycogen

Tertiary Structure

the tertiary structure is the result of interactions between side chains of the amino acids. The secondary structure is the result of hydrogen bonds in the polypeptide backbone. Tertiary is made of peptide, hydrogen, covalent, ionic, van der waals, disulfide bridges and hydrophobic interactions.

Macromolecules

the three largest molecules, they can consist of thousands of atoms and be over 100,000 daltons in mass. Macromolecules are carbohydrates, proteins and nucleic acids

Disaccharide

two monosaccharides joined together by a glycosidic linkage through dehydration reaction. Maltose is two glucose combined together. The most prevalent disaccharide is sucrose (table sugar), its monomers are glucose and fructose.

Aldose

type of monosaccharide sugar where the carbonyl group is at the end of the carbon skeleton

Ketose

type of monosaccharide sugar where the carbonyl group is within the carbon skeleton

Structural Polysaccharides

used for building strong materials in plants- not in humans we have bones

Peptide Bond

when two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other they can become joined by a dehydration reaction, the new covalent bond is called a peptide bond. AMINO ACIDS LIKED BY COVALENT BONDS. Many of these bonds combined together is called a polypeptide. A POLYPEPTIDE IS A POLYMER OF AMINO ACIDS

Disulfide Bridges

when two cysteine monomers, which include sulfhydryl groups (-SH) on their side chains, are close together because of the folding of the protein the sulfur from one cysteine bonds to the sulfur of the other and forms abridge which rivets parts of the protein together. Contributes to the tertiary structure of a protein

Hydrolysis

The process that disassembles polymers into monomers. Essentially the reverse of the dehydration reaction. It breaks the bond of the monomers by adding a water molecule. A hydrogen from water attaches to one monomer and the hydroxyl group attaches to the other. Digestion is hydrolysis. Most of the food enters our bodies comes in polymers much too large to enter our cells, in the digestive tract there are enzymes that attack the polymers and speed up hydrolysis, the released monomers are absorbed into our bloodstream to distribute to all body cells. Those cells use dehydration reactions to make new polymers that can do specific things that the cells need.

Monomer

The repeating units or building blocks that bond together to make polymers. Some monomers also have other functions of their own. -40-50 subunits

Transport Proteins

Transport substances. (hemoglobin, transports oxygen from the lungs to other parts of the body.)

Polypeptide

Unbranched polymer (long chain) of amino acids. A PROTEIN is a biologically functional molecule that consists of one or more polypeptides. Each polypeptide has a unique linear sequence of amino acids. Each polypeptide has a single amino end (n-terminus) and a single carboxyl end (c-terminus)

Trans Fats

Unsaturated fats with trans double bonds. May contribute more to atherosclerosis (a cardiovascular disease that impedes blood flow) than saturated fats. -TRANS bonds, man-made, unsaturated fats that act like saturated fats

Structural Proteins

Used for support. (Keratin, the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make cocoons and webs. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Contractile and Motor Proteins

Used in movement (responsible for the undulations of cilia and flagella. Actin and myosin are responsible for the contraction of muscles)

Glycogen

a STORAGE POLYSACCHARIDE IN ANIMALS, polymer of glucose that is like amylopectin but more EXTENSIVE BRANCHING. A storage polysaccharide. It is stored by animals. Vertebrates mainly store it in liver and muscle cells. They can't sustain an animal for very long, in humans they are depleted in about a day unless they are replenished by food consumption. -hydrolysis breaks down glycogen into glucose and sends it throughout the body.

2 smaller molecules that make up lipids:

-Glycerol: an alcohol- each 3 carbons bear hydroxyl groups -fatty acids: consists of carboxyl groups a long carbon chain (16-18)

Amino Acid

-are the building blocks of proteins. These amino acids make up polypeptides. -an organic molecule with both an amino group and a carboxyl group. An alpha carbon joins the amino and carboxyl groups. Also attached to the alpha carbon are a hydrogen atom and a variable group symbolized by R. R group or "the side chain" differ with each amino acid. Basic amino acids have amino groups in their side chain that are generally positive. All of the amino acids used in proteins are L enantiomers.

Alpha and Beta

-Alpha linkages are digestible by most animals -Beta linkages are not digestible by animals (microorganism can)

Hydrophobic Interaction

In polypeptides including side chains that are hydrophobic (nonpolar). They are the result of the shape that occurs because of the exclusion of the hydrophobic substances in the chains by water. Once nonpolar side chains are close, van der waals interactions help hold them together. The other, polar substances are stabilized by hydrogen bonds. Contributes to the tertiary structure.

Dehydration Reaction

Monomers connect to each other in a reaction where two molecules are covalently bonded to each other, with the loss of a water molecule. When the bond forms each monomer gives part of the water molecule that is released, one provides a hydroxyl group (-OH) and the other provides a hydrogen (-H), as this reaction is repeated and monomers are added to the chain a polymer is made.

Quaternary Structure

Some proteins are made of two or more polypeptide chains that combine and make up a functional macromolecule. Quaternary structure is the overall protein structure that results from the combination of polypeptide subunits

Defensive Proteins

Protect against disease (antibodies inactivate and help destroy viruses and bacteria

Enzymes

Proteins make up enzymes -are catalysts

Fatty Acid

has a long carbon skeleton, usually 16 or 18 carbon atoms long. The carbon at one end of its skeleton is part of a carboxyl group, the functional group that gives the molecules the name fatty acid. The rest of the skeleton is a hydrocarbon chain. The fatty acids in a fat can all be the same or they can be of two or three different kinds.

Denaturation

a protein may unravel and lose its shape if the conditions in its environment aren't good. The pH, salt concentration and temperature in its environment can lead to denaturation in a protein. Denatured proteins are biologically inactive. moving a protein from an aqueous environment to a nonpolar solvent usually leads to denaturation, the polypeptide chain will refold with its hydrophobic regions facing outward toward the solvent. Denaturation agents include chemicals that disrupt hydrogen bonds, ionic bonds and disulfide bridges that maintain the protein's shape. High heat can also cause denaturation, it can overpower the weak interactions that stabilize the structure. (egg whites become opaque during cooking because the denatured proteins are insoluble and solidify.)

Primary Structure

a protein's sequence of amino acids. The primary structure dictates secondary and tertiary structure.

Starch

a storage polysaccharide, a STORAGE POLYSACCHARIDE OF PLANTS a polymer of glucose monomers. A storage polysaccharide. Stored by plants as granules within plastids (cellular structures), which include chloroplasts. Synthesizing starch allows the plant to stockpile surplus glucose. Later hydrolysis can be used to break the bonds between the glucose monomers allowing them to use the glucose for energy. Most glucose monomers in starch are joined by 1-4 linkages (linkages between the 1 carbon and the 4 carbon in the glucose monomers). Amylose, the simplest form of starch is unbranched. Amylopectin, a more complexed starch, is branched with 1-6 linkages at the branch points. Is made up of Alpha glucose rings -ALPHA CONFIGURATION is largely helical

Cellulose

a structural polysaccharide. A major polysaccharide: Like starch, is a polymer of glucose. -component of the tough walls in plant cells. It is the most abundant organic compound on earth. Made of glucose like starch but the glycosidic linkages are different. There are two slightly different ring structures for glucose. Cellulose is made up of beta glucose rings, making every glucose monomer "upside down" with respect to its neighbors. Cellulose is never branched and the cellulose molecule is straight, while the starch molecule is helical. In cellulose some hydroxyl groups on the glucose monomers are free to hydrogen-bond with hydroxyls of other cellulose molecules lying parallel to it creating microfibrils. Microfibrils are strong building material for plants and they make up paper and are the only component of cotton. Enzymes that hydrolyze Alpha linkages can't hydrolyze Beta linkages because of their different shapes. All animals, including humans don't digest cellulose, it passes through the digestive tract, as it passes through it abrades the digestive tract's wall and stimulates its lining to secrete mucus helping for smooth passage of food through the tract. It is healthy even though it's not a nutrient for humans "insoluble fiber" refers mainly to cellulose. Some organism including cows can digest cellulose and break it down into glucose, cows have cellulose-digesting prokaryotes and protists in their guts. Termites have have prokaryotes or protists living in their guts that can make a meal of wood. -BETA CONFIGURATION are straight and unbranched

Cholesterol

a type of steroid. A component of animal cell membranes and is the precursor from which other steroids, like vertebrate sex hormones, are synthesized. A high level of cholesterol may contribute to atherosclerosis. Saturated and trans fats exert their negative impact on healthy by affecting cholesterol levels. EXAMPLE: sun coverts cholesterol molecules into vitamin D

Triglycerol

another name for fat

Chaperonins

chaperone proteins, proteins that assist in the folding of other proteins. they keep new polypeptides separated from chemical conditions in the cytoplasmic environment while they fold spontaneously. Chaperonins are kind of like a barrel that an unfolded polypeptide goes into and folds and then when it's done folding it leaves the chaperonin, small amounts of water are inside of the barrel as well to create a hydrophilic environment. The chaperonin is two proteins, the barrel and a lid.

Catalysts

chemical agents that speed up chemical reactions without being consumed by the reaction. These molecules can be thought of as workhorses that keep cells running, because they can be used over and over again.

Lipids

don't contain true polymers and are not composed of monomer subunits and are not generally large enough to be considered macromolecules. They are compounds that are grouped together because they share the important trait of not mixing or poorly mixing with water. Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds

Monosaccharides -ose : sugar

molecular formulas are usually some multiple of CH2O (i.e. C2H4O2). Glucose (C6H12O6) is the most common and is very important in the chemistry of life. Consists of a carbonyl (CO) and a hydroxyl (-OH) group. Depending on the location of the carbonyl group a sugar is either an aldose (aldehyde sugar) or a ketose (ketone sugar). Glucose is an aldose, fructose (an isomer of glucose) is a ketose. Another way to classify sugars is the size of the carbon skeleton which can range from three to seven carbons long. Glucose, fructose and others that have six carbons in their skeleton are called hexoses. Simple sugars also differ from each other due to the spatial arrangement of their parts around the asymmetric carbon (asymmetric carbon is a carbon attached to four different atoms or groups of atoms.). glucose and and galactose, differ only in the placement of parts around one asymmetric carbon, this is a big enough difference to give the sugars distinctive shapes, building activities and behaviors. MONOSACCHARIDES ARE MAJOR NUTRIENTS FOR CELLS. In cellular respiration cells extract energy from glucose molecules by breaking them down. Carbon skeletons also serve as material for the synthesis of other small organic molecules like amino and fatty acids.

Fats

not polymers, but large molecules assembled from smaller molecules by dehydration reactions. Fats are constructed from glycerol and fatty acids. Glycerol is an alcohol; each of its three carbons contains a hydroxyl group. The c-h bonds in the hydrocarbon chains make the fats hydrophobic. Fats separate from water because the water hydrogen-bonds to the other water and exclude the fats. Fats are made of three fatty acid molecules joined to glycerol by an ester linkage, a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group a fat is three fatty acids linked to one glycerol molecule. A fat made from saturated fatty acids is called a saturated fat. Most animal fats are saturated. Plant and fish fats are generally unsaturated meaning that they are build of one or more types of unsaturated fatty acids. A gram of fat stores twice as much energy than a gram of a polysaccharide. The hydrocarbons in fats are similar to gasoline molecules and just as rich in energy.

Storage Polysaccharide

polysaccharides that are stored by both plants and animals for later use

Receptor Proteins

response of cell to chemical stimuli (receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells)

Enzymatic Proteins

selectively accelerate chemical reactions (digestive enzymes catalyze the hydrolysis of bonds in food molecules)

Phospholipids

similar to a fat molecule but with only two fatty acids attached to glycerol instead of three. Instead it includes a phosphate group attached to the third hydroxyl group of the glycerol. The phosphate group has a negative electrical charge. Generally there is also a small charged or polar molecule linked to the phosphate group, such as choline. Has a hydrophilic head (polar) and two hydrophobic tails (nonpolar).

Enzymes

specialized macromolecules that speed up chemical reactions that make and break down polymers.

Storage Proteins

store amino acids. (casein, milk protein, is the major source of aminos for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the egg white protein, used as an amino source for the developing embryo.