Chap 5

Distinguish between a polypeptide and a protein

- A polypeptide is a linear chain of amino acids linked by peptide bonds. - A protein is a macromolecule that consists of one or more polypeptides folded into a conformation specified by the linear sequence of amino acids.

macromolecule

A giant molecule formed by the joining of smaller molecules, usually by a condensation reaction. Polysaccharides, proteins, and nucleic acids are macromolecules.

Identify a glycosidic linkage and describe how it is formed.

A glycosidic linkage is the bond between two monosaccharides, to form a disaccharide. This bond occurs through a dehydration reaction. Because of its bonds, most living organisms can digest starch but not cellulose.

triacylglycerol

A lipid consisting of three fatty acids linked to one glycerol molecule; also called a fat or triglyceride.

fat

A lipid consisting of three fatty acids linked to one glycerol molecule; also called a triacylglycerol or triglyceride.

polymer

A long molecule consisting of many similar or identical monomers linked together.

deoxyribonucleic acid (DNA)

A nucleic acid molecule, usually a double stranded helix, in which each polynucleotide strand consists of nucleotide monomers with a deoxyribose sugar and the nitrogenous bases (ACGT)

Identify a peptide bond and explain how it is formed.

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids.

polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

nucleic acid

A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA.

polynucleotide

A polymer consisting of many nucleotide monomers in a chain; nucleotides can be those of DNA or RNA.

polysaccharide

A polymer of many monosaccharides, formed by dehydration reactions.

Describe the structure and functions of polysaccharides.

A polysaccharide is a type of carbohydrate. It is a polymer made of chains of monosaccharides that are joined by glycosidic linkages. Polysaccharides are also known as glycans. The main functions of polysaccharides are structural support, energy storage, and cellular communication. Examples of polysaccharides include cellulose, chitin, glycogen, starch, and hyaluronic acid.

chaperonin

A protein complex that assists in the proper folding of other proteins

Distinguish between a saturated and an unsaturated fat and list some unique emergent properties that are a consequence of these structural differences.

A saturated fat is solid at room temp. and has no double bonds in any of its 3 fatty acids, while an unsaturated fat has at least 1 double bond in any of its 3 fatty acids, and is liquid at room temp.

cholesterol

A steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids.

starch

A storage polysaccharide in plants consisting entirely of glucose.

disulfide bridge

A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.

chitin

A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.

carbohydrate

A sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides).

x-ray crystallography

A technique used to study the three-dimensional structure of molecules. It depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule.

steroids

A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached.

ribonucleic acid (RNA)

A type of nucleic acid consisting of a polynucleotide made up of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis, gene regulation, and as the genome of some viruses.

Identify an ester linkage and describe how it is formed. Be able to recognize and draw a triglyceride.

An ester linkage is a bond between a hydroxyl group and a carboxyl group.

glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

amino acid

An organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of polypeptides

lipid

Any of a group of large biological molecules, including fats, phospholipids, and steroids, that mix poorly, if at all, with water.

Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.

Attractions between R groups contribute to bends in tertiary structure, and strong bonds called disulfide bridges reinforce the proteins conformation.

List the four major classes of macromolecules. And name their monomers and the types of linkages between the monomers.

Carbohydrates, lipids, proteins and nucleic acids.

Briefly describe the three-dimensional structure of DNA.

Cellular DNA molecules have two polynucleotides that spiral around an imaginary axis, this forms a double helix. The double helix consists of two antiparallel nucleotide strands. The nitrogenous bases in DNA for hydrogen bonds in a complementary fashion (A → T, C → G)

Describe the distinguishing characteristics of carbohydrates and explain how they are classified.

Chemical characteristics: Polyhydroxylated (1C:2H:1O) aldehydes, ketones, alcohols & acids Very polar while carrying appreciable energy Provide carbon skeletons for biosynthesis Classification: Number of carbon atoms per monomer (triose, tetrose, pentose, hexose)Number of monomers (mono-, di-, polysaccharide)Position of carbonyl (aldose vs. ketose)

Define denaturation and explain how proteins may be denatured.

Denaturation occurs when a protein becomes biologically inactive due to changes in pH, salt concentration, temperature, and other environmental factors.

List and describe the four major components of an amino acid. Be able to recognize and draw an amino acid.

Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.

Describe the unique properties, building-block molecules, and biological importance of the fats vs. phospholipids.

Fats: Made of glycerol and 3 fatty acids. Can form saturated or unsaturated fats. Serve as energy storage. Phospholipids: Made of glycerol and 2 fatty acids. Form bilayers and are found in cell membranes. Steroids: Made of a carbon skeleton with 4 fused rings. Make many hormones.

Compare dehydration synthesis (condensation reactions) and hydrolysis. Be able to draw a dehydration synthesis of any of the four macromolecules.

In dehydration synthesis reactions, a water molecule is formed as a result of generating a covalent bond between two monomeric components in a larger polymer. In hydrolysis reactions, a water molecule is consumed as a result of breaking the covalent bond holding together two components of a polymer

denaturation

In proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. In DNA, the separation of the two strands of the double helix.

What is a gene? (and its relationship to proteins?)

Most genes contain the information needed to make functional molecules called proteins. (A few genes produce other molecules that help the cell assemble proteins.)

Summarize the functions of nucleic acids. List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid.

Nucleic acids contain information for all other cell functions and for their own replication. A nucleotide is made of a nitrogenous base, a pentose sugar, and a phosphate group. These are joined by covalent bonds between a phosphate group on the 5' side and an OH/Hydroxyl group on the 3' side.

beta-pleated sheet (β-pleated)

One form of secondary structure proteins in which the polypeptide chain folds back and forth. Two regions of the chain lie parallel to each other and are held together by H+ bonds between atoms of the polypeptide backbone.

purine

One of the two types of nitrogenous bases in nucleotides, characterized by a 6 membered ring fused to a 5 membered ring. Adenine and guanine are purines.

pyrimidine

One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring. Cytosine (C), thymine (T), and uracil (U) are pyrimidines.

Explain how organic polymers contribute to biological diversity

Polymers make up DNA and proteins, so any variation in polymers will vary DNA and proteins, as well.

Explain what determines protein conformation and why it is important. What are several types of protein modification to be functional?

Protein conformation is determined by the proteins ability to recognize and bond with another molecule. However, the function of a protein also helps in the specific conformation of a protein as well. These modifications include phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, lipidation and proteolysis and influence almost all aspects of normal cell biology and pathogenesis

Describe the characteristics that distinguish proteins from the other major classes of macromolecules and explain the biologically important functions of this group.

Proteins make up over 50% of dry mass of most cells, important in every aspect of an organism. Serve for structural support, storage, transport, cellular communications, movement, and defense against foreign substances.

Using collagen and hemoglobin as examples, describe quaternary protein structure.

Quaternary protein structure differs between proteins. In collagen, 3 polypeptides combine in a rope-like structure. Meanwhile, hemoglobin, made of 4 polypeptides, forms a globular structure.

secondary structure

Regions of repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bonding between constituents of the backbone (not the side chains).

nucleotide

The building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group.

peptide bond

The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction.

Distinguish between monosaccharides and disaccharides. Be able to recognize and draw a monosaccharide and a disaccharide.

The difference between monosaccharides and disaccharides is that monosaccharides have only one molecule whereas disaccharides have two

double helix

The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

Distinguish between the glyosidic linkages found in starch and cellulose and explain why the difference is biologically important.

The glycosidic linkages in starch and cellulous are different due to their slightly different ring structures for glucose. In starch, the glucose monomers are arranged in an alpha configuration. In cellulose, the monomers are in a beta configuration. The structures are essentially flip flopped from eath other.

primary structure

The level of protein structure referring to the specific sequence of amino acids.

Explain how monomers are used to build polymers.

The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproduct

Explain what distinguishes lipids from other major classes of macromolecules.

The number one thing that makes lipids different than other macro-molecules is that lipids do not consist of monomers, so they are not polymers. Another thing that makes lipids different is that they are hydrophobic, they do not like water. If you look at oil in water, they separate. Lipids tend to be mostly hydrocarbons.

tertiary structure

The overall shape of a protein molecule due to interactions of amino acid side chains, including hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges.

quaternary structure

The particular shape of a complex, aggregate protein, defined by the characteristic three-dimensional arrangement of its constituent subunits, each a polypeptide.

monosaccharide

The simplest carbohydrate, active alone or serving as a monomer for disaccharides or polysaccharides. Also called simple sugars

monomer

The subunit that serves as the building block of a polymer.

deoxyribose

The sugar component in DNA

ribose

The sugar in RNA

Describe the two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining the structure.

The two types of secondary protein structures are the alpha helix, and the beta pleated sheets. Hydrogen bonds connect the R groups together, maintaining its shape.

Where would you expect a polypeptide rich in the amino acids valine, leucine, and isoleucine be located in a properly folded polypeptide?

These are all nonpolar amino acids, so you would expect this region to be located in the interior of folded polypeptides, where it would not contact the aqueous environment inside the cell

phospholipids

a lipid consisting of a glycerol bound to two fatty acids and a phosphate group. The hydrocarbon chains of the fatty acids act as nonpolar hydrophobic tails, while the rest of the molecule acts as a polar hydrophilic head

cellulose

a structural polysaccharide of plant cell walls, consisting of glucose monomers joined by beta glycosidic linkages

hydrophobic interaction

a type of weak chemical interaction caused when molecules that do not mix with water coalesce to exclude water

Explain how the structure of DNA and proteins can be used to document the hereditary background of an organism.

a. assume descent with modification and a constant rate of mutation b. Phyogenetic trees showing relatedness can be constructed c. Number of changes is proportional to time since divergence

Distinguish between a pyrimidine and a purine.

purine --> adenine and guanine (two rings, nine atoms) pyrimidine --> cytosine, uracil, and thymine (one ring, six atoms)

proteins

A biologically functional molecule consisting of one or more polypeptides folded and coiled into a specific three-dimensional structure.

fatty acid

A carboxylic acid with a long carbon chain. Fatty acids vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form a fat molecule, also known as a triacylglycerol or triglyceride.

dehydration reaction

A chemical reaction in which two molecules become covalently bonded to each other with the removal of a water molecule.

hydrolysis

A chemical reaction that breaks bonds between two molecules by the addition of water; functions in disassembly of polymers to monomers.

Alpha helix

A coiled region constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding between atoms of the polypeptide backbone (not the side chains).

condensation reaction

A condensation reaction is a reaction in which two molecules combine to form a single molecule. A small molecule, often water, is usually removed during a condensation reaction

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

gene

A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses).

disaccharide

A double sugar, consisting of two monosaccharides joined by dehydration synthesis.

saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.

unsaturated fatty acid

A fatty acid that has one or more double bonds between carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.