Bio Ch. 5

Phospholipid

2 fatty acids attached to a glycerol, with the third hydroxyl group of the glycerol joined to a phosphate group. The phosphate group has a negative charge, is polar, and is hydrophilic. An additional small charged/polar molecule is often linked to the phosphate group. The hydrocarbon tail is nonpolar/hydrophobic. Bilayers shield the phospholipids hydrophobic portions from water and form a boundary between a cell and its external environment.

Disaccharides

2 monosaccharides joined by a glycosidic linkage, which is a covalent bond formed between 2 monosaccharides via dehydration reaction. Usually written as some variation of 1-4 (1 carbon connected to the other monosaccharide's for carbon). Glycosidic linkages also join together polysaccharides, which few hundred to a few thousand monomers long. The position of glycosidic linkages, as well as the sugar monomers of its made up of, determine the function of polysaccharides.

Triglyceride/triacylglycerol

3 fatty acid molecules joined to 1 glycerol by an ester linkage (a bond formed by a dehydration reaction between a hydroxyl and carboxyl group). 3 dehydration reactions are needed to synthesize this molecule. The fatty acids don't all have to be the same. Saturated, unsaturated, and trans fats are all types of triglycerides.

Tertiary structure

3-D shape stabilized by interactions between side chains. Hydrophobic interactions (from amino acids with hydrophobic side chains) contributes to tertiary shape because these hydrophobic groups cluster at the core of a protein, out of contact with water. Van der Waals interactions hold the nonpolar side chains together. Hydrogen bonds between polar side chains and ionic bonds between electrically charged R groups stabilize tertiary structure. Covalent bonds called disulfide bridges form where 2 cysteine monomers, which have sulfhydryl groups on their side chains, get close. Disulfide bridges reinforce protein shape.

Aldose (aldehyde) v.s. Ketose (ketone)

Aldehydes have a carbonyl group at the end of their carbon skeleton. Ketones have a carbonyl group within their carbon skeleton.

Amino acid

An organic molecule with an amino group (-NH2), a carboxyl group (-COOH), and an a symmetric carbon connecting the 2 groups (called an alpha carbon) that's connected to a hydrogen atom. Have an R group, called the side chain, that is attached to the alpha carbon, and its make up and properties differ with each amino acid. The R group can be polar, nonpolar, or electrically charged. The amino and carboxyl groups are ionized in a cell's pH. All amino acids used in proteins are L enantiomers. Amino acid sequence is the simplest level of a protein's 3-D shape and determines what the protein's 3-D structure will be.

Glycogen

Animals store glycogen, mainly in liver and muscle cells. Glycogen is extensively branched, and their stores are depleted in about a day if not replenished. Tends to form helices in unbranched regions.

Quaternary structure

Arises only in proteins with 2 or more polypeptides.

Structural polysaccharides

Cellulose: unbranched polymer of glucose linked to each other by hydrogen bonds; found in plants. Chitin: used by arthropods to build their exoskeletons; hard when its proteins are chemically linked to each other or covered with calcium carbonate; used by fungi to protect their cell walls; has nitrogen-containing appendage. Both have beta linkages.

Dehydration reaction v.s. hydrolysis

Dehydration reaction is when 2 molecules are covalently bonded together with the loss of a water molecule. This is how monomers join together to form polymers, with a hydrogen being joined to a hydroxyl group. Hydrolysis is where a water molecule is added to break up a covalent bond. A hydrogen from the water attaches to one monomer, and the hydroxyl group from the water attaches to the other monomer.

Protein functions

Enzymatic (selectieve acceleration of chemical reactions, e.g. digestive enzymes); defensive (protect against disease, e.g. antibiotics); storage (store amino acids, e.g. casein); transport (transport substances, e.g. hemoglobin); hormonal (coordination of an organism's activities, e.g. insulin), receptor (response of cell to chemical stimuli, e.g. nerve cell receptors); contractile and motor (movement, e.g. actin and myosin); and structural (support, e.g. keratin)

Nucleic acids

Genes program amino acid sequence and are made of DNA. Nucleic acids are polymers, called polynucleotides, made of monomers called nucleotides, which join into polynucleotides by dehydration reactions. A nucleotide has 3 parts: a phosphate group, a 5-carbon sugar (pentose), and a nitrogen-containing base (nitrogenous base). A phosphate group is attached to the 5' carbon of the sugar. The portion of the nucleotide without the phosphate group is called a nucleoside. A polynucleotide has a sugar-phosphate backbone; the nitrogenous bases are variable appendages.

Phosphodiester linkages

How adjacent nucleotides are joined together. Consist of a phosphate group that links the sugars of the 2 nucleotides. The bond creates a repeating pattern of sugar-phosphate units called the sugar-phosphate backbone. One end has a phosphate attached to a 5' carbon (called the 5' end), and the other end has a hydroxyl group on a 3' carbon (called the 3' end). The sugar-phosphate backbone runs 5' to 3'. The two strains of DNA's sugar-phosphate backbones run in opposite 5' to 3' directions, making them antiparallel. The nitrogenous bases are on the inside of the 2 strands. The 2 strands are held together by hydrogen bonds between the paired bases.

Starch

How plants store sugars for later use. Joined by 1-4 glycosidic linkages. Amylose, the simplest form of starch, is unbranched; amylopectin is more complex, branched, and has 1-6 glycosidic linkages. Tends to form helices in unbranched regions.

Rings of sugars

In aqueous solutions, most 3- and 6-Carbon sugars form rings. Chemical equilibrium greatly favors rings.

3-D shape

Is determined by the interactions responsible for secondary and tertiary structure. Structure also depends on the physical/chemical conditions of a cell's environment. Unsuitable pH, salt concentration, heat, and more can cause a protein to denature, but this is usually reversed when a cell's environment returns to ideal conditions.

Steroid

Lipids characterized by a carbon skeleton of 4 fused rings. Cholesterol, a steroid, is a component of cell membranes and a precursor from which other steroids are synthesized.

Proteins

Make up 50% of a cell's dry mass. Most structurally sophisticated molecules known. All are constructed from the same set of 20 amino acids, linked in unbranched polymers. The bond between amino acids is called a peptide. The polymer of a protein is called a polypeptide. Globular proteins are spherical; fibrous proteins are shaped like long fibers. The function of a protein depends on its ability to recognize and bind to some other molecule.

Denaturation agents

Nonpolar solvents, high temperatures, and chemicals that disrupt hydrogen and ionic bonds and disulfide bridges.

Lipids

Not a true macromolecules because they're not big enough. Hydrophobic; mix poorly with water; nonpolar. Fats aren't polymers, but they're made from smaller molecules joined together by dehydration reactions. A fat is made from glycerol (an alcohol, with each of its 3 carbon bearing a hydroxyl group) and fatty acids (a long carbon skeleton usually 16 to 18 carbons long, with one carbon at the end of the skeleton part of the carboxyl group, the functional group responsible for the acid in fatty acid; the rest of the skeleton is a hydrocarbon chain). The nonpolar carbon-hydrogen bonds in the hydrocarbon chain of the fatty acids makes fats hydrophobic.

Chaperonins

Protein molecules that assist in the proper folding of other proteins. Keep new polypeptides separated from disruptive chemical conditions in the cytoplasmic environment while they fold spontaneously.

DNA

Provides direction for its own synthesis and directs RNA synthesis. Through RNA it controls protein synthesis. Each chromosome contains 1 long DNA molecule with hundreds of genes. Proteins are needed to carry out instructions on DNA.

Secondary structure

Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone. Segments of the polypeptide chain repeatedly coiled and folded as the result of hydrogen bonds between the repeating parts of the polypeptide backbone (not the amino acid chain). In the backbone, oxygen atoms have a partially negative charge, and the hydrogen atoms attached to the nitrogen have a partially positive charge, letting hydrogen bonds form between these atoms. These weak hydrogen bonds collectively support the protein's shape. The alpha helix is a delicate coil/helix held together by hydrogen bonding between every fourth amino acid. Beta pleated sheets are two or more segments of the backbone connected by hydrogen bonds between parts of the 2 parallel segments of the backbone.

Saturated, unsaturated, and trans fats

Saturated fat has no double bonds between carbon atoms in the hydrocarbon chain, letting as many hydrogen atoms as possible bond to the carbon skeleton; solid at room temperature; straight. Unsaturated fats have one or more double bonds between carbon atoms in their hydrocarbon chain, giving them 1 fewer hydrogen atom on each double-bonded carbon; most of these double bonds are cis, which creates a kink in the hydrocarbon chain wherever they occur; liquid at room temperature. Hydrogenated oils are unsaturated fats converted to saturated fats through the addition of hydrogen. Trans fats are unsaturated fats with trans double bonds.

Carbohydrates

Sugars and polymers of sugars. All sugars have a carbonyl group and multiple hydroxyl groups. Monomer is monosaccharide. Monomers joined by covalent bonds. Monosaccharides usually have molecular formulas that are some multiple of CH2O. Monosaccharides are broken down in cellular respiration to be used as energy, and their carbon skeletons serve as raw material for the synthesis of other small organic molecules, like amino and fatty acids. Most names end in -ose. Carbon skeletons range in size from 3 to 7 carbons. Hexoses (6 carbons), trioses (3 carbons), and pentoses (5 carbons) are most common. Can differ in their spatial arrangement about asymmetric carbons.

Ring structures of glucose

The hydroxyl group in a glucose is either attached to the 1 carbon below (alpha) or above (beta) the plane of the glucose ring. In beta the hydroxyl group alternates sides. All the glucose monomers in STARCH are in the ALPHA arrangement. In CELLULOSE all the glucose monomers are in the BETA configuration. Give the starch and cellulose distinct 3-D shapes. Starch is largely helical, while cellulose is straight and never branched.

Peptide bonds

The joining of one amino acid's carboxyl group to another amino acid's amino group by dehydration reaction. A polypeptide gets its backbone of alternating carboxyl and amino groups with side chains extending from it in this way. The amino end of the backbone is called the N-terminus; the carboxyl end is called the C-terminu.

Primary structure

The linear chain of amino acids. Determined by inherited genetic information, not random linking. Dictates secondary and tertiary structure.

Nitrogenous bases (purines and pyrimidines)

The purines are large, 6-membered rings fused to a 5-membered ring. Pyrimidines are smaller, 6-membered rings. Uracil is only in RNA. Thymine is only in DNA. Nitrogenous bases have 1 or 2 rings that include nitrogen atoms; these atoms tend to pick up hydrogen ions from a solution and act as bases.

Methods to determine protein shape

X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and bioinformatics