Biochemistry Flashcards

Flashcards for Biochemistry review.

Matter

Anything that takes up space and has mass.

Elements

Substances that cannot be broken down into substances with different properties.

Atoms

The smallest unit of a substance, composed of a central atomic nucleus and electrons.

Proton Charge

Positive (+1)

Neutron Charge

No charge (neutral / 0)

Electron Charge

Negative (-1)

Atomic Number (Proton Number)

Number of protons in the nucleus of an atom, symbol Z.

Mass Number

Total number of protons and neutrons in the nucleus of an atom, symbol A.

Isotopes

Atoms of the same element with the same number of protons and electrons, but different number of neutrons.

Electron Shells/Energy Levels

Regions around the nucleus where electrons move.

Atoms with incomplete valence shells

Atoms with incomplete outer shells that are more likely to react and form chemical bonds.

First electron shell capacity

Holds up to 2 electrons.

Second electron shell capacity

Holds up to 8 electrons.

Compound

Forms when atoms of two or more different elements react or bond together.

Chemical Bonds

Form when there are forces of attraction between atoms.

Ion

Charged particle produced by transfer of electrons from a metal atom to a non-metal atom.

Cations

Positively charged ions.

Anions

Negatively charged ions.

Ionic Bond

Electrostatic force of attraction between oppositely charged ions.

Covalent Bond

Forms when two non-metal atoms share a pair of electrons.

Molecule

Two or more atoms chemically bonded together by covalent bonding.

Electronegativity

The attraction of an atom for the electrons of a covalent bond.

Polar Covalent Bond

Created by the unequal sharing of electrons in a covalent bond.

Hydrogen Bond

Weak bond created when hydrogen atom in one molecule is attracted to the oxygen atom in other molecules.

Nonpolar Molecules

Interact very little with polar molecules. Attracted to one another by very weak bonds called van der Waals forces.

Van der Waals forces

Very weak bonds that nonpolar molecules are attracted to one another

Water properties

The dipole nature; awareness that the collective effect of the hydrogen bonds is responsible for the unique properties of water exemplified by importance of water as a solvent and its biological significance.

Water Molecular Structure

Consists of an oxygen atom bound to two hydrogen atoms by two single covalent bonds.

Water as a Solvent

Water is a polar molecule, and it has positive and negative ends. Can dissolve a wide range of substances, especially polar molecules and ionic compounds.

Hydrophobic Molecules

Molecules that are uncharged and non-polar, usually do not dissolve in water.

Hydrophobic Exclusion

Nonpolar molecules tend to aggregate (clump together) in water.

Specific Heat Capacity of Water

The amount of heat, measured in joules, required to raise the temperature of 1 kg of water by 1oC.

High Heat Capacity of Water

Means that a large increase in heat energy results in a relatively small rise in temperature.

Latent Heat of Vaporisation

The amount of energy needed to vaporise water, which produces a cooling effect.

Latent Heat of Fusion

A measure of the heat energy required to melt a solid, in this case ice.

Cohesion

Water molecules tend to stick together.

Adhesion

Water molecules sticking to other types of molecules.

Surface Tension

The cohesion among water molecules at the surface of ponds and lakes.

Water as a Reagent

Water is used as a source of hydrogen in photosynthesis.

Water functions in all organisms

High water content of protoplasm, solvent and medium for diffusion, reagent in hydrolysis.

Water functions in plants

Osmosis and turgidity for support, guard cell mechanism, reagent in photosynthesis.

Water functions in Animals

Transport, osmoregulation, cooling by evaporation, lubrication, support.

Organic Molecules

Molecules that contain carbon and hydrogen bonds.

Carbon Bonding

Carbon has 4 electrons in its outer shell, and it can bond with as many as four other atoms.

Functional Groups

Clusters of certain atoms that always behave in a certain way.

Isomers

Molecules that have identical molecular formula, but they are different molecules because the atoms in each are arranged differently.

Structural Isomers

Differ in the placement of their covalent bonds.

Geometric Isomers or Stereoisomers

Have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds.

Optical Isomerism

A property of any compound which can exist in two forms whose structures are mirror images.

Monomers

The smaller units from which larger molecules are made.

Polymers

Molecules made from a large number of monomers joined together in a chain.

Macromolecules

Very large molecules. They contain 1000 or more atoms and so have a high molecular mass.

Condensation Reaction

Occurs when monomers combine together by covalent bonds to form polymers (polymerisation) or macromolecules and water is removed.

Hydrolysis

Polymers are broken down by a reaction, when covalent bonds are broken when water is added

Monosaccharides

Pentoses (ribose, deoxyribose), hexoses (glucose, fructose and galactose); basic distinction between the structures of α-glucose and β – glucose.

Carbohydrates

They are substances with the general formula Cx(H2O)y, where x and y are variable numbers. All carbohydrates are aldehydes or ketones. All contain several OH groups.

Monosaccharides

Single sugar units with a carbon backbone of three to seven carbon atoms.

Carbohydrates Examples

Glyceraldehyde, contains 3 carbon atoms. It is a triose.

Pentoses

Have 5 carbons, part of the genetic molecules ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Glucose

Has 6 carbons and hence has the chemical formula C6H12O6.The subunit of which most polysaccharides are made.

Monosaccharides examples and properties

Glucose, fructose and galactose are isomers.

Disaccharides

Formed by condensation reactions between two monosaccharides. The bond formed between 2 monosaccharides is called a glycosidic bond and it normally forms between carbon atoms 1 and 4 of neighbouring units (a 1,4 bond).

Maltose Composition

Glucose + glucose

Lactose Composition

Glucose + galactose, found in milk.

Sucrose Composition

Glucose + fructose, most abundant in plants.

Oligosaccharides

Contain more than two monosaccharides. Glycoproteins and glycolipids found on the outer surface of cells have these attached to the R group of certain amino acids or lipids respectively.

Polysaccharides

Macromolecules, are polymers formed by many monosaccharides joined by glycosidic bonds in a condensation reaction to form chains.

Starch

A polymer of glucose. It is major fuel store in plants, but it is absent from animals

Amylose Compostion

Is composed of several α-glucose molecules linked together in long, unbranched chains. Each linkage occurs between the carbon 1 (C-1) of one glucose molecule and the C-4 of another, making them α-(1, 4) glycosidic linkages.

Amylopectin compostion

Makes up 80% of potato starch, is branched. The branches occur due to bonds between the C-1 of one molecule and the C-6 of another forming α-(1, 6) linkages.

Glycogen

A storage polysaccharide made from glucose in animals and in fungi. In vertebrates, stored chiefly in the liver and muscles.

Cellulose

Another polymer of glucose. It is a structural component of all plant cell walls. It consists of long chains of β-glucose joined together by 1,4 glycosidic bonds.

Chitin

A structural material found in the exoskeleton of arthropods and in the cell wall of many fungi. It is a polymer of N-acetylglucosamine which is a derivative of glucose that contains nitrogen.

Types of sugars

reducing and non-reducing. Reducing sugars act as reducing agents in chemical reactions (i.e. donates electrons to other molecules).

Benedict’s Reagent

A bright blue solution containing copper sulfate pentahydrate, sodium citrate, and sodium carbonate. Used to test for reducing sugars.

Benedict,s tests

Is performed by heating the reducing sugar with Benedict‘s reagent. The presence of the alkaline sodium carbonate converts the sugar into a strong reducing agent called enediols

Test for Starch

Add iodine in potassium iodide solution (Lugol’s iodine) to sample • If starch is present: it goes from orange/brown to blue-black It tests for starch

Lipids functions

Formation of triglycerides from alkanoic acids (fatty acids) and propane-1,2,3 triol (glycerol). Their main role as energy stores.

Lipids Properties

Contain large regions composed almost entirely of hydrogen and carbons, with nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids hydrophobic and insoluble in water.

True Lipids

Esters of fatty acids and an alcohol.

Fatty Acids (Alkanoic Acids)

Contain the acidic group —COOH (the carboxyl group) and are so named because some of the larger molecules in the series occur in fats. They have the general formula R.COOH where R is long hydrocarbon chain with many carbon atoms.

Saturated Fatty Acids

Have no double bonds between the carbon atoms.

Unsaturated Fatty Acids

Fatty acids that contain one or more double bonds (C=C).

Glycerol (Propane-1,2,3 triol)

An alcohol with three hydroxyl (-OH) groups, all of which can condense with a fatty acid to form an ester

Triglycerides

Commonest lipids in nature and if they are solid at 20°C they are called fats and if liquid they are oils.

Phospholipids

Lipids containing a phosphate group. The commonest type, phosphoglycerides, are formed when one of the primary alcohol groups (CH2OH) of glycerol forms an ester with phosphoric acid (H3P04) instead of a fatty acid.

Steroids

Consists of four rings of carbon fused together, with various functional groups protruding from them. Steroids include cholesterol, steroid hormones and Vitamin D.

Emulsion Test

Dissolve the substance by mixing it with absolute ethanol. 2. Decant the ethanol into water. If lipids are present in the mixture, it will precipitates and forms an milky emulsion.

Sudan (III) test

A red fat-soluble dye that is utilized in the identification of the presence of lipids, triglycerides and lipoproteins. The oil will stain red with Sudan III dye since it is a lipid and contains triglycerides.

Proteins and functions

General structure of an amino acid to include different properties of R groups and cysteine and methionine as examples of S- containing R groups; peptide linkage; primary structure; secondary structure to include α-helix and β-pleated sheet. fibrous proteins have a structural role e.g. collagen; globular proteins mostly function as enzymes, antibodies and hormones e.g. insulin.

Proteins structures

Polymers and the monomers building up the proteins are known as amino acids.

Essential amino acids

Plants are able to make all the amino acids that they required from simpler substances. However, animals are unable to synthesize all that they need, and therefore must obtain some ‘ready-made’ amino acids directly from their diet.

Thiols

When sulfur is present in chemical compounds

Structure of proteins

Are complex organic compounds always containing the elements carbon, hydrogen, oxygen and nitrogen and in some cases sulphur. Some proteins form compounds with other molecules containing phosphorus, iron, zinc and copper.

The primary of protiens

he number and sequence of amino acids held together by peptide bonds in a polypeptide chain. The sequence is coded by the genes. Different types of proteins have different sequences of amino acids.

Secondary structure of proteins

Hydrogen bonds cause may protein chains to form secondary structures.

Tertiary structure

Usually the polypeptide chain bends and folds extensively forming a ‘globular’ shape. This is maintained by the interaction of: ➢ Hydrogen bonds (these are between R groups) ➢ Disulphide bridges (only occurs between cysteine amino acids) ➢ Ionic bonds (occurs between charged R groups)

Quaternary structure

May highly complex proteins consist of an aggregation of polypeptide chains held together by hydrophobic interactions, hydrogen and ionic bonds and disulfide bridges.

Denaturation

Is the loss of the specific 3-dimentional conformation of proteins. Denatured by Heat Strong acids and alkali and high concentrations of salts. Heavy metals. Organic solvents and detergents.

Fibrous Proteins

Play a fundamental structural role in the body. Collagen has a unique triple- helix structure forms a sturdy, fibrous framework that provides tensile strength to tissues such as skin, tendons, and bones