Biochemistry Flashcards
Subatomic Particles in Atoms
Protons (+), Neutrons and Electrons (-)
Ground State
If all electrons in an atom are in the lowest available energy levels.
Excited State
When an atom absorbs, its electrons move to a higher energy level.
Isotopes
Atoms of one element that vary only in the number of neutrons in the nucleus. Chemically, all isotopes of the same element are identical because they have the same number of electrons in the same configuration.
Half-Life
The rate at which an isotope decays. Enables us to measure the age of fossils or to estimate the age of the Earth.
Tracer
Radioisotopes that can be incorporated into a molecule and use to trace the path in a metabolic pathway.
Atom Bonds
Atoms bond when two atomic nuclei attract the same electron/s. Energy is released when a bond is formed and energy must be supplies to break a bon. Atoms bonds to acquire a stable outer shell, a stable configuration.
Ionic Bonds
Results from the transfer of electrons. An atom that gains electrons becomes an anion and an atom that loses an electron becomes a cation.
Ions Necessary for Normal Nerve Function
Na+, Ca++, and Cl-
Ions Necessary for Normal Nerve Function
Na+, Ca++, and Cl-
Covalent Bonds
Form when atoms share electrons and the resulting structure is a molecule. Single covalent bonds results when two atoms share a pair of electrons; double occurs when two atoms share two pairs and so on.
Non-Polar Bond
Occurs when electrons are shared equally between two identical atoms. Found in diatomic molecules such as H2 or O2.
Polar Bonds
If electrons are shared unequally between two atoms.
Polar Bonds
If electrons are shared unequally between two atoms.
Polar and Non-Polar Molecules
Polar molecules are unbalanced and contain strong attractions. Non-Polar molecules are the opposite. Polar molecules will generally only dissolve in polar molecules and the opposite is true for non-polar molecules.
Polar and Non-Polar Molecules
Polar molecules are unbalanced and contain strong attractions. Non-Polar molecules are the opposite. Polar molecules will generally only dissolve in polar molecules and the opposite is true for non-polar molecules.
Hydrophobic and Hydrophilic
Substances that are polar will dissolve in water while substances that are non-polar will not. Lipids are hydrophobic and don’t dissolve in water this is the reason why oils separate when mixed with water. This is also the reason why only non-polar substances can pass through the plasma membrane. Large polar molecules must pass through hydrophilic protein channels.
The Water Molecule
One side of the molecule has a negative charge (O) and one has a positive charge (H).
The Water Molecule
One side of the molecule has a negative charge (O) and one has a positive charge (H). In addition, two molecules of water can be held together by hydrogen bonding.
Hydrogen Bonding
A weak bond created as a result of the electrostatic attraction between a negative molecule and a positive molecule.
Specific Heat Definition
The amount of heat a substance must absorb to increase one gram of the substance by one degree celsius.
Water and Specific Heat
Water has a high specific heat and therefore, can provide a stable environmental temperature for the organisms that live there. In addition, because large bodies of water exhibit little temperature change, they moderate the climate of the nearby land.
Water and Vaporization
Water has a high heat of vaporization. This means that evaporating water required a relatively great amount of heat. As a result, the evaporation of sweat significantly cools the body.
Water as a Solvent
Since water is a highly polar molecule, it dissolves all polar and ionic substances.
Water and Tension
Water exhibits a very strong cohesion tension. This means that water molecules attract each other.
Transpirational-Pull Cohesion
Water moves up a tall tree from the roots to the leaves without the expenditure of energy due to water’s cohesion. As a molecules of water is lost from the leaves through transpiration another molecules is drawn in from the roots.
Capillary Action
Results from the combined forces of cohesion and adhesion.
Surface Tension
Allows insects to walk on water without breaking the surface. A result of cohesion.
Water as Ice
Ice floats because it is less dense than water.
Spring Overturn
In the winter, ice allows the liquid under it to be insulated. Then, in the spring the ice melts and sinks to the bottom of the lake causing water to circulate. Oxygen is returned to the depths and nutrients from the bottom of the lake move upwards. The cycling of nutrients in the lake is know as spring overturn.
pH Values
Anything less than a pH of 7 is an aid and anything over is basic/alkaline. 7 is a neutral pH. The value of pH is the negative log of the hydrogen ion concentration in moles per liter.
pH of Stomach Acid
2
pH of Human Blood
7.4
pH of Acid Rain
1.5-5.4
Internal pH of most living cells is…
about 7
Buffer
Substances that resist changes in pH by absorbing excess hydrogen ions or donating hydrogen ions when there are too few.
Most Important Buffer in Human Blood
bicarbonate ion
pH Values
Anything less than a pH of 7 is an aid and anything over is basic/alkaline. 7 is a neutral pH. The value of pH is the negative log of the hydrogen ion concentration in moles per liter. As H+ concentration increases pH decreases.
Most Important Buffer in Human Blood
bicarbonate ion - Donor/Acid: H2CO3; Acceptor/Base: HCO3-
Most Important Buffer in Human Blood
bicarbonate ion - Donor/Acid: H2CO3; Acceptor/Base: HCO3-
Isomer
Organic compounds that have the same molecular formula but different structure, therefore, different properties.
Structural Isomers
Organic compounds that differ in arrangement of their atoms.
Geometric Isomers
Organic compounds that differ only in spatial arrangements around double bonds which are not flexible like single bonds.
Optical Isomers or Enantiomers
Organic compounds that are mirror images of each other. The images are called the left-hand and the right-hand. Amino-acids are all left-handed.
Optical Isomers in Pharmaceuticals
Two mirror images of compounds may not be equally effective. L-dopa can treat Parkinson’s disease but R-dopa is useless in treatment of the disease.
Optical Isomers in Pharmaceuticals
Two mirror images of compounds may not be equally effective. L-dopa can treat Parkinson’s disease but R-dopa is useless in treatment of the disease.
Classes of Organic Compounds
carbohydrates, lipids, proteins and nucleic acids
Classes of Organic Compounds
carbohydrates, lipids, proteins and nucleic acids
Carbohydrate Structure
Carbon, hydrogen and oxygen are the main three elements. The number of hydrogen atoms to the number oxygen atoms is 2 to 1. C(n)H(2)O is the empirical formula.
Carbohydrate Function
It is used in the body for quick energy. One gram of a carbohydrate will release 4 calories when it is burned.
Sources of Carbohydrates
Rice, pasta, bread, cookies, and candy are the dietary sources.
Three Classes of Carbohydrates
monosaccharides, disaccharides and polysaccharides
Monosaccharides
Chemical Formula: C6H12O6. Glucose, galactose and fructose are isomers of each other.
Disaccharides
Chemical Formula: C12H22O11. They are formed by two monosaccharides joined when one molecule of water is released through dehydration synthesis/condensation.
Dehydration Synthesis and Disaccharides
C6H12O6 + C6H12O6 = C12H22O11 + H2O
Disaccharides
Chemical Formula: C12H22O11. Maltose, lactose and sucrose are examples. They are formed by dehydration synthesis/condensation.
Dehydration Synthesis and Disaccharides
Two monosaccharides joined when one molecule of water is released. C6H12O6 + C6H12O6 = C12H22O11 + H2O
Hydrolysis
The breakdown of a compound by adding water. The opposite of dehydration synthesis/condensation.
Hydrolysis
The breakdown of a compound by adding water. The opposite of dehydration synthesis/condensation.
Polysaccharides
Polymers of carbohydrates and are formed as many monosaccharides join together by dehydration synthesis. Important polysaccharides are cellulose, chitin, starch and glycogen.
Cellulose as a Polysaccharide
Makes up plant cell walls.
Starch as a Polysaccharide
Found in plants; two forms are amylose and amylopectin
Chitin as a Polysaccharide
Makes up the exoskeleton in arthropods and cell walls in mushrooms.
Glycogen
“Animal Starch”; In humans this is stored in the liver and skeletal muscle.
Lipid Examples
They include fats, oils, waxes and steroids. They are grouped together because they are all hydrophobic and are not soluble in water.
Lipid Structure
Consist of 1 glycerol and 3 fatty acids. Phospholipids are lipid molecules with a phosphate attached.
Glycerol
Alcohol; C3H8O3
Fatty Acid
A hydrocarbon chain with a carboxyl group at one end.
Saturated
All the carbons are attached by single bonds to molecules. Saturated fats from animals are solids at room temperature and in large, ingested quantities may cause heart disease. (Ex. butter)
Unsaturated
Carbons are attached by double bonds to molecules formed by the removal of hydrogen atoms in the carbon skeleton. In general, these are extracted from fats and are liquid at room temperature.
Tropical Oils and their Saturation
Coconut oil and Palm oil are saturated, somewhat solid at room temperature and as unhealthy as animal fats. This contradicts the usual idea that plant oils are unsaturated and healthy at room temperature.
Steroids
Lipids that consist of four fused rings. Examples are cholesterol, testosterone and estradiol.
Lipid Functions
Energy storage; one gram of any lipid will release 9 calories per gram. Structural; a major component of the cell membrane such as the plasma membrane of animal cells. Endocrine; some steroids are hormones.
Protein Function
Growth and repair; signaling from one cell to another; defense against invaders; catalyzing chemical reactions; etc..
Protein Function
Growth and repair; signaling from one cell to another; defense against invaders; catalyzing chemical reactions; etc..
Sources of Protein
fish, poultry, meat and certain plants such as beans and peanuts
Protein Energy
one gram of a protein releases 4 calories
Protein Structure
The main elements contained by a protein are Sulfur, Phosphorus, Carbon, Oxygen, Hydrogen and Nitrogen. They are polymers/polypeptides consisting of units called amino acids joined by peptide bonds.
Amino Acid Structure
They consist of a carboxyl group (CHO2), an amine group (NH2) and a variable (R) attached to a central asymmetric carbon atom. The R group called the side chain differs with each amino acid. The 20 amino acids can build thousands of different proteins.
Protein Conformation
Each protein has a unique shape that affects how it performs and functions. Four levels of protein structure a responsible for a protein’s unique conformation.
Protein Conformation
Each protein has a unique shape that affects how it performs and functions. Four levels of protein structure a responsible for a protein’s unique conformation.
Protein: Primary Structure
The unique linear sequence of amino acids. The slightest change can have dire consequences. Fred Sanger was the first to sequence the protein, insulin.
Protein: Secondary Structure
The secondary structure of a protein results from hydrogen bonding within the polypeptide molecule. The polypeptide coils and folds into either an alpha helix of beta pleated sheets.
Fibrous Proteins
Proteins that exhibit either alpha helix or pleated sheet. Examples are wool, claws, beaks, reptile scales, collagen and ligaments. The proteins that make up human hair is called keratin and is composed of alpha helixes.
Protein: Tertiary Structure
The tertiary structure of a protein is the intricate three-dimensional shape of conformation of a protein that is superimposed on its secondary structure. This determines a protein’s specificity.
Factors that Contribute to Tertiary Structure
Hydrogen bonding between R groups of amino acids; Ionic bonding between R groups; Hydrophobic interactions; Van de Waals interactions; Disulfide bonds between cysteine amino acids
Protein: Quaternary Structure
The quaternary structure refers to proteins that consist of more than one polypeptide chain. Hemoglobin, for example, consists of four polypeptide chains each forming a heme group.
The Protein-Folding Problem
The area of studying how proteins spontaneously folding into their unique shapes.
Chaperone Proteins
Molecules that assist in folding other proteins.
Chaperone Proteins
Molecules that assist in folding other proteins.
The two Nucleic Acids
ribonucleic acid or deoxyribonucleic acid
Nucleic Acid Structure
Repeating units called nucleotides make up nucleic acids.
Nucleotide Structure
Consist sof a phosphate, a 5-carbon sugar (ribose/deoxyribose) and a nitrogenous base. Carbon atoms of deoxyribose are numbered from 1 to 5.
Nitrogenous Bases
Adenine, Cytosine, Guanine and Thymine (DNA) or Uracil (RNA)
Nitrogenous Bases
Adenine, Cytosine, Guanine and Thymine (DNA) or Uracil (RNA)
Functional Groups
Components of organic molecules that are most often involved in chemical reactions. They are attached to the carbon skeleton and replace one or more hydrogen atoms.
Functional Group - Amino
NH2; Name of Compound: Amine
Functional Group - Carboxyl
COOH; Name of Compound: Carboxyl
Functional Group - Hydroxyl
OH; Name of Compound: Alcohol
Functional Group - Phosphate
PO4 (3-); Name of Comound: Organic Phosphate
Functional Group - Phosphate
PO4 (3-); Name of Compound: Organic Phosphate
First Law of Thermodynamics (Law of Conservation of Energy)
Energy cannot be created nor destroyed only transferred.
Second Law of Thermodynamics
In the course of energy conversions the universe becomes more disordered (greater entropy).
Gibb’s Free Energy
ΔG = ΔH - TΔS ΔG - change in free energy ΔH - change in heat content T - absolute temperature ΔS - change in entropy
Negative ΔG
Energy releasing reactions. Exergonic or exothermic.
Positive ΔG
Energy absorbing equations. Endergonic or endothermic.
Coupled Chemical Reactions
Cellular reactions in which the exergonic reactions power the endergonic ones.
Metabolism
The sum of all the chemical reaction that take place in cells. Metabolic reactions controlled by enzymes that take place through pathways that serve a special function an are controlled by enzymes.
Catabolism and Anabolism
Reactions that break down molecules or build them up.
Enzymes
Serve as catalytic proteins that speed up reactions by lowering the energy of activation.
Energy of Activation
The amount of energy needed to begin a reaction.
Negative ΔG
Energy releasing reactions. Exergonic or exothermic. In a potential energy diagram the potential energy of the products is less than the potential energy of the reactions so the reaction is exothermic.
Positive ΔG
Energy absorbing equations. Endergonic or endothermic. In a potential energy diagram the potential energy of the products is greater than the potential energy of the reactants.
Enzymes
Globular proteins that exhibit tertiary structure; They serve as catalytic proteins that speed up reactions by lowering the energy of activation. Dotted lines on a potential energy diagram represent catalysts. Enzymes can catalyze in both directions.
Energy of Activation
The amount of energy needed to begin a reaction.
Induced-Fit Model
As a substrate enters an active site, it induces the enzymes to alter its shape slightly so the substrate fits better.
Enzymes and Substrates
Enzymes are substrate specific. They are named after their substrate and the name ends in the suffix “ase”.
Cofactors/Coenzymes
Cofactors are inorganic molecules that help enzymes and coenzymes are vitamins that help enzymes.
Enzyme Efficiency
Enzymes are affected by pH and temperature. 37 degrees celsius is optimal for human enzymes. If temperature is too high enzymes denature and lose their conformation. Gastric enzymes becomes active at low pH while intestinal amylase works best in alkaline environments.
Competitive Inhibition
Inhibition of an enzyme due to some compounds resemble the normal substrate molecule and compete for the same active site on the enzyme. These mimics reduce the productivity of enzymes by preventing the substrate from combining with an enzyme. They can be reversible or nonreversible.
Noncompetitive Inhibition
When an enzyme contains more than one active site and the substrates do not resemble each other. Binding of either substrate presents the other from binding to the enzyme. The substrate that binds to the enzyme is ransom and a function of the concentration of each substrate.
Noncompetitive Inhibition: Operon
The binding of a repressor to the operator on the DNA strand blocks the binding site for RNA polymerase and no transcription can occur.
Allosteric Inhibition
Two active sites are present; one for a substrate and one for an inhibitor. The enzyme oscillates between two conformations; active or inactive. When the inhibitor binds the substrate site is altered and the enzyme cannot catalyze the reaction.
Allosteric Inhibition: phosphofructokinase
Catalyzes step three in the production of pyruvic acid and is inhibited by ATP. This is an example of feedback inhibition where a metabolic pathway is switched off by its end product.
Cooperativity
Substrates can stimulate an enzyme with quaternary structure to be more effective. For example, when oxygen bing to hemoglobin it can rapidly bind to three more oxygen atoms.
