biochem review

Matter anything that has mass and occupies space Composed of atom 90 naturally occurring atom (elements) About 26 “man-made” elements Organized on the periodic table of elements Atoms are composed of smaller particles Proton (+) - in the nucleus ; Mass: 1.0u Neutron (o) - in nucleus; Mass: 1.0u Electron (-) - outside nucleus ; Mass: 0.00054u

ELEMENTS Defined by # of protons in nucleus (atomic #) Electrically neutral NOTE #p+ = #e- also, atomic mass = #p+ + #no 12 C mass 6 #

ISOTOPES Has same # of protons (atomic #), but different number of neutrons (atomic mass) For eg. carbon has 3 isotopes 12 C 13 C 14 C 6 6 66no 7no 8no All isotopes have some chemical properties, just different masses, with the expectation of radioactivity.

RADIOISOTOPES : CHEMICAL BONDS (IONIC) Radioisotopes - have an unstable nucleus and emit subatomic particles or energy as they decay into more stable atoms radioactive emissions include : 3 types Alpha particles ( ) : a helium nucleus 2 proton and neutron being released Can be stopped by paper Beta particles ( ) : high speed electrons Can be stopped by lead Gamma rays ( ) - energetic electromagnetic radiation Brick of lead RADIOISOTOPES IN MEDICINE Radiation can damage cells Extremely useful in diagnosis and treatment of diseases Ex1 : inject radioactive material into patient and traces its movement in the body Ex 2: energy emitted from radioactive decay can be directed to a tumor Short half-life preferred

Radioisotopes Uses 146C Traces movement of carbon through biological pathways, like respiration and photosynthesis 4530Ca Measures rate of bone formation 4019K Half-life of 13 billion year (decays into 40Ar) ratio of 40K : 40Ar used to date fossils 13153I Taken up by thyroid gland can be imaged to detect abnormalities 22688Ra Emits radiation that can destroy living cells used to treat cancer tumors

HOW ARE THEY TRACED? Tracers - radioisotope placed in body on biologically active molecule (glucose, water, or ammonia) Give off gamma rays as they -easily detectable

CHEMICAL BONDS Chemical bonds are formed between atoms by interaction of their respective electrons Three types of intrAmolecular bond that hold atoms in a molecule together: Ionic bonds Covalent bonds Polar covalent bonds IONIC BONDS Occurs when there is a transfer of one or more electrons from one atom to another Transfer leads to formation of a cation and anion Resulting electrostatic attraction between these two oppositely charged ions is an ionic bond

COVALENT BONDS Involves sharing of electrons between atoms to achieve a stable electron configuration (stable octet) For example, Two hydrogen atoms combine to form a molecule of hydrogen gas Electrons always attempt to move as far away from one another as possible creating different molecular shapes (VSEPR theory) Each hydrogen atom has one electron of its own and shares, for some time the electron of the other hydrogen atom Each has full outer energy level Equal sharing of electrons, so bond is purely covalent

POLAR COVALENT BONDS Occurs when there is an unequal sharing of electron within a molecule For ex. In water, polar bonds are formed b/c O has a greater attraction for shared electrons (electronegativity) than H.

IONIC, COVALENT OR POLAR COVALENT Type of bond that forms is determined by the difference in electronegativity of the two involved If there is essentially no difference (<0.5), bond is covalent If difference is between 0.5 - 1.7 bond is polar covalent If the difference is equal to or greater than 1.7 bond is ionic

POLAR AND NON POLAR MOLECULES Polar molecules - has a slight positive charge on one side and slight negative charge on the other - unequal distributions of charge How to determine if a molecule is polar or non polar: Draw lewis dot diagram for each pair Determine structural formula of molecule Does molecule have a positive end and a negative end Polar molecules are good solvents because they can disrupt ionic bonds

POLAR MOLECULES = GOOD SOLVENTS When salt and water are mixed, negative end of water molecules are attached to Na+, while positive end of water molecule are attracted to CL- Water molecules from “spheres of hydration” around ions, causing the slats to dissolve

INTERMOLECULAR BONDS - SPECIAL PROPERTIES OF WATER INTERMOLECULAR BONDS Intramolecular bonds - holds atoms in a molecule together Intermolecular bonds - hold two or more molecules together Much weaker and determine physical state of substances 3 types of intERmolecular bonds: Collectivity known as Van der waals forces

London force Causes bonds thats are formed due to a temporary unequal distribution of electrons in an atom Very weak, occu between small nonpolar molecules (ex: methane) Ex: Ch4 : each molecule is weakly attracted to its neighbor That is why methane is a gas at room temperature Cumulative effect of london forces become more significant in larger nonpolar molecules (ex: octane) Ex: C8H18 In larger molecules, many weak attractive forces result in a clear association As a result, octane is a liquid at room temperature Dipole - dipole forces Occurs between polar molecules, like HCl Slightly positive end if one polar molecule is attracted to slightly negative end of another polar molecule Stronger than london forces Hydrogen bonds Dipole -dipole forces that form between electropositive H of one polar molecule and an electronegative N, O, or F of another Strongest intermolecular force Ex: H2O

IntRAmolecular IntERmolecular Holds one molecule together Holds many molecule together Strong attraction between atoms Weak attraction between molecules Commonly called ‘bonds’ Known as van der waals forces Determines if electrons are transferred or shared Determines state of substance Ex: ionic, covalent, polar covalent Ex: london forces, dipole-dipole, hydrogen bond

SPECIAL PROPERTIES OF WATER Hydrogen bonding and the angular shape of a water molecule gives it unique properties essential to existence of living things Water is an excellent solvent Solvent - substance that is able to dissolve other substances Water is a polar molecule Break ionic bonds Water is both adhesive and cohesive Adhesive - tendency of dissimilar particles/ surfaces to cling to one another Cohesive - tendency of similar or identical particles/ surfaces to cling to one another Water has a high specific heat capacity Specific heat capacity - amount of energy needed to change the temp of 1 kg of substance by 1oC Water resists change in temperature Water has a high heat conductivity Water has a high boiling/freezing point Water is more dense as a liquid then as a solid

ACIDS, BASES, AND BUFFERS Glass of water does not only contain H2O molecules H2O molecules can collide to form OH- and H3O+ ions This process is called autoionization A glass of pure water has an equal concentration of OH- and H3O+ ions and is therefore neutral

THE pH SCALE Acidity is a measure of the hydronium ion concentration [H3O+] of a solution A logarithmic scale is used due to the wide range of [H3O+] pH is given by the following formula: pH = -log10[H3O] At 25oc, pure water has a [H3O+] of 1.0 * 10-7 mol/L So, the pH of pure water would be pH = -log10 (1.0*10-7) pH = 7 pure water is neutral pH is on a negative logarithmic scale When [H3O+] increases, pH decreases A 10x increases in [h3o +] increases, pH decreases A 10x increase in [h30+] decreases pH by only one unit pH = -log10[H30+] Acids solutions have a low pH Basic solutions have a high pH ACIDS Acids increases the [H3O+] when dissolved in water HCl is a strong acid b/c it ionizes completely in water

A weak acid, CH3COOH (acetic acid) only partially ionizes

The ‘strength’ of an acid is unrelated to its concentration It depends on its ability to dissociate into H3O+

BASES Bases increases the [OH-] when dissolved in water A strong bases NaOH (sodium hydroxide) ionizes completely in water

A weak base, NH3 (ammonia) only partially ionizes in water

A strong base is as dangerous as a strong acid

ACID - BASE BUFFERS Blood pH must remain within a narrow range (7.35 -7.45) A buffer is a substance that helps resist changes in pH Buffers usually consist of conjugate acid-bicarbonate buffer is very important When extra H+ ions enter the body (in food for example), they bond with HCO-3 ions to form H2CO3

In the same way, if a base enters the body and remove H+ ions H2CO is ionized to replace them. A buffer system in living things requires specific enzymes.

FUNCTIONAL GROUPS Reactive clusters of atoms attached to the carbon backbone of organic molecules Reactivity results from the polar nature of the cluster or the presence of multiple bonds (double or triple) Hydroxyl - found in alcohol and sugars

Amino - found in protein and bases

Sulfhydryl -found in rudder and protein

Phosphate - found in ATP, DNA and RNA

Carboxyl - found in acids (eg. vinegar)

Aldehyde - found in sugars and formaldehyde

Ketone - found in sugars and acetone

STRUCTURAL ISOMERS Structural isomers - molecule with same molecular formula but with different arrangement of atoms Differences in shape of isomers leads to differences in their physical and chemical properties For ex: glucose, galactose and fructose have same molecular formula (C6H12O6) but different structures Glucose itself has 3 diff structural isomers In dry state, glucose has linear structure, but when dissolved in water, molecule folds on itself to form one of two possible ring structure :

Two isomers of glucose differ only in orientation of a single hydroxyl (-OH) group Small structural difference leads to large differences in chemical properties Scratch found in mushrooms ( amylopectin is a polymer of -glucose - can be easily digested Starch - digestible Cellulose (found in celery) is a polymer of beta glucose can’t be digested by most animals Cellulose - not digestible Isomers illustrate that structure of a molecule determines function of that molecule ⭐ STRUCTURE = FUNCTION

THE MOLECULE OF LIFE Macromolecules - large molecules that often have complex structure Many are polymers Polymers - long chain like molecules composed of many smaller molecules (monomers ) linker together Monomer - small molecules; when linked together from polymers

CARBOHYDRATES Carbohydrates - carbon, hydrogen, and oxygen in 1:2:1 ratio Made up of simple sugar monomers (monosaccharides) Monosaccharide - single ringed; at least 2 hydroxyl groups, and an aldehyde or ketone Disaccharides - two simple sugars units linked together Oligosaccharide - 3-10 sugar units linked together Sugars are linked by covalent bonds Hydroxyl groups on adjacent sugars react to production a molecule of water and link sugars through a shared oxygen Condensation/ dehydration reaction - builds larger molecules from smaller units while producing water Sucrose - disaccharide made up of glucose and fructose Polysaccharides - formed when dozens, hundreds or thousands of simple sugars are linked together Complex carbs - provide vitamins, mineral and fiber Mono, di, and oligosaccharides -used for quick energy Polysaccharides used for energy storage (starch in plants, glycogen in animals) or structural components (cellulose in plants)

LIPIDS (FATS) Lipids - class of greasy, oily or waxy compounds that are non-polar and water insoluble Composed of C,H,O “CHO” Functions: energy storage, insulation, structural components, absorption of vitamins and mineral and hormones 2 major classes: those with fatty acids and those without

WHAT ARE FATTY ACIDS? Fatty acids - made of a ‘backbone’ of a carbon atoms (up to 36) Ending in a carboxyl group Saturated fats - fatty acids that contain only single - bonded carbons (e.g. stearic acid) Solid at room temperature Unsaturated fats - have one or more double -bonded carbons (eg. oleic acid) Liquid at room temperature

LIPIDS (WITH FATTY ACIDS) Phospholipids -consists of a phosphate ‘head’ (hydrophilic) attached to 2 fatty acids ‘tails’ (hydrophobic) Main components of cell membranes Head → water loving Tail → water hating Triglycerides - glycerol joined to 3 fatty acids “tails” Condensation reactions - occurs between hydroxyl groups on the glycerol and the carboxyl group on each fatty acid.

Resulting bonds are called ester linkages Triglycerides contain twice the stored energy as same mass of carbohydrates Waxes - long fatty acid chains linked to alcohols or carbon rings

Hydrophobic, extremely non -polar, soft solids Function -water resistance and protection Ex: wax-coating on fruits, leaves and stems (cutin), beeswax

LIPIDS (WITHOUT FATTY ACIDS) Steroids - lack fatty acids, have 4 fused hydrocarbon rings Cholesterol -important structural components of cell membranes and functional groups People with elevated levels of wrong type of cholesterol are more likely to experience heart disease or stroke Other steriods inculde sex hormones (testosterone, estrogen, progesterone)

PROTEINS Basic building blocks are amino acids Amino acids - composed of central carbon atom linked to amino group, carboxyl group, hydrogen atom and variable group of atoms called side chain or R-group 20 different amino acids Amino acids differ only in their R-group 6 polar, a non-polar, 5 electrically charged Essential amino acids, we must get these in our diet R groups males one amino acids different from another Series of amino acids link together to form a protein Structure and function of protein are determined by sequence of amino acids Amino acids are joined together through condensation reactions between a carboxyl group and amino group Called a peptide bond

FUNCTIONS OF PROTEINS: Structural components (muscle tissue, collagen in skin) Transport of materials ( channels in cell membrane Carrier molecule (hemoglobin carries oxygen) messenger molecules (hormones) Antigens ( used in immune response) Enzymes (catalyze biochemical reactions)

Structural proteins generally form strands or sheets, other have globular shape Globular proteins - four levels of structure, primary, secondary, tertiary, quaternary Primary structures - sequences of amino acids in polypeptide chain Secondary structure - caused by hydrogen bonding between adjacent amino acids May cause polypeptide chain to develop a helical orr a pleated shape Tertiary structure - result of further folding of polypeptide chain to cause interaction of R-groups Quaternary structure - caused by interaction of 2 or more polypeptide globules Overall result is a protein with a very specific 3 dimensional shape with unique surfaces and pockets All other levels of a protein structure are a consequences of primary structure Structure and functions of a protein are determined by sequence of amino acids

NUCLEIC ACIDS Basic building blocks are nucleotides Contain a 5-carbon sugar, a phosphate group and a nitrogenous base Functions include: Biochemical energy carriers (ATP, NABH & FADH2) Encoding genetic information (DNA, RNA, mtDNA) DNA IS AN EXAMPLE OF A NUCLEIC ACID DNA (deoxyribonucleic acid) is a polymer of nucleotides Contains the sugar deoxyribose, a phosphate group and one of 4 nitrogenous bases PURINES( double ringed) Adenine (A) - Guanine (G) PYRIMIDINES (single ringed) Thymine (T) - Cytosine (C) BOND PAIRS A -T G - C DNA is normally double stranded and twisted into a helix The two strands are held together by hydrogen bonds Genetic code is the sequence of bases (i.e. ATGAC)

RNA IS ANOTHER EXAMPLE OF A NUCLEIC ACID RNA (Ribonucleic acid) is polymer of nucleotides Contain the sugar ribose, a phosphate group and one of 4 nitrogenous bases Adenine (A), guanine (G) and Cytosine (C) [same as DNA] Thymine is replaced by uracil in RNA RNA is normally single stranded Three types of RNA are involved in protein synthesis Messenger (mRNA) Transfer (tRNA) Ribosomal (rRNA)

INTRO TO METABOLISM Catabolic reactions -complex substance broken down into something less complex Combustion of gasoline (octane) is an example:

Anabolic reactions -complex substances is built from something less complex Production of sugar (glucose) in photosynthesis is an example:

THERMODYNAMICS Metabolism - sum of all catabolic and anabolic reactions in an organism These reactions, as all reactions in universe, follow laws of thermodynamics FIRST LAW OF THERMODYNAMICS Total amount of energy in universe in constant Energy cannot be created or destroyed; it can only be converted from one form to another For example, burning of gasoline does not create energy; it just converts potential energy in chemical bonds to heat SECOND LAW OF THERMODYNAMICS Energy in universe is spontaneously flowing from higher to lower energy content Universe is becoming more disordered (entropy is increasing) For example, it is common to see a wine glass (ordered system) break into pieces (disordered system), but you will never see the broken pieces reforming into a wine glass on their own

SPONTANEITY OF REACTIONS AND COUPLED REACTIONS METABOLISM All processes of life require energy (growth, reproduction etc) Energy -ability to do work Organisms must capture, store, and use energy to function Reactions that transform matter and energy in our cells occur in step by step sequences called metabolic pathways

SPONTANEITY OF REACTIONS spontaneous reaction: reaction that will continue to completion without further energy input once initiated Example: oxidation of glucose

Nonspontaneous reaction: reaction that can only continue as long as it receives a continual energy input Example: electrolysis of water (using an electric current to break down water into oxygen and hydrogen gas)…

MANY chemical reactions that are exothermic (ie, give off heat) occur spontaneously So, how do you know if a reaction will be spontaneous? Three factors determine if a reaction is spontaneous or not: Enthalpy (H): total value of energy of a system (decreases in # tend toward spontaneity) Total of all kinetic and potential energy in system You can't calculate If the absolute value of H can’t be measured then what good is it? Not value of H that matters, it’s how it changes during a reaction Change in enthalpy ( H) can be measured When H is positive - reaction is endothermic When H is negative - reaction is exothermic

EXOTHERMIC REACTION

ENDOTHERMIC REACTION

2. Entropy (S): a measure of randomness of a system (increases in S tends towards spontaneity)
3. Temperature (T) : a measure of molecular motion (increase in T tend towards spontaneity)

GIBBS FREE ENERGY (G) - energy in system that can do useful work
Ex. before combustion, free energy in gasoline higher than in products of combustion Gasoline can do more useful work than carbon dioxide and water G decreases in this reaction Spontaneity can be determined mathematically with Gibbs free energy equation:

G = H - T S

WHEN G IS POSITIVE - REACTION IS NONSPONTANEOUS WHEN G IS NEGATIVE - REACTION IS SPONTANEOUS

BIOCHEMICAL COUPLING Non Spontaneous reactions require continual input of energy - metabolically expensive To conserve energy spontaneous reactions used to ‘drive’ nonspontaneous reactions For example: Synthesizing an ATP molecule is a nonspontaneous reaction ( G = +31kJ) Reaction can be coupled to a spontaneous reaction ( G = -49kJ) Overall, coupled reaction will be spontaneous ( G = -18kJ)

biochemical coupling of reactions occurs on surface of enzyme

ENZYMES enzymes are protein catalyst Speed up rate of reaction by lowering activation energy Reactants converted into products faster than without enzymes presents Enzymes not consumed in reaction - Continue to work indefinitely. Enzymes have very specific three-dimensional structure Precisely shaved, active site specific to substrate that enzyme works on Enzyme can only catalyze a single specific reaction For example, amylase is a enzyme which catalyzes following reaction

Amylose [a starch] – substrate Amylase – enzyme Maltose – product Enzymes different from other catalyst because they are a delicate organic molecules Very high temperature or a change in pH alter 3-D structure of enzyme – useless Denaturation – irreversible Models of enzyme function Early models of enzyme activity – lock and key model Propose exact fit between enzymes and subtract When combined Substrate converted into product an enzyme left unchanged Evidence suggest models does not accurately describe action of enzymes When substrate molecules enters active site, functional groups interact with functional groups of enzymes Currently accepted model – induced fit model Causes enzyme to change shape to better accommodate substrate Enzymes , then returns to original shape

ENZYME ACTIVITY AND COLLISION THEORY WHAT IS THE REACTION RATE? Rate of reaction – speed of a chemical reaction (how quickly a reactant is consumed as you convert into a product) WHY DO REACTIONS REQUIRE? Particles are constantly moving – collide with each other With enough energy and in right orientation – from larger molecules/compounds COLLISION MODEL Collision model – the more collisions, the more likely the particles have enough kinetic energy and will be oriented property for a reaction to occur Activation energy – minimum energy required for a reaction to occur

EFFECT OF SUBSTRATE CONCENTRATION As the number of subtract molecules increase, so does the chance of a successful reaction [collision theory] Enzyme molecules are saturated with substrate. [all enzymes and molecules are occupied at any given time.] EFFECT OF TEMPERATURE As temperature increases so the molecular motion This increases the probability of a successful reaction. [collision theory] High temperature denatures enzymes. They will no longer catalyze reaction. EFFECT OF PH Pepsin functions within pH range 0.4–4. pepsin optimal pH is 1.8. Trypsin functions within pH range 6– 10. Trypsin optimal pH is 8.2. Outside of these pH range is the enzymes will denature