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Chapter 2

 

 

Chemical basis of life

 

chemicals compose the structures of the body, and the interactions of chemicals with one another are responsible for the functions of the body.

 

 

 

Basic chemistry

 

  1. Matter – all living things are composed of matter which is anything that occupies space and has mass
  2. mass – the amount of matter in an object
  3. weight – the gravitational force acting on an object of a given mass
  4. kilogram – kg – the international unit of mass
  5. gram – 1/1000 the mass of the kilogram
  6. element – the simplest type of matter with unique chemical properties
    1. body is mostly made up of carbon, hydrogen, nitrogen, and oxygen
    2. 98%
  7. atom – the smallest particle of an element that has the chemical characteristics of that element
    1. elements are made up of one type of atom only
    2. carbon is made up of only carbon atoms
  8. an element or atom is often represented by a symbol
    1. usually the 1st letters of the element’s name
    2. sometimes Greek, Latin, or Arabic

 

 

Atomic Structure

 

1.      Subatomic particles that compose atoms:

a.      proton – 1 positive charge

b.      neutron – neutral or no charge

c.      electron – 1 negative charge

                                                                          i.      the positive charge of the proton is equal in magnitude to the negative charge of the electron

                                                                        ii.      the numbers of protons and electrons in each atom is equal

                                                                      iii.      the charges cancel each other out

                                                                       iv.      an atom is electronically neutral

2.      nucleus – formed by protons and neutrons

a.      accounts for 99.97% of an atom’s weight

b.      only 1 ten-trillionth of its volume

3.      electron cloud – the region where any given electron is located at any particular moment

a.      likelihood of locating an electron at a specific point in a region correlates with the darkness of that region

b.      the darker the color, the greater the likelihood of finding the electron there at a given moment

 

Atomic number and Mass number

 

  1. atomic number – is equal to the number of protons in each atom
    1. because the number of electrons and protons is equal it is also the number of electrons
  2. mass number – the number of protons plus the number of neutrons in each atom
    1. carbon is 12. 6 protons and 6 neutrons

 

 

Chapter 2 continued

 

 

 

Isotopes and atomic mass

 

  1. Isotopes – 2 or more forms of the same element that have the same number of protons and electrons, but a different number of neutrons.
    1. Have the same atomic number but different mass numbers
    2. 3 isotopes of hydrogen

                                                              i.      Hydrogen – 1 proton, 1 electron, no neutrons

                                                            ii.      Deuterium – 1 proton, 1 electron, 1 neutron

                                                          iii.      Tritium – 1 proton, 1 electron, 2 neutrons

    1. Isotopes denoted using the symbol of the element preceded by the mass number of the isotope.

                                                              i.      Hydrogen 1H,

                                                            ii.      Deuterium 2H

                                                          iii.      Tritium 3H

 

  1. unified atomic mass unit (u) or Dalton (D)
    1. Individual atoms have very little mass. To avoid using very small numbers, a system of relative atomic mass is used.
    2. is 1/12 the mass of 12C, a carbon atom with 6 protons and 6 neutrons
    3. 12C has an atomic mass of exactly 12u
  2. Atomic mass – is the average mass of its naturally occurring isotopes, taking into account the relative abundance of each isotope.
    1. Atomic mass of carbon is 12.01u because the additional mass of the small amount of other carbon isotopes.
    2. Because atomic mass is an average, carbon can be treated as if all carbon atoms have atom mass of 12.01u

 

 

Electrons and chemical bonding

 

1.      Chemical bonding: the outermost electrons of an atom determine its chemical behavior. When they are transferred or shared between atoms, chemical bonding occurs.

a.      two major types

2.      ionic bonding

a.      if an atom loses or gains electrons, the number of protons and electrons are no longer equal – creating a charged particle – an ion

b.      if it loses an electron, this makes the atom be positively charged like sodium -- cations

c.      if the atom gains an electron, this makes the atom be negatively charged like chloride – anions

d.      opposites attract and cations and anions stay close together in iconic bonding

e.      sodium and chloride ions are held together this way to form sodium chloride -- salt

3.      covalent bonding – results when atoms share one or more pairs of electrons

a.      resulting combo of atoms is called a molecule

b.      2 hydrogen atoms form a covalent bond to form a hydrogen molecule

c.      The positively charged nucleus of each hydrogen atom attract the electron of the other atom.

d.      At an optimal distance the 2 nuclei mutually attract the 2 electrons, and each electron is shared by both of them. They’re not held by a covalent bond

4.      single covalent bond

a.      an electron pair is shared between 2 atoms

b.      represented by a single line between the symbols of the atoms involved

c.      H—H (hydrogen)

5.      double covalent bond

a.      results when 2 atoms share 4 electrons

b.      2 from each atom

c.      Represented by a single line between the symbols of the atoms involved

d.      O==C==O (carbon dioxide)

6.      nonpolar covalent bonds

a.      electrons are shared equally between atoms – i.e. hydrogen molecule

7.      polar covalent bonds

a.      do not share their electrons equally between atoms

b.      the nucleus of one atom attracts the electrons more strongly than the other

c.      common in living and non-living matter

d.      can result in polar molecules which are electronically asymmetric

                                                                          i.      oxygen atoms attract electrons more strongly than hydrogen atoms

                                                                        ii.      in a water molecule, the electrons are located nearer the oxygen nucleus

                                                                      iii.      the electrons have a negative charge making the oxygen side of the molecule slightly more negative than hydrogen side

 

 

 

Molecules and Compounds

 

  1. Molecule – formed when 2 or more atoms chemically combine to form a structure that behaves as an independent unit.
    1. Can be same type – 2 hydrogen atoms for 1 hydrogen molecule
    2. Typically a molecule consists of 2 or more different types of atoms – 2 hydrogen atoms and 1 oxygen atom form water
  2. compound – substance composed of 2 or more different types of atoms that are chemically combined
    1. not all molecules are compounds – hydrogen is not
    2. water is a covalent compound – 2 hydrogen and 1 oxygen
    3. ionic compounds are not molecules

                                                              i.      they’re held together by force of attraction

                                                            ii.      sodium chloride is a compound but not a molecule

  1. the kinds and numbers of atoms or ions in a molecule or compound are represented by a formula consisting of symbols of the atoms or ions plus the subscripts denoting the number of each type of atom or ion
    1. glucose is C6H12O6
    2. meaning 6 carbon, 12 hydrogen, and 6 oxygen atoms
  2. molecular mass (of atom or ion)
    1. can be determined by adding up the atomic masses of its atoms or ions
    2. the term is a convenience for iconic compounds even though they are not molecules
    3. atomic mass of sodium 22.99 + atomic mass of chloride 35.45 = sodium chloride (NaCl) 58.44

 

 

 

Intermolecular forces

 

1.      intermolecular forces –

a.      result from weak electrostatic attractions between the oppositely charged parts of molecules

b.      or between ions and molecules

c.      weaker than the forces producing chemical bonding

2.      hydrogen bonds

a.      molecules with polar covalent bonds have positive and negative “ends” the oppositely charged ends are attracted to each other

b.      when the positively charged hydrogen of 1 molecule is attracted to the negatively charged oxygen, nitrogen, or fluorine of another molecule

c.      positive charged hydrogen atoms of water molecule form hydrogen bonds with the negatively charged oxygen atoms of another water molecule

d.      important in determining shape of complex molecules

e.      provides a cohesiveness

3.      solubility – the ability of one substance to dissolve in another

a.      i.e. sugar dissolves in water

b.      charged substances (sodium chloride) and polar substances (glucose) dissolve in water readily

c.      non polar substances such as oils do not

d.      substances dissolve when surrounded by water molecules and the positive and negative ends of the water molecules are attracted more to the charged ends of the other molecule than they are to each other

e.      the hydrogen bonds in the water molecule are broken and the water molecules then surround the other molecules which become dissolved

f.        most molecules (covalent compounds) remain intact even though surrounded by water molecules

4.      dissociate (separate) –

a.      when iconic compounds dissolve in water their ions separate from each other

b.      the cations are attracted to the negative ends of the water molecules

c.      the anions are attracted to the positive ends of the water molecules

d.      the sodium and the chloride ions separate and the water molecules surround and isolate them – keeping them in solution

5.      electrolytes –

a.      cations and anions that dissociate in water

b.      they have the capacity to conduct an electric current – the flow of charged particles

c.      ECG is a recording of the electric currents produced by the heart

6.      nonelectrolytes – molecules that do not dissociate

a.      form solutions that do not conduct electricity

b.      pure water is a nonelectrolyte

 

 

 

 

 

 

 

 

 

 

 

 

Chemical reactions and Energy

 

  1. chemical reaction – atoms, ions, molecules, or compounds interact with each other to form or to break chemical bonds
  2. reactants – the substances that enter into a chemical reaction
  3. products – substances that result from the chemical reaction

 

 

Types of chemical reactions

 

  1. synthesis reaction – less complex reactants combine to from a larger, more complex product
    1. synthesis of complex molecules of the body from basic building block of food
    2. two amino acids combining to form a dipeptide

                                                              i.      water is removed from the amino acids as they are bound together

  1. dehydration reactions – water out –
    1. synthesis reactions in which water is a product
    2. old chemical bonds are broken and new ones formed as atoms rearrange
  2. ATP – the energy currency of cells
    1. Synthesized from ADP and an inorganic phosphate P
    2. ADP + P = ATP
  3. anabolism – all of the synthisesis reactions that occur within the body
    1. growth, maintenance, and repair of body could not take place without anabolic reactions
  4. decomposition reactions– a reactant can be broken down, or decomposed, into simpler, less complex products
    1. the reverse of synthesis reactions
    2. break down of food molecules into basic building blocks
    3. ATP breaking down back into ADP and an inorganic phosphate are decomposition reactions
    4. disaccharide into glucose is another example

                                                              i.      water must be split into two parts and each part contributed to one of the new glucose molecules

                                                            ii.      hydrolysis reactions -- use water in this way

  1. catabolism – all the decomposition reactions that occur in the body
    1. include digestion of food molecules in the intestines and within cells
    2. breakdown of fat stores
    3. breakdown of foreign matter and microorganisms in certain blood cells that function to protect the body
  2. metabolism – all the anabolic and catabolic reactions in the body
  3. reversible reactions – is a chemical reaction in which the reaction can proceed from reactants to products or from products to reactants
  4. equilibrium – when the rate of the product formation is equal to the rate of the reverse reaction, the reaction system is at equilibrium
    1. the amount of reactants relative to the amount of products remains constant
    2. carbon dioxide (CO2) and water (H2O) form carbonic acid (H2CO3)
    3. carbonic acid then separates by reversible reaction to form hydrogen ions (H+) and bicarbonate ions (HCO3-)
    4. CO2 + H2O <>H2CO3<>H+ + HCO3-
    5. Maintaining a constant level of H+ is necessary for proper function of the nervous system. Achieved partly by regulating CO2 levels thru respiration
  5. oxidation-reduction reactions – chemical reactions that result from the exchange of electrons between the reactants.
    1. The complete or partial loss of an electron by an atom accompanied by the gain of that electron by another atom
    2. Can be Synthesis and/or decomposition reactions
  6. oxidation – the loss of an electron by an atom
  7. reduction – the gain of an electron by an atom
    1. complete transfer – ionic bond
    2. partial transfer – covalent bond
  8. energy – the capacity to do work
    1. that is, to move matter
    2. energy occupies no space and has no mass
    3. Energy cannot be created nor destroyed, only converted.
  9. potential energy – 1 form of energy
    1. stored energy that could do work but is not doing so
  10. kinetic energy – 2nd form of energy
    1. energy that actually does the work and moves matter
  11. mechanical energy – energy resulting from the position or movement of objects
    1. moving a limb, breathing
    2. circulating blood
  12. other forms of energy
    1. chemical
    2. heat
    3. electric
    4. electromagnetic (radiant)
  13. chemical energy – of a substance is a form of stored (potential) energy within its chemical bonds
    1. ATP has potential energy in the form of chemical energy
    2. If chemical energy in reactants is at a higher level than the chemical energy of the products, energy is released during the reaction.

                                                              i.      i.e. from food

    1. if the chemical energy in reactants is at a lower level than the chemical energy of the products, energy is used during the reaction

                                                              i.      i.e. muscle contractions

  1. heat energy – the energy that flows between objects that are at different temperatures
    1. always transferred from hotter object to cooler object
    2. temperature is a measurement of heat
  2. All other forms of energy can be converted to heat.
    1. Kinetic energy is converted to heat when a moving object comes to rest
    2. Some of the potential energy of chemical bonds is released as heat energy during chemical reactions
    3. Body temp is maintained by heat produced this way
  3. speed of chemical reactions – molecules are constantly in motion and have kinetic energy
  4. activation energy – the minimum energy that the reactants must have to start a chemical reaction
    1. sparkplug is an activation energy so gas and oxygen can explode
  5. catalysts – substances that increase the rate of chemical reactions without being permanently changed or deleted
    1. energy activation problem is that it requires a catalyst
  6. enzymes – protein catalysts
    1. they increase the rate of chemical reactions by lowering the activation energy necessary for the reaction to begin
    2. with an enzyme, the rate of chemical reaction can take place more than a million times faster

 

 

Inorganic chemistry

 

 

  1. inorganic chemistry – generally deals with those substances that do not contain carbon
  2. organic chemistry – the study of carbon containing substances
  3. exceptions:
    1. carbon monoxide (CO)
    2. carbon dioxide (CO2)
    3. bicarbonate ion (HCO3)
  4. water – 1 atom of oxygen joined to 2 atoms of hydrogen by covalent bonds
    1. water molecules are polar with a partial negative charge associated with the oxygen atom and a partial positive charge associated with the hydrogen atoms
    2. hydrogen bonds form between the hydrogen atoms of 1 water molecule and the oxygen atoms of another water molecule
    3. forms a lattice that holds the water molecules together
    4. water accounts for approximately 50% of the weight of a young adult female and 60% of a young adult male
  5. functions of water
    1. stabilizing body temperature

                                                              i.      Water has a high specific heat meaning a relatively large amount of heat is required to raise its temperature. Therefore it resists large temperature fluctuations

                                                            ii.      when water evaporates, heat is required

                                                          iii.      the evaporation of water from the surface of the body gets rid of excess body heat

    1. protection

                                                              i.      water is an effective lubricant for protection from friction damage

                                                            ii.      tears protect the eye from the eyelid

                                                          iii.      forms a cushion around organs to protect them from trauma

                                                           iv.      i.e. cerebrospinal fluid surrounds brain

    1. chemical reactions

                                                              i.      many chemical reactions necessary for life do not take place unless the reacting molecules are dissolved in water

                                                            ii.      sodium chloride must dissociate in water into Na+ and Cl- before they can react with other ions

                                                          iii.      water directly participates in many chemical reactions

                                                           iv.      dehydration reaction is synthesis reaction that produces water

                                                             v.      hydrolysis reaction is a decomposition reaction that requires a water molecule

    1. Mixing medium – the ability of water to mix with other substances enables it to act as a medium for transport, moving substances from one part of the body to another.

                                                              i.      Mixture – a combination of two or more substances physically blended together, but not chemically combined.

                                                            ii.      Solution – any mixture of liquids, gases, or solids in which the substances are uniformly distributed with no clear boundary between the substances.

1.      the solute dissolves in the solvent

2.      water is the solvent and salt the solute in a salt solution

                                                          iii.      suspension – a mixture containing materials that separate from each other unless they are continually, physically blended together

1.      blood is a suspension liquid containing red blood cells suspended in liquid (plasma)

2.      it will separate into layers if allowed to sit

                                                           iv.      colloid – a mixture in which a dispersed (solutelike) substance is distributed throughout a dispersing (solventlike) substance

1.      the dispersed particles are larger than a simple molecule but small enough that they remain dispersed and do not settle out

2.      proteins – which are like large molecules – and water form colloids

a.      plasma and the liquid portion of cells are colloids containing many important proteins

  1. Solution concentrations – concentration of solute particles dissolved in solvents an be expressed in several ways.
    1. 1 common way is to indicate the percent of solute by weight per volume of solution
    2. A 10% solution of sodium chloride is 10g of sodium chloride in enough water to make 100ml of solution
  2. osmoles – expresses the number of particles in a solution.
    1. Particles can be atom, ion, or molecule
    2. An osmole (osm) is 6.022 x 10(to the 23rd) particles of a substance in 1 kg of water
    3. Chemists group atoms in lots of 6.022 x 10(to the 23rd)
  3. osmolatiy – a reflection of the number, not the type, of particles in a solution
    1. 1 osm glucose solution and a 1 osm sodium chloride solution both contain 6.022 x 10(to the 23rd) particles per kg of water
    2. The glucose has 6.022 x 10(to the 23rd) molecules of glucose
    3. The sodium chloride dissociates into 3.011 x 10(to the23rd) sodium ions and 3.011 x 10(to the 23rd) chloride ions
  4. milliosmole – measurement of concentration of particles in body fluids
    1. milliosmole (mOsm) 1/1000 of an osmole
    2. concentration of particles in body fluids are very low
    3. most body fluids have concentration of about 300 mOsm
    4. The concentration influences the movement of water into or out of cells.

 

 

Acids and Bases

 

  1. Acids – defined as a proton donor
    1. Hydrogen ion is a proton because of the loss of the electron from the hydrogen atom, which consists of a proton and an electron
    2. A molecule or compound that releases H+ is an acid
  2. Base – defined as a proton acceptor
    1. Any substance that binds to (accepts) hydrogen ions (H+) is a base
    2. Most bases function as a proton acceptor by releasing hydroxide ions (OH-) when they dissociate
  3. Classifications of acids and bases
    1. Strong – dissociate almost completely when dissolved n water

                                                              i.      They release almost all of their H+ or OH- (hydrogen or hydroxide)

                                                            ii.      The more completely the acid or base dissociates, the stronger it is

                                                          iii.      HCl is a strong acid because it completely dissociates in water

    1. Weak – only partially dissociate in water

                                                              i.      They release only some of their H+ or OH-

                                                            ii.      Acetic acid when dissolved in water, some dissociates but some remains in undissociated form. An equilibrium is established between the ions and undissociated weak acid

                                                          iii.      For a weak acid or base, the amount of dissociated ions relative to the weak acid or base is a constant

                                                           iv.      Vinegar is a weak acid

  1. when acids and bases come together, they form water and a salt
  2. PH Scale – means of referring to the H+ concentration in a solution
    1. Scale runs from 0 to 14
    2. The higher the number, the more basic the solution
    3. Pure water is a neutral solution and has a PH of 7. there are equal concentrations of H+ and OH-
    4. Solutions with PH of less than 7 are acidic. They have a greater combo of H+ than OH-
    5. Alkaline or basic – solutions with a PH greater than 7. they have fewer H+ or OH-
    6. A change in the PH of a solution by 1 PH unit is a 10 fold change in the H+ concentration.

                                                              i.      Solution with PH of 6 has H+ concentration 10 times greater than a solution with PH of 7 and 100 times greater than a solution with PH of 8


 

    1. Normal PH range for blood is 7.35 to 7.45

                                                              i.      Acidosis – blood PH drops below 7.35

1.      nervous system is depressed

2.      person can become disoriented and possibly comatose

                                                            ii.      Alkalosis – blood PH rises above 7.45

1.      nervous system is overexciteable

2.      person can be extremely nervous or have convulsions

 

  1. Salts – are ionic compounds held together by ionic bonds
    1. Consist of cation other than H+ and an anion of other than OH-
    2. Formed by the interaction of an acid and a base in which the H+ of the acid are replaced by the positive ions of the base
    3. When salt dissociates in water it dissociates into a cation and an anion. They form positively and negatively charged ions.
    4. I.e.: HCl (hydrochloric acid) reacts with base sodium hydroxide (NaOH), the salt, sodium chloride (NaCl) is formed
  2. buffers – resist changes in PH when an acid or base is added to a system
    1. decreases the magnitude of PH change for a given addition of acid or base
    2. helps maintain PH in our blood
    3. can be described as a conjugate acid-base pair

                                                              i.      buffer is a solution of a conjugate acid-base pair in which the acid component and the base component occur in similar concentrations

                                                            ii.      a conjugate base is everything that remains of an acid after the H+ (proton) is lost

                                                          iii.      a conjugate acid is formed when a H+ is transferred to the conjugate base

                                                           iv.      carbonic acid (H2CO3) and a bicarbonate ion (HCO3-) formed by the dissociation of H2CO3 are a conjugate acid-base pair

    1. the greater the buffer concentration, the more effective it is to resisting change in PH
    2. buffers cannot entirely prevent some change in the PH of a solution
    3. buffers found in living systems have bicarbonate, phosphates, amino acids, and proteins as components

 


 

 

Oxygen (O2) –

a.      is an organic molecule consisting of two oxygen atoms bound together by a double covalent bond.

b.      21% of the gas in the atmosphere is oxygen and is essential for most animals

c.      Required by humans in the final step of a series of reactions in which energy is extracted from food molecules

 

Carbon Dioxide (CO2) –

a.      consists of two oxygen atoms bound to one carbon atom.

b.      Each oxygen atom is bound to the carbon atom by a double covalent bond

c.      CO2 produced when organic molecules such as glucose are metabolized within the cells of the body

d.      The energy stored in the covalent bonds is transferred to other organic molecules when glucose is broken down

e.      CO2 is a metabolic by product, transferred to lungs by blood, and exhaled during respiratioin

f.        CO2 build up in cells can be toxic

 

 

 

 

Organic Chemistry

 

The ability of carbon to form covalent bonds with other atoms makes possible the formation of the larger, diverse, complicated molecules necessary for life.

 

The backbone of large molecules

 

4 major groups: carbohydrates, lipids, proteins, and nucleic acids

 

 

Carbohydrates

 

  1. carbohydrates
    1. primarily carbon, hydrogen, and oxygen
    2. polar – primarily because of the oxygen.
    3. Soluble in polar solvents such as water
    4. carbos break down into energy
    5. range in size large to small
    6. in most carbos for each carbon atom there are approximately two hydrogen atoms and one oxygen atom. The same as in water
    7. called carbohydrates because carbon atoms are combined with the same atoms that form water. Carbo+hydrated
    8. undigested carbos provide bulk in feces, which helps to maintain the normal function and health of the digestive system
  2. monosaccharides
    1. simple building blocks
    2. usually have 3 (trioses), 4 (tetroses), 5 (pentoses), or 6 (hexoses) carbon sugars
    3. mono means one saccharide means sugar
    4. isomers – common 6 carbon sugars

                                                              i.      glucose, fructose, and galactose

                                                            ii.      molecules that have the same number and types of atoms but differ in their 3D arrangement

                                                          iii.      glucose – blood sugar – the major carbo found in the blood and is major nutrient for most cells of the body

    1. some important 5 carbon sugars

                                                              i.      ribose and deoxyribose

                                                            ii.      both components of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), respectively

  1. Disaccharides
    1. Composed of 2 simple sugars bound together through dehydration reaction
    2. Sucrose – formed by glucose and fructose plus 1 water molecule
    3. Sucrose, lactose, and maltose are important
    4. Lactose – milk sugar – glucose combined with galactose
    5. Maltose – malt sugar – is 2 glucose molecules joined together
  2. Polysaccharides
    1. Many monosaccharides bound together to form chains or branched chains
    2. Glycogen – animal starch – glucose molecules covalently bound in chains

                                                              i.      Important energy storage molecule

                                                            ii.      Can be metabolized rapidly and the resulting energy can be used by cells.

                                                          iii.      Substantial amount is metabolized to produce energy during exercise and stored in the cells of the liver and skeletal muscles

    1. Starch and cellulose

                                                              i.      2 important polysaccharides found in plants

                                                            ii.      Both composed of long chains of glucose

                                                          iii.      Starch is broken down and used as energy

                                                           iv.      Cellulose is not broken down because humans don’t have the necessary digestive enzymes – eliminated in feces

 

 

 

Lipids

 

1.      Lipids –

a.      composed primarily of carbon, hydrogen, and oxygen

b.      less polar due to a lower ratio of oxygen to carbon

c.      relatively insoluble in water

2.      roles of lipids in the body

a.      protection – fat pads surround vital organs

b.      insulation – fat under skin prevents heat loss. myelin surrounds nerve cells and electrically insulates the cells from one another

c.      regulation – steroid hormones regulate many physiologic processes

                                                                                      i.      estrogen and testosterone are sex hormones responsible for many differences between male and female

                                                                                    ii.      prostaglandins help regulate tissue inflammation and repair

d.      vitamins – fat soluble vitamins perform variety of functions

                                                                                      i.      vitamin A forms retinol which is necessary for seeing in the dark

                                                                                    ii.      active vitamin D promotes calcium uptake in the small intestine

                                                                                  iii.      vitamin E promotes wound healing

                                                                                   iv.      vitamin Kathryn necessary for the synthesis of protein responsible for blood clotting

e.      structure – phospholipids and cholesterol are important components of plasma membranes

f.        energy – lipids can be stored and broken down later for energy

                                                                                      i.      per unit of weight, they yield more energy than carbos or proteins

3.      Fats – major type of lipid

a.      fats are ingested and broken down by hydrolysis reactions in cells to release energy for use by those cells

b.      stored for later use if needed

c.      protection by padding organs and preventing heat loss

4.      triglycerides – constitute 95% of the fats in the body

a.      sometimes called triacylglycerols

b.      consist of 2 different types of building blocks – 1 glycerol and 3 fatty acids

c.      glycerol – 3 carbon molecules with a hydroxyl group attached to each carbon atom

d.      fatty acids – consist of a straight chain of carbon atoms with a carboxyl group attached at one end

e.      carboxyl group – consists of both an oxygen atom and a hydroxyl group attached to a carbon atom

                                                                                      i.      responsible for acidic nature of the molecule because it releases hydrogen ions into solution

5.      Glycerides described according to number and kinds of fatty acids that combine with glycerol through dehydration process

a.      Monoglycerides have 1 fatty acid

b.      Diglycerides have 2 fatty acids

c.      Triglycerides have 3 fatty acids

6.      Fatty acids –

a.      differ from one another according to the length and degree of saturation of their carbon chains

b.      most naturally occurring fatty acids have an even number of carbon atoms

c.      14 to 18 carbon chains being the most common

d.      Saturated fatty acid – contains only single covalent bonds between the carbon atoms

                                                                                      i.      Sources include: beef, pork, whole milk, cheese, butter, eggs, coconut oil, and palm oil

e.      Unsaturated fatty acid– the carbon chain is unsaturated if it has 1 or more double covalent bonds between carbon atoms

                                                                                      i.      Double bonds can occur anywhere along the carbon chain so many types of unsaturated fatty acids with an equal degree of unsaturation are possible

1.      Monounsaturated fats – olive oil and peanut oil – have one double covalent bond

2.      polyunsaturated fats – safflower, sunflower, corn, or fish oils – have 2 or more double covalent bonds

                                                                                    ii.      the best type of fats in the diet because they do not contribute to development of cardiovascular disease

7.      Phospholipids

a.      Similar to triglycerides, except one of the fatty acids bound to the glycerol is replaced by a molecule containing phosphate and usually nitrogen

b.      Important structural components of the plasma membranes

c.      Polar at the end of to which the phosphate is bound

d.      Non polar at the other

e.      Polar end attached to water and said to be hydrophilic (water loving)

f.        Non polar end repelled by water and said to be hydrophobic (water fearing)

 

 

 

 

Proteins

 

1.      Proteins

a.      all proteins contain carbon, hydrogen, oxygen, and nitrogen bound by covalent bonds. Most contain some sulfur as well.

b.      most are very large and complex molecules

c.      tend to form collids and not solutions

d.      proteins are polypeptides composed of hundreds of amino acids

2.      role of proteins in body

a.      regulate body processes

                                                                                                  i.      enzymes control chemical reactions

                                                                                                ii.      hormones regulate may physiologic processes

1.      insulin affects glucose transport into cells

b.     act as transportation system

                                                                                                  i.      hemoglobin transports oxygen and carbon dioxide in the blood

                                                                                                ii.      plasma proteins transport many substances in the blood

                                                                                              iii.      proteins in the plasma membranes control the movement of materials into and out of the cell

c.      provide protection

                                                                                                  i.      antibodies and complement protect against microorganisms and other foreign substances

d.     help muscles contract

                                                                                                  i.      actin and myosin in muscle are responsible for muscle contraction

e.      provide structure

                                                                                                  i.      collagen fibers form a structural framework in many parts of the body

                                                                                                ii.      keratin adds strength to skin, hair, and nails

f.        provide energy

                                                                                                  i.      proteins can be broken down for energy

                                                                                                ii.      per unit of weight they yield as much energy of carbos

3.      protein structure

a.      basic building blocks are the 20 amino acid molecules

b.      each amino acid has an amine group, a carboxyl group, a hydrogen atom, and a side chain – designated by the symbol R – attached to the same carbon atom

c.      the side chain can be a variety of chemical structures

d.      differences in the side chains make the amino acids different from each other

4.      peptide bonds –

a.      covalent bonds formed between amino acids during protein synthesis

b.      dipeptide – 2 amino acids bound together by a peptide bond

c.      tripeptide – 3 amino acids bound together by peptide bonds

d.      polypeptide – many amino acids bound together by peptide bonds

e.      proteins are polypeptides composed of hundreds of amino acids

5.      primary structure – of a protein is determined by the sequence of the amino acids bound by the peptide bonds

a.      potential number of different proteins is huge because the 20 amino acids can be located at any position along a polypeptide chain

b.      characteristics of the amino acids in a protein determine the 3D shape of the protein – and the shape of the protein determines its function

c.      changing 1 or a few of the amino acids in a primary structure can alter protein functions – making it less or even non functional

6.      secondary structure – results from the folding or bending of the polypeptide chain caused by the hydrogen bonds between amino acids.

a.      2 common types –

                                                                                                  i.      Helices – coils

                                                                                                ii.      Pleated sheets – folded sheets

b.      If the hydrogen bonds are broken, the protein becomes non functional

c.      Denaturation – the change of the shape –

                                                                                                  i.      Can be caused by high temp

                                                                                                ii.      Changes in PH of body fluids

                                                                                              iii.      Egg whites cooked is a good example

7.      tertiary structure – results from folding of the helices or pleated sheets

a.      some acids are very polar and form hydrogen bonds with water

b.      polar portions of proteins tend to remain unfolded, maximizing their contact with water

c.      the less polar portions tend to fold into globular shape, minimizing their contact with water

d.      formation of covalent bonds between sulfur atoms of 1 amino acid and sulfur atoms in another amino acid located at a different place in the sequence can also contribute to the tertiary structure

e.      tertiary structure determines the shape of a domain, which is a folded sequence of 100 to 200 amino acids within a protein

f.        the function of proteins occur at 1 or more domains

g.      changes in the primary or secondary structure that affect the shape of the domain can change protein function

8.      subunits – 2 or more proteins associate to form a function unit

9.      quaternary structure – refers to the spatial relationships between the individual subunits

 

 

Enzymes

 

  1. Enzyme – is a protein catalyst that increases the rate at which a chemical reaction proceeds without the enzyme being permanently changed
    1. 3D shape of enzyme catalyst critical for normal function because it determines the structure of the enzyme’s active site
    2. Activation energy required by chemical reaction to occur is lowered by enzymes because they orient the reactants toward each other in such a way that it is more likely a chemical reaction will occur
    3. Enzymes are highly specific because their active site can bind only to certain reactants. Each catalyzes a specific chemical reaction and no others
    4. Many different enzymes are needed to catalyze the many chemical reactions of the body
    5. Enzymes named by adding the suffix –ase to the name of the molecules on which they act

                                                              i.      Lipase – enzyme that catalyzes the breakdown of lipids

                                                            ii.      Protease – enzyme that breaks down proteins

    1. Control the rate at which most chemical reactions occur in living systems – essentially control all cellular activities
    2. Enzymes are regulated by several mechanisms that exist inside the cells

                                                              i.      Some control enzyme concentration by influencing rate at which the enzymes are synthesized

                                                            ii.      Some alter the activity of existing enzymes

                                                          iii.      Much of what is known about regulation of cellular activity involves knowledge of how enzyme activity is controlled

  1. active site
    1. at active site, reactants are brought into close proximity
    2. when they combine, they are released from the active site
    3. the enzyme is again capable of catalyzing additional reactions
    4. slight changes can destroy the ability of the active site to function

                                                              i.      sensitive to PH and temp which can break their hydrogen bonds

                                                            ii.      breaking the hydrogen bonds changes the relationship between the amino acids, making a change in shape, and that prevents the enzyme from functioning properly

  1. Lock and key model
    1. Says a reaction occurs when the reactants (key) bind to the active site (lock) on the enzyme
    2. Viewed as a rigid structure
  2. induced fit model
    1. the enzyme is able to slightly change shape and better fit the reactants
    2. like a glove that achieves functional shape when the hand – the reactant – moves into place
  3. Cofactors
    1. Nonprotein substances which help some enzymes to function
    2. Normally form a part of the enzymes active site and required to be functional
    3. Can be an ion such as zinc or an inorganic molecule such as vitamins
    4. Organic molecules that are cofactors are called enzymes

 

 

 

Nucleic Acids – DNA and RNA

 

1.      Deoxyribonucleic acid (DNA)

a.      is the genetic material of cells and copies are transferred from one generation of cells to the next

b.      contains the info that determines the structure of the proteins

2.      Ribonucleic acid (RNA)

a.      Structurally related to DNA

b.      3 types play important roles in synthesis

3.      Nucleic acids – large molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus

4.      nucleotides –

a.      composed of a monosaccharide to which a nitrogenous organic base and a phosphate group are attached

                                                                          i.      5 carbon monosaccharide deoxyribose for DNA

                                                                        ii.      5 carbon monosaccharide ribose for RNA

b.     Nitrogenous organic bases

                                                                          i.      Consist of carbon and nitrogen atoms organized into rings

                                                                        ii.      Bases because the nitrogen atoms tend to take up H+ from solution

                                                                      iii.      The nitrogenous organic bases are thymine, cytosine, and uracil – all single ringed pyrimindines. and adenine and guanine – both double ringed purines

c.      basic building blocks for both RNA and DNA

5.      basic structure of DNA

a.      2 strands of nucleotides joined together to form a twisted ladder like structure – the double helix

b.      Uprights of ladder are formed by covalent bonds between the deoxyribose molecules and the phosphate groups of adjacent nucleotides

c.      Rungs are formed by the bases of the nucleotides of one upright connected to the bases of the other upright by hydrogen bonds

d.      Each nucleotide of DNA contains one of the organic bases

                                                                          i.      Adenine

                                                                        ii.      Thymine

                                                                      iii.      Cytosine

                                                                      iv.      guanine

e.      Adenine binds only to thymine because the structure of these organic bases allows 2 hydrogen bonds to form between them

f.        Cytosine binds only to guanine because the structure of these organic bases allows 3 hydrogen bonds to form between them

g.      The sequence of organic bases in DNA molecules stores genetic info and each DNA molecule consists of millions of organic bases, their sequence determines the type and sequence of amino acids in the protein molecules

h.      Enzymes are proteins so DNA structure determines the rate and type of chemical reactions that occur in cells by controlling enzyme structure

i.        The info in DNA ultimately defines all cellular activities

6.      RNA structure

a.      Similar to a single strand of DNA

b.      4 different nucleotides make up the RNA molecule and the organic bases are the same – except that thymine is replaced with uracil

c.      Uracil can bind only to adenine

 


 

 

Adenosine Triphospate ATP

 

  1. ATP – important organic molecule found in all living organisms
  2. a modified nucleotide – energy currency that powers cells
  3. consists of adenosine and 3 phosphate groups
  4. adenosine is the sugar ribose with the organic base adenine
  5. the catabolism of glucose and other nutrient molecules results in chemical reactions that release energy
    1. some of that energy is used to synthesize ATP from ADP and an inorganic phosphate group (P1)
    2. ADP + P1 + energy from catabolism --> ATP
    3. Transfer of energy to ATP involves a series of oxidation-reduction reactions in which a high energy electron is transferred from one molecule to the next molecule in the series
  6. once produced ATP is used to provide energy for other chemical reactions – anabolism
  7. also used to drive cell processes such as muscle contraction
  8. when used, ATP is converted back to ADP and an inorganic Phosphate group
    1. ATP --> ADP + P1 + energy (for anabolism and other cell processes)
  9. energy currency
    1. capable of both storing and providing energy
  10. concentration of ATP maintained within narrow range of values
  11. all energy requiring chemical reactions stop when there is an inadequate quantity of ATP