BioChemistry UNIT TEST

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 13 14
C C C
6 6 6

6no 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
14
C
6 Traces movement of carbon through biological pathways, like
respiration and photosynthesis
45
30 Ca Measures rate of bone formation
40
19 K Half-life of 13 billion year (decays into 40Ar) ratio of 40K : 40Ar used to
date fossils
131
53 I Taken up by thyroid gland can be imaged to detect abnormalities
226
88 Ra 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:
a. Draw lewis dot diagram for each pair
b. Determine structural formula of molecule
c. 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 Determines state of substance

shared

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
I. Water is an excellent solvent
➔ Solvent - substance that is able to dissolve other substances
➔ Water is a polar molecule
➔ Break ionic bonds
II. 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
III. 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
IV. Water has a high heat conductivity
V. Water has a high boiling/freezing point
VI. 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)
1. Hydroxyl - found in alcohol and sugars

2. Amino - found in protein and bases

 3. Sulfhydryl -found in rudder and protein

4. Phosphate - found in ATP, DNA and RNA

5. Carboxyl - found in acids (eg. vinegar)

6. Aldehyde - found in sugars and formaldehyde

7. 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:
1. 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