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AP  BIOLOGY  NOTES  
 
Introduction  
• Atomic  Structure:  Atoms  are  the  building  blocks  of  all  matter
...
 
o An  atom  in  its  elemental  state  is  neutral  (with  equal  number  of  
protons  and  electrons
...
 
o Excited  State:  When  electrons  move  to  a  higher  energy  level
...
   
§ Some  isotopes  are  radioactive  and  decay  at  a  rate  known  as  
half-­‐life
...
 
• Bonding:  A  bond  is  formed  when  two  elemental  nuclei  share  electrons
...
   An  atom  that  gains  electrons  
becomes  an  anion  (a  negative  ion)  and  the  atom  that  looses  electrons  
becomes  a  cation  (a  positive  ion
...
   This  results  in  a  molecule
...
 
• Nonpolar  molecules  are  balanced  or  symmetrical
...
   
• Polar  molecules  are  unbalanced
...
 
• Hydrophilic  Substances:  “Water-­‐loving”  substances  that  a  polar  and  
dissolve  in  water
...
   The  two  hydrogen  molecules  are  held  together  
with  hydrogen  bonding  which  is  a  weak  bond  singularly,  but  strong  in  large  
numbers
...
High  specific  heat:  Large  bodies  of  water  resist  changes  in  
temperature  and  are  stable  environments
...
High  heat  of  vaporization:  Water  is  also  able  to  absorb  great  
amounts  of  heat
...
Universal  solvent:  Because  water  is  highly  polar,  it  dissolves  all  polar  
and  ionic  substances
...
Strong  cohesion  tension:  Water  molecules  attract  other  water  
molecules
...
Ex:  Transpiration  in  trees  
5
...
 
 

•

•

•

 
 
 
pH:  The  measure  of  acidity  and  alkalinity  of  a  solution
...
   
§ Ex:  Level  6à10^6        
o Slight  pH  levels  can  be  detrimental  to  
an  environment
...
 
§ Bicarbonate  ion:  In  human  blood  regulates  levels  of  H+  
(basic)  of  Carbon  levels  (acidic)  
Isomers:  Organic  compounds  that  have  the  same  molecular  formula  but  
differ  in  shape
...
 
o Cis-­‐trans:  Differ  in  the  spatial  arrangement  around  double  bonds
...
 
Organic  Compounds:  All  living  organisms  are  made  up  of  organic  molecules,  
or  molecules  that  contain  Carbon
...
 
§ Contain  Carbon,  Hydrogen  and  Oxygen
...
     
• Ex:  glucose  (isomers:  galactose/  fructose)  
§ Disaccharides:  The  second  stage  of  carbohydrates  that  consist  
of  two  monosaccharides
...
   
• Hydrolysis:  The  adding  of  a  water  molecule  to  
breakdown  a  compound
...
 
• Plants:  
o Structural:  Cellulose-­‐makes  up  cell  wall  
o Storage:  Starch  
• Animals:  
o Structural:  Chitin-­‐makes  up  exoskeleton  
o Storage:  Glycogen-­‐“animal  starch”  

o Lipids:  Diverse  class  of  organic  molecules  that  includes  fats,  oils,  
waxes,  and  steroids
...
   Lipids  consist  of  a  glycerol  (Alcohol  head)  with  fatty  
acid  tails  
§ Saturated:  Solid  at  room  temperature,  come  from  animals,  and  
straight  due  to  the  sing  bonded  Carbon  molecules
...
 
§ Steroids:  Lipids  with  4  fused  rings  that  act  differently  than  
other  lipids
...
 
• Structural:  Phospholipid  layers  make  up  the  cellular  
membranes  in  animal  cells
...
 
§ Phospholipids:  Modified  lipids  that  contain  a  hydrophobic  
head  (phosphate/glycerol)  with  hydrophobic  tails  (fatty  acids)
...
   
§ Polymers  or  polypeptides,  consists  of  amino  acids,  which  
are  joined  by  peptide  bonds
...
 
§ Amino  acids  consist  of  a  carboxyl  group,  amine  group,  and  
an  R  group
...
 
§ Conformation:  
 
• Primary:  Linear  sequence  of  amino  acids
...
   It  
creates  a  coiled  shape  (alpha  helix/beta  pleated  
sheet)  
• Tertiary:  Creates  an  intricate  3D  shape  that  determines  
specificity
...
 
o Ex:  globular  proteins  (hemoglobin)  

  
 
 
 
 
 
 
 

o Nucleic  Acids:  Encode  for  all  hereditary  material  that  include  
ribonucleic  acid  (RNA)  and  deoxyribonucleic  acid  (DNA)
...
 
• Nucleotides  consists  of  a  phosphate,  5-­‐carbon  sugar  
(deoxyribose  or  ribose)  and  a  nitrogen  base  
(adenine,  guanine,  cytosine,  thymine  [or  uracil  in  
RNA])  
• Nitrogenous  bases  attach  with  hydrogen  bonds
...
 
 
 
 
 
 
 
 
 
 
 

 
•
•

Functional  Groups:  Specific  groups  of  elements  that  make  up  organic  
compounds
...
 
Energy/Enzymes,  and  Metabolism:  
o First  Law  of  Thermodynamics:  Energy  cannot  be  created  or  
destroyed
...
 
o Gibb’s  Free  Energy:  Amount  of  free  energy  that  can  be  used
...
 
§ Endergonic:  Absorption  of  energy
...
 
§ Catabolism:  Break  down  of  molecules
...
 

§ Pathways:  Metabolic  serious  that  each  serve  a  purpose
...
   
§ Enzymes  are  globular  proteins  that  exhibit  tertiary  
structure
...
 
 
• This  forms  the  enzyme-­‐substrate  complex
...
”  
§ Competitive  Inhibition:  Substrate  “imposters”  fight  for  
enzymes
...
 
§ Noncompetitive  Inhibitors/Allosteric  Regulators:  Bind  to  
another  part  of  enzyme  to  change  its  shape,  stopping  function
...
 
• All  cells  contain  protective  membranes,  cytosol,  ribosomes,  and  DNA  
material
...
 
Eukaryotes  
Prokaryotes  
Contain  distant  organelles  
DNA  wrapped  into  chromosomes  
Ribosomes  are  larger  

Ribosomes  are  very  small,  simple  

Metabolism  is  aerobic  

Metabolism  in  anaerobic  or  aerobic  

Cytoskeleton  

No  cytoskeleton  

Cells  are  large  (Animal/Plant  cells)  

•

No  internal  membranes;  no  nuclear  
membrane,  E
...
)  
Circular,  naked  DNA  

Cells  are  small  (Bacteria)  

 
Structure  &  Function:  
o “Function  dictates  form”  
§ The  different  shape  of  cells  helps  in  their  functions
...
   However  surface  area  
increases  slower  than  volume,  which  is  harmful  to  the  cell
...
   
The  best  cell  is  one  that  has  a  large  surface  area  and  small  
volume
...
   
Subunits  of  ribosomes  are  also  created  here
...
   When  free  in  the  cytosol,  they  produce  
proteins,  when  attached  to  the  E
...
   
o Peroxisomes:  Contain  catalase,  which  converts  hydrogen  peroxide  
into  water,  and  detoxifies  alcohol  in  liver  cells
...
   
It  is  surrounded  by  a  nuclear  envelope  that  separates  the  nucleus  
from  the  cytoplasm
...
   
o Endoplasmic  Reticulum  (E
...
   
§ Rough  E
...
R:    
• Assists  the  synthesis  of  steroid  hormones  (sex  
hormones)    
• Detoxifies  drugs  
• Stores  Ca  ++  ions  in  muscles  that  facilitate  contractions  
o Golgi  Apparatus:  Process  and  package  substances  produced  in  the  
rough  E
...
 
o Lysosomes:  Sacs  of  hydrolytic  (digestive)  enzymes
...
     
§ Autophagy:  Cell  breaking  down  dead  parts  of  itself
...
 
o Mitochondria:    Energy  site  of  the  cell
...
)    Contain  their  own  
DNA  that  supports  the  Theory  of  Endosymbiosis
...
   Freshwater/plant  cells  
generally  have  large  contractile  vacuoles  to  pump  out  excessive  

•

water
...
 
o Chloroplasts:  Contain  green  pigment,  chlorophyll  that  absorb  light  
and  synthesize  sugar
...
   Contain  a  double  
membrane  (inner  membrane  in  a  thylakoid
...
 
o Cytoskeleton:  Complex  mesh  of  protein  filaments  that  extend  
through  the  cytoplasm
...
 
The  cytoskeleton  includes  microtubules  and  microfilaments
...
)  
§ Spindle  Fibers:  help  separate  chromosomes  in  mitosis  and  
meiosis
...
 
§ Microfilaments:  assembled  from  actin  microfilaments  and  
help  support  the  shape  of  the  cell
...
   They  organize  spindle  fibers  and  give  rise  to  spindle  
apparatus  in  cell  division
...
   
(Chitin  in  fungi)      
o Plasma  Membrane:  Selectively  permeable  membrane  that  regulates  
the  steady  traffic  that  enters  and  leaves  the  cell
...
   Cholesterol  molecules  
are  also  on  the  membrane  to  stabilize  it
...
   Proteins  in  the  plasma  membrane  provide  a  wide  range  of  
functions
...
R  and  then  to  the  Golgi  apparatus,  which  creates  a  
transport  vesicle,  which  leaves  the  cell
...
 
o Passive:  Movement  down  the  concentration  gradient  
§ Diffusion:  
• Simple:  Does  not  involve  protein  channels  
• Facilitated:  Involves  protein  channels  

•
•

•
•

o Hydrophilic  protein  channel:  specifically  
permeable    
§ Osmosis:  term  used  for  water  down  the  concentration  
gradient  
o Active:  Movement  against  the  concentration  gradient  
§ Sodium-­‐potassium  Pump:  Pumps  sodium  and  potassium  
molecules  into  or  out  of  the  cell
...
 
§ Exocytosis:  Release  of  something  out  of  the  cell  
§ Phagocytosis/Pinocytosis:  Cell  drinking/eating  
Solvent:  Dissolving  substance  
Solute:  Substance  that  dissolves  
o Hypertonic:  more  solute  than  the  surrounding  solution  
o Hypotonic:  less  solute  than  the  surrounding  solution  
o Isotonic:  equal  amounts  of  solute  than  the  surrounding  solution  
Water  Potential:  the  movement  of  water  from  higher  water  potential  to  
lower  potential
...
 
Cell  Communication:  
o Quorum  Sensing:  Bacteria  secrete  molecules  that,  once  reach  a  
threshold,  enable  them  to  respond  to  changes  in  their  population  
density
...
   
§ Ex:  Urinary  bladder  cells  
o Gap  Junctions:  Permit  the  passage  of  materials  directly  from  the  
cytoplasm
...
 
o Signal  Transduction  Pathways:  Pathways  the  activities  within,  
between,  and  among  individual  cells  and  support  the  entire  organism
...
   This  ligand  binds  to  a  receptor  either  on  
the  cell  membrane  of  inside  the  cytoplasm
...
   Ultimately,  this  signal  
transduction  pathway  leads  to  a  cellular  response
...
 
• Two  types  of  cellular  respiration:  aerobic  (with  the  presence  of  oxygen)  
and  anaerobic  (without  the  presence  of  oxygen
...
 
o ATP  becomes  ADP  with  the  process  of  hydrolysis  
o ATP  provides  the  energy  for  all  the  activities  in  the  cell
...
   The  energy  of  activation  for  this  cycle  
is  2  molecules  of  ATP
...
     
o Glycolysis  occurs  in  the  cytoplasm  without  the  use  of  oxygen
...
   
Anaerobic  Respiration:  Glycolysis  with  the  processes  of  Lactic  Acid  and  
Alcohol  Fermentation
...
     
o Fermentation  can  generate  ATP  during  anaerobic  respiration  as  long  
as  there  is  NAD+  to  accept  electrons
...
   This  is  used  in  bread  baking  
with  the  ability  of  yeast  to  undergo  this  type  of  fermentation
...
   
Human  skeletal  muscles  use  it,  when  the  red  blood  cells  cannot  carry  
enough  oxygen  to  them
...
   
o Takes  place  in  the  mitochondrial  matrix  and  requires  pyruvate,  the  
product  of  glycolysis
...
   CO2  is  
given  off,  and  acetyl  co-­‐A  enters  the  cycle
...
 
o The  Krebs  cycle  takes  place  in  the  matrix
...
   Without  them,  the  cell  would  die  
o Coenzymes  that  carry  protons  or  electrons  from  glycolysis  and  the  
Krebs  cycle  to  the  electron  transport  chain
...
   It  does  not  make  ATP  directly,  but  sets  the  stage  
for  the  process  of  chemiosmosis
...
   NAD  
and  FAD  bring  electrons  to  the  Electron  Transfer  Chain
...
     
Oxidative  Phosphorylation  and  Chemiosmosis:  Most  of  the  energy  is  
produced  in  this  stage  of  cellular  respiration
...
   As  protons  flow  
through  the  synthase,  they  generate  energy  that  phosphorylates  ADP  
into  ATP
...
 
o Carotenoids:  Yellow,  orange  and  red  pigments  that  absorb  all  
wavelengths  but  those  colors
...
 
§ Absorption  Spectrum:  All  of  the  wavelengths  compared  
within  a  plant
...
   Event  though  PS  I  acts  secondly  in  the  
process,  it  was  discovered  first
...
 
1
...
 
2
...
     

3
...
Chemiosmosis:  ATP  is  formed  during  the  light  
reactions
...
   As  these  protons  
flow  down  a  gradient,  through  ATP  synthase,  ATP  
is  produced
...
NADPH:  Reduced  form  of  NADP  that  carries  
hydrogen  to  the  Calvin  cycle  to  make  sugar  in  the  
light-­‐dependent  reactions
...
Photosystem  I:  Energy  is  absorbed  and  goes  
through  the  same  process,  however  instead  of  ATP,  
NADPH  is  created
...
   
Excited  electrons  from  the  PS  II  ETC  are  brought  to  the  
PS  I  and  are  then  accepted  by  the  primary  acceptor
...
 
o Light-­‐independent  Reactions  (Calvin  Cycle):  
§ Cyclical  process  that  produces  a  3-­‐carbon  sugar  (G3P)
...
 
§ CO2  enters  the  cycle  and  becomes  attached  to  a  5-­‐carbon  sugar  
(RuBP),  by  Rubisco,  forming  a  6-­‐carbon  molecule
...
     
§ C-­‐4  Plants:  Modification  in  hot,  dry  environments  
• Most  plants  are  C-­‐3  plants  in  that  the  CO2  entering  is  
fixed  to  a  3-­‐PGA  
• CO2  enters  the  mesophyll  cell  of  the  leaf  and  combines  
with  a  3-­‐carbon  pyruvate  to  form  a  4-­‐carbon  molecule
...
     
• The  mesophyll  cell  produces  malate,  which  is  pumped  
into  the  bundle  sheath  cell  where  little  oxygen  is  
present
...
   
§  CAM  Plants:  Adaption  to  dry  conditions  
• Plants  keep  stomata  closed  during  the  day  and  open  
during  the  night
...
   During  the  day,  when  the  light  
reactions  can  supply  energy  for  the  Calvin  cycle,  CO2  is  

released  from  the  organic  acids  made  in  the  night  to  
become  incorporated  into  sugar
...
     
• Mitosis:  Production  of  two  genetically  identical  daughter  cells  that  preserve  
the  chromosome  number;  (diploid)  
• Meiosis:  Sexually  reproducing  organisms  and  resulting  in  cells  that  are  
haploid;  (the  have  half  the  chromosome  number  of  a  parent  cell
...
     
o A  replicated  chromosome  consists  of  two  sister  chromatids
...
 
o Kinetochore:  Disc-­‐shaped  protein  on  the  centromere  that  attached  
the  chromatid  to  the  mitotic  spindle  during  cell  division
...
   Most  cells  are  constantly  
growing/dividing,  however  cells  arrested  in  the  G0  Phase  (like  heart  
and  liver  cells)  do  not
...
   It  is  important  to  have  more  of  a  surface  are  in  comparison  
to  its  volume  because  of  the  factor  of  nutrient  exchange  over  its  
membrane
...
   
§ Interphase:  
• G1:  A  period  of  growth  and  biochemical  activity
...
 
• G2:  Continued  growth  in  preparation  for  division
...
 
• Prophase:    
o Nucleus  unwraps,  chromosomes  begin  to  
condense  
o Nucleolus  disappears  
o Mitotic  spindles  begin  to  form,  extending  from  
one  centrosome  to  the  other
...
   
o Centrosomes  are  positioned  at  the  opposite  
poles  of  the  cell
...
   
• Anaphase:  

o Centromeres  of  each  chromosome  separate,  as  
spindle  fibers  pull  apart  the  sister  chromosomes
...
     
§ Cytokinesis:  The  dividing  of  the  cytoplasm
...
 
• In  plant  cells,  a  cell  plate  will  create  a  new  cell  wall,  
splitting  the  two  daughter  cells
...
   Cancer  cells  do  not  have  
this  reaction  and  grow  uncontrollably
...
     
§ Gametes:  Sex  cells  that  are  produced,  have  a  haploid  number  
§ Meiosis  I:    
• Prophase  I:    
o Synapsis:  Pairing  of  homologous  chromosomes  
o Crossing-­‐Over:  Exchange  of  pieces  of  DNA  
forming  Chiasmata  
• Metaphase  I:    
o Homologues  line  in  a  double  line  along  the  
metaphase  plate  
o Spindle  fibers  from  the  poles  of  the  cell  are  
attached  to  the  centromere  of  each  pair  of  
homologues  
• Anaphase  I:  
o Separation  of  homologous  chromosomes  is  
pulled  by  the  spindle  fibers  as  they  migrate  to  
opposite  poles
...
   Each  pole  has  a  
haploid  number  of  chromosomes
...
 
§ Meiosis  II:  Functionally  the  came  as  mitosis  and  consists  of  the  
came  phases
...
     
o Genetic  Variation:    

Independent  Assortment:  During  meiosis  homologous  pairs  
of  chromosomes  separate  depending  on  the  random  way  in  
which  they  line  up  on  the  metaphase  plate  during  metaphase  I
...
     
§ Random  Fertilization:  One  human  represents  millions  of  
possible  chromosome  combinations  that  could  be  passed  
down
...
   The  
cell  is  chopped  up  from  the  inside  and  packaged  into  vesicles
...
 
o Multiplication   Rule:   When   finding   the   probability   of   two  
independent   events,   multiply   the   chance   of   one   happening   by   the  
chance  that  the  other  will  happen
...
     
• Law   Of   Dominance:   When   two   organisms,   each   homozygous   for   the  
opposing   traits   crossed,   the   offspring   will   be   hybrid,   but   only   express   the  
dominant  trait
...
 
o Monohybrid   Cross:   A   cross   between   two   organisms   that   are   each  
hybrid  for  one  trait
...
     
o Dihybrid  Cross:  A  cross  with  more  than  one  allele
...
     
• Codominance:  Both  traits  show  
• Multiple  Alleles:  When  there  are  more  than  two  alleles  for  a  certain  gene
...
     
o Epistasis:  Two  different  genes  control  one  trait,  but  one  gene  masks  
the  other
...
     
Linked  Genes:  Genes  on  the  same  chromosome  that  tend  to  be  inherited  
together  and  do  not  assort  independently
...
   Traits  carried  on  the  X  chromosome  are  called  
sex-­‐linked
...
     
Mutations:  Any  changes  in  the  genome  
o Deletion:  When  a  fragment  lacking  
a  centromere  is  lost  during  division  
o Inversion:  When  a  fragment  
reattaches  to  its  original  
chromosome  but  in  the  reverse  
orientation  
o Translocation:  When  a  fragment  of  
a  chromosome  becomes  attached  to  
a  nonhomologous  chromosome  
o Polyploidy:  When  a  cell  or  organism  has  extra  sets  of  chromosomes  
Nondisjunction:  An  error  that  sometimes  occurs  in  meiosis  in  which  
homologous  chromosomes  don’t  separate
...
     
Extranuclear  Genes:  Genes  located  in  the  mitochondria  and  chloroplasts

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