biology 1500

  1. 6 major funcitons of proteins 
    structure  transport, catalysis, regulation and signalling, motors, protection
  2. polypeptide chain
    a linear unfoled chain of 30+ amino acids 
  3. peptide 
    a short chain of 2-30 amino acids
  4. how many different amino oacids are there 
    over 20 
  5. what does an amino acid consist of 
    • a central carbon surronded by a hydrogen
    • amindo (NH2) group
    • carboxyl (COOH) group
    • a unique r group
  6. different r groups have different....
    biochemical properties
  7. three main classes of amino acids
    • hydrophillic
    • hydophobic,
    • unique
  8. describe a polar hydrophillic R group/amino acid
    • found on the surface of a protein
    • some are charged others are not 
    • charged ones act as an acid or base
    • uncharged ones hydrogen bond wiht water
  9. describe nonpolar hydophobic amino acids/R groups
    • usually buried in a protein to get a way form the water 
    • have hydrocarbon rings or chains
  10. describe unique r groups/ amino acids
    have a unique biochemical protein that can alter the function of the entire protein
  11. how do peptides and polypeptides form
    • the amino group of on amino acid reacts with the carboxyl group of an agjacent amino acid 
    • water is removed and the peptide bond is formed 
  12. where does the formation of polypeptides and peptides take place 
    in the ribosomes
  13. all polypeptides have two ends what are they 
    n terminus and c terminus 
  14. n terminus
    free NH2 group 
  15. c terminus 
     free COOH group
  16. the function of a protein is extremely depentant on its ...
    specific shape
  17. primary structure of a polypeptide 
    • a linear string of amino acids 
    • order determined by dna
    • linking of amino acids is not random
  18. secondary structure of polypeptide
    • hydrogen bonds between two different amino acids in the polypeptide chain bettween amino and carboxyl 
    • hydrogen bonds cause two different structures  called secondary structures
  19. what are the two types of secondary structures 
    alpha helix  and beta sheet 
  20. tertiary structure of a polypeptide 
    interactions between amino acid side chain r groups  leads to further twisting allowing secondary structures to interact
  21. what are the 5 tyoes of interactions between r groups in the tertiary structure of polypeptides
    • hydrogen bonding 
    • hydrophobic interactions
    • van der waals interactions
    • ionic bonds
    • disulfide bridges----covalent bonds
  22. quaternary structure of polypeptide
    2 or more polypeptide chains bonded together
  23. it is very difficult ot disrupt a polypeptides....
    primary structure
  24. the disruption of hte bonds in the 2-4 structures of polypeptides leads to....
    unwinding/ changing of hte polypeptide shape, disrupting the proteins 3D structure -----denaturing 
  25. denaturing usually results in a loss of 
    protein function 
  26. what are nucleic acids
    long polymers made up of small monomers called nucleotides
  27. what are the two major types of nucleic acids
    • Deoxyribonucleic acid
    • Ribonucleic acid
  28. describe DNA
    • stores heretidary information 
    • double stranded
    • contains four types of nucleotides 
    • strands interact via hydrogen bonds
    • contain deoxyrobse sugar
  29. describe RNA
    • transfers the herediary information 
    • single stranded 
    • 4 types of nucleotids
    •  contains the sugar  ribose
  30. what are nucleotides
    • a sugar, five carbon ring (ribose or deoxyribose)
    • one or more phosphate groups 
    • a nitrogen containing base-- single or double carbon ring structure ---makes them different from eachother
  31. what tyoes of bases does DNA have
    A T C G 
  32. what types of bases does RNA have 
    A C U G 
  33. all cells have a similar -----
    basic structure,chemical composition, and a set of metabolic pathways
  34. what is magniication 
    increasing apparent size
  35. what is resolution 
    distinguishing two parts 
  36. what does resolution depend on 
    wavelength of light
  37. what are the two kinds of microscopes used today 
    light microscopy and electron microscopy 
  38. light microscopy can intensify the objecy_____times
  39. what are the three kinds of light microscopes
    • visible light, 
    • uv light
    • light laser
  40. describe visible light microscope
    enhances contrast in unstained cells 
  41. describe a uv light microscope 
    flourescence, for tagging proteins
  42. describe light laser microscope
    confocal ised to observe thin section of a thick sample
  43. what are the two types of electron micropscopes
    • scanning EM
    • transmission EM 
  44. describe scanning em 
    • gives great 3D images 
    • surface topography 
    • electrons shoots the surface of the sample 
  45. describe a transmission em microscope 
    • gives fine detail on internal cellular components 
    • electrons shoot through a thin sample 
  46. samples must me ____ in electronmicroscopy
    fixed, dead 
  47. electron micropscopes can see ___ than light microscopes (1000x) 
  48. the greater the suface area of the plasma membrane the _____ that are brought in and the cell is healthier 
    nutrients is brought in 
  49. as the cells diameter expands so does the ...
    suface area and volume 
  50. based on math equations , as the the volume of a cell ____ ____ than the surface area of the plasma membrane 
    increases faster
  51. if a cell grows too large what happens
    the plasma membrane will be unable to bring in nutrients fast enough to support hte increased amount of hte cytoplasma  the cell will die 
  52. what does the plasma membrane do for the cell
    • protects the interior form the outside
    • allows biochemical reactions to proceed in a controlled environment
  53. where ar chromosomes found in both eukaryotic and prokaryotic cells
    in teh nucleus (e) or in the cytoplasm around the nuceolus (p) 
  54. what do ribosomes do
    they are machines that construct polypeptides from amino acids
  55. all cells have 
  56. what two types of organisms are made up of prokaryotic cells 
    eubacteria (monera) and archeabacteria
  57. what type of cell is thought ot evolved first 
  58. what are four thiings the plasma membrane does 
    • controls movement
    • separates chemical reactions form harsh environment
    • helps relay messages into the cell
    • regulates chemical compostion of the cytoplasm
    • ---controls the volume of the inside of hte cell
  59. what does the plasma membrane consist of 
    phospholipids, cholesterol, embedded proteins (liipid bilayer)
  60. what does the nucleus do
    • protects and organizes genetic material
    • organizes production of ribosomes
    • the site where the genetic code is read and captured to RNA
  61. what does the nucleus look like
    • spherical 
    •  visible 
  62. what are the four key features of the nucleous
    • nuclear envelope 
    • nuclear lamina
    • chromosomes
    • nucleolus
  63. describe the nuclear envelope
    • double layer membrane 
    • has nuclear pores
    • selects substances to go in and out of nucleus
  64. describe the nuclear lamina
    • meshwork of protein filaments that line th inner layer of hte envelope
    • gives nucleus its structural support and shape
  65. describe chromosomes
    • DNA inside the nucleus is coiled around proteins that protect the DNA from toxins
    • the split pieces of DNA and its associated proteins are called chromosomes  
  66. describe the nucleolus 
    • dense mass in nucleus
    • where ribosomal subunits are assembled 
  67. how are ribosomal subunits made?
    mad eof protein and rRNA that is shipped into the nucleolus 
  68. what do  ribosomes do
    they read the genetic message in mRNA and assemble amino acids in to specific proteins
  69. what do ribosomes look like
    • solid granules of protein adn rRNA 
    • composed of one large nad one small subunit
  70. where are ribosomes found
    attacted to internal cellular membranes or free in the cytosol
  71. what are membrane bound ribosomes 
    • the make proteins that are destined to be inserted into membranes 
    • shipped to the inside of organelles or shipped out of the cell
  72. what are free ribosomes
    generally make proteins that stay in cytosol 
  73. what does endoplasmic reticulum (ER) look like 
    network of sacs that are connect ot eachother some are studded with ribonsomes 
  74. what are the individual sacs of ER called 
  75. what is the empty space in cisternae called 
    ER lumen
  76. smooth ER looks like...
  77. what are the four things smooth ER does
    • synthesis of proteins 
    • metabolism of carbohydrates
    • detox of drugs and poisens 
    • store calcium ions in certain cell types
  78. what are the two things rought ER does
    • protein synthesizer 
    • membrane synthesis
  79. little tiny sacs of membrane are called...
  80. what does the golgi apparatus look like 
    • flattened interconnected cisternae (pancaked)
    • one side close to ER the other away from 
  81. what is the cis face 
    the side of the golgi apparatus that is close to the ER 
  82. what is the transface
    the side of the golgi apparatus that is facing away form teh ER 
  83. what are the three things the golgi apparatus does
    • makes several types of carbohydrates 
    • receives proteins form the rough ER (via vesicles from the ER                ------to the cis face) and puts finishing touches on them 
    • packages proteins and directs where they need to go in the cell 
  84. what are glycoproteins 
    ER made proteins that have sugar  groups attached to them 
  85. what do lysosomes have in them 
    • acid
    • hydrolic (digestive) enzymes 
    • other toxic substances 
  86. what do lysosomes look like 
    typical vesicles
  87. where are lysosomes derived from 
    the trans golgi 
  88. what are the two things lysosomes do
    • destroy large  items brought in from the outside of the cell 
    • destroy ol organells and recycle them 
  89. what do peroxisomes look like
    similar to lysosomes
  90. what is the function of peroxisomes 
    • the convert substances to H2O2
    • they help tetoxify the cell by removing hydroogen form the toxins and transfers that to O leaving H2O2 which is further broke down to water

    breakdown of fatty acids and transports them to the mitochondria 
  91. what do the mitochondria do 
    • they are major ATP producers  fo the cell. 
    • they breakdown organic compunds in to CO2 / H2O  extract the energy and make ATP 
  92. what do mitochondria look like
    • a bean
    • double membrane
    • inner membrane is folded 
  93. what is the inner folds of the mitochondria called 
  94. what is the inner space of the mitochondria called 
  95. the mitochondria is inherited form the 
  96. most plant cells contain a category of organelles call ____ that specialize in photosynthesis and food storage 
  97. what are the three main types of plastids 
    • chloroplasts 
    • chromoplasts
    • amyoplasts
  98. what is chloroplast
    the structures responsible for photosynthesis 
  99. what is chromoplast
    they lack chloroplast but have other photosynthetic pigments
  100. what is amyoplast
    lack all pigment --no photosynthesis-- help store starch 
  101. what is the structure of  chloroplast 
    • double outer membrane (smooth)
    • third internal membrane forms sacs 
    • a fluid filled space outside of the sacs
    • process their own DNA and ribosomes 
  102. what are the individual sacs of chloroplast called 
  103. what is the fluid filled space outside of the thylakoid called 
  104. a stack of thylakoid is called...
  105. describe a vacuole
    • gigantic vesicle found in plants
    • has similar degradative enzymes as lysosomes 
    • they degrad polymers,proteins,carbs and fats into monomers
    • regulates cell size 
  106. what  is the universal storage facility for plant cells 
  107. what do vacuoles store
    amino acids, sugars, ions toxic substances ect
  108. what is the cytoskeleton 
    a dense network of interconnecting protein filiments and cylinders
  109. what are the three functions of hte cytoskeleton
    • give the cell overall shape and structural support
    • helps organize cellular components
    • cellular movements
  110. what are microtubules 
    large hollow rods composed of the protein tublin
  111. what protein makes up microtublues 
  112. what are the functions of the microtubules 
    • shape and support of the cell (push and pull) 
    • provide organized framework for travel
    • moving parts or whole cell
  113. what are cilia and flagella 
    extensions from the plasma membrane that move and as a result creat movement of hte cell 
  114. what is the 9 to 2 arrangemetn 
    microtubules made up of 9 doublets arranged in a cylindar wiht another in the middle 
  115. microtublues are associated with the motor protein....
  116. cilia---
    small hair like structures
  117. flagella 
    longer whip like structures 
  118. what type of movement does flagella create
    whip like motion moves whole cells 
  119. what type of movement does cilia create
    beating motion that can move hte whole cell or substances around the cell 
  120. who do cilia move 
    like oars 
  121. how do flagella move 
    like propellers
  122. what are microfiliments
    • large solid rod composed of actin 
    • huge networks
  123. what are the two functions of microfiliments
    • shape and support
    • ---under the plasma membrane , supports against pulling --supports microvilli
    • cell movement via pseudopodia or microvilli 
  124. what is the intermediate filament
    • made of different proteins mostly keratin 
    • makes up nuclear lamina 
  125. what does the intermediate filaments do
    • mostly structural support 
    • help cell maintain shape 
    • anchor the nucleus and other organelles in place 
  126. what are the nonmembrane enclosed structures found outside the plasma membrane 
    cell wall, extracellular matrix, and intracellular junctions
  127. plant cell walls contain lots of _____ embedded in their polysaccharides and various proteins 
  128. describe the cell wall 
    surrounds the plasma membrane and rovides strength , support and protection 
  129. the cell wall is made by ... 
    themselves and sent out
  130. animal cells have a ____ instead of a cell wall
    extracellular matrix
  131. what is an extracellular matrix 
    thick loosley arranged network of various glycoproteins outside of plasma membrane 
  132. what are four components of the extracellular matrxi
    • -collegen (most abundant) 
    • -proteoglycans  
    • -fibronectin
    • -integrins
  133. what is a proteoglycan
    long sticky glycoprotein that keep the other parts ofhte ECM stuck together 
  134. what does fibronectin do
    attach some ECM proteins tot he plasma membrane 
  135. what do integrins do 
    embedded in the membrane they can signal to the inside if something is happending outside the cell 
  136. what are intercellular junctions 
    connections between cells that help them stick together and communicate with one another 
  137. what are the 3 major types of intracellular junctions in animals 
    • tight junctions
    • desmosomes
    • gap junctions
  138. tight junctions
    • super glue
    • encircles entire cell
    • water tight seal 
    • composed of adhesion protein filaments
  139. desmosomes 
    • elasic bands between cells
    • allow for stretching 
    • consists of glycoprotein filaments that do not completely surround the cell
  140. gap junctions 
    •  protein complexes that form a channel (pore) between 2 neighboring cells 
    • allows communication and exchange of nutrients
    • do not encircle
  141. what is the only type of intracellular junction in plants
  142. plasmodesmata
    • channels between 2 adjacent [plant cells 
    • connects cytoplasm
    • allows water, ions and nutrients to flow form cell to cell (like gap) 
    • helps cell wall keep plant cells glued ot eachother 
    • share a cell wall with neighbor 
  143. what really holds cell walls together 
  144. what are the two groups that cellular chemical reactions can be placed in
    • -those that involve the breaking down of large molecules into simpler ones
    • -those that are involved in building up of larger more complex molecules 
  145. breakdown reactions are called ---- and ----
    catabolic reactions ---- release lots of energy 
  146. build up reactions are called ____ and ______
    anabolic reactions---- require energy 
  147. what are the three types of cellular work?
    • anabolism macromolecules synthesized 
    • mechanical work
    • electromechanical work
  148. what is anabolism macromolecules synthesized
    • making of proteins from amino acids 
    • making of DNA from nucleotides 
  149. what is mechanical cell work
    • movement
    • growth 
  150. what is electromechanical cellular work
    active transport (shipping things in and out of the cell) 
  151. what is a catabolic pathway
    the long series of controlled steps that a cell goes through to extract energy 
  152. why do cells follow the catabolic pathway 
    • to prevent damage from extractng too much energy at once 
    • and to maximize efficiency 
  153. a cell must constantly _____ their anabolic and catabolic reactions 
    balance and regulate
  154. define metabolism 
    the sum of hte anabolic and catabolic reactions in a cell 
  155. how is energy pransfered from one process to another 
  156. what is ATP 
    • Adenosine triphosphate 
    • contains the sugar ribose
    • a nitrogenous base adenine
    • three phosphate groups 
    • very stable 
  157. how is ATP made
    the energy produced from catabolic reactoins is used to take a phosphate group and add onto a molecule of ADP 
  158. what does ADP stand for 
    adenosine diphosphate 
  159. how do you use the energy in ATP 
    the last phosphate is taken off breaking the bond (by hydrolysis)--releasing all the energy you put in
  160. define a chemical reaction 
    the process that leads to the changing / making and or breaking of chemical bonds ----requires energy 
  161. what is activation energy 
    the energy required to get a reaction going
  162. where do reactants acquire thier activation energy 
    heat from surrounding environment
  163. most chemical reactions have a very_____ activation energy requirement
  164. what is a catalyst
    a substance that can speedup a reaction with out being used up 
  165. catalysts in cells are called 
  166. how do enzymes speed up the chemical reaction 
    they lower teh activationenergy barrier and allow reactions to happen with  much less energy 
  167. what are the three ways enzymes lower the activation energy 
    • -the bind to reactants  (substrates) and twist them so that the existing bonds are destabalized 
    • -the find substrates and orient them properly so that they are more likely to interact
    • -provide a microenviroment that is conductive to the reaction 
  168. what are 5 properties of enzymes 
    • -very specific (lock and key) an enzyme usually only catalizes one reaction
    • -binding to substrates is temporary -recycled
    • -the speed up reactions without the need for an increase in temp,press, ect
    • -extremely fast and efficient
    • -exist in active and inactive forms
  169. what 5 factors affect enzyme activity 
    • temp
    • pH
    • salt concentration 
    • coenzymes
    • inhibitors
  170. enzyme activity ____ as temp____
  171. too high of a temp can cause enzymes to 
  172. most enzymes work best at a pHs of 
  173. pepsin works best at a pH of 
  174. most enzymes dont work very well in ____ water 
  175. why do enzymes not work well in pure water 
    they need ions to allow for proper ionic and hydrogen bondong between enzymes and substrates
  176. if the salt concentration is too high it can interfere with enzyme activity by---
    interfering with enzyme substrate interactions
  177. some inhibitors are _____ 
  178. how do competitive inhibitors work
    they resemble the substrate and block the acitve site
  179. what is another name for noncompetative inhibitors
  180. how do noncompetative inhibitors work 
    binds to enzyme in a p;lace other than the active site and indirectly causes the active site to change  no longer recognizing the substrates 
  181. what is feedback inhibition 
    the final product of the enzymatic reaction goes back and allosterically inhibits the first enzyme in the series
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biology 1500
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