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Cell Biology (Bard) > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

L1 What are the three “tenets” of the “Cell Theory” of life on Earth?

A
  1. All living Organisms are composed of cells. 2. Cells are the (smallest) structural unit of life. 3. Cells arise from other cells.
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2
Q

L1 What three general “features or functions” are shared by ALL living cells on Earth?

A
  1. Boundary or limiter i.e. cell (plasma membrane) 2. Mechanism for harvesting/utilizing energy resources from their environment (Metabolism) 3. A mechanism of inheritance capable of “faithful” replication (DNA)
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3
Q

L1. The presence of what organelle is commonly used to distinguish prokaryotes from eukaryotes?

A

Nucleus- a membrane-bound organelle enclosing their DNA

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4
Q

L1. Phase contrast microscopy and differential interference microscopy use differences in the ________ of cellular constituents to generate contrast.

A

Refractive index.

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5
Q

L1. _______ microscopy uses fluorescently-labeled antibodies to “stain”, identify and reveal the location, of specific cellular components such as proteins.

A

Immunofluorescense

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6
Q

L1. __________ Electron microscopy can be used to examine the surface topography of cells at resolutions of________

A

Scanning 2-20 nanometers

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7
Q

L1. __________ Electron microscopy resolves details of cytoplasmic organization down to _________

A

Transmission 1-2 nanometers

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8
Q

L1. Draw a simple diagram comparing the construction of a transmission electron microscope with a typical light microscope

A

Diagram ECB4 panel 1-1

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9
Q

L1. Why is there a limit to the “useful” magnification obtainable with a light and electron microscope? Why do you think the useful magnification of a TEM is so much higher than a light microscope?

A

The purpose of a microscope is to enlarge cells (or their components) sufficiently to be “seen” by a detector, which might be an eye or a camera, the resolution of the average human eye is 100 microns. The resolution limit for a typical light microscope is .2 microns. Reye/Rscope tells us a magnification of 500x will enlarge all details resolved by the microscope sufficiently to be resolved by our eyes. Addt’l magnification beyond 500x reveals no additional detail. The R for a TEM is much smaller, and allows us to see even more detail.

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10
Q

L1. How is a scanning electron microscope (SEM) different from transmission electron microscopy (TEM)? What cellular features are best examined by SEM?

A

Transimission microscope only focuses on one point, scanning microscope scans a whole topography due to the scan generator and sensor (?) The SEM is most useful for details of cell surface topography. ECB4 panel 1-1

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11
Q

L1. List three organelles or features found in cells of both plants and animals and breifly describe their function

A

Nucleus (contains genetic material, and mechanism for replicating and transcribing it) Plasma membrane: acts as a barrier between inside and outside of the cell Rough and Smooth Endoplasmic Reticulum: produce/synthesize proteins and lipids Golgi: sort and transport proteins Cytoskeleton: actin and microtubules-provide structure Ribosomes: translation

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12
Q

L1. List three organelles or features found only in plant cells. Briefly describe their function

A

Chloroplasts: site of photosynthesis. Vacuole: Regulate ion balance Provide turgor pressure and provide support and do some of the same things as lysosomes. Cell wall: composed of cellulose and polysaccharaides, provides more support, counters turgor pressure.

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13
Q

L1. What is the significance of Miller and Urey’s experiment investigating the origin of organic compounds on the primordial Earth?

A

It proved that abiotic synthesis of organic compounds. Proved abiotic assembly of “bio”polymers was possible. It helped give credence to the theory that under the understood conditions of primordial Earth, the abiotic synthesis of organic compounds was possible. Miller and Urey (and others that followed) simulated conditions on early earth by combining exposing a reducing atmosphere rich in CO2, H2, and N2, and water to an energy source such as heat/electricity/UV. Combining these ingredients resulted in the abiotic synthesis of many precursors to biological macromolecules, including amino acids (proteins), glyceraldehyde and other simple sugars (carbohydrates), purines (nucleic acids), etc. Their results provided compelling evidence for the abiotic synthesis/origin of many building blocks for biomolecules found in modern cells

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14
Q

L1. Which features of the mitochondria and chloroplasts are consitent with their evolution from endosymbiotic prokaryotes/

A

They have their own circular DNA. They have their own double membranes, including an outer one that contains porin proteins similar to prokaryotes. 3)prokaryote-like translation machinery ???

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15
Q

L1. Do you think chloroplasts and mitochondria could live independently from their “host” cells?

A

NO. They have lost the ability to create necessary proteins to live independtly. The symbiotic relationship is so strong, that they have yielded the synthesis of certain necessary proteins to their host cells.

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16
Q

L3. Rank Strengths of following chemical interactions: Van der Waals, Covalent bond, hydrogen bond, ionic bond, hydrophobic interaction

A

strongest: covalent, ionic(in water), h-bond, van der waals, hydrophobic interaction

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17
Q

L3 How can weak bonds such as van der Waals forces, ionic and hydrogen bonds contribute to the structure of biomolecules such as proteins?

A

The summation of thousands of these forces end up being strong enough to contribute to the structure. “The summation of weak bonds, can create strong binding forces.

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18
Q

L3. Which of the above interactions holds the atoms of a water molecule together? which of the above interactions are primarily responsible for water being a liquid at room temperature?

A

Oxygen and Hydrogen bond together through polar covalent bonds. H-bonds are responsible for water being a liquid at room temp. By rotating and continuing to form, break, and reform H-bonds, keeping molecules moving and therefore liquid (?)

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19
Q

Why are some covalent bonds polar? How does the presence of polar bonds influence interactions the structure and association of biomolecules?

A

Covalent bonds that are polar are a product of one of the elements that share electrons being more electronegative than the other and pulling the electron density more toward it, resulting in a partial negative charge on the more EN element and a partial positive charge on the less EN element. These partial charges result in and allow van der Waals and H-bonds to form.

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20
Q

L1. How could you unambiguosuly determine whether each cell was a prokaryote or eukaryote?

A

Sequence their genomes and compare them to those of archae, eubacteria and eukaryotes.

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21
Q

L3. Describe how the structure of some compounds, and it’s molecular interactions, result in their distinct physical properties?

A

Propane has no polar bonds, thus it only interacts by VdW which results in a low BP Propanol has one OH. Polar bonds of that OH allow propanol molecules to forma a limited number of H-bonds keeping it a liquid at Room Temp Glycerol has 3 OH. Allows for extensive H-bonding. Actually will decompose before it reaches its BP

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22
Q

L3. What distinguishes Hydrophobic, hydrophilic and amphipathic molcules?

A

Hyrdophobic molecules have non-polar bonds. They interrupt h-bonds of water, and are insoluble. Hydrophilic compounds are charged or have polar bonds, allowing them to H-bond. are soluble Ampipathic: have regions that are hydrophobic and others that are hydrophilic, i.e. lipids and detergents.

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23
Q

L3. What is the mathmatical defintiion of pH?

A

pH = -log[H]

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24
Q

L3. What is the [H] in an aqueous solution at a) pH 7 b) pH 4 c) pH 10 ??

A

a) 10E-7 b) 10E-4 c) 10E-10

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25
L3. How are acids and bases defined for the purpose of this class?
Acids increase [H+], decrease pH Bases decrease [H+], increase pH
26
L3. Is the group either acidic or basic? a) methyl group b) carboxyl group c) amino group d) inorganic phosphate
a) neither b) acidic c) basic d) acid-loses to protons in water
27
L3. Draw structures of each of the following functional groups or linkages a) alcohol b) carboxylic acid c) amine d) ketone e) ester bond f) phosphoester bond g) phosphaoanyhdride
ECB4 panel 2-1 lecture 3 notes slide 15-16
28
L4. Draw the structure of a generic amino acid in water at neutral pH, labeling the amino group, carboxyl group, alpha carbon, and the position of the side chain
H3N-C-COO R N is amino group, carboxyl group is COO, R is side chain.
29
L4. Which amino acids contain acidic side chains? Draw the structure of these amino acids as they would appear in water at neutral pH. Where might you expect to find these amino acids in the 3D structure of a protein/
Asparic acid (Asp or D) CH2-COO- Glutamic Acid (Glu or E) CH2-CH2-COO These would be found in the hydrophilic parts of the membrane, they're charged and would interact with water. On the outer portion.
30
L4. Which amino acids contain basic side chains? Draw the structure of these amino acids as they would appear in water at neutral pH. Where might you expect to find these amino acids in the 3-D structure of a protein? Why
Lysine (Lys or K) CH2-CH2-CH2-CH2-NH3+ Arginine (Arg or R) CH2-CH2-CH2-NH-C=NH2 NH2 Histidine (His or H) CH2-C=CH-NH+=CH-NH- l Terminal amino groups are protonated!!!! These would be found on the outside of a protein, where it would interact with water.
31
L4. Which amino acids are nonpolar? Which might be considered hyrdrophobic? Where might you expect to find these amino acids in the 3D structure of a protein?
NONPOLAR and not hydrophobic: Glycine (Gly or G) Alanine (Ala or A) Cysteine (Cys or C) Can be in aqueous or non-aqueous regions of the protein. NONPOLAR/HYDROPHOBIC: Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) These would be found inside or within the protein, where they wouldn't interact with water.
32
L4. Mutations that cause changes in protein sequence can dramatically alter protein structure and function. Replacement of a non-polar amino acid with a charged amino acid often results in a non functional protein. Briefly explain why.
This may be due to the fact that if a polar amino acid replaces a nonpolar one, it will cause the protein to form or fold in a different way and thus render it impossible for the protein to serve its original function.
33
L4. Briefly define/describe the four levels of proteins structure discussed in class, indicating which chemical bonds/interactions stabalize or contribut to that level or protein structure.
Primary: Linear order of amino acids. Bonded by peptide bonds, which are just covalent bonds. Secondary: either Alpha helix or beta sheet. caused by H-Bonds between peptide (amide) bonds Tertiary: 3D conformation of the the protein. Folding of helices or sheets into domains, involving weak interactions: H-bonds between AA side chains, ionic interactions, VdW and hydrophobic interactions. Also disulfide bonds between cysteine side chains. Quaternary: the joining of two or more polypeptides. this is due to VdW and all the other weak interactions and disulfides potentially
34
L4. In both alpha helices and beta sheets, the N-H and C=O groups of each peptide bond are H-bonded. What distinguishes the organization/orientation of H-bonds in these two secondary structures?
HELIX: H-Bonds are formed by AA along the length of the polypeptide, the amide H is H-bonded to the carboyn O 4 amino acids along the helix. Sheet: H-bonds link amino aicds from different strands of the sheet.
35
L4. Draw structure of 2 cystine side chains linked by a disulfide bond
ECB4 PANEL 2-5 PAGE 75
36
L4. Antibodies bind extremely tightly and specifically to antigens, and yet this binding does not involve any covalent bonds between the antibody and antigen molecules. Explain how such tight and specific interactions could be generated using weak bonds
Antibodies contain a binding pocket or cleft whose surface is complementary to that of their antigen. The tight and specific binding of antibodies to their corresponding antigens results from the summation of a multitude of weak bonds... including vdW, H-bonds, hydrophobic interactions, and in some cases, ionic bonds
37
L4. Briefly describe how SDS-PAGE is used to analytically separate protein mixtures. Why are proteins to be separated first heated in SDS and 2-mercaptoethanol (2-ME)? What property of the proteins is then used to separate them? How can the proteins be visualized/identified
Step 1: Denature proteins by heating in SDS and 2-ME SDS denatures and unfolds the protein 2-ME breaks disulfide bond Step 2: Load protein samples to cross-linked polyarcylamide gel Step 3: Apply Electric field Step 4: SDS-coated proteins migrate towards positve pole.. smaller proteins migrate faster Step 5: Stain with dye or antibodies.
38
L5. What is meant by the term amphipathic as it is applied to biomolecules?
It is meant to describe a molecule that has both hydrophilic and hydrophobic regions/domains.
39
L5. Draw and label the hydrophobic and hyrdophilic regions of each a) Sodium Doceyl sulfate (SDS) b) Palmitic acid a C16 fatty acid c) Phosphatidic Acid d)Phosphatidycholine (lecithin) e) Phosphatidylserine
Lecture 5, slides 4,7,8,20
40
L5. Draw a simple stick diagrams showing the orientation of phosphatidycholine molecules in: 1) a micelle in water 2) a bubble in air 3) a lipid bilayer in water 4) a biological membrane.
Lecutre 5 slide 10. A soap bublle in air is simply a lipid bilayer turned inside out
41
L5. What chemical interactions are responsible for the organization of a biological membrane?
Hydrophobic lipid tails interact laterally via VdW interactions. Polar heads interact with water via H-bonds, ionic interactions, but primarily hydrophobic effect that is responsible for the organization of a lipid bilayer membrane.
42
L5. Why are biological membranes referred to as fluid mosaics?
They are mosiacs of lipids and membrane proteins and have diffusional characteristics of a two-dimensional "fluid"
43
L5. Why is there a higher percentage of unsaturated phospholipids in organisms that exist in cold temperatures?
More double bonds in the lipid, the more fluid the membrane.
44
L5. What effect does length of fatty acid chain have on membranes?
Shorter fatty acid tails increase membrane fluidity. Cold organisms have shorter chains, those in hot environments have longer fatty acid chains
45
L5. What effect does cholesterol have on the structure and function of animal cell membranes?
Cholesterol inserts itself into the lipid bilayer with its polar hydroxyl group associated with the polar heads, and sterol ring and hydrocarbon tail in the hydrophobic interior. The rigidity of the sterol ring interferes with movement and packing of the lipid tails. CHOLESTEROL THUS DECREASES FLUIDITY AT RT, BUT BROADENS THE TRANSITION TEMPERATURE OF THE MEMBRANE, keeping it more fluid at colder temps. Cholesterol also decreases the permeability of the membrane to small molecules
46
L5. What characteristic of bilyar membranes allows cells to maintain the phsopholipid distribution implied by your data?
Generation and maintenance of the lipid distributions in the inner and outer membranes requires that flipping between the two leaflets is slow. Cells use membrane-associated enzymes to flip lipids from th cytoplasmic to the outer leaflet during membrane synthesis (scrambalase) and to remove phosphatidyl ethanolamine and phosphatidylserine from the non-cytoplasmic leaflet (flippase), which leaves the outer leaflet enriched in phosphatidycholine and sphingomyelin.
47
L5. What distinguishes an integral from a peripheral membrane protein?
Peripheral can be removed without disrupting the membrane, due to their weaker association. Integral proteins are tightly associated and disrupt the membrane when they're removed
48
L5. Draw a diagram of what integral proteins look like compared to peripheral
DIAGRAM slides 22 or 25 lecture 5
49
L5. How would you experimentally determine whether a membrane protein was "integral" or peripheral?
Wash membrane with salt and separate the membrane fraction from the soluble fraction in a centrifuge. If it's released, it is peripheral. Also, staining of the membrane and then bleaching it to see if it moves. "Fluorescence recovery after photobleaching (FRAP)
50
L5. If a single membrane spanning domain, what would you expect its structure to be
hydrophobic alpha helix
51
L5. Describe the features of alpha helices and beta barrels that allow them to span the lipid bilayer. How long must an alpha helix be to span a cell membrane? How many amino acids does this require?
All of the polar components of the peptide bonds linking amino acids in the polypeptide chain are shielded from water by H-bonding with nearby peptide bonds. Crossing the membrane requires an alpha helix to be approx. 3 nm in length, requires about 20 AA (.15nm/AA)
52
L5. Do proteins or lipids diffuse faster in the membrane?
LIPIDS
53
L5. What are the 2 major classes of transport proteins found in cell membranes?
Channels and carriers
54
L5. Compare and contrast the function of the two classes of membrane transporters. which is faster, which functions as active transport, etc.
Channels form an open pore through membrane, allowing molecules to flow down a gradient. They may be gated by signals or small ligands. Faster. Carriers do not form an open channel and transport requires a change in protein conformation. May be coupled with energy, used for active transport.
55
L5. Provide 3 examples of energy sources coupled to active transport.
Electrochemical gradient: many amino acid transporter use energy of the Na+ gradient to power amino acid import. ATP hydrolysis: The Na+-K+ ATPase pumps Na+ out and K+ in Electron Transport: mitochondria use the flow of high energy eletrons down a redox chain to power transport of H+ across the inner mitochondrial membrane Light: photosynthetic organisms use the energy stored in light to power H+ transport across the thylakoid membrane
56
L5. How do cells use the Na+ gradient to power amino acid import? Is this an example of passive/active transport? How does cell maintain Na/K gradient across cell membrane?
Na is high outside the cell, low inside. [AA] is low outside the cell and high inside. Thus, AA's must go up gadient (Active transport) Na goes down gradient, and this energy allows AA transporter to let AA go up gradient. SYMPORT (they both enter the cell) Na-K pump with ATPase uses ATP hydrolisys to pump Na out and K into the cell to maintain gradient
57
L5. If Na can't get out of the cell, what happens?
Cell depolarizes, membrane potential becomes less negative. Na gradient is diminished
58
L5. How would a reduced Na gradient effect amino acid import into animal cells?
As Na gradient decreases, amino acid import will slow and eventually come to a halt.
59
L5. Why would a cell burst if the Na-K-ATPase pump stopped working?
Na gradient helps maintain osmotic balance, as [Na] becomes equal outside and inside the cell, water will be drawn in into the cell by osmosis.
60
Lysine
Lys or K Basic- NH3+
61
Arginine
Arg or R basic c=Nh2+
62
Histidine
His or H basic NH+ with 3 bonds to 2 carbons
63
Aspartic Acid
Asp or D Acidic Coo-
64
Glutamic Acid
Glu or E Acidic coo-
65
Asparagine
Asn or N uncharged polar
66
Glutamine
Gln or Q Uncharged polar
67
Serine
Ser or S Uncharged polar
68
Threonine
Thr or T Uncharged polar
69
Tyrosine
Tyr or Y Uncharged polar
70
Glycine
Gly or G nonpolar
71
Alanine
Ala or A nonpolar
72
Valine
Val or V nonpolar
73
Leucine
Leu or L nonpolar
74
Isoleucine
Ile or I nonpolar
75
Cysteine
Cys or C nonpolar
76
Methionine
Met or M nonpolar
77
Phenylalnine
Phe or F nonpolar
78
Tryptophan
Trp or W nonpolar
79
Proline
Pro or P nonpolar
80
L6. What is delta G for ATP --\> ADP + pi
-7.3 kcal/mol
81
L6. How much energy does the hydrolysis of ATP yield under cellular conditions?
-10 to -13kcal/mol due to cellular conditions and how far the rxn is from equilibrium.
82
L6. Why does the ATP reaction never reach equilibrium in a living cell?
Cells continuously harvest energy from the environment to make ATP. [ATP] is above what it would be at equilibrium, therefore driving the reaction towards products
83
L6. Structure of ATP
DIAG
84
L6. Hydrolysis of the gamma phosphate releases how much energy?
-10--13 kcal/mol
85
L6. How much energy is released when the bond between alpha and beta phosphates is hydrolyzed?
-26kcal/mol
86
L6. Diagram of oxidation of glucose that depicts the role cellular enzymes play in the metabolism of glucose to CO2 and water cells
DIAGRAM Lecture 6/7 slide 33 Energy Activation diagram. lots of small mole hills continually decreasing
87
L6. Why is the conversion of pyruvate to lactate crucial?
Under anaerobic conditions, as NAD+ is consumed, it won't be regenerated and glycolysis will grind to a halt. When pyruvate is reduced to lactate, NADH is oxidized to NAD+ allowing cells to continue glycolysis to produce energy.
88
L6. How do cells regulate the flow of glucose through glycoysis? How can ATP serve as both substrate and regulatory ligand for an enzyme?
by "allosterically" regulating key enzymes. ATP acts as both substrate and regulatory ligand. Substrate: binds in the active site, and donates a phosphate to fructose 6 phosphate to make fructose 1,6 bisphosphate. Regulatory ligand: ATP binds in a regulatory site on the enzyme, causing an allosteric change in the enzyme structure which turns the enzyme off.
89
L6. What reaction(s) couples the reactions of glycolysis to those of the citric acid cycle? Where does these reactions take place?
Pyruvate is converted to acetylcoA by the pyruvate dehydrogenase complex, releasing CO2 and reducing NAD+ to NADH. These reactions occur in cytoplasm of prok. and in mitochondrial matrix of euks.
90
Glycolysis
* Glucose (6C) * hexose kinase uses energy- * Glucose 6-Phosphate (6C) * Fructose 6-phosphate (6C) - * phosphofructokinase (uses energy) * Fructose 1,6-bisphosphate (6C) * either Dihydroxyacetone phosphate or Glyceraldehyde 3-phosphate * converts to glyceraldehyde * Glyceraldehyde-3-Phosphate (3C) - * Glyceraldehyde 3-P dehydrogenase- (produces NADH) * 1,3-bisphosphoglycerate (3C) * --Phosphoglycerate kinase (produces Energy)-- * 3-phosphoglycerate (3C) * 2-phosphoglycerate (3C) * Phosphoenolpyruvate (3C) * --pyruvate kinase (produces energy)-- * pyruvate
91
Citric Acid Cylce
* Acetyl-CoA (2C) * Citrate (6) * Isocitrate (6) * -CO2 * -NADH * alpha-Ketoglutarate (5) - * CO2 * -NADH * Succinyl-CoA (4) - * GTP * Succinate (4) * -FADH2 * Fumarate (4) * Malate (4) - * NADH * Oxaloacetate (4)
92
Citric Acid Cycle reminders
A Car in Kanab Should Stop for Moving Objects. 2 6's 5 4's NADH with CO2 FADH2 w/ fumurate GTP succs
93
Citric Acid Cylce
94
Fatty Acid Structure
95
Choline
96
Ethanolmine
97
Serine
98
Phosphate Functional Groups
99
Light Microscope diagram
100
Scanning Electron Micrscope Diagram
101
Transmission Electron Microscope Diagram
102
L4. Which amino acids are polar but uncharged? Draw the structure of these amino acids as they would appear in water at neutral pH. Identify the polar chemical bonds, and indicate the distribution of partial charges. Diagram an H-bond between water and one of these amino acid side chains, showing the distribution of partial charges on both water and amino acid side chain. Where might you expect to find these amino acids in the 3-D structure of a protein? Why
Asparagine Glutamine Serine Threonine Tyrosine Most likely to be found on the outside of a protein, where it could interact with water.

Cell Biology (Bard) (4 decks)

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