Exam 1 Flashcards
L1 What are the three “tenets” of the “Cell Theory” of life on Earth?
- All living Organisms are composed of cells. 2. Cells are the (smallest) structural unit of life. 3. Cells arise from other cells.
L1 What three general “features or functions” are shared by ALL living cells on Earth?
- 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)
L1. The presence of what organelle is commonly used to distinguish prokaryotes from eukaryotes?
Nucleus- a membrane-bound organelle enclosing their DNA
L1. Phase contrast microscopy and differential interference microscopy use differences in the ________ of cellular constituents to generate contrast.
Refractive index.
L1. _______ microscopy uses fluorescently-labeled antibodies to “stain”, identify and reveal the location, of specific cellular components such as proteins.
Immunofluorescense
L1. __________ Electron microscopy can be used to examine the surface topography of cells at resolutions of________
Scanning 2-20 nanometers
L1. __________ Electron microscopy resolves details of cytoplasmic organization down to _________
Transmission 1-2 nanometers
L1. Draw a simple diagram comparing the construction of a transmission electron microscope with a typical light microscope
Diagram ECB4 panel 1-1
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?
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.
L1. How is a scanning electron microscope (SEM) different from transmission electron microscopy (TEM)? What cellular features are best examined by SEM?
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
L1. List three organelles or features found in cells of both plants and animals and breifly describe their function
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
L1. List three organelles or features found only in plant cells. Briefly describe their function
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.
L1. What is the significance of Miller and Urey’s experiment investigating the origin of organic compounds on the primordial Earth?
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
L1. Which features of the mitochondria and chloroplasts are consitent with their evolution from endosymbiotic prokaryotes/
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 ???
L1. Do you think chloroplasts and mitochondria could live independently from their “host” cells?
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.
L3. Rank Strengths of following chemical interactions: Van der Waals, Covalent bond, hydrogen bond, ionic bond, hydrophobic interaction
strongest: covalent, ionic(in water), h-bond, van der waals, hydrophobic interaction
L3 How can weak bonds such as van der Waals forces, ionic and hydrogen bonds contribute to the structure of biomolecules such as proteins?
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.
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?
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 (?)
Why are some covalent bonds polar? How does the presence of polar bonds influence interactions the structure and association of biomolecules?
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.
L1. How could you unambiguosuly determine whether each cell was a prokaryote or eukaryote?
Sequence their genomes and compare them to those of archae, eubacteria and eukaryotes.
L3. Describe how the structure of some compounds, and it’s molecular interactions, result in their distinct physical properties?
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
L3. What distinguishes Hydrophobic, hydrophilic and amphipathic molcules?
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.
L3. What is the mathmatical defintiion of pH?
pH = -log[H]
L3. What is the [H] in an aqueous solution at a) pH 7 b) pH 4 c) pH 10 ??
a) 10E-7 b) 10E-4 c) 10E-10
L3. How are acids and bases defined for the purpose of this class?
Acids increase [H+], decrease pH Bases decrease [H+], increase pH
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
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
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.
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.
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.
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.
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.
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
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.
L4. Draw structure of 2 cystine side chains linked by a disulfide bond
ECB4 PANEL 2-5 PAGE 75
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
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.
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.
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
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
L5. Draw a diagram of what integral proteins look like compared to peripheral
DIAGRAM slides 22 or 25 lecture 5
Citric Acid Cylce
Fatty Acid Structure
Choline
Ethanolmine
Serine
Phosphate Functional Groups
Light Microscope diagram
Scanning Electron Micrscope Diagram
Transmission Electron Microscope Diagram
