module 1 (outcomes, asgn, practice Qs) Flashcards
basic properties shared by all cells
- Highly complex and organized
- Possess a genetic program and the means to use it
- Are capable of reproducing more copies of the same cell
- Acquire and use energy
- Carry out a variety of chemical rxns
- Engage in numerous mechanical activities
- Able to respond to stimuli
- Capable of self-regulation
- Capable of evolving
what is the source of E that supports life on Earth and how is it passed on b/ organisms
- Electomagnetic radiation from the sun (trapped by photosynthetic cells)
- Light energy —-trapped bylight absorbing pigment in photosynthetic cells —> chemical energy —stored as–>energy rich carbs —via glycolysis–>ATP
common features of pro/euk.
- Similar structure of plasma membrane
- Genetic info is encoded in DNA using identical genetic code
- Ribosomes
- Similar transcription/translation
- Shared metabolic pathways
- Apparatus for conserving energy as ATP (pro: plasma membrane; euk: mitochondrial membrane)
- Similar photosynthesis; synthesis and insertion of membrane protein
- Similar proteasomes
- Cytoskeleton filaments: actin and tubulin
- Genetic material condensed to chromosome
cell differentiation
Cell specialization to carry out certain function, contain certain material
why are cells always microscopic
The greater cytoplasmic volume of a cell, the longer it will take to move substances in/out, synthesize number of messages required by that cell.
Endosymbiotic theory:
- Euk arose after prok: evidence by fossils
- Prok gave rise to euk: share many complex traits
- Similarities b/ pro and euk show that euk evolved from prok. (share identical genetic code that uses DNA and RNA, common set of metabolic pathways, many similar structural features)
- Mitochondria and chlorop originated from the smaller prok cell:
- Have own DNA (similar to bacterial)
- Similar size to the bacterial
- DNA, RNA, ribosomes and protein synthesis
- Have double phospholipid bilayer
Types of viral infections:
Lytic cycle:
- Virus infects
- Uses host to replicate viral genome
- Assembly
- Cell lyses releasing virions
Lysogenic cycle:
- Incorporation of viral DNA into host DNA
- Provirus=integrated viral DNA
- Can lead to
- Normal cell growth until stress conditions -> lytic cycle to follow
- Budding of virions w/t cell rupture
- Host loses control over mitosis -> malignancy
Cell theory:
- Schleiden and Schwann
- Virchow
- tenets:
- Cells organisms are composed of 1 or more cells
- Cell is strucutral unit of life
- Cells can only arise by dividing from preexisting cells
4 classes of macromolecules:
- Lipid (monomer: hydrocarbon and glycerol)
- Nucleic acid (monomer: nucleotide)
- Carbohydrates (monomer: monosaccharide)
- Protein (monomer: aminoacid)
Glycogen, starch and cellulose
- made of glucose, but have different properties
- Glycogen: highly branched ( alpha linkage: 1,4 for straight chain and 1,6 for branches), can form H bonding, insoluable, purpose: storage
- Starch: in plants for energy storage, helical arrangemens, mixture of 2 polymers
- Cellulose: unbranched, highly extended; structural support in plants; beta linkage
lipids
- Diverse group of nonpolar biological molecules
- Include fats, steroids, phospholipids
fats
- Saturated: have only SB, solids in room t
- Unsaturated: can have DB, liquid in room t
- Consists of glycerol + 3 FA
- Amphipathic molecule (both hydrophobic and hydrophilic parts)
- Storage of E on longer terms
- Rich in chem E
Steroids:
- Precursor: cholesterol (has 4 fused rings)
- Steroid hormones: testosteron, estrogen
- Components of animal cell membrane
- Cholesterol involved in membrane fluidity
Phospholipids:
- Function primarily in the cell membrane
- Amphipathic molecule
- Glycerol + 2 FA + P
Protein Function:
- enzyme (increase rxn rate)
- Structural: mchanical support
- Hormones, growth factors, gene activators: regulation
- Membrane receptors and transporters: determine what a cell reacts to and how it regulates what substances enter r leave the cell
- Contractile filaments and molecular motors: machinery for biological movements
- Ab
- Toxins
- Blood clots
- Absorb/refract light
Why proteins can have so many functions:
b/c they have unliited shapes and exhibit high degree of specificity
Secondary protein:
- Include conformations ( 3D arrangement of molecules and atoms) alpha helix and beta pleeted sheets
- Descrie conformation of the portion of the polypeptide
- Conformation is chosen to max # H bonding
- Alpha helix:
- R handed
- Side chain point outwards
- H bonding b/ atoms of the same polypeptide
- Turn has 3.6 AA
- H bond b/ every 4th AA
- Subject to pulling forces
- Beta pleeted sheets:
- Several segments of polypeptide laying side by side
- H bond perpendicular to the chain axis
- Parallel or antiparallel
- b/c of structure -> good at resisting pulling Force
- R groups project upwards and downwards from the chain
- Other conformation: hinges, turns, loops, finger-like extentions
Ribozymes
- RNAs that have a catalytic role
- Aka RNA enzymes
- Have led to speculation that early in the evolution neither DNA nor protein existed in Earth, instead RNA served as genetic material and enzymes
Structure of nucleotide and how they form a nucleic acids:
- Structure: sugar (ribose vs deoxyribose), phosphate group, base
- Links 5’ phosphate w/ 3’ OH of sugars in two nucleotides
magnification
- Increase the size of the object
- As magnification increases, the quality of the image decreases
- Produces enlarged image of an object
resolution
- How well we can see fine details
- Limited by the diffraction
- Ability to see two neighbouring points as two distinct points w/t overlapping
Why is it necessary to stain the specimen to be viewed in tge bright-field microscope?
- Specimen that have been thinly sectioned are translucent
- Need to stain w/ dye in order to see
fluorophores
a molecule that absorbed photon of a certain wavelength and releases some of the energy in longer wavelength. It is used in the fluorescence microscopy. The fluorescence microscope enables viewing molecules that are fluorophores themselves or that are linked to fluorophores
Describe two ways that scientists can determine the location of specific proteins in cell. What are the main differences b/ these techniques?
I_mmunofluorescence microscopy:_
- Uses Ab made to specific proteins
- Ab are labeled w/ fluorofluores
- Cells are fixed (not living)
Protein fusions to the fluorescent protein GFP:
- Cells are alive
- Protein movement can be tracked in vivo
What is the difference b/ fluorescence/epifluorescence and confocal microscopy in terms of the clarity of the image?
Fluorescence/epifluorescence microscopy:
Light emitted by the sample originated from the molecules located throughout the entire sample (including areas above and below the focal plane)
Confocal microscopy:
Uses a pinhole in front of the detector to block light that does not originate from the focal plane
Images are not blurry b/c only light from structures within focal plane is observed
TEM vs SEM
TEM
- Forms images using electrons that are transmitted thru the specimen
- Visualization of the inner structures
SEM
- Forms images from electrons that bounce off the surface of the specimen
- Visualization of the outer surfaces of the objects
Isotope
- Is a radioactive version of a molecule that can act as a tracer revelaling its location by a radioactive signal
- Used in cell and molecular biology to localize or monitor changes during the experiment
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Procedure of Differential centrifugation:
- Cell is broken down by mechanical homogenization: various membranous organelles become fragmented anf form spherical membraneous vesicles
- Low speed centrifugation (to pellet larger particles). Will leave smaller particles in supernatant on the top and heavy particles at the bottom of the tube
- Transfer of the supernatant to the other tube
- Centrifugation at the higher speed to send small particles (ex. microsomes) to the bottom of the test tube
Homogenization vs cell fractionation
- Homogenization: breaking of the cell by mechanical disruption
- Cell fractionation: the purification of the specific parts of a homogenate usually containifg organelles
How do you separate cellular components after fractionation
Using centrifugation and density gradient centrifugation
x-ray crystallography is used to
determine proteins and DNA strucutre at atominc resolutions
You are observing a cell. Its cell wall is not made of cellulose; rather, it is constructed of a long-chain polysaccharide called peptidoglycan. This type of cell has the ability to make all but the simplest molecules and can make all of the 20 amino acids.
- what kind of cell it is
- would it contain pigment capable of photosynthesis? which one?
- it’s a bacteria cell since it contains peptidoglycan cell wall
- It would be called photoautotroph since it’s capable of both photosynthesis and can make the simplest molecules. Cyanobacteria is a well-known photoautotroph
Cite three cellular features that suggest that all living organisms are evolutionarily derived from a common ancestral cell. Which term often is used in reference to this cell?
- share identical genetic code that uses DNA/RNA
- similar plasma membrane
- ribosomes
it’s called last universal common ancestor (LUCA)
why is an electron microscope superior to a light microscope
- light microscope is limited only to one wavelenth
- electron microscope has different wavelength (shorter wavelength and produces better resolving power)
- wavelength is directly related to resolution
Under certain conditions, some proviruses can be activated to enter the lytic pathway, which ends with lysis/death of the host cell. What circumstances can lead to this shift?
under stressful conditions (ex. t, ph, UV radiation)
Some viruses remain as proviruses and reproduce without lysing the host cell. Explain how this is accomplished and give one example of such a virus.
. It replicates and exits the cell by budding off from the host cell membrane
what is the smallest known cell (+characteristics)
- mycoplasma
- .2microm
- 500 genes
- no cell wall
- bacteria
3 major differences b/ viriods and viruses
- viroid has no protein coat, while viruses have capsid
- viroid genome does not encode any proteins, while viral does
- virion is 1/10 of virus size
amphipathic
molecule has both hydrophobic and hydrophilic components
Briefly explain why many mammals are herbivores and eat grass and other plants for nutrition, whereas humans are unable to use cellulose as a food source.
- cellulose which is made of beta (1,4) glycosidic linkage between its glucose residues. Humans don’t have an enzyme to digest beta glyosidic linkage
- enzyme that digest cellulose is called cellulase, and many organism do not have genes to encode for cellulase and therefore it is not synthesizes
which techniques are used to determine the arrangements of atoms witin aproteins
- X-ray diffraction (X-ray crystallography);
- NMR spectroscopy.
What is the net charge of DNA and RNA and which chemical group is responsible for this charge
DNA and RNA are both nucleic acids that are composed of a sugar (DNA - deoxyribose; RNA – ribose), bases (DNA – C, G, A, T; RNA – C, G, A, U) and a phosphate.
The presence of the phosphate in those molecules gives them a negative charge.
On what basis are DNA fragments separated when subjected to agarose gel electrophoresis?
- Gel electrophoresis separates molecules based on their effective size
- Negative charge of the DNA (due to the phosphate group) will be attracted to the anode, which is a positive pole.
- The smaller the segment of the DNA, the further down it will travel (it will be located closer to the anode and further away from the well)
molecular chaperones
- help misfolded or unfolded proteins to achieve their final conformation by preventing them from interacting with other molecules in the cytoplasm until the protein is fully synthesized
- ex. Hsp70
chaperonin
- it’s the location where larger polypeptides fold in order to decrease misfolding of the protein due to the interactions with other molecules.
- ex. TRiC
Which level of structure of DNA would be disrupted by a reagent that breaks apart hydrogen bonds
there would be no more of double helix since H bond b/ based would be broken
what effect would reagent that breaks H bond have on the function of ribozyme
This reagent would eliminate the double helical segments of the RNA and eliminate its 3D shape and the ribozyme would be incapable of self cleavage
Give three examples of non-covalent bonds that participate in tertiary structure.
- van der Waals
- H bonding
- ionic interaction
Of what are the lenses of an electron microscope composed
The lenses of the electron microscope are composed of coil shaped electromagnets that transmit electrons in comparison to the light microscope lenses that just bend light.
what technique would you use to study surface features of fruit fly head
SEM (electron microscopy) in which the electrons bounce off the surface of the specimen and are then detected by the detector providing information about the outer structure of the specimen
what technique would you use to study interior and exterior of surfaces of the plasma membrane
- freeze-fracture replication with freeze etching step in which some of the ice is removed allowing to visualize both external surface and internal structures of cellular membranes
what technique would you use to studystructures in living cells
phase contrast microscopy that provides one of the best contrast and resolutions and enable better viewing of the structures of the living cell
Why is laser scanning confocal microscopy superior to conventional fluorescence microscopy
- It produces the image of the thin plane within a thicker plane of the specimen and therefore the produced images are very sharp and there is no need to constantly refocus the microscope;
- It accomplishes this by the use of a pinhole aperture in front of the detector which eliminates the light not originating from the focal plane.
- The laser scans the specimen only at a single depth;
The secondary light source increases resolution
Freeze fracture replication with freeze etching step
- Study inner and outer surface of the plasma membrane
- A layer of ice is removed
- Less ice clearer view of the inner and outer structures of the plasma membrane
Phase contrast microscopy
- Good contrast and resolution
- Enables viewing of structures of living cells
