BIO 215 EXAM 1
Provide evidence in support of the endosymbiotic theory.
1. mit/cp similar to prokaryotes 2.Replicate by binary fission 3.Double membrane -.Inner membrane similar to PM of prokaryotes -Outermembrane may have been derived from host "phagosome" 4. 70S ribosomes - sensitive to some antibiotics 5. Circular genome: prokaryotic promoters, no histones 6. Genome sequence similarity: cp cyanobacteria mit proteobacteria 7. Reduction of organellar genomes - Gene transfer between host and endosymbiont - Many genes needed by mit/cp are nuclear encoded - Sequence similarity between genes in nucleus and cyanobacteria/proteobacteria
What is "symbiosis'?
A close, long term interaction between two different species
What is a protist? Why is it no longer correct to classify all protists together into one phylogenetic group?
A diverse grouping of eukaryotic organisms. Many diverse lineages of various eukaryotic organisms. Can be unicellular or multicellular. They are so diverse that they are not closely related enough to group them into one group.
Describe a glycosidic bond. Be able to identify the type of glycosidic bond present in a given disaccharide or polysaccharide (e.g. alpha 1-->4 glycosidic linkage)
A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.
Define "peptide".
A short chain of amino acids
Define 'electronegativity'.
Affinity of an atom/molecule for electrons Greater the EN, the stronger the affinity for e
Explain the difference between an alpha and a beta isomer.
Alpha : -OH on opposite side of ring vs the CH2OH at C6 Beta: -OH on same side of ring vs the CH2OH at C6
Explain the importance of alpha and beta linkages in polysaccharides. How does this influence our ability to digest polysaccharides?
Alpha and beta linkages affect the structure of the polysaccharides. Certain enzymes can digest some types of linkages and not others. For example, enzymes that digest starch hydrolyze alpha linkages but can't hydrolyze beta linkages in cellulose. Therefore, cellulose in human food passes through the digestive tract as fiber.
Describe the structure/function of the plasma membrane
Boundary of lipids and proteins between a cell and its external environment Defines the 'cell' Regulated movement in/out Mediates communication with external environment
Identify and describe the monomer units used to construct the polymeric macromolecules.
Carbohydrates = monosaccharides Nucleic acids = nucleotides Proteins = amino acids
Identify and describe the different functional groups found in organic molecules.
Carboxyl & phosphate = negatively charged Amino = positively charged group Hydroxyl, sulfhydryl, carbonyl, aldehyde = neutral but polar groups
Describe the general structure of an amino acid.
Carboxyl group Amino group R group (different for each amino acid)
Differentiate between a carboxylic acid and a carboxylate. Which one is protonated? Which one is charged?
Carboxylic acid = protonated, uncharged form of molecule Carboxylic ion = deprotonated, charged form
Who is credited with redrawing the tree of life into 3 domains?
Carle Woese & George Fox.
Describe the evidence used to reclassify organisms into the 3 domains. Why were rRNA gene sequences used for to analyze phylogenetic relationships?
Carle and Woese and George Fox redrew phylogenetic relationships based on analysis of rRNA gene sequences. They used rRNA because 1) all cells require rRNA 2) they change very slowly over time (not much room for variation bc their sequence is so closely related to its function). Bc of this, any slight changes in sequence reflect an evolutionary "step." rNA can be used to establish evolutionary relationships between all species. 3) conserved regions enable easy in virto replication
Explain why cell size is limited.
Cell size is limited by 2 things: resource availability and surface area to volume ratio. A cell can be limited by resource availability such as limited space, nutrients, etc. that keep the cell from growing past a certain size. Surface area to volume ratio is critical to the metabolism of the cell. As cells increase in size, volume increases proportionally more than SA, which leads to a lower SA to V ratio. This can lead to a problematic exchange of substances between cells and their environment, which in turn affects the localized concentrations of molecules which affects the diffusion rates of molecules which affects the rates of chemical reactions -- slow reaction rates are BAD for living things.
Give a brief overview of the historical events that contributed to modern cell biology. Recall the associated names and dates involved in the events discussed in class.
Cells were first observed in 1665 by Robert Hooke. He is credited with coining the term "cell" in Micrographia. After 1665 there were not many discoveries in cell biology because they were limited by optical instruments (limited resolving power of microscopes & a lack of detail) and their way of thinking (more observation, less asking 'why'). 1830's there was advancement in optics & in 1831, Robert Brown described the nucleus. 1838 : Schleiden & Schwann put forth the 'Cell Theory'. Cell Theory - Schwann (1839) 1) The cell is the unit of structure, physiology, and organization in living things. 2) The cell retains a dual existence as a distinct entity and a building block in the construction of organisms. 3) Cells form by free-cell formation, similar to the formation of crystals #3 was wrong and revised by Virchow in 1855. Replaced #3 with "All cells arise from only preexisting cells".
Describe the various modifications that can occur to a protein during post-translational modification (e.g acetylation, etc.)
Chaperone-assisted folding Addition of functional groups Acetylation Phosphorylation glycosylation = adding lipid groups → lipoproteins Proteolytic cleavage= proteo=protein; lysis=to break apart Ex; insulin
Describe the structure/function of the chloroplasts
Chloroplasts Change energy from one form to another Found only in photosynthetic organisms Site of photosynthesis
Describe a cofactor. Describe a coenzyme. Do all proteins need these?
Cofactors= non-protein components of proteins - Can be inorganic or organic (coenzyme) Not all proteins need them
Describe the structure/function of the endoplasmic reticulum
Contiguous w outer nuclear membrane (connected) Two distinct regions: smooth and rough
Describe the events involved in properly targeting a protein to the endomembrane system...**describe to the level of detail we discussed in class
Cotranslational import - As polypeptide is produced, it has 'address label' signal peptide. - Proteins in the cytoplasm called 'signal recognition particles' (SRP) recognize the sequences and bind to it. - Everything then migrates to the rough ER - Pore in ER membrane opens up and protein will be deposited into the lumen of the rough ER as it is getting translated. - Ribosomes and signal particles detach and are recycled to translate something else.
Describe covalent bonds (polar and nonpolar)
Covalent bonds - E are shared between atoms Polar covalent bonds - E are unequally shared which results in one part of the molecule being more negative than the other - Hydrophilic Nonpolar covalent bond - Electrons are equally shared - atoms have same EN values - No one part of the molecule is distinctly charged - Hydrophobic
Describe the structure/function of the cytoplasm
Cytoplasm = internal contents of the cell Contains cytosol, organelles, and subcellular structures
Describe the structure/function of the cyoskeleton
Cytoskeleton Network of protein fibers and associated proteins Network extends throughout the cytoplasm and underlie nuclear envelope
Describe the three possible localization pathways for a polypeptide synthesized from mRNA exported from the nucleus into the cytoplasm.
Cytosolic (default) All ribosomes begin translation in the cytoplasm Endomembrane system mitochondria/chloroplast/nucleus/peroxisome
Describe in general the properties of lipids. What are the functions of lipids? How are they different from the other types of macromolecules that make up cells?
Defined in terms of solubility characteristics (not structural) All lipids are primarily hydrophobic molecules - Little affinity for water - Not soluble in water - Readily soluble in nonpolar solvents Some lipids are amphipathic (having polar and nonpolar regions) Functions: - Energy storage - Membrane structure - Signal transduction
Explain why certain elements are 'reactive'. What makes them reactive? Explain the role played by valence electrons when determining reactivity.
Electrons are attracted to positively charged nucleus (e have potential energy in their e cloud bc of their attraction to the nucleus) Can have only certain amounts or levels of energy (shells) Valence e are e in the last shell Important determinant of reactivity Can be gained/lost in a chemical reaction Atoms tend to react in ways that result in a filled outer shell
Elements of the cytoskeleton
Elements of cytoskeleon Microtubules: spacial organization and intracellular transport Microfilaments: cell shape, cell locomotion, muscle contraction Intermediate filaments: mechanical strength, nucleus shape
Describe the various factors that could influence protein conformation.
Environment can influence protein folding patterns pH: Temperature Solute concentration Solvent Aqueous? Lipid bilayer? Redox status Space Crowding can influence folding patterns Mechanical stress
Define "epithelial" and "endothelial"
Epithelial cells are those that come from the surfaces of the body such as skin, hair, blood vessels, etc. Endothelial cells are cells on the inside that line blood vessels.
Describe the structure/function of the extracellular matrix
Fibrous network made of various proteins found outside the PM, in the extracellular space support/structure adhesion/anchorage to surrounding medium
Describe the structure/function of the ribosome
Found in all cell types and certain organelles (NOT AN ORGANELLE ITSELF) Ribosomes are RNP (ribonucleoprotein) complexes Sizes of ribosomes differ between prokaryotes and eukaryotes (euk are bigger) Prokaryote size = 50S + 30S = 70S Eukaryotic size = 60S + 40S = 80S
Describe the basic details of the RBC structure and function.
Function to carry oxygen throughout the body Contain large amounts of hemoglobin protein Iron-containing protein that reversibly binds O2 RBC structure Bioconcav, disk shaped, very flexible Highly reduced subcellular contents @ maturity Lack nucleus, ribosomes, etc why?--> so it can carry as much hemoglobin (O2) as possible
Nonpolar amino acids
Glycine Alanine Valine Leucine Isoleucine Methionine Phenylalanine Typtophan Proline
Review redox reactions. How is Hydrogen used as an indicator of redox in this class?
H indicates whether the reaction is oxidized or reduced Oxidation can involve Loss of electrons Gain of O Loss of H Reduction can involve Gain of electrons Loss of O Gain of H LeO says GeR
List the 5 elements found in all living things.
Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus
Describe the process of translation (this should be review material).
Initiation: During initiation, the components of the translational apparatus (ribosome) come together with an mRNA, and a tRNA carrying the first amino acid binds to the start codon (AUG) Elongation: During elongation, amino acids are brought to the mRNA by tRNAs and are added, one by one, to a growing polypeptide chain Termination: During termination, a stop codon in the mRNA is recognized by a protein release factor, and the translational apparatus comes apart, releasing a completed polypeptide.
Describe ionic bonds
Ionic bond - Formed through electrostatic attraction between oppositely charged ions - Electrons are not shared
Describe the structure/function of the rough endoplasmic reticulum
Large flattened sheets Ribosomes temporarily bound to cytosolic side ('rough' appearance) Produces proteins and glycoproteins Products are distributed throughout Endomembrane system by transport vesicles
Convert between the different SI/metric prefixes. Recall the prefixes appropriate for describing cells, subcellular structures and molecules. Convert between standard notation and scientific notation.
Larger subcellular structures/cells : micrometer (1x10^-6 of a meter) Smaller subcellular structures ; nanometer (nm) (1x10^-9 of a meter) & Angstrom ( 1/10th of a nm) Dalton (Da) - unified atomic mass unit ( commonly used to describe size of proteins) = 1.66 x 10^-24 g
qDistinguish the various types of macromolecules found in living things.
Lipids Nucleic acids Carbohydrates Proteins
Describe the structure/function of the Lysosome
Lysosome: Digestive compartments Membranous sac of hydrolytic enzymes Function is digestion Are part of endomembrane system - bud off from golgi
Define the sedimentation coefficient and explain its usage in cell biology.
Measure of how rapidly a particle sediments when subjected to centrifugal force. Large/denser particles tne to sediment faster and thus have higher S values Use in cell biology to determine the size of certain particles or cell structures when separating components of a cell
Describe the structure/function of the mitochondria
Mitochondria Change energy from one form to another Site of cellular respiration Found in most eukaryotes, including photosynthetic organisms
Describe in general a 'carbohydrate'.
Most abundant organic molecules on earth Main function : structural components & storage (major energy source)
Identify the N- and C-terminus of a polypeptide. Explain which terminus is associated with the 5' or 3' end of the corresponding gene.
N terminus = amino end (5') C terminus = carboxyl end (3')
Polar, charged amino acids
Negative - Aspartate - Glutamate Positive - Lysine - Arginine - Histidine
Describe the structure/function of the nuclear lamina
Network of intermediate filaments Lies beneath inner layer of nuclear envelope Scaffolding that supports nuclear structure
Are viruses considered living organisms? Why or why not? Explain.
No, they do not exhibit multiple characteristics of living things. These characteristics are : growth/development, response to environment, metabolism, homeostasis, and they do not contain one or more cells.
Why are lipids not considered polymers?
Not formed by the same type of linear polymerization as proteins, nucleic acids, and polysaccharides
Explain the strategies cells/organisms can use to overcome the limitations imposed by surface area:volume constraints.
Once a cell reaches a certain size, cell division occurs. Growth stops : cells enter Go phase. Cells in this phase may become quiescent. This is when the cell basically is waiting for the appropriate signal. This phase is reversible, as some cells can re-enter the cell cycle and begin division (ex. Stem cells). Cells in the Go phase may also be terminally differentiated. These cells are specialized cells that are in a permanent Go phase (nonreversable). Membrane folding : increases the amount of SA Change in shape : long, thin cells = greater SA:V ratio Active Transport : active process = expenditure of E by the cell. The cell doesn't rely on simple diffusion for the exchange of materials in and out of the cell. Multicellularity: SA:V sets an upper limit on cell size. The only way to get larger is for different cells to cooperate. (thought to be a driving force behind the evolution of multicellularity!)
Describe the main elemental composition of the human body, i.e. those that comprise 99% (students do not need to memorize the ~1% elements)
Oxygen= 65% Carbon= 18.5% Hydrogen= 9.5% Nitrogen= 3.3% Calcium= 1.5% Phosphorus= 1.0%
Define and describe the function of a signal peptide or a transit peptide.
Particular stretch of amino acids within a protein Functions as an 'address' for protein's final destination
Describe the structure/function of the peroxisomes
Peroxisomes - Similar in size/shape to lysosome - NOT part of endomembrane system - Compartmentalize hydrogen peroxide (H2O2) producing reactions - Certain enzymes found in peroxisome catalyze the breakdown of organic molecules to generate H2O2 -H2O2 breakdown -H2O2 is toxic to us -H2O2 produced in peroxisome is then degraded into H2O and O2 - Other functions : breakdown of long-chain fatty acids via B-oxidation pathway and detoxification of oxidizable substrates
Describe the structure and function of the various carbohydrates found in cells (monosaccharides, disaccharides, polysaccharides).
Poly-hydroxyls - one per carbon Aldehyde or ketone Often have - ose ending Monosaccharides - 1 Disaccharides - 2 Polysaccharides -many
What is a protein domain? Recognize different structural/functional regions of a polypeptide as independent domains (where applicable).
Portions of the polypeptide chain can fold into compact, semi-independent units called 'domains' - Discrete structural/functional unit within a polypeptide - Domains form their own confirmation within a polypeptide - Domains are NOT separate subunits
What is a protein domain? Recognize different structural/functional regions of a polypeptide as independent domains (where applicable).
Portions of the polypeptide chain can fold into compact, semi-independent units called domains Discrete structural/functional unit within a polypeptide Domains form their own 3D conformation within a polypeptide NOT separate subunits
Recognize the primary structure of proteins. Identify the types of interactions that are responsible for stabilizing this level of protein structure.
Primary Structure - Sequence of amino acids linked together by peptide bonds, forming a polypeptide
Define a 'prion'. Describe the current model to explain prion diseases.
Prion= infectious disease-causing proteins Result from misfolded PrP proteins No change in corresponding PrP gene sequence Prion diseases cause neurological breakdown Different prion variants; All are transmissible 9 known human variants, which can be familial Spontaneous Latrogenic BSE-acquired (eating tainted meat products) What we know Normal prion protein, PrPc Cell surface protein w high expression level in CNS Secondary structure is rich in alpha helices Soluble Disruption of secondary structure results in a misfolded pathogenic protein, PrPsc→ a prion Changes in secondary structure lead to subsequent disruption in tertiary structure PrPsc is highly insoluble, and protease resistant PsPsc is thought to act as a template that promotes the conversion of PrPc to PrPsc
Describe the fundamental differences between eukaryotic and prokaryotic cells.
Prokaryotes lack the internal complexity seen in Eukaryotes and are on average much smaller than eukaryotes. They also lack a nucleus but instead have a "nucleoid region." Eukaryotic cells have a nucleus and various membrane bound organelles. They are also much larger than prokaryotes on average.
Describe the structure/function of the various subcellular structures found in prokaryotic and/or eukaryotic cells that we discussed in class today.
Prokaryotic Cell: Cell wall : rigid protective layer of carbohydrate surrounding plasma membrane Plasma membrane DNA in nucleoid region: not enclosed, some species have extrachromosomal plasmids May/may not have motility structure Eukaryotic cell: Nucleus, plasma membrane, endoplasmic reticulum,ribosomes,golgi apparatus, etc
Explain why protein structure is so important for protein function. Describe the examples discussed in class (i.e. prions, sickle cell anemia).
Protein structure <-> protein function What happens if protein structure is disrupted? Ex1) Sickle cell anemia An altered primary structure - mutated amino acid sequence Results in rigid sickle shaped cells Lack of blood flow→ less O2→ anemia
Describe the events involved in post-translational import of proteins...**again, describe to the level of detail discussed in class.
Proteins are imported into organelle AFTER translation Process is utilized for mitochondria, chloroplast, nucleus, peroxisome, any other compartment that is NOT part of the endomembrane system Also involves signal sequences called 'Transit sequence'
Recognize the quaternary structure of proteins. Identify the types of interactions that are responsible for stabilizing this level of protein structure.
Quaternary structure For multimeric proteins, the quaternary structure describes the association of 2+ polypeptides as they interact to form the final, functional protein Stabilized by same attractive forces involved w tertiary structure - Ionic bonds - Hydrophobic interactions - Covalent bonds (not frequent in quaternary)
Given a DNA sequence, identify the coding strand and template strand. Given a DNA sequence, transcribe into the corresponding mRNA sequence. Given a DNA or mRNA sequence, translate into the corresponding polypeptide sequence.
Rna polymerase recognizes and bind wto promoter sequences on the Template Strand Promoter indicates Where gene starts Which strand is ti be used as template when/where a gene is to be expressed By convention, gene sequences are represented in literature by the coding strand sequence Read 5'-->3' Even if not indicated, you assume sequence is 5'' → 3'
Calculate the surface area (SA), volume (V) and SA to V ratio of a given cell. Given their dimensions, compare the SA:V of different cells.
SA: (height x width) x # of sides x number of cells V: (H x W x L) x # of cells SA:V = SA/V
Recognize the secondary structure of proteins. Identify the types of interactions that are responsible for stabilizing this level of protein structure.
Secondary - Local regions of the resulting polypeptide can then be coiled into an alpha helix, one for mof 2ndary structure (beta pleated sheets as well) - stabilized by H bonds
Polar, uncharged amino acids
Serine Threonine Cysteine Tyrosine Asparagine Glutamine
Explain the role of molecular chaperones. Propose scenarios to explain their role (e.g. Heat shock proteins? Chaperone for post-translationally-imported proteins?).
Some proteins cannot fold into their native form spontaneously Molecular chaperones= protein molecules that assist in the folding of other proteins Ex. Heat shock proteins Why would cells induce molecular chaperones in response to heat shock? Chaperones are expressed to help proteins that are denatured by the heat to fold correctly ex ) import into the mitochondrial matrix As polypeptide is synthesized, Hsp70 binds along its length Why is this necessary? Keeping the protein unfolded so it an linearly fit through membrane pore Transit sequence directs polypeptide to membrane receptor Hsp70 molecules detach as polypeptide passes through membranes Transit sequence cleaved Mitochondrial hsp70 molecules bind and release polypeptide as it enters matrix Polypeptide fold aided by Hsp60
Describe the structure/function of the nucleus
Stores dna = control center Large organelle Surrounded by nuclear envelope Double membrane layer Supported by nuclear lamina Punctures at intervals by nuclear pores Regulated openings in nuclear envelope Control movement of substances in/out of nucleus
Describe the structural features shared by all cells.
Surrounded by lipid-based plasma membrane Metabolic machinery DNA as hereditary information Ribosome as protein-synthesizing machinery
Describe the process by which polymers are synthesized and the process by which polymers are broken down in cells.
Synthesis of Organic macromolecules occurs by 1. condensation reactions - H and OH are removed - Subunits join into a polymer -Components are 'dehydrated' - Left w ether and water byproduct 2. Breakdown of polymers are by hydrolysis rxn - Polymer is split into smaller subunits by adding H and OH (water) - Polymer is hydrolyzed
Recognize the tertiary structure of proteins. Identify the types of interactions that are responsible for stabilizing this level of protein structure.
Tertiary structure Regions of 2ndary structure associate w each other in a specific manner to form the tertiary structure , which describes the final folding of the polypeptide Stabilized by various types of interactions - Interactions may occur between - Primary R group-R group interactions - R groups-polypeptide backbone interactions
Describe cystic fibrosis. Describe the structure and function of the CFTR protein.
The cystic fibrosis transmembrane conductance regulator (CFTR) is a 1480 amino acid membrane bound glycoprotein. The protein is comprised of two, six span membrane bound regions each connected to a nuclear binding factor which binds ATP. Between these two units is an R-domain which is comprised of many charged amino acids.
Describe lactose intolerance.What are some management options for people who are lactose intolerant?
The inability to digest lactose due to a missing/defective lactase enzyme Management options: -avoid dairy, - lactase supplements, treat dairy w lactase
Identify characteristics of living things that distinguish them from non-living things.
There are 9 characteristics of living things that distinguish them from non-living things. 1. Organization 2.Evolution of populations 3. DNA 4. Reproduction 5. Response to environment 6. Metabolism 7. Homeostasis 8. Contain one or more cells.
What information did we learn from the analysis of the rRNA gene sequences pioneered by Woese and Fox?
There were two separate prokaryote groups (Bacteria and Achaean domains) that were actually very different from each other, although before that they had always been grouped together bc they are prokaryotes. Suggested that eukaryotes and archaea are actually more closely related to each other than to bacteria Allowed a better understanding of how protists should be organized Revealed how incorrect it was to classify them all together in one kingdom Some protists are not even closely related at all
what needs to happen for the C-terminus to be cytoplasmically localized and the N-terminus to be localized in the lumen of the ER?
Type 1: N-terminus located in the lumen of the ER and C-terminus localized in the cytoplasm Signal sequence targets polypeptide to translocation Stop transfer sequence halts translocation, signal sequence removed Protein released laterally into ER membrane, N-terminus is in the ER lumen; C terminus is in the cytoplasm
what needs to happen for the N-terminus to be cytoplasmically localized and the C-terminus to be localized in the lumen of the ER?
Type 2: N-terminus located in the cytoplasm and C-terminus located in the lumen Start transfer sequence starts polypeptide transfer Protein continues translocation until the c-terminus moves through translocation Protein is released laterally into the ER membrane
Correctly predict the orientation of a trans-membrane protein, How would multiple membrane-spanning domains be achieved?
Type 3: Multi-pass transmembrane protein: multiple internal start & stop-transfer sequences Start-transfer sequence starts polypeptide transfer Protein continues translocation until stop-transfer sequence is encountered Portion of the protein is released laterally into the ER membrane. Next start-transfer sequence repeats process to initiate a second transmembrane region.
In terms of disease transmission, explain why prion diseases are unlike any other type of disease that is bacterial- or viral-based.
Unique diseases- all other known disease causing agents contain nucleic acids
Describe the structure/function of the vacuoles
Vacuoles: Diverse Maintenance Compartments Function is cell specific Ex. central vacuole in plants, food vacuoles (phagocytosis), contractile vacuole Animal vacuoles are much smaller than central vacuole in plants
Identify whether a given amino acid structure is shown in solution (aq) or not.
When placed in solution, the amino acids classified as 'negatively charged' behave as acids and the AA classified as 'positively charged' behave as bases
What is the "lumen" of an organelle?
a lumen is a membrane-defined space that is found inside several organelles, cellular components, or structures: thylakoid, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondrion, or microtubule.
Describe the 'peptide backbone' of a polypeptide. How are the 'R' groups oriented along the peptide backbone of a polypeptide?
backbone= repeating sequence of atoms along polypeptide chain Held together by peptide bonds between amino acids R groups emanate from backbone
Distinguish between a polypeptide and a protein.
polypeptide= polymer of amino acids - not necessarily a functional protein protein= a functional polypeptide or group of polypeptides
Using the appropriate nomenclature, describe a protein according to the number and type(s) of subunits present.
# of subunits 1=monomer (tertiary only) 2=dimer 3=trimer 4=tetramer 5=pentamer 6=hexamer 7=heptamer 8=octamer Types of subunits homo-meric= all same subunits hetero-meric=different subunits
Define a protein 'conformation'. What is a protein's 'Native' conformation? What does it mean to 'denature' a protein? 'Renature' a protein? Which levels of protein structure are altered during denaturation?
- Conformation = overall, 3D shape of a polypeptide - Native conformation= conformation that represents the most stable state for a particular polypeptide - Denaturation= loss of conformation, usually resulting in loss of function - Caused by a change in cell environment(ex. pH) - Renaturation = return of a denatured polypeptide to its native confirmation, usually with restoration of function
Describe the Gram stain and its purpose
- Gram stain is a technique used to ID bacteria based on cell wall characteristics -Cell wall stained w purple dye -Rinsed w alcohol -Stain again w counterstain Can be used to establish presence/absence of bacteria Can broadly differentiate bacteria as Gram (+) or (-) (CANNOT ID SPECIES) To confirm/rule out bacterial infection
Define and describe an 'organic' molecule (*as defined in Biol 215).
-Hydrocarbon based -The presence of carbon alone does not guarantee it is an organic molecule (ex. CO2q
Describe the pathway(s) molecules can take through the endomembrane system (e.g. targeting of the hydrolase to the lysosome, or targeting of a secreted protein).
-Inside the ER, the proteins fold and undergo modifications, such as the addition of carbohydrate side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell. -If the modified proteins are not destined to stay in the ER, they will be packaged into vesicles, or small spheres of membrane that are used for transport, and shipped to the Golgi apparatus. The rough ER also makes phospholipids for other cellular membranes, which are transported when the vesicle forms. When vesicles bud off from the ER, where do they go? Before reaching their final destination, the lipids and proteins in the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. This sorting, tagging, packaging, and distribution takes place in the Golgi apparatus (Golgi body).The receiving side of the Golgi apparatus is called the cis face and the opposite side is called the trans face. Transport vesicles from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. -As proteins and lipids travel through the Golgi, they undergo further modifications. Short chains of sugar molecules might be added or removed, or phosphate groups attached as tags. -Finally, the modified proteins are sorted (based on markers such as amino acid sequences and chemical tags) and packaged into vesicles that bud from the trans face of the Golgi. Some of these vesicles deliver their contents to other parts of the cell where they will be used, such as the lysosome or vacuole. -The lysosome is an organelle that contains digestive enzymes and acts as the organelle-recycling facility of an animal cell. It breaks down old and unnecessary structures so their molecules can be reused. --- -Lysosomes are part of the endomembrane system, and some vesicles that leave the Golgi are bound for the lysosomes.
Explain the endosymbiotic theory for the origin of mitochondria and chloroplasts.
-Mitochondria and chloroplasts originated as free-living prokaryotes -Smaller prokaryote engulfed by a larger prokaryote and a symbiotic relationship developed -Dependency increased over time and the cells became one
Summarize the currently accepted cell theory.
1) The cell is a unit of structure, physiology, and organization in living things 2)The cell retains a dual existence as a distinct entity and a building block in the construction of organisms. 3)All cells arise from only preexisting cells
Review of hydrolase homework - pathway taken by a hydrolase enzyme in order to properly target it to the lumen of the lysosomes.
1. Starts in the nucleus. DNA contains hydrolase gene Transcription occurs and mRNA is produced and leaves nucleus through nuclear pore to the cytoplasm Small ribosomal subunit finds mRNA and the attaches. Large subunit attaches afterwards. Translation is initiated and a polypeptide chain begins to form. Some amino acids signal to the cell that the protein belongs in the ER (or endomembrane system) Everything (while translation is still happening, ribosomes included) are redirected to the rough ER While in the ER, translation is completed and the hydrolase protein is synthesized and deposited into the lumen of the rough ER. A carbohydrates 'tag' gets added to the protein (mannose) A vesicle containing hydrolase buds off of rough ER and fuses to the Golgi apparatus At the golgi: As glycosylated hydrolase moves through the golgi, mannose 'tag' is phosphorylated by golgi-specific enzymes Results in hydrolase with a mannose-6-phosphate 'tag' The tag serves as a recognition system Phosphate group binds to the receptor in trans golgi membrane Receptor specifically recognizes the M-6-P 'tag' Binding triggers packaging of hydrolase into a vesicle The vesicle fuses to acidified compartment; endosome Low pH causes dissociated of hydrolase from receptor Endosome matures into a lysosome.
Describe a positive and negative gram test
Gram positive bacteria : thick CW w large amounts of peptidoglycan - Traps violet dye in cytoplasm, masks counterdye, cells appear purple Gram negative : complex cell walls Cell wall located between PM and outer membrane Cell wall is thinner w less peptidoglycan Violet dye is rinsed away w alcohol so counterdye appears Cell appears red
Recognize that monosaccharides can exist as both linear and ring structures.
In aq environments, ring structures are more energetically favorable (more stable) Rings can exist in 2 forms alpha and beta
Describe the structure/function of the smooth endoplasmic reticulum
Lack ribosome (smooth) Lipid synthesis Carbohydrate metabolism Stores calcium (signal transduction) Detoxifies poison (ex. alcohol)
Describe the structure/function of nucleolus
Region within nucleus Clustered regions of rRNA genes surrounded by specific RNA's and proteins Site of ribosomal subunit synthesis
Describe the structure/function of nuclear pores
Regulated openings through nuclear envelope Openings controlled by nuclear pore complex (NPC) NPC controls movement of substances in/out of nucleus
Describe the structure/function of the Golgi apparatus
System of flattened membranous sacs Receives many of the transport vesicles produced in the ER Cis golgi network (CGN) = close to ER Trans (TGN) - other side Modifies ER products Manufactures polysaccharides Sorts and packages molecules for transport to final destinations
Describe the properties of carbon that make it well suited to form the backbone of organic molecules.
apable of forming 4 bonds Relatively neutral electronegativity Covalent bonds Forms stable molecules
Describe how cells are fractionated in order to study their individual components. What does it mean to "lyse" a cell? What is homogenization? What is centrifugation?
Cell Lysis: cells are broken open (by chemicals, enzymes, sound waves, etc) Homogenization : subcellular contents are blended together ('cell soup') Centrifugation : use of centrifugal force to differentially sediment heterogenous mixture (different densities and sizes cause the components to settle differently).
Describe in detail the peptide bond formation
Condensation (dehydration) reaction between amino acids. This occurs inside the ribosome H and OH are removed Subunits join into a polymer Components are 'dehydrated' End with polymer and h2o byproduct
Describe the 3 domains of life.
Bacteria = Prokaryotes Archaea = Prokaryotes, many extremophiles Eukarya = Eukaryotes (Protists, plants, fungi, animals)
