NS3: BBCF Flashcards
restriction enzymes
Restriction enzymes cut near or at their recognition sequences. However, if the gene is methylated, this cutting cannot occur.
Sex linked traits
- specifically X linked recessive
X-linked recessive conditions affect males more often. This is because females inherit one X chromosome from their mother and one from their father, while males only get their single X chromosome from their mother.
Thus, females have a chance to obtain a dominant X chromosome, such that the recessive mutation won’t manifest. Since males only have one X chromosome, having a single mutated allele will suffice to manifest a recessive mutation.
carrier properties of ETC
mobile and hydrophobic
mobile bc carriers travel inside the inner mitochondrial membrane, passing electrons from one to another and pumping protons across the inner mitochondrial membrane
hydrophobic bc they need to be able to travel inside the hydrophobic interior of the membrane ;; remember, like interacts w like
However, cytochrome c is a highly water-soluble protein, unlike other cytochromes.
where in the body does glucagon act in a high concentration
Glucagon is released by the pancreas as a response to low blood glucose levels. Its main purpose is to increase glycogenolysis to increase blood glucose. The glycogen stored in the liver is broken down to create glucose that is released into the bloodstream; therefore, most of glucagon’s action occurs in the liver.
what is an organic compound
- also, what is an organic acid
An organic compound must contain carbon and hydrogen in its formula. Furthermore, there must be a covalent bond between a carbon and hydrogen atom in the molecular structure.
Organic acids are weak acids, generally having formulas of R-CO2H, with the acidic hydrogen bonded to an oxygen atom.
Viruses
obligate intracellular parasites, thus must hijack host cells to replicate
The genetic material of viruses can be in the form of either single-stranded or double-stranded DNA or RNA
Single-stranded RNA viruses are further subdivided into positive-sense and negative-sense viruses. Positive-sense RNA viruses contain mRNA that can immediately be translated by the cell.
Negative-sense RNA viruses contain RNA that is complementary to mRNA, meaning that mRNA must be synthesized by an enzyme known as RNA replicase that is carried in the virion.
define the following:
- bacteriophage
- retrovirus
Bacteriophages: viruses whose host cells are bacteria → Instead of entering the cell completely, they inject their genetic material into their host through a syringe-like structure known as a tail sheath
– Two distinct life cycles: lytic and lysogenic
Retroviruses: distinct class of single-stranded RNA viruses that use an enzyme known as reverse transcriptase to synthesize DNA from their RNA genome → eg. HIV
post transcriptional modifications
vs post TRANSLATIONAL
Post-transcriptional modifications: occur in mRNA, specifically in nucleus→ addition of the 5’ cap, poly A tail and splicing
Post-translational modifications: occur after protein has been formed from mRNA, can happen in many areas of the cell → groups being added to the protein by covalent bonds or cleavage of protein
Lifecycle of bacteriophages
During the lytic cycle, the bacteriophage essentially works to replicate at full speed, making full use of the host cell’s machinery. Eventually, the host cell is filled with virions to the point that it bursts or lyses, and a tremendous number of new virions spill out into the environment.
Alternately, in the lysogenic cycle, bacteriophages can integrate themselves into the host genome, at which point they are referred to as a prophage or a provirus. In response to environmental signals, the prophage can re-emerge from the host genome and resume a lytic cycle.
define the following:
- transduction
- transformation
- conjugation
Transduction is a form of horizontal gene transfer in bacteria in which bacteriophages (viruses that infect bacteria) transmit genomic material.
Vs. Transformation involves direct uptake of genetic material from the environment and is not mediated by viruses.
Vs. Conjugation is a horizontal gene transfer process in bacteria in which plasmid DNA is transferred from one bacterium to another through a pilus. Viruses are not involved.
reaction rate
+ order of reactions
Reaction rate itself has units of M/s or mol/L∙s. [A] and [B] are concentrations of the reactants in units of M or mol/L. The exponents x and y must be experimentally determined; they do not correspond to the stoichiometric coefficients a and b in the reaction formula.
The order of a reaction is defined by the sum of the exponents (x + y) in the rate law. If the exponents sum to zero, the reaction is zero-order. If the reactants sum to 1, the reaction is first-order. If they sum to 2, it is second-order, and so on.
Note that at low substrate concentrations, the reaction approximates first-order kinetics, as described above. In contrast, at very high substrate concentrations (where the enzyme is nearly or entirely saturated), the reaction approximates zero-order kinetics, since reaction rate ceases to depend on substrate concentration.
are viruses living??
Viruses are unique in that they occupy a gray area between living and non-living. They have been described as non-living. Prions, or pathogenic misfolded proteins, are also non-living biological substances that are pathogens, but they are not considered organisms.
triglycerides
saponificiation
Triglycerides are composed of 1 glycerol molecule and 3 fatty acid molecules. So, if we start with 3000 triglyceride molecules, we would expect to have 9000 molecules of fatty acids and 3000 molecules of glycerol after hydrolysis.
Saponification: carboxylic acids are deprotonated and their conjugate bases form salts, according to the following template: RCOOH + Na+ + OH− → RCOO−Na+ + H2O
– the process can be combined with the base-catalyzed hydrolysis of a triglyceride containing three fatty acid chains
malonyl coA
Malonyl-CoA, an indicator of ongoing fatty acid synthesis, inhibits β-oxidation by preventing the movement of long-chain acyl groups into the mitochondrial matrix, thereby preventing a futile cycle of fatty acid synthesis followed by immediate β-oxidative catabolism of those newly synthesized fatty acids.
can a purine turn into a pyrmidine?
no, not even by methylation or deamination bc purines and pyrimidines differ based on whether they have a 1-ring structure (pyrimidines) or a 2-ring structure (purines), and the loss or addition of a single functional group (as in (de)methylation or (de)amination) is insufficient to convert between these very different structures.
BUT you should know that purines are likely to mutate into other purines
sds-page discrepancies
Recall that SDS-PAGE is used to grant a uniform negative charge to all proteins in an assay.
However, if the protein has enough charged residues on its own, it causes the measurements to be less accurate.
If there are enough positive charges, the negative charge of the protein will not be as great as anticipated and the molecule will travel a smaller distance, which, to the individual running the assay, usually means the mass of the protein is greater and would lead to a discrepancy in the actual observed distance.
beta barrel
beta sheet that is twisted to form a closed barrel-like structure
what are the five enzymes involved in DNA replication
semiconservative; begins at the origin of replication
Helicase unwinds the DNA helix and separates the two strands of DNA. Single-stranded DNA-binding proteins keep the separated strands from immediately re-annealing.
Primase then synthesizes a short RNA primer with a free 3’ OH group that is used as the starting point for the synthesis of a new strand.
DNA polymerase reads the DNA template in a 3’ to 5’ direction and synthesizes the complementary strand in the 5’ to 3’ direction.
DNA gyrase, also known as DNA topoisomerase II, alleviates the supercoiling that would otherwise be created as helicase works its way down the DNA molecule.
Ligase links together Okazaki fragments, which are created from the lagging strand of DNA replication.
name the major hormones
ICE STAG LPC3 mnemonic
from endocrine system
insulin
cortisol
epinephrine
sex
thyroid
atrial naturietic
glucagon
leutinizing prolactin calcium-related hormones: -- calcitonin -- parathyroid -- vitamin D3
ICE hormones
Insulin promotes transport of glucose from the bloodstream into cells.
The stress response, involving increased blood glucose and sympathetic nervous system activation, is mediated by cortisol for long-term stress and by epinephrine for short-term stress.
STAG hormones
the sex hormones estrogen and testosterone contribute to the development of secondary sex characteristics
Thyroid hormone increases the basal metabolic rate
Atrial natriuretic protein promotes fluid excretion. Vs aldosterone and antidiuretic hormone promotes fluid retention.
Glucagon promotes gluconeogenesis.
LPC3 hormones
Luteinizing hormone (LH) is a hormone produced by gonadotropic cells in the anterior pituitary gland. In females, an acute rise of LH triggers ovulation and development of the corpus luteum.
Prolactin is the hormone responsible for stimulating the mammary glands to produce milk.
C for CALCIUM RELATED HORMONES
- Calcitonin is a thyroid hormone responsible for lowering blood calcium concentrations.
- Parathyroid hormone and vitamin D3 increase blood calcium concentrations
divisions of hormones
Steroid hormones are derived from cholesterol and are lipid-soluble. They diffuse through the plasma membrane and influence gene transcription. Thus, their effects tend to be slow-onset and long-lasting.
3 S’s: sex, salt, sugar
Amino acid-derived hormones include T3/T4 and (nor)epinephrine.
Peptide hormones are larger polar molecules that cannot enter cells directly. Therefore, they bind with membrane receptors and trigger secondary messaging cascades, exerting relatively rapid-onset and shorter-lasting effects.
Types of immunity:
- passive
- natural
- cell-mediated
- innate / non-specific
Passive immunity is the transfer of active humoral immunity in the form of ready-made antibodies, from one individual to another.
Vs. Natural immunity is immunity that is present in the individual at birth, prior to exposure to a pathogen or antigen, and that includes intact skin, salivary enzymes, neutrophils, natural killer cells, and complement.
Vs. Cell-mediated immunity is an immune response that does not involve antibodies, but rather involves the activation of phagocytes, antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen.
Vs. The innate (non-specific) immune system includes anatomical barriers, secretory molecules, and cellular components. Among the mechanical anatomical barriers are the skin and internal epithelial layers, the movement of the intestines, and the oscillation of bronchopulmonary cilia.
define the following structures:
- nucleolus
- lysosome
- centriole
The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells.
Vs. The lysosome is the organelle in the cytoplasm of eukaryotic cells containing degradative enzymes enclosed in a membrane.
Vs. A centriole is composed of short lengths of microtubules arranged in the form of an open-ended cylinder, designed to help chromosomes separate during cell division.
plasma membrane structure
composed of amphipathic phospholipids that have a polar head and a nonpolar tail that are organized in such a way that the polar phosphate heads face the intracellular and extracellular environments (which are both aqueous solutions), while the nonpolar tails remain inside the membrane
In addition to phospholipids, the presence of cholesterol and lipid rafts within the plasma membrane help contribute to the fluidity of the membrane at lower temperatures and to its stability at higher temperatures.
plasma membrane permeabilty
Permeable to small uncharged or lipid-soluble molecules
Not permeable to larger, hydrophilic molecules → these require specialized transporters
Thus, the lipid bilayer results from entropically-favorable interactions between phospholipids ultimately allows the body to perform the physiologically essential task of closely regulating what goes into and out of the cell
types of cell junctions
Gap junctions: formed by connexin proteins, which connect cells in a way such that diffusion can take place between them, enabling communication, without involving direct contact between the cytoplasmic fluids of each cell → important in cardiac muscle cells, where gap junctions allow for for simultaneous cell contraction
Tight junctions: found in epithelial cells and prevent solutes from being able to move freely from one tissue into another
Anchoring junctions: connect cytoskeletal components of the cell with other cells and/or the extracellular matrix, thereby contributing to the overall structural stability of tissues
– 3 types: adherens, desmosomes, and hemidesmosomes
three types of anchoring junctions
Adherens junctions: involve cadherin-mediated connections between actin filaments and other cells and the extracellular matrix
Desmosomes: also involve cadherin, but in this case cadherin connects intermediate filaments to other cells
Hemidesmosomes: junctions in which integrins connect the intermediate filaments of cells to the extracellular matrix
motility and structures involved
cell’s ability to move → eg. Flagella and cilia, formed from microtubules in a 9+2 structure (outer ring of nine pairs of microtubules surrounds an inner ring of two microtubules)
Flagella (singular = flagellum) are tail-like appendages that protrude from a cell and allow it to move, although they also can serve as sensory appendages.
- In eukaryotes: flapping motion, powered by ATP
- In prokaryotes: rotary motion, powered by a proton gradient, and made of flagellin (instead of microtubules)
Cilia are relatively small projections that help move substances along the cell surface.
