B MCAT- Bio, Biochem Flashcards
Endoplasmic Reticulum
A membrane-bound organelle within a cell.
The ER is a series of membranes continuous with the nuclear envelope.
Rough ER is decorated with ribosomes for generating secreted proteins. (Note that many OTHER proteins are made by ribosomes in the cytoplasm.)
Smooth ER is for detoxification and lipid synthesis. Majority of steroid synthesis reactions are carried out by enzymes in the smooth ER.
Intracellular vesicles deliver what is make by the ER to the Golgi apparatus.
ligase
Category of enzymes that join things together.
A+B>AB
Ligating is joining things together. Usually requires energy in the form of ATP.
isomerase
Category of enzymes that facilitates an isomerization.
A > B
Isomers are the broad category of molecules with the molecular formula, different structure.
eg. Could change a compound from R to S form.
eg. Converting glucose-6-P to fructose-6-P in glycolysis using phospho-glucose isomerase.
lyase
Category of enzymes that break compounds apart WITHOUT water.
A > B+C
eg. argininosuccinate > arginine + furmarate
in urea cycle, via enzyme argininosuccinate lyase.
Generate either a double bond or a ring structure in order to work.
transferase
Category of enzymes that moves a group from one molecule to another.
A + BX > AX + B
eg. KINASE moves a phosphate group from one molecule to another, or takes a phosphate from ATP.
eg. tRNA transfers an amino acid to a growing peptide chain via peptidyl transferase.
hydrolase
Category of enzymes that break compounds apart by adding water to the compound.
A + H2O > B + C
Lots of digestive enzymes (eg. lipase, pepsidase) fall into this category.
eg. serine hydrolase/protease
oxidoreductase
Category of enzymes that move electrons around–oxidation and reduction reactions. Two reactions.
A + B: <=> A: + B
These are heavily involved in the electron transport chain and citric acid cycle.
*If an enzyme has dehydrogenase in its name, it is moving around electrons in NADH or FADH2
lysosome
Membrane-bound organelle within the cell that recycles proteins and other materials for reuse.
Also maintain pH and protect the cell from these contents.
The garbage disposal.
Nucleus
A membrane-bound organelle within the cell that contains all genetic material for cellular replication.
Mitochondrion
A membrane-bound organelle within the cell.
Carries out aerobic respiration, generating ATP via the ETC. Major role in metabolism.
Have their own genome and a symbiotic relationship with the cell.
All mitochondria in humans comes only from the egg, the mother. There are mitochondria in sperm, but only behind the head to help with motility, never enter egg.
(plural: mitochondria)
Peroxisomes
Membrane-bound organelle within the cell.
Break down long chain fatty acids for beta oxidation (acetyl Co-A) and making other lipid molecules.
Cytoskeleton
Part of cell that regulates shape and rigidity.
Polymerized actin fibers.
Also used during annophase of miosis and mitosis. Drives cleavage furrow of cytokinesis.
Microtubules
Polymerized tubule fibers.
Tube-shaped.
Components of mitotic spindles.
Intermediate Filaments
Diverse proteins that function in adhesion within a cell; make cells stick together (or to a plate). Help in cytoskeletal integrity.
Prokaryotic cell classification
Two categories of prokaryotes:
bacteria and
archaea.
Bacteria can be gram positive (thick peptidoglycan cell wall, less dangerous, show up purple with dye), or
gram negative (thin peptidoglycan double membrane cell wall, much more dangerous to humans, show up red with dye)
So far, no archaea that are human pathogens have been discovered. There are archaea that live in humans.
3 shapes of bacteria
Bacteria typically subcategorized by shape:
chocci spherical
bactilli –oblong
spirilli–spiral
binary fission in bacteria
asexual reproduction in bacteria. The single chromosome in a single bacteria cell divides and each half attaches to the cell wall. The cell then divides and two full-sized daughter cells are formed.
transformation in bacteria
Bacteria bring foreign material (e.g. plasmids) FROM THE ENVIRONMENT into themselves and integrate it into their genome.
conjugation in bacteria
a form of sexual reproduction in bacteria where two cells join via a conjugation bridge and a pilus and DNA is passed from one (with an F-plasmid) to the other.
Also called cell-to-cell exchange.
transduction in bacteria
Gene transfer (integration of foreign material) via a VIRUS (viral vector).
growth in bacteria (4 stages)
1) lag phase –bacteria adapting to conditions
2) exponential (log phase)–fast growth
3) stationary –growth can’t be sustained because lack of resources
4) death –resources are depleted
In research, you want to keep your samples in the exponential (log phase), or early stationary phase.
bacteria phage (i.e. phage)
A virus that infects a bacteria.
transfection
The process by which genetic material is introduced into animal cells.
plasmid
A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell’s chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance.
ribosome
Site of protein synthesis within a cell.
Ribosomes are made from rRNA, which are made in the nucleus during transcription.
Western Blot
Experiment which shows you the presence and relative amount of a specific protein.
First, run sample on electrophoresis gel.
Second, introduce antibody conjugated to a florescent probe, which will bind specifically to protein of interest.
Left Lane»_space;> Right Lane:
purified sample >
sample of normal cell nuclear lysate>
sample of whole cell lysate from normal cell>
sample of affected cell nuclear lysate >
sample of affected whole cell lysate.
Intensity of band indicates amount of protein present.
Lower band indicates part of protein missing.
lysate
the product of lysis, a cell that has been broken down.
Bohr Effect on Oxyhemoglobin Disassociation Curve
The Bohr Effect describes what happens when there is an off-loading of oxygen from hemoglobin to surrounding tissues.
The sigmoidal curve shifts RIGHT (partial pressure of oxygen in surrounding tissue on x axis; % hemoglobin oxygen-bound on y axis).
An INCREASE of the following conditions lead to this Bohr effect right shift of the curve:
-temperature
-pCO2 (i.e. active muscles)
-acid
-exercise
-(2,3) DPG
Effect of Carbon Monoxide poisoning on the Oxyhemoglobin Disassociation Curve
CO causes the sigmoidal curve to shift left and peak at a lower point.
Hemoglobin’s affinity for CO is more than 200x that of O2. Therefore, there is less hemoglobin available for O2 to bind to, causing the curve to peak at a lower point.
However, a CO bound at the first of four binding sites on a hemoglobin protein will still increase affinity for the remaining sites and the curve will initially rise faster (shift left) than without CO. This leads to the O2 not as readily leaving the hemoglobin to go to surrounding tissue.
What is the term for the effect that causes the upslope in a sigmoidal curve?
cooperativity
Ex. Oxyhemoglobin Disassociation Curve
endonuclease
An enzyme involved in DNA excision repair that cut at specific DNA sequences (e.g. to remove a dimer caused by UV radiation).
Operons
Tool to start DNA transcription to RNA.
4 pieces (genes) to any operon: regulator > promoter > operator > structural (e.g. enzyme that performs respective duty of the particular operon).
2 categories of operons:
1) Inducible systems–default is that the receptor is bound to the operator and keeps it in the “off” position; the RNA polymerase can not travel past the promoter region of the operon. When inducer is present, receptor binds to it instead and the operon can transcribe.
2) Repressible systems–the repressor can not bind to the operon by itself.
2 prokaryotic operons to know:
1. Lac Operon
2. Trp Operon.
paracrine vs. autocrine vs. endocrine vs. direct signaling via gap junctions
There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions.
Paracrine signaling is between cells that are close together, via Diffusion through the extracellular matrix. Fast acting, short lasting.
Signals from distant cells are called endocrine signals, and they originate from endocrine cells. (In the body, many endocrine cells are located in endocrine glands, such as the thyroid gland, the hypothalamus, and the pituitary gland.) These types of signals usually produce a slower response but have a longer-lasting effect. The ligands released in endocrine signaling are called hormones, signaling molecules that are produced in one part of the body but affect other body regions some distance away.
Autocrine signals are produced by signaling cells that can also bind to the ligand that is released. This means the signaling cell and the target cell can be the same or a similar cell. Ex. pain sensation.
Gap junctions in animals and plasmodesmata in plants are connections between the plasma membranes of neighboring cells. These water-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules, such as calcium ions (Ca2+), are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels. The specificity of the channels ensures that the cells remain independent but can quickly and easily transmit signals.
peptide hormones
Tend to end in “-in”. Water soluble, can not cross cell membrane. Require receptor to communicate across a cell membrane.
Act very fast.
glucagon vs. insulin
Hormone insulin and its opposite glucagon are both peptide hormones.
Steroid hormones
Water soluble. Carried around bloodstream by molecules that are not water soluble.
Can cross cell membranes.
Slower acting, longer lasting.
Secreted by three “steroid glands”—the adrenal cortex, testes, and ovaries—and during pregnancy by the placenta.
All steroid hormones are derived from cholesterol.
Tend to end in “-one” or “-ol” or “-oid”?
