Biology Systems Flashcards
Classification of Organisms
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (dear king philip cried out for good soup)
Domains
Bacteria, Archaea, and Eukarya
Kingdoms of Eukarya Domain
Protista, Fungi, Plantae, and Animalia
Class and phylum of mammals
Class- mammalia; phylum- chordata
Species
loosely limited to all organisms that can reproduce to create fertile offspring
Causes for differentspecies being unable to mate
geographic isolation, temporal isolation (mating in different seasons), genetic incompatibility
Genotype
describes the chromosomes of an organism
Phenotype
describes the products of the genes that can be observed
Allele
copy of a gene
Polymorphism
a gene that has multiple alleles corresponding to distinct forms of a phenotype whose existence in a population makes evolution possible
Gene pool
the total of all alleles in a population
Evolution
the change in a population’s gene pool
Speciation
the formation of a new species which is when members from a single species have evolved into different groups that can no longer produce fertile offspring
Mechanisms that contribute to speciation
inbreeding, bottleneck situation, specialization, and adaptation
Inbreeding
the mating of relatives which increases the number of homozygous individuals in a population without changing the allele frequency
Outbreeding
mating of nonrelatives which maintains genetic flow between populations and so would not be expected to contribute to speciation
Bottleneck
sharp reduction in the population size where the allelic frequencies of the survivors are not representative of the original population
Specialization
the process by which the members of a species tailor their behaviors to exploit their environment; when distinct groups within a population specialize such that they differ substantially ie. in habits or locations, speciation may result
Adaptation
genetic or behavioral changes that are advantageous in a given environment
Assumptions of Hardy-Weingberg Equilibrum
- mutational equilibrium 2. large population 3. random mating 4. immigration or emigration must not change the gene pool 5. no natural selection
Measurement of evolutionary time
by comparing the genomes of species that share a common ancestor can be used to determine how long ago they diverged due the gradual changes in the genome
Genetic drift
changes in the gene pool in a small population owing to the chance of disappearance of alleles for individuals who fail to reproduce or die
Sexual selection
selection of certain phenotypes for mating
Fitness concept
the fittest organism is the one that can best survive to reproduce offspring who will in turn reproduce offspring and son generation after generation
Measure of gene fitness
increase in percent representation in the gene pool of the next generation
Natural selection
genes that are advantageous in a given environment are preferentially passed down from generation to generation
Differential reproduction
those organisms best adapted to an environment will be most likely to survive to reproductive age and have their own offspring
Viruses
tiny infectious agents from 1 to 100s of genes in the form of DNA or RNA (not both) that have the ability to transfer genetic material and are comparable in size to large proteins
Capsid
protein coat of a virus
Viral particle/virion
a mature virus outside the host cell
Structure of a virus
capsid (containing nucleic acid), lipid-rich protein envelope (for some viruses), and tail, base plate, and tail fibers for most bacteriophages
Host cell
the cell that is being infected by a virus
Receptor that virus binds to
usually a specific glycoprotein on the host cell membrane
Bacteriophage
a virus that infects bacteria which typically injects nucleic acids into the host cell through its tail after viral enzymes have digested a hole in the cell wall
Bacteriophage Injection Mechanism
Landing, Attachment, Tail contraction and penetration, injection
Eukaryotic Virus Infection Mechanism
being engulfed by an endoctytotic process
Lytic infection
the virus comandeers the cell’s synthetic machinery to translate its RNA into proteins which self-assemble to form a new virus; the cell may fill with new viruses until it lyses
Latent period
the period from infection to lysis
Virulent virus
a virus following a lytic cycle and which is capable of causing disease
Lysogenic infection
the viral DNA is incorporated into the host genome where the host cell replicates its DNA in addition to the viral DNA; may show no symptoms of infection
Temperate virus
a virus in the lysogenic cycle
Provirus (or prophage in bacteria)
when the viral DNA remains incorporated in the host DNA (dormant/latent)
Activation of dormant virus
potentially when the host cell is under stress in which the virus then takes on a lytic phenotype
Synthetic machinery
parts of cell used to produce protein
Viral envelope
formed as viruses undergo exoctyosis from the cell and to a certain extent protects the virus from detection by the immune system
Enveloped virus
protects virus from detection by the host cell’s immune system and allows it to bind to a new host cell and start the process all over again
Nonenveloped virus
typically lyse a cell and cause cell death on their release
Viral RNA
may have plus-strand RNA which only requires translation to produce proteins or it may have a minus-strand RNA which involves transcription/replication of RNA and then translation of that RNA to produce protein
Retrovirus
able to transcribe their RNA into double stranded DNA
Reverse transcriptase
enzyme that transcribes RNA into DNA
HIV
human immunodeficiency virus is a retrovirus that attacks cells involved in the immune response
Subviral particles
infectious agents related to viruses which include viroids and prions
Viroids
small rings of naked RNA without capsids which only infect plants
Prions
naked proteins which cause infections in animals and are capable of reproducing themselves without DNA or RNA
Prokaryotes
do not have membrane bound organelles including a nucleus and are split into two domains: bacteria and archae
Archae
prokaryote with similarities to both bacteria and eukaryotes which are typically found in extreme environments such as salty lakes and boiling hot springs
Shapes of Bacteria
cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped)
Symbiotic
mutually beneficial relationship ie. bacteria in the intestinal tract of humans
Parasitic
the relationship is beneficial to one organism but hurts the other
Anaerobic
not dependent on oxygen for growth and survival
Aerobic
requires oxygen for growth and survival
Protoplast
the bacterial plasma membrane along with everything it contains
Bacterial envelope
surrounds the protoplast
Cell wall
component of the bacterial envelope adjacent to the plasma membrane
Peptidoglycan
makes up the cell wall of bacteria and consist of a series of disaccharide polymer chains with amino acids and these chains are crosslinked by an interbridge of more amino acids
Gram positive bacteria
the cell wall is located just outside the cell membrane and have a thick peptidoglycan cell wall; stain purple
Gram negative bacteria
contain a thin peptidoglycan cell wall which is located in between two plasma membranes, the outer membrane possesses lipopolysaccharides which protrude outward and form a protectibe barrier from antibodies and antibiotics; stain pink
Flagella
long, hollow, rigid, helical structures that rotate counterclockwise to propel the bacterium in a single direction
Flagellin
globular protein which flagella are made from in bacteria
Flagellar propulsion
allows bacteria to move toward favorable products such as food sources
Chemotaxis
the directed movement of a motile cell or organism toward substances that will promote its survival and growth
Binary fission
a type of asexual reproduction (by bacteria) which results in 2 genetically identical daughter cells
Genetic recombination
examples are sexual reproduction, conjugation, transformation, and transduction
Origin of replication
point where DNA replication begins
Growth of bacterial population
exponential growth, meaning that each bacteria produces 2 offspring and so on
Conjugation
the transfer of a plasmid from one bacterium to another
Plasmid
small circles of extragenomic DNA which are not essential to the survival of bacteria that carry them
Extragenomic DNA
DNA that exist and replicate independently from the chromosome
Episome
a plasmid that can integrate into the chromosome
F plasmid
the fertility factor or F factor because it codes for the sex pilus (a conjugative plasmid)
R plasmid
donates resistance to certain antibiotics (also a conjugative plasmid)
Transformation
the process by which bacteria incorporate DNA from the external environment into their genomes
Transduction
the transfer of genetic material by a virus when a bacteriophage mistakenly encapsulates a DNA fragment of the host cell and injects this bacteria DNA into another cell
Vector
a virus that mediates transduction
Transposons
provides a way for nucleotides to move from one position to another along the genome
Transposase
the enzyme that catalyzes the transposon’s removal from and incorporation into the chromosome
sex pilus
a hollow protein tube that connects two bacteria to allow the passage of the plasmid from one to the other (conjugation)
Photosynthetic autotroph
organisms that obtain energy from sunlight
Nucleus
contains all of the DNA in a eukaryotic cell, other than a small amount in the mitochondria
Nuclear envelope
double phospholipid bilayer wrapped around the nucleus
Nuclear pores
large holes in the nuclear envelope in which RNA can exit but DNA cannot
Nucleolus
an area within the nucleus where rRNA is transcribed and the subunits of the ribosomes are assembled
Endoplasmic Reticulum
organelle that is a thick maze of membranous walls in the eukaryotic cell separating the cytosol from the ER lumen; proteins that will ultimately be exported from the cell or sequestered in a vesicle are translated on the ER
Cisternal space
ER lumen
rough ER
ER near the nucleus which has many ribosomes attached to its cytosolic side, giving it a granular appearance; synthesizes all proteins that do not belong in the cytosol; proteins synthesized in rough ER are pushed into ER lumen and sent to Golgi; also synthesizes peptide hormones
Golgi apparatus
a series of flattenened, membrane bound sacs whose major functions are packaging and secreting proteins within vesicles to be expelled from the cell, to mature into lysosomes, or transported within the cell ; may alter proteins by glycosylation or by removing amino acids;
Lysosomes
type of vesicle that contain hydrolytic enzymes particularly acid hydrolase that digest substances taken in the cell by endocytosis; come from Golgi apparatus
Apoptosis
programmed cell death where lysosomes are seen in high concentration as they rupture their contents to kill the cell
Smooth ER
plays a role in lipid metabolism and storage, as well as detoxification
Adipocytes
cells containing predominantly fat droplets which contribute to energy storage and body temperature regulation
Peroxisome
vesicles in the cytosol that are involved in both lipid and protein storage and are involved in the production and breakdown of hydrogen peroxide
Hydrogen peroxide
a byproduct that has potential to harm the cell, broken down by peroxisomes
Mitochondria
site of ATP production
Endosymbiotic theory
mitochondria may have evolved from a symbiotic relationship between ancient prokaryotes and eukaryotes and contain ciruclar DNA that replicates independently from nuclear DNA and contain no histones or nucleosomes; have their own ribosomes
Inner mitochondrial membrane
invaginates to form cristae and holds the electron transport chain of aerobic respiration
Intermembrane space
space between inner and outermembrane of mitochondria
Cytoskeleton
network of filaments that contributes to a cell’s structure and motility; consists of microtubules, microfilaments, and intermediate filaments
Microtubules
provide a platform for transport within cells and also support the shape of the cell; made up of globular protein tubulin
Microtubule organizing center (MTOC)
- end of microtubule attaches to MTOC and the the microtubule grows away from MTOC at is + end
Centrosome
major MTOC in animal cells, composed of a pair of centrioles
Centrioles
function in the production of flagella and cilia but are not necessary for microtubule production
cilia
specialized structure made from microtubules (along with flagella); they function to move fluid, causing the cell itself or nearby substances to move
9+2 arrangement
9 pairs of microtubules that forma circle around 2 lone microtubules where each outer pair is connected to its neighbot by dyneinthat are the major portion of each flagellum and cilium
Dynein
protein that connects each outer pair of microtubule to its neighbor in the 9+2 arrangment causing microtubule pairs to slide along their neighbors creating a whip action in cilia that causes fluid to move laterally or wiggle action in flagella which causes fluid to move directly away from the cell
Microfilaments (actin filaments)
interact with myosin to cause muscle contraction and are responsible for cleavage during cytokinesis
Intermediate filaments
maintain the cell’s shape and primarily serve to impart structural rigidity to the cell
Eukarytoic flagella vs prokaryotic flagella
eukaryotic: 9+2 arrangement, whip-like action; prokaryotic: thin strand of flagellin, rotate
Micelle
when placed in aqueous solution, amphipathic molecules spontaneously aggregate, turning their polar ends toward the solution and their nonpolar ends toward each other resulting in a spherical structural
Integral or intrinsic protein
amphipathic proteins that can cross the membrane from inside of the cell to the outside
Peripheral or extrinsic protein
located on the surfaces of the membrane and are generally hydrophilic; generally ionically bonded to integral proteins or the polar group of a lipid
Fluid mosaic model
the fluid part refers to the phospholipids and proteins which can slide past each other since the forces holding the entire membrane together are intermolecular; the mosaic part refers to the asymmetrical layout of a membrane’s lipids and proteins
Functions of membrane proteins
transporter, receptor, attachment, identifier, adhesion, and enzyme
Brownian motion
the random movement of molecules moving rapidly and in all directions and leads to the tendency of solutions to mix completely with each other over time
Chemical concentration gradient
series of vectors pointing in the direction of lower concentration
Electrical gradient
pointing in the direction that a positively charged particle will tend to move
Semipermeable
membrane slows the diffusion of X but does not stop it
Factors that determine permeability of compound
size and polarity
Leakage channels
most of the diffusion of polar or charged molecules across a membrane take place through incidental holes created by the irregular shapes of integral proteins
Passive diffusion
when molecules move across a membrane through random motion such as through a leak channel
Membrane channels/carrier proteins
facilitate the diffusion of specific molecules or ions across the membrane
Facilitated diffusion
use of carrier or membrane channels for passive diffusion; contributes to the selective permeability of the membrane by selecting between molecules of similar size and charge
Active transport
requires expenditure of energy
Secondary active transport
powered indirectly by ATP to create an electrochemical gradient which is then used to acquire or expel a molecule down its concentration gradient ie. sodium potassium pump
Isotonic
aqueous solution of their cytosol contains approximately the same concentration of particles as the aqueous solution surrounding them
Hypertonic cells
cells that are more concentrated than their environment
Hypotonic cells
cells that are less concentrated than their environment
Osmotic pressure
minimum pressure which needs to be applied to a solution to prevent the inward flow of its pure solvent across a semipermeable membrane
Colligative property
a property that is based on the number of particles present rather than the type of particle
Endocytosis
how cells acquire substances from the extracellular environment
Phagocytosis
the cell membrane protudes outward to envelop and engulf particulate matter; triggered by the binidng of particulate matter to protein receptors on phagocytic cell; performed by particular cells
Phagosome
the membrane bound bond of a particulate mater that is engulfed by phagocytosis
Pinocytosis
extracellular fluid is engulfed by small invaginations of the cell membrane and is typically performed by most cells and random, non-selective
Receptor-mediated endocytosis
specific uptake of macromolecules such as hormones and nutrients; in this process the ligand binds to a receptor protein on the cell membrane and is then moved to a clathrin-coated pit which then invaginates to form a coated vesicle
Exocytosis
reverse of endocytosis; provides a way for substances to leave the cell
Interphase
G1, S, and G2
G1 stage
cell has just divided and begins to grow in size, producing new organelles and proteins; RNA and protein synthesis are highly active
G0 stage
a non-growing state distinct from interphase; responsible for variations in the length of cell cycle between different types of cells
S stage
the cell devotes most of its energy to DNA replication; organelles and proteins are produced more slowly
M stage
mitosis or meiosis which is defined by the division of the nucleus
G2 stage
the cell prepares to divide; organelles continue to duplicate, RNA and proteins are actively produced
Cancer
unchecked cell growth
Mutations that cause cancer
tumor repressor: the deactivation of a checkpoint protein; oncogene: the activation of a gene that causes the proliferation of the cell
Tissue
group of similar cells that work together
Fibroblasts
secrete fibrous proteins such as elastin and collagen which form a molecular network that holds tissue cells in place (the extracellular matrix)
Basal lamina
a thin sheet of matrix material that separates epithelial cells from support tissue; also found around nerves, and muscle and fat cells; usually acts as a sieve-like barrier, selectively allowing the passage of some molecules but not others
Epithelial cells
separate the outside environment from the inside of the body
Support tissue
composed of the cells adjacent to epithelial cells on the inside of the body
Types of intercellular junctions
tight, desmosomes, and gap
Tight junctions
form a watertight seal from cell to cell that can block water, ions, and other molecules from moving around and past these cells; often found in epithelial tissue of bladder, intestines, and kidneys
Apical surface
the part of a cell facing the lumen of a cavity
Basolateral surface
the part of a cell opposite of the lumen of a cavity
Desmosomes
join 2 cells at a single point; attach directly to the cytoskeleton of each cell, and are found in tissue that typically experience a lot of stress ie. skin or intestinal epithelium; strongest type of junction
Gap junctions
small tunnels that connect cells, facilitating the movement of small molecules and ions between the cells; found in cardiac muscle to propagate action potential from cell to cell, and in some kinds of smooth muscle allowing fibers to contract as a unit
Intracellular second messenger
activates or deactivates enzymes and/or ion channels and often creates a cascade of chemical reactions that amplifies the effect of the hormone
Epithelial tissue
separates free body surfaces from their surrounidngs; includes endothelium which lines vessels of the body such as the heart
Connective tissue
characterized by an extensive matrix such as blood, lymph, bone cartilage, and connective tissue proper
Positive sense virus
contain coding RNA that can be immediately transcribed by the host ribosomes and thus do not require RNA-dependent RNA polymerase (RdRP)
Negative sense virus
contain the complement of the coding strand; since human cells do not normally make RNA from other RNA, there is no way for these viruses to begin replication without RdRP
Speed of communication of nervous system
specific and fleeting; somatic more so than autonomic
Nervous system
includes the brain, spinal cord, nerves, neural support cells and sense organs such as the eye and the ear
Neuron
the smallest functional unit of the nervous system; a highly specialized cell capable of transmitting a signal from one cell to another through a combination of electrical and chemical processes
Dendrites
stubby structures that receive a signal to be transmitted
Structure of neuron
dendrites, cell body, and axon
Summation
provides a way for the nervous system to screen for the most important stimuli
Spatial summation
occurs when multiple dendrites receive signals at the same time
Temporal summation
adds up the effects of signals that are received by a single dendrite in quick succession
Frequency of firing
codes the intensity of a stimulus of sensory neurons
Axon hillock
the site of connection between the cell body and the axon
Axon
carries action potentials to a synapse; having a single axon minimizes error and maximizes efficiency since multiple synapses would provide opportunities for information to be transferred incorrectly and would also slow down the signal
Receptors
bind substances (ligands) such as neurotransmitters and respond by triggering responses within the cell
Ion channels
open to allow ions to travel from one side of the membrane to the other, facilitating the transmission of signals; vary in how quickly they open and close
Concentration cell
differences in concentration initiate the movement of charge, creating a voltage
Concentrations of Na and K across membrane
more Na outside the cell and more K inside the cell
Resting potential
the electric potential or voltage across the neuronal membrane at rest; a stored potential that is used by the neurons to transmit a signal
Sodium potassium pump
functions to maintain or reestablish the chemical gradient that is lost by diffusion; the pump moves ions against their concentration gradients using ATP; moves 3 Na+ out and 2 K+ in
Resting potential of neuron
set up by the diffusion of K; K diffuses out of the cell, dragging along negatively charged proteins that get stuck along the inner side of the membrane; when the chemical gradient of K equilibriates, the inner side of the membrane is negatively charged compared to the outer side; resulting potential across the membrane is very close to equilibrium potential of K
Action potential
mechanism by which a signal travels down the length of a neuron and ultimately is transferred to the next cell; generated by a change in voltage across the neuronal membrane
Voltage gated Na channels
these proteins change configuration when the voltage across the membrane is disturbed allowing Na+ to flow through the membrane
Depolarization
the process of the activation of multiple voltage gated Na channels causing more sodium channels to change configuration, allowing more sodium to flow into cell so that the cell becomes positive on the inside
Voltage gated K Channels
less sensitive to voltage change than sodium channels, so they take longer to open
Repolarization
the process of K+ flowing out of the cell, moving the potential back towards the negative equilibrium potential of K
Hyperpolarization
the process when the potassium channels are so slow to close that the membrane potential becomes even more negative than the resting potential
Threshold stimulus
in order to create an action potential, the stimulus to the membrane must be greater than the threshold
Excitatory
depolarizing effect
Inhibitory
hyperpolarizing effect
Accommodation
if the threshold is reached but it is reached very slowly so that an action potential may not occur
Absolute refractory period
period in which no stimulus will create another action potential because the membrane potential is already more positive than the resting potential, so the driving force of the action potential is absent
Relative refractory period
the time during which only an abnormally large stimulus will create an action potential because the membrane is hyperpolarizing, requiring a greater threshold stimulus
Steps of action potential
- membrane is at rest, voltage gated sodium and potassium channels are closed 2. voltage gated sodium channels open and the cell depolarizes 3. voltage gated potassium channels open as sodium channels begin to inactive 4. voltage gated sodium channels are inactivated, open potassium channels repolarize the membrane 5. voltage gated potassium channels close and the membrane equilibriates to its resting potential
Electrical synapse
composed of gap junctions between cells and are often used when coordinated action is required from a group of cells ie. cardiac muscle, visceral smooth muscle
Chemical synapse
consists of a space between 2 neurons that is crossed by neurotransmitters; unidirectional
Motor end plate
the connection between a neuron and a muscle
Neurotransmitters
chemicals that are often derived from amino acids which are released into the synapse by a presynaptic neuron and attach to receptors on the post-synaptic cell; required because the electrical signal of the action potential cannot be transferred across the synapse
Fatigue (of presynaptic neuron)
when a presynaptic cell is fired too often and it is not able to replenish its supply of neurotransmiter vesicles so the impulse is not passed to the postsynaptic cell
G protein second messenger system
a G protein is attached to the receptor protein along the inside of the postsynaptic membrane, when the membrane is stimulated by neurotransmitter, part of the G-protein called the alpha subunit breaks free and may activate separate specific ion channels, activate a second messenger, activate intracellular enzymes or activate gene transcription
Glial cells/neuroglia
support cells in nervous tissue; different types carry out immune functions, circulate cerebrospinal fluid, support ganglia, give physical support to neurons, help maintain the mineral and nutrient balance in the interstitial space, and create myelin
Myelin
electrically insulating sheaths in the central nervous system that wrap many times around axons which acts as a insulator around the axon, increasing resistance to the passage of ions through the membrane
Schwann cells
produce myelin in the peripheral nervous system which wrap their entire bodies around the axons
White matter
refers to areas of the nervous system that are composed of myelinated axons of neurons
Grey matter
refers to bundles of the cell bodies of neurons
Nodes of Ranvier
tiny gaps between the myelinated areas and are the only places along the myelinated axon where ions cross the neuron’s membrane
Saltatory conduction
the phenomenon when action potentials jump from one node of Ranvier to the next
Sensory/afferent neurons
receive signals from a receptor cell that interacts with the environment and then transfers this signal to other neurons; located dorsally on the spinal cord
Interneurons
transfer signals from neuron to neuron
Motor/effector neurons
carry signals to a muscle or gland; located ventrally on the spinal cord
Effector
muscle or gland
Nerves
neuron processes (axons and dendrites) bundled together
Reflex
a quick response to a stimulus that occurs without direction from the CNS
Supraspinal circuits
circuits above the spinal cord
Central Nervous System
consists of the neurons and support tissue within the brain and spinal cord; a major function is to integrate nervous signals between sensory and motor neurons
Peripheral Nervous System
handles the sensory and motor functions of the nervous system and is further divided into the somatic nervous system and autonomic nervous system
Somatic nervous system
contains sensory and motor functions and primarily functions to respond to the external environment
Autonomic nervous system
coordinates an involuntary response to environmental stimuli, altering processes within the body to produce the most adaptive physiological state and behavior; further divided into the sympathetic and parasympathetic nervous systems