Chapter 3 Flashcards
the nucleus
contains genome enveloped by the nuclear membrane. Where replication, transcription and splicing occur
the genome
organized into linear molecules of dsDNA in eukaryotes and sDNA in prokaryotes
the nucleolus
“little nucleus” functions as a ribosome factory, not separated from the nucleus.
nucleolus is composed of
loops of DNA, RNA, polymerase, rRNA and the protein components of the ribosome
the nucleolus is largest in cells that are producing large amounts of proteins (T/F)
True, the bigger the size the more synthesis of ribosomes
Site of transcription of rRNA byRNA pol I
nucleolus
where does all translation take place?
cytoplasm
nuclear envelopes is composed of
Two lipid bilayers, the inner nuclear membrane and the outer nuclear membrane
orientation of the nuclear envelope
the inner nuclear membrane faces the nuclear interior. Outer nuclear membrane faces the cytoplasm and is contiguous “sharing a common border” with the ER lumen
Nuclear envelope structure
punctuated w large nuclear pores to allow passage of materials in out of the nucleus. Molecules < 60 kilodaltons can freely diffuse
How do molecules larger than 60 kilodaltons enter the nucleus
if they contain the nuclear localization sequence (lysine rich)
mitochondria
site of oxidative phosphorylation. Singular circular DNA molecule, exhibits maternal inheritance
the matrix
interior of the mitochondria bounded by the inner and outer mitochondrial membrane. Contains pyruvate dehydrogenase and enzymes of the Krebs cycle
Krebs Cycle
location of the electron transport chain and ATP synthase
Endoplasmic reticulum (ER)
large system of folded membrane accounting for over half of the membrane of some cells
Plays a role in directing traffic to different parts of the cell
endoplasmic reticulum
Rough ER
site of protein synthesis for proteins targeted to enter the secretory pathway
Smooth ER
contains enzymes involved in steroid hormone biosynthesis (gonads) or degradation of environmental toxins (liver)
The two sites of proteins synthesis in eukaryotic cells
(1) ribosomes free in the cytoplasm (2) ribosomes bound to the surface of the rough ER
Destinations of ribosomes bound to the surface of the rough ER
(1) are secreted into extra cellular environment (2) integral membrane proteins (3) membrane interior of ER, Golgi or Lysosomes
the interior of the ER, Golgi apparatus, lysosomes and the extra cellular environment are not continuous (T/F)
false
Proteins start translation
in the cytoplasm
Signal recognition particle (SRP)
ER has SRP receptors which doc the complex and is pushed through the ER lumen and moved through the Golgi to the plasma and released by exocytosis
removed after translation and at the N-terminus
Transmembrane domains
sections of hydrophobic amino acid residues. threaded through the ER lumen during translation and undergoes secretory pathways.
not at the N-terminus and not removed after translations
ER functions
(1) initial post translational modification of proteins (2) some glycosylation (3) disulfide bond formation
glycosylation
addition of saccharides to proteins (usually in the Golgi)
Golgi Apparatus
(1) modification of proteins in the RER (2) sorting; sending proteins to their correct destinations (3) synthesizes certain macromolecules to secrete
the route taken by a protein once it leaves the trams face is determined by
signals within the protein
exocytosis
vesicles move from the Tran’s Golgi towards the cell surface, then fuses w/ the cell membrane and dumps its contents into the extracellular environment.
Endocytosis
materials are taken into the cell by an invagination of a piece of the cell membrane to form a vesicles (endosome)
three types of endocystosis
phagocytosis, pinocytosis, and receptor mediated endocytosis
phagocytosis
macrophages of the immune system
pinocytosis
cell drinking; nonspecific uptake of small molecules and extracellular fluid via vagination
receptor mediated endocytosis
very specific; the site is marked with clathrin (inside cell) and with receptors (outside cell)
constitutive secretory pathways
proteins sent in vesicles from the Golgi immediately to the cell surface through unregulated membrane fusion
regulated secretory pathways
specialized secretory cells (pancreatic cells, B- cells of the immune system) store secretory proteins in secretory vesicles and release them only at certain times, usually in response to change in the extracellular environment
lysosomes
membrane bound organelle that degradates biological molecules.
lysosomal proteins are made in the
RER and modified in the Golgi and releases from the trans face of the Golgi
Autophagy
self eating; organelles are degraded in lysosomes
phagocytosis
cell eating; degradation of large particulate matter engulfed by the cell
macrophages
from the immune system, engulf bacteria and viruses
crinophagy
lysosomal digestion of unneeded (excess) secretory products
after hydrolysis the lysosomes will
release molecular building blocks into the cytoplasm for reuse
degradation in lysosomes occurs due
to acid hydrolysis
acid hydrolysis
enzymes only hydrolyze substances when they are in an acidic environment
peroxisomes
contain enzymes that produce H2O2 which is converted into H2O + O2. Detoxify drugs and chemicals in the liver, protects the rest of the cell from damage by peroxides or oxygen radical
membrane structure
all membranes are composed of lipid bilayers. The 3 most found lipids are phospholipids, glycolipids, and cholesterol
fatty acid arrangement
hydrophilic head is facing outward and the hydrophobic tails facing inwards, away from the water
fatty acids arrrange in a lipid bilayer due to
steric hindrance. this arrangement allows them to reseal or repair any ruptured areas of the membrane
what molecules are not soluble in the plasma membrane
hydrophilic molecules (ions, carbohydrates & amino acids). This makes the membrane a barrier to these molecules
which molecules can cross the plasma membrane easily
non polar molecules ( CO2, O2 and steroid hormones)
how does water pass through the plasma membrane
through membrane specialized protein channels
what are big components of the membrane
proteins; they act to mediate interactions of the cell with other cells
cell- surface receptors
bind extracellular signaling molecules such as hormones and relay signals into the cell
channel proteins
selectively allow ions or molecules to cross the membrane
membrane proteins are classified as
either peripheral or integral
integral membrane proteins
are embedded in the membrane and held by hydrophobic interactions
membrane crossing regions are
transmembrane domains
peripheral membrane proteins
are not embedded in the membrane. They are stuck to integral membrane proteins, held by hydrogen bonding and electrostatic interactions
Fluid Mosaic model
lipids and proteins are free to diffuse laterally, in 2D but are not free to flip flop
what is a major determinante of plasma membrane fluidity
Van der Waals interactions between fatty acid side chains on the membrane
cholesterol plays a key role in
maintaining optimal membrane fluidity by fitting into the membrane interior
transmembrane transport
integral membrane proteins transport material through membranes that cannot diffuse on their own.
two types of transport
passive (does not require cellular energy) and active (requires cellular energy)
hypertonic solution
has more total dissolved solutes than the cell
hypotonic
solution has less total dissolved solutes in the cell
forms of passive transport
(1) simple diffusion (2) facilitated diffusion
simple diffusion
diffusion of a solute through a membrane without help from a protein
facilitated diffusion
movement of a solute across a membrane, down a concentration gradient with the help of a protein when the membrane is otherwise impermeable to solute
two types of proteins involved in facilitated diffusion
channel and carrier proteins
channel proteins
allow for facilitated diffusion by forming a narrow opening in the membrane surrounded by the protein. Channels are very selective
ion channels
Are gated if the channel is open in response to specific environmental stimuli. Only involved in facilitated diffusion
voltage- gated channel
opens in response to a change in the electrical potential accross the memebrane
ligand-gated channel
opens in response to the binding of a specific molecule like a neurotransmitter
Carriers
bind the molecule to be transported at one side of the membrane
Uniports
Carry only one molecule
Symports
Carry two molecules
Antiports
Carry two molecules in opposite directions
Pore
Tube through the membrane, large and non selective. All molecules below a certain size can pass through. Pores are formed by polypeptides known as porins.
Which membrane does not contain pores
Eukaryotic plasma membrane. Pores destroy the barrier function.
Active Transport
Movement of molecules through the plasma membrane against the gradient. Requires energy input usually thermodynamically favorable.
Primary Active Transport
transport of a molecule coupled to ATP hydrolysis (release of ATP)
Secondary active transport
Not coupled to ATP hydrolysis. ATP released in primary active transport is used to create a gradient an then the potential energy in the gradient is used to drive the transport of other molecules across the membrane.
NaK/ATPase and the resting membrane
Transmembrane proteins in the plasma membrane of all cells in the body. Pumps out 3+ Na ; 2K+ in and hydrolyses one ATP to drive the pumping of these ions against their concentration gradients. Some potassium ions leak out of the cell through potassium leak channels.
Resting membrane potential
As potassium leaves the cell the movement of positive charge out of the cells creates an electric potential across the plasma membrane with a net (-) charge on the inside of the cell
Driving force behind secondary active transport of different molecules (sugars, amino acids)
Concentration gradient of high sodium outside the cell
Catalytic receptors
have an enzymatic active site on the cytoplasmic side of the membrane. When a ligand binds at the extra cellular surface enzyme activity is initiated.
Usually behaves similar to a protein kinase; enzymes that covalently attach phosphate groups to proteins. (serine, threonine, tyrosine)
G-protein linked receptor
does not directly transduce a signal. It transmit it into the cell with the aid of a second messenger
The second messenger
relays instructions from the cell surface to enzymes in the cytoplasm
The cytoskeleton
provides structural support. Allows for movement of the cells and its appendages (cilia & filaments).
Animal cell’s internal cytoskeleton is composed of these proteins
Microtubules, Intermediate filaments & microfilaments
(all are composed of no covalently polymerized proteins)
Microtubules
Hollow rod composed of gobular proteins: alpha tubulin and beta tubulin. Once formed the Microtubules can elongate by adding alpha-beta tubulin dimers to one end.
The other end cannot elongate because its anchored to the MTOC (nicrotubulue organizing center)
Microtubules mediate what
transport of substances within the cell. Transport is driven by proteins that hydrolysis ATP and act as molecular motors along the Microtubules.
Cilia and Flagella
Cilia are small hairs on the cell surface that move fluids past the cell surface.
Flagellum is a large tail which moves the cell by wiggling (the only human one is the sperm)
Both have 9+2 arrangement of Microtubules. Prokaryotic flagellum is different in structure and its motion is driven by a different mechanism.
Intermediate Filaments
heterogeneous, composed of a wide range of polypeptides. They are more permanent and involved in providing strong cell structure, such as in resisting mechanical stress.
Microfilaments
Rods formed in the cytoplasm from polymerization of the globular protein actin. Responsible for gross movements of the entire cell such as pinching the dividing parent cell into two daughters during cell division and amoeboid movement.
Changes in the cytoplasmic structure which cause cytoplasm & the rest of the cell to flow in one direction.
Amoeboid movement
Tight Junctions
form tight seal preventing items from moving freely between the intestinal lumen and the body
Desmosomes
Intercellular junctions that provide strong adhesion between cells.
Do not form a seal, but merely hold cells together
Gap Junctions
form pore-like connections between adjacent cells, allowing the two cells’ cytoplasma to mix. Permits exchange of solutes such as ions, amino acids and carbohydrates. NOT polypetides and organelles.
Cells reproduce themselves by
first doubling everything in the cytoplasm and the genome and then split it in half
S Phase (synthesis)
when the cell actively replicates its genome
M Phase
Mitosis is the partitioning of cellular components into two halves.
Prophase
genome becomes visible upon condensing into densely packed chromosomes. Nucleolus disappears, spindle & kinetochore fibers appear.
Centriole pairs begin to move to opposite ends of the cell. At the end of prophase the nuclear envelope converts itself into many tiny vesicles
Metaphase
All the chromosomes line up at the center of the cell, forming the metaphase plate. They are pushed and pulled by the mitotic spindle.
Anaphase
spindle fibers shorten, and the centromeres of each sister chromatid pair are pulled apart.
The cell elongates, and cytokinesis beings with the formation of a cleavage furrow.
Telophase
nuclear membrane forms around the bunch of chromosomes at each end of the cell.
Chromosomes decondense and nucleolus becomes visible within each new daughter nucleus. Each daughter has n chromosomes
Cytokines
physical process of cell division
Interphase is made by
Gap phase and S phase
The cell spends most its time in
Interphase. Some cells become permanently stuck in interphase (Go)
During Interphase
the genome is spread out and is not visible. DNA is accessible to the enzymes replication.
The more specialized the cell becomes
the less likely it is to remain capable of reproducing itself.
Oncogenes
Inappropriate cell division and unregulated cell growth can cause disastrous consequences; like inducing cancer.
Sister Chromatids
identical copies of chromosomes, attached to each other at the centromere.
Homologous chromosomes
are equivalent but non identical and do not come anywhere near each other during mitosis.
Karyotype
display of an organism’s genome
Prokaryotes
do not contain membrane bound organelles. “before the nucleus”
Posses all the machinery required for life (unlike viruses).
True cells and true living organisms, bacteria, archea & blue-green algae
Prokaryotic Genome is a
single-double stranded circular DNA chromosome
What processes occur in the same pace in bacteria
transcription and translation. Ribosomes begin to translate mRNA before it’s completely transcribed.
elongation of mRNA proceeds 5’ to 3’
Polyribosome
many ribosomes translating. Bacterial ribosome is structurally different from the eukaryotic ribosome, but both function in the same way.
Plasmid
extra chromosomal genetic elements.
Encode gene products which may confer an advantage upon bacterium carrying the plasmid (antibiotic resistance)
Orchestrate bacterial exchange of genetic information; conjugation (allows for exchange of genetic information).
The bacterial cell wall is composed of
peptidoglycan (a complex polymer unique to prokaryotes). Contains amino acid D-alanine which is not found in animal cells.
Protoplast
a wall less vulnerable cell whose peptidoglycan has been destroyed by lysozyme
Gram- Positive
stain strongly (dark purple) and have a thick peptidoglycan layer outside the cell membrane and no other layer
Gram-Negative
stain weakly (light pink) have a thinner layer of peptidoglycan in the cell wall but have an additional layer containing lipopolysaccharides
Capsule/Glycocalyx
sticky layer of polysaccharide surrounding the bacterial cell and often surrounding an entire colony of bacteria.
Makes bacteria more resistant to eradication from the immune system. Allows bacteria to adhere to smooth surfaces
Flagella
involved in motility, only in bacteria. Can be either monotrichous (only located at one end) or amphitrichous (located at both ends) or peritrichous (have multiple flagella)
Chemotaxis
Motion can be directed towards attractants, such as food, or away from toxins, such as acid.
Chemoreceptors
bind attractants repellents and transmit a signal which influences the direction of flagellar motion.
This is not dependent on an absolute concentrations but to a change in the concentration over time
Pili
Long projections on the bacterial surface involved in attaching to different surfaces
Sex Pilus
special Pilus attaching F+ (male) and F- (female) bacteria that facilitates the formation of conjugation bridges.
Fimbraie
smaller structures that are not involved in locomotion or conjugation but are involved in adhering to surfaces
Mesophiles
moderate temperature lover (30C)
Thermophiles
heat lovers (100C)
Pyschrophiles
cold lovers (0C)
Chemoautotrophs
build organic macromolecules from CO2 using energy of chemicals.
They obtain energy by oxidizing inorganic molecules like H2S.
Chemo Heterotrophs
require organic molecules such as glucose made by other organisms as thei carbon source and for energy.
Humans are chemo heterotrophs
Photoautotrophs
use only CO2 as a carbon source and obtain their energy from the sun (Plants)
Photoheterotrophs
are odd in that they get their energy from the Sun, like plants, but require an organic molecule made by another organism as their carbon source
Auxotroph
cannot survive on minimal medium because it can’t synthesize a molecule it needs to live. Requires an auxiliary trophies substance to live
Obligate aerobes
bacteria that requires oxygen
Anaerobes
bacteria that does not require oxygen
Facultative anaerobes
will use oxygen when it’s around but don’t need it
Tolerant anaerobes
can grow in the presence or absence of oxygen but do not use it in their metabolism
Obligate anaerobes
are poisoned by oxygen. (commonly infect wounds)
Binary Fission
Bacteria reproduce asexually. Each bacterium grows in size until it has synthesized enough cellular components for two cells rather than one|it then replicates it genome, then divides into two
Log phase
bacteria grow exponentially
Lag phase
bacteria that were not previously growing enter this phase and cell division does not occur even if the growth condition is ideal
Stationary Phase
Once the medium is depleted the cells cease to divide and go into this phase
if the environment is isotonic to the cell
the solute concentration is the same inside and outside
Endospores
Have a though, thick external shell compromised of peptidoglycan.
Germination
reactivation of an endospore
How do bacteria aquire new genetic material
Transduction, transformation and conjugation
Transduction
transfer of genomic DNA from one bacterium to another by lysogenis phase
Transformation
if pure DNA is added to a bacterial culture, the bacteria internalize the DNA in certain conditions and gain genetic information in the DNA.
Conjugation
bacteria make physical contact and form a bridge between cells.
Hfr cell
a cell with the F factor integrated into its genome is considered a high frequency of recombination cell
