List the four tenets of cell theory
1) All living things are composed of cells
2) The cell is the basic functional unit of life
3) Cells arise only from preexisting cell
4)Cells carry genetic info in the form of DNA. This genetic material is passed from parent to daughter cell
Characteristics of Eukaryotes
-uni or multicellular
-contain true nucleus enclosed in a membrane
-linear DNA
Prokaryotes characteristics
no nucleus
no membrane bound organelles
circular DNA contained in nucleoid region
Nucleoid region
space within a prokaryotic cell where its circular DNA can be found, not enclosed in a membrane
cytosol and function
fluid within cell
allows for diffusion of materials within cell
cytoplasm
term for cytosol and organelles
nucleus characteristics
surrounded by nuclear membrane/envelope
where DNA is located
Where transcription occurs
Nuclear pores
in nuclear membrane, allows for selective 2 way exchange of molecules between cyto and nucleus
nucleolus
dark spot in nucleus
where ribosomal RNA (rRNA) is produced
Where is ribosomal RNA produced?
nucleolus
histones
organizing proteins of DNA
mito
powerhouse of cell
parts of the mito
outer membrane-barrier between cyto and mito environment
inner membrane-ETC/cristae
matrix-space inside inner membrane
intermembrane space-space between inner and outer membrane
What kind of DNA does the mito carry
double stranded circular DNA
cristae and function
foldings on the inner membrane of mito, increases surface area for ETC enzymes
ETC
protons from matrix flow through ATP synthase to generate ATP during OXIDATIVE PHOSPHORYLATION
proton motive force
pumping of p+ from matrix to intermembrane space
How are mitochondria different from other organelles?
they are semi autonomous, contain their own genes and replicate independently of nucleus via binary fission
theory of how mitos came to be
evolved from anaerobic prokaryote engulfing an aerobic prokaryote creating a symbiotic relationship
two main functions of mito
energy production
APOPTOSIS- mito releases ETC molecules to kick start apoptosis (cytochrome c activates caspases which activate auto degradation of cell)
What molecule releases the caspases in mito for autodegradation of cell during apoptosis
CYTOCHROME C
lysosomes charcteristics
membrane bound
contain hydrolytic enzymes that can break down substances from endocytosis and waste products to prevent cell damage
also plays role in apoptosis via autolysis (release of its enzymes to degrade cell components)
which two organelles are most involved in apoptosis?
mito and lysosomes
ER
Contiguous with nuclear envelope
SINGLE membrane folded into numerous invaginations with CENTRAL LUMAN inside
process proteins destined to ER, GOLGI, LYSOSOMES, PM, SECRETION)
Rough ER
studded with ribosomes for protein translation destined for secretion into its LUMEN
smooth ER
no ribosomes
lipid synthesis
detox of certain drugs/poisons
transport of proteins from rough ER to golgi
where in a cell does drug/poison detox occur?
smooth ER
Golgi
stacked membrane bound sacs
materials from ER transfered to Golgi for MODIFICATIONS including carbs, phosphates and sulfates
exocytosis for secretion products, golgi packages proteins in secretory vesicles that merge with cell membrane to release content
Where are proteins packaged in secretory vesicles?
in the GOLGI
Where are lipids synthesized
in the Smooth ER and in peroxisomes
Signal sequences
hydrophobic area of protein that initially directs proteins destined to ER GOLGI LYSOSOMES PM or SECRETION to the ER so it can be modified/exported.
SRP proteins recognize the signal sequences and take it to the rough ER to be processed.
used to direct delivery of a product to specific cellular location (ER, GOLGI, LYSOSOMES, PM, SECRETION)
peroxisomes
contain hydrogen peroxide which it converts to H20 and 02
break down LONG chain fatty acids via BETA OXIDATION
self replicate
synthesize phospholipids
contains enzymes in pentose phosphate pathway (involved in breakdown of glucose to create a pentose DNA/RNA precurser and NADPH)
Pentose Phosphate pathway
(involved in breakdown of glucose to create a pentose DNA/RNA precurser and NADPH)
What is beta oxidation?
catabolic process by which fatty acid molecules are broken down in the mitochondria to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in the electron transport chain
short chain fatty acids undergo this in mito
long chain fatty acids under go this in peroxisomes
Cytoskeleton
structure and shape of cell
Main functions of each cytoskeletal componant
microfilaments
microtubules
intermediate filaments
microfilaments-resist against tension and compression, cleavage furrow and muscle contraction
microtubules-cilia, flagella, mitotic spindle
intermediate filaments- important for cell-cell interactions, tissue structuring, and is scaffold for Z-disk
microfilaments
ACTIN
organized into bundles and networks
resistant to compression and fracture to protect cell
myosin
interacts with actin in muscle contraction to generate force for movement
cytokinesis
division of matirials between daughter cells dependent on ACTIN filaments
during mitosis, the cleavage furrow is formed of microfilaments and organize as a ring at site of division between 2 daughter cells
actin in this ring contracts and becomes smaller until pinching connection between daughter cells
Which cytoskeletal structure forms the cleavage furrow during mitosis?
MICROFILAMENTS
INTERMEDIATE FILAMENTS
filamentous proteins like KERATIN AND DESMIN
cell-cell adhesion
maintenance of cyto integrity
withstands tension to make cell RIGID
anchores organelles including nucleus
cell and is tissue specific
MICROTUBULES
tubulin polymers
provide pathways for motor proteins like KINESIN AND DYNEIN to carry vesicles accross cell
cilia/flagella are what kind of cytoskeletan
microtubules
cilia
projections from cell involved in movement of materials along surface of cell (eg rispratory tract cilian help move mucus)
flagella
movement of cell itself (ex sperm through repro tract)
structure of cilia/flagella
9 pairs of microtubules forming outer ring, 2 microtubules in the center
EUKARYOTIC CELLS ONLY cuz structure of flagella in bacteria has diff structural and chemical composition.
Centrioles
found in centrosomes, organizing center for microtubules
9 triplets with hollow center
centrioles in mitosis
migrate towards opp poles of dividing cells and organize mitotic spindle
kinetochore-microtubules emanating from centrioles attach to chromos and exerts force on sister chromatids to tear them apart
Epithelial tissue
covers body, lines cavities
protects against pathogen invasion
involved in absorption, secretion and sensation
PARENCHYMA of most organs i.e. the functional part
basement membrane
layer of connective tissue that joins epithelial cells
Parenchyma+ examples
functional part of an organ (epi cells)
nephrons in kidney, hepatocytes in liver, acid producing cells of stomach
epi cells
polarized, one side faces lumen (hollow inside of organs) OR the outside world, the other side interacts with blood vessels and structural cells
eg)in small intestine, one side absorbs nutrients, the other releases those nutrients into circulation
Types of epithelia
simple, stratified, pseudostratified
simple epithelia
one layer of cells
stratified epithelia
multilayered cells
pseudostratified epithelia
looks like multiple layers of cells due to cell height differences but really is just one layer
epithelial cell SHAPES
cuboidal, columnar, squamous (flat, scalelike)
CONNECTIVE TISSUE
supports body, gives framework for epi cells
STROMA (supportive structure of body as compared to PARENCHYMA, functional part)
bone, cartilage, tendons, ligaments, adipose tissue, blood,etc
connective tissue cells secrete
collagen or elastin to form EC matrix
prokaryotes
simplest organisms, including bac., no membrane bound organelles, circular DNA
Nucleoid region
in prokaryotes, non membrane bound region where circular DNA is contained
Archae
single celled
LOOK LIKE bacteria structurally
contain GENES and METABOLIC pathways similar to Eukaryotes
many are extremophiles
some in human body
circular DNA
divide via binary fission or budding
resistant to antibiotics
energy source of archae
alternative sources such as photosynthesis, chemosynthesis (energy from inorg. compounds like sulfure or nitrogen like ammonia)
how are archae similar to euks
have similar genes/metab pathways
start translation with methionine
contain similar RNA polyms
associate DNA with histones
bacteria
contain cell membrane and cyto
some have flagella and fimbriae (like cilia)
circular DNA
Why does the presence of a membrane on the outer surface of a cell not a distinguishing factor between a prokaryotic cell and euk cell
Because gram negative cells contain a third membrane made of phospholipids and lipopolysaccharides
euks contain a phospholipid bilayer membrane
why is it hard to develop medicines that target bacteria
beause they have analogous structures to euks, so the structures that are diff (like flagela) are used to target them
other antibiotics target ribosomes which are SMALLER than euks
mutualist symbiotes and example
bbacteria and humans both benefit from relationship (eg human gut bacteria creates Vit K and biotin and prevents overgrowth of harmful bacteria)
role of Vit K
involved in blood clotting, vit k injections for babies who have not yet developed a fully functional bacterial ecosystem in gut and thus are vit k deficient
Pathogens
no advantage, benefit to host
(eg Chlamydia-livesinside rep tract
Clostridium tetani-lives outside cell, produces toxins to enter blood stream)
Bacterial shapes
cocci (spherical), bacilli (rod-shaped), spinilli (spiral)
obligate aerobes
need oxygen to survive
anaerobes
use fermentation/ellular metabolism that does not requier oxygen
obligate anaerobes
cannot live in oxygen environment because it creates oxygen readicals leading to cell death
facultative anaerobes
switch between oxygen and non-oxygen metabolism
aerotolerant anaerobes
cant use oxygen but isnt harmed by it
prokaryotic structure
no organelles, no nucleus, cell wall and membrane, nucleoid region, ribosomes
cell wall of prokaryote
outer barrier
provides structure and controles movement of solutes in and out of cell, thereby giving concentration gradients with respect to environment
cell/plasma membrane of prokaryote
inner barrier made of phospholipids
envelope of prokaryote consists of
cell wall and PM
types of cell walls for prokaryotes
gram positive, gram negative
test for cell walls of prokaryotes
gram staining,
Step 1: crystal violet stain (purple)
Step 2: safranin counter stain (pink)
Step 3: gram+ is purple, gram- is pink
Gram positive cell wall
thick layer of peptidoglycan (AAs and sugars)
protection from hosts immune system
contains lipoteichoic acid which ACTIVATES the human immune system
How does penicillin work
it attacks enzymes that catalyzes crosslinking of peptidoglycan so cell wall deteriorates, effective on strep and syphilis
Gram negative cell wall
thin
contains less peptidoglycan
third OUTER MEMBRANE containing phospholipids and lipopolysaccharides IN ADDITION to cell wall and membrane
lippopolysaccs triggers human immune response which is STRONGER than lipoteichoic acid
what triggers human immune response in gram positive and negative cells respectively, AND WHICH IS STRONGER RESPONSE
lipoteichoic acid, lippopolysaccs, lippopolysaccs
how are archaea simlar to bacteria
both single celled
no nucleus or membrane bound organelles
circular chromos
divide by binary fission or budding
similar structure
difference between gram + and gram-
gram+:thick layer of peptidoglycan and lipoteichoic acid, but NO OUTER MEMBRANE
gram-:thin layer of peptidoglycan but has oUTER MEMBRANE containing lipopolysaccharides and phospholipids
Flagella in bacteria
moves cell towards food and away from toxins/immune cells through CHEMOTAXIS
chemotaxis
the way flagella detects chemical stimuli to move cell in response
structure of flagella in bacteria
filament-flagellin
basal body-anchors flagellum to membrane and acts as motor
hook-connects filament to basal body and creates torque from basal body to filament for propulsion
similar in gram+ and gram- cells
difference between flagella in bacteria and euks.
eukks contain microtubules composed of tubulin and organized in 9+2 arrangement, bacterial flagella are made of flagellin and consist of a filament, basal body and hook, use chemotaxis to move
Plasmids
DNA from external sources that is not necessary for survival and is not part of genome but gives advantage such as against antibiotics
which organelles do prokaryotes lack
mitochondria, instead, ETC is on cell membrane to generate ATP
prokaryotes reproduce through
binary fission or budding
binary fission is (list steps of process)
simple form of asexual reproduction in prokaryotes
1) circular chromosomes attach to cell wall and replicates while cell grows
2=PM and Cell wall grow inward at midline to produce 2 daughter cells
How is binary fission different from mitosis
fewer events and thus happens more rapidly
plasmids and what they carry
extragenomic material that carry genes veneficial to the bacterium such as
1)anitbiotic resistance
2)virulence factors
what are virulence factors
traits that increase how pathogenic a bacterium is
toxin production, projections that allow bacterium to attach to certain cells, evasion of host immune system
episomes
subset of plasmids capable of integrating into the genome ofbacterium
what is the advantage of bacteria genetic recombo
increase bacterial diversity, evolution
types of bacterial genetic recombo
transformation conjugation transduction transposons
Transformation
integration of foreign genetic material into host genome, usually done after a bacterial cell lyses and spills its content in the vicinity of another cell capable of transformation, which can then uptake that genetic material and integrate it into its genome
many GRAM NEGATIVE RODS can carry this out, but it can also be done by gram positive cells too
conjugation
sexual reproduction of bacteria.
1)two cells form CONJUGATION BRIDGE to transfer gen. material
2) transfer is unidirectional from donor male (+) to donor female (-).
3) bridge made of SEX PILI (appendages) found on donor male
4)Pili formed via SEX FACTORS (necessary genes)
F factor
the best studied sex factor, found in E coli,
F+ cell
E coli cell containing the F factor plasmid
describe conjugation in E Coli
1) Fertility factor present in F+ cells.
2) Fertility factor transfered on a plasmid to F- cells making that cell now a F+ cell which can transfer the given genes to other cells
3) this method also allows other plasmids to be passed through conjugation bridge
4) F factor via transformation can become integrated into genome of certain recipient cells, turning the cell into an HFR cell.
HFR cell
high frequency of recombo, when the F factor has integrated into the genome of a recipient cell after conjugation
these cells that have the F factor integrated into the genome during conjugation will actually try and transfer an entire copy of its genome, however the bridge usually breaks before all the DNA can be transfered
Transduction
REQUIRES a vector IE a virus to carry gentic material from one bacteria to another
in this process,
1)virus infect bacteria
2)chop up its dna
3) traps some of the bacteria dna into virus copies
4) cell lyses and the viruses leave the cell
5)find new cell to attack
6)releases the dna from initial bacteria into a new cell
7)this trapped DNA from the original host can then integrate into the genome of the new host cell.
bacteriophages
viruses that infect BACTERIA, specifically
perform transuction
Transposons
genetic elements capable of inserting and removing themselves from the genome, IN BOTH EUKS AND PROKS
issue with transposons
if it inserts itself within the coding region of a gene, that gene will be disrupted
Stages of bacterial growth
1) Lag phase, when the bacteria adapt to new conditions
2)exponential phase, once bacteria adapt and growth increases
3)stationary phase when the reduction of resources slows production
4)death phase, when the resources in the environment have depleted
Picture representation:
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Virus
nonliving, acellular, no organelles or nucleus
structure of virus
genetic material (cirular, linear, single strand double strand, dna, rna), protein coat (called caspid), and SOMETIMES lipid envelope
caspid
protein coat of a virus
what are envelopes sensitive to/why important
some viruses contain envelopes around their caspids, which are susceptible to heat, detergents and desiccation. This makes the viruses with envelopes easier to kill than viruses without envelope
why cant viruses reporduce independently
they dont have ribosomes to do protein synthesis
virions
viral progeny after virus uses cell machinery to reproduce
structure of bacteriophages
caspid,
nucleic acid within caspid
tail sheath that acts as syringe for genetic material,
tail fibers to help bacteriophage recognize and connect to correct host cell
positive sense virus
single stranded RNA virus, genome can be directly translated to proteins by ribosomes like mRNA
negative sense virus
RNA viruses that require sythesis of a COMPLETMENTARY RNA strand which can then be used in protein synhesis
This can be accomplished through RNA replicase, which is contained within the virion
RNA replicase
protein in negative sense virus that synthesizes complementary strand to the RNA carried by virus
retrovirus
a single strand RNA viruses (usually 2 identicals in one virus), These viruses carry reverse transcriptase which synthesizes DNA from its RNA. the DNA can then integrate into host cell genome
ONLY WAY TO GET RID OF VIRUS IS TO KILL THE CELL
viral life cycle (HIV)
1)envelope proteins bind to CD4 and CCR5 cell surface proteins
2)reverse transcriptase from virus copies virus RNA genome into double stranded DNA and makes errors that generate diversity in virus copies
3)integrase inserts viral DNA into host DNA
4) cells machinery transcribes viral genes back into RNA which travels to cytoplasm to be translated
5)proteins from translation move toward cell membrane and gather to make a virus copy that will bud from the cell
6)After budding, HIV protease enzymes modify protein chains to enamble virion maturity.
7)repeat.
infection stage of virus (3 types)
1) cell specificity for viruses which interact with cell surface proteins and fuse with PM of cells OR
2) are endocytosed by cell that thinks it is a nutrient OR 3) use tail fibers to attach to the cell membrane, leaves caspid out
how to bacteriophages anchor themselves to bacteria cell membrane
with tail fibers
how to bacteriophages inject their genome
via tail sheat
how do enveloped viruses differ from bacteriophages in terms of injection
enveloped viruses, such as HIV, fuse with the PM and remain in tact
Bacteriophages actually use their tail fibers to anchor themselves and then the tail sheath to inject the viral genome into the host, leaving their caspids outside the host cell
Translation stage of virus (for the different types of viruses)
for
DNA viruses-they must go to nucleus to be transcribed into mRNA, which then goes to cyto to be translated
Positive sense RNA-stays in cyto directly translated by ribosomes
negative sens RNA- synthesis of complementary RNA strand via RNA replicase, then translation via ribosomes
retroviruses-DNA formed through reverse transcription travels to the nucleus and integrates into host genome
Viral progeny release
Initiation of cell death so that the virions spill out
or
host cell may lyse as a result of so many virions
OR
virus can leave via EXTRUSION or fusing to PM
productive cycle of virus
when the host cell survives because the virus leaves by extrusion and thus can be continued to be used by the virus
Lytic Cycle FOR bacteriophage
bacteriophage uses at max the cells machinery, the virions build up and then the cell lyses.
virulent cells
bacteria in the lytic phase
Lysogenic cycle for bacteriophage
bacteriophage integrates into the genome as a PROVIRUS/PROPHAGE. The virus is replicated when the bacteria reproduce.
UNTIL, environmental factor (radiation, light, chemicals) cause the virus to leave the genome and enter the lytic cycle
superinfection
simultaneous infection of bacterium with other phages, infection with one phage makes it less susceptible to superinfection
Prions
infectious proteins, non-living, causes misfolding of other proteins by converting alpha helical structure to beta pleated sheet. this causes solubility and degradability to decrease and thus causes protein aggregates to form and reduces cell function
Viroids
plant pathogens consisting of short circular single stranded RNA. They can bind to RNA and silence those genes in the plant genome necessary for metabolism and cell structure.
example of human viroid
HDV which can silence human hapatocytes when coinfected with HBV
photoautotroph
energy source is light, carbon source is CO2
chemoautotroph
energy source are chemicals, carbon source is CO2
photoheterotroph
energy source from light, carbon from organic compounds
chemoheterotroph
energy source from chemicals and carbon from organic compounds