Unit 1 Flashcards
Why are cells the smallest units exhibiting life characteristics?
Because they are able to reproduce themselves by their own efforts
Why are Organelles are NOT the smallest units exhibiting the characteristics of life?
they are NOT able to reproduce themselves by their own efforts outside of the host cell. Has a specific function in a cell.
Why are Viruses are NOT the smallest units exhibiting the characteristics of life
Because they’re NOT able to reproduce themselves by their own efforts; they use the host reproductive machinery
Hooke made the _____, _____ refined it.
Light microscope,
Leeuwenhoek
1m = ____
10^10 A’s
Basic properties of cells (1 & 2 most basic)
- Life: Can grow and reproduce in culture for long periods
- Highly complex, regulated and organized. Cells of similar structure have conserved metabolic and compositional features that has been conserved over evolutionary time.
Basic properties of cells (3-10 )
- Posses a genetic program and means to use it
- Capable of producing more of themselves
- Acquire and utilize energy
- Carry out rxn’s. Sum of rxn’s called metabolism
- Engage in mechanical activities
- Able to respond to stimuli
- Capable of self-regulation
- They evolve
Two types cells and what distinguishes them
- Prokaryote (all bacteria)
- Eukaryote (protists, animals, plants, fungi)
* Distinguished by cell size and organelles present
In prokaryotes, DNA is
NOT segregated within a nucleus
In eukaryotes, DNA is
segregated within a defined nucleus
Prokaryotes contain a single
Membrane-limited compartment and nucleuoid
Nucleiod
(in prokaryotes) which is a single circular DNA molecule not surrounded by a membrane separating it from the cytoplasm.
Features common to prokaryotes and eukaryotes
- Plasma membrane of similar construction
- Genetic information in DNA, using identical genetic code
- Both store chemical energy in the form of ATP
- Shared metabolic pathways (glycolysis, TCA cycle)
- Proteasomes (for protein degradation) of similar construction
Features of eukaryotic cells not found in prokaryotic cells
- Nuclear envelope, separating nucleus from cytoplasm
- Complex chromosomes that compact into mitotic structures
- Membrane-bound cytoplasmic organelles
- Cytoskeleton with associated motor proteins
Features of genetic material distinguishing eukaryotic cells and prokaryotic cells
- Packaging: Prokaryotes have a nucleoid region whereas
eukaryotes have a membrane-bound nucleus. - Amount: Eukaryotes have much more genetic material
than prokaryotes. - Form: Eukaryotes have many chromosomes made of both DNA and protein (histones) whereas prokaryotes have a single, circular DNA with no histone proteins.
The Nucleus is surrounded by a
double membrane, called the nuclear envelope
The nucleus communicates with the cytosol via
Nuclear pores that perforate the envelope
Nuclear envelope consists of:
- 2x Concentric membranes (inner and outer) with perinuclear space in between.
- Nuclear lamina for structural support
- Nuclear pores with a central granule perforations in envelope.
What does the nuclear lamina do (function)
- Supports the nuclear envelope, composed of lamins.
Integrity of nuclear lamina regulated by
phosphorylation/dephosphorylation.
Human conditions Re: Nuclear lamina
- Lamin A/C mutation causes Hutchinson-Gilford Progeria syndrome
- Lamin B mutation causes leukodystrophy (loss of myelin)
– Mutations in lamin binding protein emerin cause Emery-Dreifuss muscular dystrophy (elbows, neck and heels become stiff, heart problems)
Mutations in emerin cause
Mutations in this lamin binding protein (emerin) cause Emery-Dreifuss muscular dystrophy (elbows, neck and heels become stiff, heart problems)
Emerin
Lamin binding protein
NPC stand for:
Nuclear pore complexes
NPC types of transport
- Passive diffusion (small molecules)
- Energy-dependent transport (proteins, mRNA, lamins and components of nucleus, importins)
NPC transport receptors are called, and what is their purpose
Importins; deliver other proteins to the nucleus.
rRNA subunit complexes
40S + 60S ribosomal subunits
NPC in vertebrates contains
scaffold (anchors) to the nuclear envelope, rings bext to cytoplasm and nucleus, nuclear basked and octagonal cytoplasmic filaments.
NPC structure size and channel info:
15-30x size of ribosome
Octagonal
Channel 20-30mm wide
F-G (phenylalanine and glycine) hydrophobic domains ~ sieve that blocks larger macromolecules
NPC size exclusion
> /= 40kDa
Proteins that import are called
Importins
The outer _____ is continuous with the _________. And, the space between the outer and inner _______ is continuous with the ______ of the ______ ER
nuclear membrane,
Rough ER,
Nuclear membranes,
Lumen,
Rough ER
Prokaryote ribosome components that must be bound to function
50S + 30S ~ 70S
Eukaryote ribosome components that must be bound to function
60S + 40S ~ 80S
Nucleolus
the sub-organelle of nucleus, where ribosomes are assembled
Chromatin
The complexes of eukaryotic DNA and proteins. Contains 2x amount of proteins vs DNA
Major component (proteins) of chromatic are called
Histones
Histones are (and what they’re known to have lots of)
Small proteins (11-23kDa) with lots of basic AA’s (Arg and Lys), facilitate binding to -vely charged DNA molecules
Chromatin = ____ + ______
DNA + Histones
How many types of histones?
5 types:
H1, H2A, H2B, H3, H4
Basic structural unit of chromatin is the
Nucleosome
Nucleosome contents:
DNA wrapped around octamer of H2A, H2B, H3 and H4 in a nucleosome core particle, then sealed by H1.
Nonhistone particles bind to linker DNA between nucleosome core particles.
Compaction of DNA amount with histones (first step):
7-fold
Higher order structures of chromatin and how much they compact it
Step 2: Histone interactions forming 30nm fibers by zig-zags and solenoids result in 6-fold more compaction
Step 3: 30nm fibers organized into 80-100nm supercoiled loops (cohesion ring) stabilized by protein called Cohesin
Overall mitotic chromosome compactness of DNA into chromatin
10 000:1
As a cell prepares to divide into two daughter cells… ____
chromatin condenses into chromosomes
Euchromatin is chromatin that was
In a nucleus
Euchromatin returns to a _____ after Mitosis
Dispersed state
Heterochromatin is even more
Compact than euchromatin
When DNA is more compacted, it is less likely that
those genes are being expressed.
Heterochromatin is condensed during
Mitosis
Two types of heterochromatin
- Constitutive heterochromatin (stays condensed). Usually around
-Centromeres, telomeres - Facultative heterochromatin (activates/inactivates during certain phases of organism’s life)
Example of Facultative heterochromatin:
X-activation on a Barr body on X chromosome. One is activated and more compact.
Mitochondria plays this critical role
in the generation of metabolic energy (ATP) in eukaryotic cells via cellular respiration
Why can’t you get sense of live action w/ a micrograph?
Because cell is dead.
Major determinant of mitochondrial morphology
Balance between fusion and fission (which occurs constantly)
Single mitochondrion length
~4 μm length
Where ER meets mitochondria is where _____ collects and fission with _____ will separate mitochondria via fission.
DRP1,
ER tubule
How do mitochondria arise?
By fission from existing mitochondria
Steps of process of mitochondria fission
Induced by contact with ER tubules
-GTPase binds to Drp1and Drp1 surrounds fission site and squeeze it into separate mitochondria.
Mitochondria surrounded by a
double-membrane system, consisting of inner and outer mitochondrial membranes separated by an intermembrane space.
inner membrane of mitochondria folds called
Cristae
Interior of the mitochondria
Mitochondrial matrix
Mitochondrial matrix contains
Enzymes for TCA and for expression of mitochondrial genes
Several identical copies of mitochondrial genome (circular)
Mitochondrial ribosomes.
Inner mitochondrial membrane is the main site of
ATP synthase
ATP is not made in the membrane because it is
highly polar and membrane is hydrophobic
Why is ATP synthesized in the matrix?
because it is a more hydrophilic environment…
Even though ATP synthase is on the inner mitochondrial membrane between there and intermembrane space
Outer mitochondrial membrane contains
enzymes that convert lipid substrates into forms that are subsequently metabolized in the matrix
What is the driving force to make ATP in Mito-Matrix?
H+ gradient (more in Intermembrane space)
ATP Production in mitochondrial matrix mechanism overview
Food consumed. Oxidative phosphorylation results in electrons pumping H+ into IMS, gradient in IMS creates pH difference between IMS and inner membrane. This gradient is such that H+ will want to move back from IMS to inner membrane… Then ATP synthase makes pathway to relieve this electrochemical gradient. Energy captured to produce ATP.
ATP production
Pyruvate and fatty acids enter mitochondrion, broken down by Acetyl-CoA and go in TCA. Produces NADH and FADH2
Then, oxidative phosphorylation takes electrons from NADH and FADH2 and passes them along ETC in inner membrane to O2. This transport generates a proton gradient across the inner membrane, which is used to drive the production of ATP by ATP synthase
Glycolysis overview:
1 (6C) Glucose broken down to 2x(3C)Pyruvate to enter into TCA cycle. + 2ATP (net gain) + 2 NADH
*Total ATP produced = 4 in glycolysis, but 2 are used thus a net 2 ATP produced
What happens to pyruvate (pyruvic acid)?
- O2 present~Oxidative phosphorylation
- anaerobic conditions~fermentation
What enters TCA cycle from glycolysis?
Acetyl-CoA (2C)
What will 1 molecule of pyruvate produce after 1 round TCA cycle?
4NADH
1FADH2
1GTP
Thus, five electrons in a cycle can be used in ETC
Glycolysis + TCA cycle products =
10 NADH
2 FADH2
2ATP
2GTP
Why 1.5 ATP generated with each FADH2 vs. 2.5 with each NADH
Because FADH2 enters downstream of NADH in ETC.
What from TCA cycle important for mitochondrial DNA and encodes for a ETC complex ___
Succinate dehydrogenase, ETC complex II
Four complexes in ETC chain
- Complex 1 (NADH dehydrogenase)
- complex II (Succinate dehydrogenase)
- Complex III (cytochrome bc1)
- Complex IV (cytochrome C oxidase
ETC step 1:
Electrons derived from NADH (via C1) or FADH2 (C2) passed to ubiquinone (aka Q)
Ubiquinone is a
lipid soluble molecule, thus doesn’t span the lipid bilayer and doesn’t get coupled by movement of protons from the matrix to IMS. Only responsible for generating electrons.
ETC step 2:
electrons passed from Q to C3 (cytochrome b-c1 complex)
ETC step 3:
Electrons transferred to CYT C (in IMS) carries electrons to C4
ETC step 4:
Complex IV transfers electrons to molecular oxygen to form H2O within the matrix
ETC step 5:
The electron transfers in complexes I, III and IV generate energy, which is used to pump H+’s from the matrix to the intermembrane space, establishing a proton gradient across the inner membrane. The energy stored in the proton gradient is then used to drive ATP synthesis as the protons flow back to the matrix through complex V (or ATP synthase)
DNP
Can dissipate H+ gradient and prevent ATP production.
Endosymbiont theory of origin of mitochondria and chloroplasts
smaller prokaryotes that took up residence in eukaryotic cell.
Evidence for endosymbiont theory
- Outer membrane of bacteria and mitochondria contain porins
- Inner membrane of bacteria and mitochondria contain the lipid cardiolipin 3. Mitochondria arise from pre-existing mitochondria via fission
- Mitochondria and bacteria contain a single, circular DNA
- Mitochondrial ribosomes are similar to those of bacteria (70S)
Chloroplasts resemble…
mitochondria in that both contain a permeable outer membrane and a relatively impermeable inner membrane (double-memb)
Stroma akin to
Mitochondrial matrix
Third membrane formed in chloroplasts by the
Thylakoids, orderly stacks are grana
Chloroplasts function
Sites of photosynthesis (light rxns) in plant cells, using CO2 and water to make ATP and NADPH and sugars.
In plant cells, chloroplasts and mitochondria
collaborate to supply cells with metabolites and ATP. Because the plant relies mostly on exporting sugars from mitochondria (dark rxns) to carbon fixation.
What 3 of 4 stages in photosynthesis take place in the thylakoid membranes?
- absorption of light by chlorophylls (green pigment)
- Electron transport to generate H+ gradient across thylakoid membrane with lumen containing higher H+ compared to the stroma.
- ATP and NADPH synthesis
photosynthetic units are found in two (large) protein complexes, which are embedded in the _______
PS1 and PS2
Thylakoid membrane
Steps of ETC in thylakoid membrane
- Light photon excites PS1, splits 2 H2O into O2 and 4H+ into thylakoid lumen, electrons transfer to…
- Plastoquinone (lipid soluble), transfers electrons to…
- Cytochrome b6-f complex, spans membrane and increases proton gradient.
- Plastocyanin (lumenal protein) transfers electrons to PS1, leads to passing electrons to H2O soluble ferrodoxin (Fe-S), which associates with ferrodoxin-NADP+ reductase (FNR) to produce NADPH
- ATP synthase of thylakoid membranes couples proton movement into the stroma to synthesize ATP.
Similarities (four) of mitochondria (OP) and chloroplasts (PSLR)
- Both generate ATP, and both use a proton pump to do so.
- Both contain DNA and ribosomes.
- Both are surrounded by a double membrane.
- Chloroplasts contain an additional third membrane (thylakoid) while the
inner mitochondrial membrane forms cristae
Differences of (four) of mitochondria (OP) and chloroplasts (PSLR)
The main difference is where the electrons go at the end:
* Mitochondria rely on both a proton gradient and a charge gradient across the inner membrane to generate ATP, while chloroplasts rely on a proton gradient (the charge is neutralized by the permeability of the thylakoid membrane to ions such as Cl- and Mg2+).
* The electron transfer chain of both organelles is composed of a number of large protein complexes.
* The terminal electron acceptor (OP) is O2 and (PSLR) is NADP+.
* OP requires O2 and produces CO2 as a byproduct while PSLR produce O2
and (in the Calvin cycle) utilize CO2.
Rubisco is highly inefficient, but needs abundant amounts of leaf proteins. Why inefficient and why does it work?
Lots of energy consumed 18 ATP per glucose molecule, but payoff is good (net gain with 30 ATP made via oxidative phosphorylation
Endomembrane system includes
Which all function as a part of a coordinated unit:
ER
Golgi
Endosomes
Lysosomes
Vacuoles
Why could the plasma membrane be part of Endomembrane system?
because it also started its journey on the ER.
All endomembrane system components
start their life from the ER.
In endomembrane system… every
vesicle knows where to go, even if bumping into each other.
Important for understanding protein function
Orientation of protein once embedded in lumen of ER will stay the same. It will always be on the lumenal side of whatever vesicle.
Extracellular proteins that are produced in rough ER will go to the
lumen of the golgi, vesicle derived from golgi and then fused with the membrane and can do outside extracellularly
In the endomembrane system, you can always see in the same
configuration in the lumen of the transport.
Cytosol facing will always be cytosol facing, lumenal facing will always be lumenal facing
Organelles of the endomembrane system are part of an integrated network in which materials are
shuttled back and forth between organelles in membrane-bound transport vesicles.
Upon endomembrane materials reaching their destination, the vesicles
fuse with the membrane of the acceptor compartment.
ER is a
network of interconnected internal membranes that extends from the nuclear membrane throughout the cytoplasm
Describe the the ER lumen
ER membrane forms a continuous sheet enclosing a single internal space,
The ER spans
Practically the entire surface of the cell
3 types of ER
- Rough ER (ribosomes bound, generates proteins)
- Smooth ER (generates lipids, no ribosomes
- Transitional ER (region where secretory vesicles exit ER enroute to golgi)
Many proteins are _____ within ER by ___________ .
Glycosylated,
Covalent attachment of sugars (glucose and mannose to proteins)
Proteins destined to any other Endomembrane system are built
on ribosomes on rough ER
Proteins synthesized on free ribosomes (in ____) either:
cytosol,
Stay in cytosol or are transported to nucleus, mitochondria, chloroplasts, peroxisomes
Smooth ER functions to
generate lipids for the cell, not just for the endomembrane system.
Three mechanisms to modify lipid composition of membranes
- Enzymatic modification
- modification during vesicle formation
- modification by phospholipid transfer proteins.
Smooth ER forms ______, whereas Rough ER forms a ________
Fine network of tubules connected to rough ER,
Oriented stacks of flattened cisternae
Transitional ER function
Part of ER that a vesicle will bud from, receptors in ER membrane that grab to those proteins that will bud them off and take them places.
Transport vesicles (for both proteins and lipids) bud from the _____ . Which are then carried to the
Transitional ER.
ER-Golgi Intermediate compartment, then to Golgi
ERGIC
ER-Golgi Intermediate Compartment
Main functions of ER once protein is inside is for:
Quality control, monitoring proper protein folding.
Folding of protein steps (in ER) after glycosylation in ER
protein goes through ribosome as 1e chain, then in lumen folded into 2e and 3e structure (done by calnexin)
Once monoglucosylated…
Chaperone calnexin binds, folds protein. Terminal glucose is removed and if protein is not folded properly:
-UGGT adds glucose back, refolding attempted again
If protein folds, can be transported to the next compartment
-After several attempts, more sugars (mannose) removed. Protein is dislocated from ER lumen, into cytoplasm and degraded by Proteasome enyzme.
If too many unfolded proteins accumulate in the ER
Unfolded protein response (UPR) is activated:
* Stops translation
* Degrades misfolded proteins
* Produces more chaperones
Prolonged UPR ~ apoptosis
How to induce unfolding response rapidly in lab conditions:
use small molecule to interfere with UGGT, Calnexin… or act way upstream and not let them get glycosylated (can’t fold properly).
Golgi complex is
Perinuclear; right up against the nucleus
What is golgi composed of:
Cisternae (flattened membrane enclosed sacs)
and
Vesicles
Golgi is usually near the
Cell nucleus
Golgi functions:
- proteins received from the ER are:
-Further glycosylated through golgi (further modification)
-sorted for transport to destinations - Some lipids synthesized in golgi complex
- Site of complex polysaccharides of cell wall are synthesized (in plants)
Destinations of golgi proteins:
-Lysosomes
-Plasma membrane
-Extracellular medium
Golgi has ordered series of compartments, which the faces are either:
Cis: entry facing (adjacent to ER)
Trans: exit facing (points towards plasma membrane)
Five functionally distinct compartments:
- the cis Golgi network (before cis golgi stack)
- the cis compartment of the Golgi stack
- the medial compartment of the Golgi stack
- the trans compartment of the Golgi stack
- the trans Golgi network (after trans golgi stack)
(Facing lysosomes, plasma memb, cell exterior)
Movement of proteins within golgi:
- Proteins and lipids enter the cis Golgi network in transport vesicles from the ER
- The proteins and lipids then progress to the cis, medial and trans compartments (cisterna) of the Golgi stack
- The proteins and lipids then move to the trans Golgi network, which acts as a sorting and distribution center, directing molecular traffic of transport vesicles to lysosomes, the plasma membrane and cell exterior
Two models in vesicles of transport through golgi complex:
- Vesicular transport model: cargo is shuttled from the CGN to the TGN in vesicles
- Cisternal maturation model: each cisterna matures as it moves from the cis face to the trans face, mediated by vesicles traveling from trans face to cis face
Lysosomes are
Membrane-enclosed organelles that contain degradative enzymes that can hydrolyze:
1. nucleic acids (nucleases)
2. proteins (proteases)
3. lipids (lipases)
4. carbohydrates (glycosidases)
in lysosomes, All lysosomal enzymes are
acid hydrolases, which are active at acidic pH (~5) that is maintained within lysosomes but not at neutral pH (~7.2) characteristic of the cytosol
The lumen of the lysosome is maintained at acidic pH by a
H+ (proton) ATPase in the membrane that pumps H+ ions (protons) into the lumen
Integral membrane proteins of the lysosome are
highly glycosylated. This is thought to shield the membrane from the degradative enzymes of the lysosome.
Lysosomes can display considerable variation in size and shape as a result of
differences in the materials that have been taken up for degradation.
Primary lysosomes
roughly spherical and do not contain obvious particulate or membrane debris.
Secondary lysosomes
larger and irregularly shaped, result from the fusion of primary lysosomes with membrane-engulfed aged and defective organelles; they contain particles of membranes in the process of being digested (autophagy).
Three pathways to deliver materials to lysosomes for degradation:
- The digestion of molecules taken up from outside the cell by endocytosis
- The digestion of large particles, including bacteria, cell debris, and aged cells
(taken up from outside the cell), by phagocytosis - The digestion of aged or defective organelles (the cell’s own components) by
autophagy
Peroxisomes are the site of
synthesis and degradation of hydrogen peroxide (H2O2), which is highly reactive and toxic. Hydrogen peroxide is produced during the oxidation of several substrates.
Peroxisomes have
catalases which degrade H2O2 into O2 and H2O
Four functions of peroxisomes:
- Oxidation of very long chain fatty acits
- Decomposition of H2O2
- Biosynthesis of plasmalogens (abundant lipid in myelin)
- Conversion of stored fatty acids to carbohydrates in germinating seeds of plants (in this case it is called glyoxosome)
Similarities between peroxisomes and mitochondria
Both:
- are formed from a pre-existing organelle
- import preformed proteins from the cytosol
- oxidize fatty acids
Differences between peroxisomes and mitochondria
- Peroxisomes have a single phospholipid bilayer but mitochondria have two
- Peroxisomes do not contain DNA or ribosomes but mitochondria do
Cytoskeleton is a network of
protein filaments extending throughout the cytoplasm
Cytoskeleton functions:
- Provides cell’s structural framework: determines
- cell shape
- the general organization of the cytoplasm - Responsible for the movements:
- entire cells
- organelles
- transport vesicles
- chromosomes during cell division
Three kinds of cytoskeletal filaments
- Microtubules (made of tubulin, central and radiate in cell for transport, cell div)
- Actin filaments (made of actin, for movement mostly in periphery of cell)
- Intermediate filaments (structural support and mechanical strength).
