Cell Bio Exam 2 Flashcards
What is the function of mRNA?
encoded by genes in DNA and carry information for many proteins
What is the function of rRNA?
structural and catalytic core or ribosomes that translate mRNA into proteins
What is the function of tRNA?
attach encoded/selected amino acids to make a growing amino acid chain
What is the function of microRNA?
regulator for eukaryotic gene expression
What is the function of small iRNAs?
provide protection against viruses and proliferating transposable elements
Where does RNA transcription begin?
Upstream from point of RNA synthesis at PROMOTER
Where does RNA transcription end?
At stop site called TERMINATOR where RNA strand will be released
What makes the terminator more special than the promoter?
The terminator is transcribed so that the RNA polymerase will know to let go of the strand. Promoter is NOT transcribed
What recognizes the promoter? (in bacteria)
The sigma factor recognizes the promoter (each DNA base has unique features the present to the outside which allows sigma factors to identify the promoter without separating DNA)
How many RNA polymerases are there?
3 (RNA polymerase I, II, III)
What are the functions of RNA polymerase I and III?
The transcribe genes that encode tRNA, rRNA, and other RNA with important structural and catalytic roles in cells
What is the function of RNA polymerase II?
Transcribe the rest of the genes, including the ones that encode proteins
What is the difference between prokaryotic and eukaryotic RNA polymerases?
Prokaryotic RNA polymerase has one accessory factor (sigma factor), has short regulatory sequences, does not need to unpack DNA template
Eukaryotic RNA polymerase has many accessory factors (gen. transcription factors), long regulatory sequences, and has to unpack nucleosomes
What is the function of the TATA box?
RNA polymerase II uses it to determine the orientation of transcription
TFIID binds to it (TBP, its subunit binds and bends DNA) then other factors assemble on the polymerase and create the transcription initiation complex
What is the function of TFIIH?
RNA polymerase needs to be released from the transcription initiation complex so TFIIH adds a phosphate group to its C terminal tail
Also functions to separate DNA strand
Explain the importance of elongation factors
They load onto actively transcribing RNA polymerase and help it move along DNA packaged in nucleosomes
What happens when RNA transcription is complete?
RNA polymerase is released and the protein phosphatase takes the phosphate at the C terminal tail then RNA polymerase is ready to find a new promoter
What are the 3 RNA processing steps?
RNA capping, RNA splicing, and polyadenylation
What is RNA capping?
The 5’ end of the RNA transcript is modified by adding a cap after about 25 nucleotide sequences have been produced
What is RNA splicing?
carried out by snRNPS which also form spliceosome in the nucleus
removes introns and stitching exons back together to create functional mRNA, before splicing it is known as pre-mRNA
What is polyadenylation?
Poly A tail
enzyme at 3’ end cut RNA chain at specific sequence of the nucleotide then another enzyme adds repeated adenine to the end
What is the importance of RNA capping and polyadenylation?
Increases stability of eukaryotic mRNA and allows it to be transported into cytosol
What is the importance of alternative splicing?
Allows different proteins to be produce from the same gene
What is the function of aminoacyl tRNA synthases?
There are 20 aminoacyl tRNA synthases that couple each amino acid to an appropriate set of RNA
Also creates a charge tRNA
What is the function of small ribosomal subunits?
Matches tRNAs to codons on mRNA
What is the function of large ribosome subunits?
Catalyzes formations of peptide bonds that link amino acids
How are ribosomes decoded?
From 5’ to 3’, one codon at a time
What are the steps for RNA translation?
Step 1: charged tRNA (aminoacyl tRNA) binds to the A site in the ribosomal subunit
Step 2: peptidyl transferase forms a peptide bond with the amino acid on the tRNA to the growing chain at the P site
Step 3: the large ribosomal subunit shifts forward moving the tRNA into the E site
Step 4: The small ribosomal subunit moves forward to realign with the large ribosomal subunit and eject the tRNA
Cycle repeats until a stop codon is reached
How do proteasomes in eukaryotes know which proteins to degrade?
Proteins are marked with ubiquitin for degradation
What are the two main biochemical reactions that can be catalyzed by ribozymes?
Peptide bond formation = rRNA
Splicing = snRNAs, self-splicing RNA
What are housekeeping proteins?
Proteins that are expressed in all cell types
What is the first step in gene expression?
Transcriptional control
What are transcription regulators?
Transcription regulators bind to regulator DNA sequences that are intact double helix, form noncovalent interactions with the nucleotides, and often bind to the major groove
Why are dimers important for transcription regulators?
Dimers increase contact are which also increases strength and specificity of binding
What is the Trp operator?
A regulatory DNA sequence
What is the Trp repressor?
A transcriptional regulator that is always present while Trp is not
Is controlled by Trp (feedback inhibition)
How does a transcriptional activator protein work?
Promoters would not be very active without transcriptional activator protein.
Increase the transcription of genes by binding to specific sites on DNA and interacting with other protein
Binding of activators to DNA are controlled by metabolites or other small molecules (like cAMP)
Explain the lac operon
Has a lac repressor and CAP activator
Lac repressor binds when lactose is absent and glucose is present (Lac operon not able to be transcribed) but when lactose is present and glucose is absent then the operon is transcribed
CAP activator has to be switched on by cAMP which increases when glucose decreases (this allows activation of genes that can metabolize sugars other than glucose)
What is the function of eukaryotic transcription regulator?
Control gene expression from a distance
What are eukaryotic activators called?
Enhancers because they can enhance transcription from 1000 nucleotides away
Enhancers are the binding site for eukaryotic activator proteins
What is a mediator?
A protein complex that binds activator and other general transcription factors to promote transcription
Eukaryotic repressor can also work with mediator to block transcription
What is the function of chromatin-remodeling complexes?
They modify the histones tightly packed to DNA
Reposition the nucleosome on DNA, can lead to activation or repression of transcription
Explain histone modifications that lead to activation or repression
Histone acetyltransferases attach an acetyl group to the histone and activate transcription
Histone deacetylases remove a group of acetyl from the histone and represses transcription
What is the importance of DNA loops?
It holds specific genes and regulator regions together
It prevents one gene regulator from acting on an inappropriate gene
Loops are called Topological Associated Domains
Changes in transcription are remembered (true/false)
False
What is combinatorial control?
A group of transcriptional regulators that work together to determine the expression of a gene (ex: lac operon)
What is signal integration?
Determines transcriptional status of a gene
What is a reporter gene?
A gene that tells when and where a particular gene is expressed
What are the transcriptional repressions and activators of stripe 2 of the eve?
Repressor = Giant and Krupel
Activator = Bicoid and Hunchback
The expression of different genes can be coordinated by a single protein (true/false)
True
What is pluripotency?
The ability to become any cell type
Formation of an entire organ can be triggered by a single transcriptional regulator (true/false)
True
What can generate cell memory?
Positive feedback loop
What nucleotide base does methylation occur on?
Cytosine bases
What are the 3 cell memory mechanisms?
Positive feedback loop, DNA methylation, and histone modification
Explain translation control
(bacterial) gene expression can be controlled by regulating translation of mRNA
ex: some RNA-binding proteins can repress translation of specific mRNAs
What is the significance of thermosensors?
They control the translation of the mRNAs for proteins needed during infections
What is the function of microRNAs?
Direct destruction of target mRNAs
Later become part of RNA-induced Silencing Complex (RISC)
Base pair with target mRNAs to destroy target and block translation of target so that no protein is produced from target mRNA
What is the function of small interfering RNAs?
Protect cell from infections
Used to eliminate foreign RNAs and target long ds RNAs (RNA produced dsRNA during infection)
Explain the regulatory RNA siRNAs
RNA interference cuts long dsRNA into small pieces by Dicer protein and produced small interfering RNAs which then join RISC proteins then degrade target RNAs
What is the function of long-noncoding RNAs?
The regulative mammalian gene activity
Xist - long-noncoding RNA involved in X-inactivation of one female X chromosome
Coats the chromosome and attaches proteins that form heterochromatin
Can also serve as scaffolds, bringing together proteins that function in the same cell process
What is the function of CRISPR Cas in viral infections?
They are small noncoding RNAs (crRNAs) that record past viral infections and collect them in the CRISPR locus
(Clustered Regularly Interspersed Palindromic Repeated sequences)
The Cas enzyme, guided by crRNAS, destroy the viral DNA when encountered
Why is the plasma membrane important?
It compartmentalizes the internal of the cell
Receives info for communication, allows for import and export of small molecules, and has capacity for for movement and expansion (important for cell growth and motility)
What are the most abundant membrane lipids?
Phospholipids
What is a key characteristic of the lipid bilayer?
It is a flexible 2D layer and allows for free movement of molecules within the PLANE of the bilayer
What is the significance of the hydrocarbon tail of lipids?
No double bonds = saturated
Double bonds have kinks (bends) = unsaturated and more fluid with looser packing
How does the length of the hydrocarbon tail affect fluidity?
Longer tails = less fluid
Shorter tails = more fluid
How do microbes adjust phospholipid composition?
Adaptations to temperature changes
low temp = shorter tails mean more double bonds, more fluidity
higher temp = longer tails mean fewer double bonds, less fluidity
How can animal cells modulate membrane fluidity?
By adjusting cholesterol levels
Why is membrane fluidity important?
For many cell processes like cell signal, membrane protein distribution, cell division, and membrane fusion (endocytosis and exocytosis)
What are the types of movement that phospholipids can make in a lipid bilayer? Which occurs the least?
Lateral diffusion, rotation, flip flop, and flexion
Flip flip occurs the least
Where does lipid membrane assembly occur?
In the ER
Phospholipids are deposited into cytosolic side of bilayer than phospholipids are flipped to face noncytosolic side
What are the two enzymes used to flip the lipid bilayer?
- scramblases = transporter protein that removes randomly selected phospholipids and 1/2 of bilayer and inserts them in the other half –> newly made phospholipids are redistributed between each layer in ER membrane
- flippases (enzymes in golgi membrane) = use ATP hydrolysis energy to transfer specific phospholipids from one side of bilayer to the other –> move selected lipids from layer facing exterior to layer facing cytosol
What is an important characteristic of membrane phospholipids?
They are asymmetric and this process begins in the golgi apparatus
What enzymes do flippases move?
Phosphatidylserine (PS) and phosphatidylethanolamine (PE) –> both are concentrated on cytosolic face
NOT PC or SM (concentrated on lumen/exterior)
Establish and maintain asymmetric distribution of phospholipids
Explain the significance of membrane retained orientation
Membranes and proteins can retain their orientation
What are the two plasma membrane lipids that are asymmetrically distributed?
Glycolipids = faces exterior (noncytosolic face)
Inositol phospholipids = faces interior (cytosolic face), important in cell signaling
Explain the significance of lipids and proteins in the cell membrane
Lipids are 50x more abundant than proteins and provide the basic structure and membrane permeability barrier
Proteins constitute to 50% of the membrane mass and perform all the other membrane functions
What are some examples of membrane proteins?
Channels (K+ leak channels) and transporters (Na+ pump), anchors (integrin), receptors (platelet-derived growth factor receptor), and enzymes (adenylyl cyclase)
What are the types of membrane proteins?
Integral proteins
- transmembrane (amphipathic, alpha helix, beta sheets)
- monolayer-associated (amphipathic alpha-helix)
- lipid-linked (NH2, COOH)
Peripheral proteins
- protein attached (protein extends into extracellular space and cytosol)
Explain the significance of protein structure in the lipid bilayer
The polypeptide chain crosses the bilayer as alpha helix
Each protein has a specific orientation
Hydrophobic side chains of the helix face the hydrophobic tails of the phospholipid
The backbone of phospholipid is hydrophilic, the alpha helix maximizes hydrogen bonding possibilities
Most transmembrane segments are…
Alpha helical
Explain the significance of multipass proteins in the lipid bilayer
hydrophilic pores can form multiple amphipathic alpha helices (hydrophilic cores and hydrophobic side chains facing lipid bilayer)
some transmembrane proteins have beta-barrel structures (like alpha helices where hydrophilic side chains face interior and hydrophobic side chains face exterior)
ex: porin proteins
How are integral and peripheral proteins removed from the membrane?
Integral proteins require the use of detergent to disrupt the lipid bilayer and remove them from the membrane
Peripheral proteins do not require detergents because they are indirectly bound to the membrane
Explain detergents
Detergents have a single tail (common detergents = SDS and milder is Triton X-100)
Detergent molecules form micelles which are aggregates formed from small clusters of detergent molecules
DOES NOT FORM BILAYERS
Explain the significance of the cell cortex
Protein cortex is on the cytosolic side of the membrane and it stabilizes the plasma membrane and provides shape
Most other animal cells have a cortex containing actin and myosin proteins (better for shape changes, movement, etc.)
Why is the Human RBC cortex important?
Spectrin is the main component and a mutation in the spectrin protein results in anemia
Transmembrane proteins attach to spectrin via actin (cortex confers shape)
What is the significance of the exterior cell wall?
The exterior cell wall serves the same purposes for bacteria, yeast, and plant cells
Protein movement in the lipid bilayer with mouse and human cell
Involves fusing a mouse cell with a human cell. At first, both remain separates but after awhile become a hybrid
Many membrane proteins are…
Confined to particular locations (domains)
- tethering (to cell cortex, to extracellular matrix, and protein to protein)
- diffusion barriers (tight junctions)
What are cell surfaces coated with? And what is its significance to the cell?
Carbohydrate layer is used for cell identity, function, protection, motility, cell-cell recognition and adhesion
Some lipids and proteins have sugars attached to them
- glycolipids
- glycoproteins (attach to short, oligosaccharide chains, ex: lectin membrane proteins bind particular oligosaccharides)
- proteoglycans (attach to long, polysaccharide chains)
Lipid bilayers are…
impermeable to water-soluble molecules
What affects the diffusion rate across the lipid bilayer?
Size and solubility (small, hydrophobic = faster rate)
Ordered by diffusion rate from greatest to least –> small nonpolar, small uncharged, large uncharged, and ions
What do the transport proteins in the cell membrane do?
Selectively promote facilitated transport
- passive diffusion
- pumping
Name the important ions and their concentrations inside/outside the cell
Na+ = higher concentration outside and is partly balanced by Cl-
K+ = higher concentration inside and partly balanced by negatively charged ions in the cell
Ca2+
What is membrane potential?
Voltage difference across membrane
Charges are not completely balanced across membrane
Differences in concentration of inorganic ions near cell membrane create membrane potential
What is the resting potential?
Between -20 mV to -200 mV
The interior is slightly more negative than the exterior which is useful for cell functions like transport of metabolite and cell-cell communication
What is CFTR?
CFTR is a protein that controls the flow of H2O and Cl- in and out of cells in the lungs
Reduced/malfunctioning CFTR can cause cystic fibrosis (buildup of thick mucus)
CFTR is expressed in cells of respiratory epithelia and exocrine glands
What are the two types of membrane transport proteins?
Channels (selective based on size and charge)
Transporters (selective based on molecules/ions that fit the specific binding sites)
Transporters can be active and passive, channels are only passive
Active transporter (aka pumps) couples with energy-producing process (ATP hydrolysis, ion gradient, and sunlight)
What makes the electrochemical gradient?
The membrane potential and concentration gradient
Na+ electrochemical gradient work in the same direction because of steep electrochemical gradient, but K+ work in the opposite direction because of low gradient
Explain the movement of water across the cell membrane
Water diffuses slowly across the membrane and uses aquaporins which are specialized channels for water
Total concentration of solutes inside a cell is high, because of osmolarity water is pulled inside cells
Move of H2O is low solute (high H2O concentration) to high solute (low H2O concentration)
How is osmotic swelling avoided?
Protozoans eliminate excess water using contractile vacuoles, discharging contents to exterior
Animal cells maintain equilibrium by using transmembrane pumps to expel solutes (like Na+ ions drawing H2O in cell)
Turgor pressure keeps plants from wilting and helps drive their movements
How does a transporter mediate passive transport?
Through conformational changes
Ex: glucose transporter will randomly switch between conformation depending on the concentration gradient for the direction (more glucose outside of cell when full and inside cell when hungry)
What are the 3 types of active transports?
gradient-driven pump, ATP-driven pump, light-driven pump
Give examples of active transports
In animal cells, ATP-driven Na+ pump transports Na+ out of the cell and creates an Na+ gradient that powers the gradient-driven pump
In plants, fungi, and bacteria, ATP-driven H+ pump transports H+ out of the cell and creates an H+ gradient that powers the gradient-driven pump
Explain the Na+ pump
Na+ pump uses energy supplied by ATP hydrolysis from the phosphate that is released, undergoes series of conformational changes
Na+-K+ ATPase = Na+-K+ pump
Operates in the plasma membrane
Na+ difference and the resting potential result in a large Na+ electrochemical gradient that is an energy store for operating other gradient-driven pumps
What inhibits the Na+ pump and by doing what?
Ouabain blocks K+ binding
Explain the significance of Ca2+ pumps
Ca2+ is important for cell functions but has a lower concentration than Na+
The low concentration (done by plasma membrane and ER membrane) makes the cell sensitive to an increase in Ca2+ concentration
Ca2+ binds and regulates many proteins
Influx of Ca2+ will regulate muscle contraction
Ca2+ pump only binds Ca2+, no second ion
What are the types of active transporters? Give an example of each
Antiport - Na+-H+ exchanger uses Na+ electrochemical gradient to pump H+ cells out of cell (to control cytosolic pH)
Symport - glucose-Na+ symport transports glucose from lumen to epithelial cells and use Na+ gradient to transport glucose against its gradient
What are the two types of glucose transporters?
Active glucose-Na+ transporter = apical epithelial cells that transport glucose into cells
Passive glucose uniport transporter = basal and lateral epithelial cells that transport glucose to bloodstream
Explain the H+ gradient in plants, fungi, and bacteria
They use H+ pumps instead of Na+ pumps
H+ pump creates proton gradient for symporters to transport sugar and amino acids into cell
H+ pump creates an acidic environment outside of the cell and used in organelle membranes to acidify interior of organelle (lysosomes)
What is important about ion channels?
They are ion-selective so they select based on size/diameter, charge, and amino acid side chains (water molecules attach to the ions and flow depends on electrochemical gradient)
They are gated so they open due to a special stimulus and close quickly
PUMPS ESTABLISH GRADIENT
Explain the electrochemical gradient for K+
Na+-K+ pump establishes high Na+ concentration outside of cell and high concentration of K+ inside cells
K+ will move out of cells via K+ leak channels until electrochemical gradient for K+ reaches zero
K+ leak channels are MAIN CHANNELS OPENED DURING RESTING STATE
What is the Nernst equation? What happens when there is a 10x change in an ion’s concentration?
V= 62 log(sub 10)*(Co/Ci)
It would change the membrane potential by 62 mV
What is the patch-clamp technique?
It is a technique that can be used to record the ion activity of a channel through a recording
A microelectrode extracts a part of the plasma membrane containing an ion channel and puts it into an apparatus to record the electrical current of the channel which shows that they are all or none (fully opened or fully closed)
What are the types of ion-gated channels?
- voltage gated (responds to membrane potential)
- ligand-gated (responds to ligand binding)
- mechanically-gated (responds to mechanical stress)
Give examples of a mechanically-gated channel
Auditory hair cells
Touch-sensitive Mimosa pudica are mechanically-gated and voltage-gated
Explain voltage-gated ion channels
Voltage-gated ions open due to small changes in membrane potential –> flow of ions further change the membrane potential –> new membrane potential activates or inactivates other voltage-gated channels (circuits couple ion channel activities)
Explain cell signaling of a neuron
Dendrites receive information, cell body processes the information, and the axon transmits the information to the terminal axon branches
Explain the action potential of a neuron
Initial stimulus = Voltage-gated Na+ channels open allowing Na+ to flow into the cell and cause a membrane potential change make the inside more positive/less negative –> depolarization
More Na+ flowing in then action potential will be reached and flow until electrochemical gradient of Na+ reaches 0
Channels then stay inactive until the membrane returns to the resting potential
What is significant about voltage-gated Na+ channels?
They are able to flip from one conformation to another depending on the membrane potential/action potential
Explain the significance of voltage-gated K+ channels
Voltage-gated K+ channels open in response to depolarization created by the voltage-gated Na+ channel
K+ ions will flow through voltage-gated K+ channels and allow the cell to return to its resting state (K+ leak channels not involved)
Na+-K+ pumps will then restore the concentration gradients of Na+ and K+ in the resting cell
Explain the significance of voltage-gated Ca2+ channels
Voltage-gated Ca2+ channels are located at nerve end terminals where they convert electrical signals into chemical signals
Neurotransmitters are stored in synaptic vesicles that can cross the synaptic cleft with the triggering of voltage-gated Ca2+ channels
What is transmitter-gated ion channels?
They couple ion receptors
They are a subclass of ligand-gated ion channel where neurotransmitters bind to the neurotransmitter receptor on the post-synaptic cell
Give an example of a transmitter-gated ion channel
ACh receptor in plasma membrane of skeletal muscle cells open when ACh neurotransmitter binds to receptor
What is the function of curare?
Blocks excitatory of ACh receptors resulting in muscle paralysis
What is the function of psychoactive drugs?
Affect synaptic signaling by binding to neurotransmitter receptor
What is the function of strychnine?
Blocks inhibitory glycine receptors
What is the function of GABA-gated Cl- channels?
inhibitory synaptic signaling
What is the function of prozac?
Blocks Na+ symport for serotonin uptake
What is oxidative phosphorylation?
Membrane-based process that drives the formation of ATP by transferring electrons from food molecules to O2
Occurs in the mitochondria and depends on the ETC
ADP + phosphate –> energy conversion in inner membrane –> ATP
Explain the first step of ATP formation via membrane
High energy electrons (from oxidation of food, sunlight, or other chemical sources) transferred along the ETC
Electron transfers released, energy is used to pump protons across membrane and generate an electrochemical gradient (a form of stored energy)
Explain the second step of ATP formation
Protons flow back down their electrochemical gradient through the ATP synthase which will catalyze the energy-requiring synthesis of ATP from ADP and phosphate
What is chemiosmotic coupling?
Using energy from stored in the transmembrane proton gradient to drive energy-requiring processes like ATP synthesis and transport of a molecule across the membrane
What is endosymbiosis?
When one organism lives inside another organism
What makes mitochondria special?
It can change shape, location, and number according to what the cell needs
What is the structure of the mitochondria?
- matrix
- inner membrane
- outer membrane
- intermembrane space
How is ATP produced from high-energy electron generation?
It is produced by the flow of electrons from burning foodstuff
The high-energy electron is provided by the activated carriers generated by glycolysis and the citric acid cycle
Pyruvate produced by glycolysis and fatty acids from fats can enter intermembrane space through porins, transported across inner membrane into matrix where they are converted into acetyl-CoA and is oxidized to CO2 via citric acid cycle
Some of this energy is saved by NADH and FADH2
Why is the matrix significant?
It only contains molecules that were selectively transported across the inner membrane
Explain stage 1 of chemiosmotic coupling
Pyruvate and fatty acids enter intermembrane space then transported across inner membrane to matrix were it is converted into acetyl-CoA
Acetyl-CoA broken down in the citric acid cycle to make activated carriers NADH and FADH2 which donate their electrons to the ETC and become oxidized NAD+ and FAD
Electron is passed along the ETC to O2 and form H2O
A proton gradient is generated during electron transport and energy can be used to make ATP via ATP synthase
What are the three ETC complexes in order by which the receive electrons?
- ATP dehydrogenase complex
- Cytochrome C reductase complex
- Cytochrome C oxidase complex
Explain the process of the ETC complexes
High energy carrier like NADH is donated to the NADH dehydrogenase complex where the electrons are extracted from NADH and make H- which is converted into H+ and 2 electrons (these electrons are used
electron carriers to power the movement throughout the complexes)
Electrons then combine with O2 and make H2O
What is the proton motive force?
Sum of forces generated by membrane potential and pH gradient which are works in the same direction
Aka electrochemical H+ gradient
How does ATP synthase produce ATP?
It is located in the inner membrane of the mitochondria where movement of the protons creates mechanical motion of the stalk which drives ATP synthesis
What happens when the proton gradient is small?
ATP synthase will function in reverse like how ATPase pumps protons to intermembrane space
Direction of ATP synthase depends on the electrochemical H+ gradient
What is true about the concentration of ATP to ADP?
The concentration of ATP must be kept 10x higher than the concentration of ADP
What is the difference between NADH and FADH2 in ATP synthesis?
NADH produced during citric acid cycle pass their high energy electron to the NADH hydrogenase
FADH2 can bypass the NADH hydrogenase complex and pass its electrons to the membrane-embedded carrier, ubiquinone
Explain the role of redox reactions in the ETC
What is the movement of the electrons?
Proteins of the regulatory chain guide the electrons to move from one complex to the next in a series of redox reactions
Electrons pass from carriers with low (high G, low redox potential) affinity with carriers with high affinity (low G, high redox potential)
Which carrier in the ETC has the highest redox potential?
cytochrome C oxidase
What are the electron carriers in each ETC complex?
- NADH hydrogenase = uses an iron-sulfur center
- Cytochrome C reductase = iron in a heme group bound to a cytochrome protein
- Cytochrome C oxidase = uses copper atom in a heme group
What is the terminal electron acceptor?
O2
Why is the cytochrome C oxidase complex important?
At the end of the ETC, it holds the O2 until all the electrons are received to reduce it to 2H2O
What is the importance of O2 in respiration?
O2 supports oxidative phosphorylation in animals, plants, and aerobic bacteria
What is the function of chloroplasts?
They capture light energy and use it to produce ATP and NADPH
It produces almost all of plant’s amino acids and synthesizes fatty acids, purines, and pyrimidines
Describe the structure of the chloroplast
Highly permeable outer membrane, less permeable inner membrane, inner membrane is surrounded by large space called stroma which is analogous to the mitochondrial matrix
What makes the stroma different from the mitchondrial matrix?
It doesn’t contain molecular machinery needed for the generation of energy
Where is ATP energy contained in photosynthesis?
Light-capturing systems, ETC, and ATP synthase all convert light energy into ATP during photosynthesis and this is all contained in thylakoid membrane (arranged in stacks called grana)
What is stage 1 of photosynthesis?
Aka light-dependent reactions
Similar to the oxidative phosphorylation
ETC in thylakoid membrane harnesses energy from the electron transport to pump H+ into thylakoid space, resulting in H+ gradient that drives the synthesis of ATP by ATP synthase
High energy electron is donated to photosynthetic ETC which is supplied by the chlorophyll that has absorbed light
What is stage 2 of photosynthesis?
ATP and NADPH produced in stage 1 are used to drive the production of sugars from CO2
Carbon fixation reactions begin in chloroplast stroma where they generate 3-carbon sugar called glyceraldehyde-3-phosphate (DO NOT DIRECTLY REQUIRE SUNLIGHT)
Sugar produced is exported to cytosol to produce organic molecules in leaves to nourish the plant
What light wavelength does chlorophyll absorb?
Red and blue wavelengths
High energy state is…
UNSTABLE
Excited chlorophyll will rapidly release excess energy and return to more stable, unexcited state
What are the large multiprotein complexes that chlorophyll are held in?
Photosystems that contain antenna complexes that capture light energy and convert it into chemical energy
What is the antenna complex?
Hundreds of chlorophyll are arranged so that light energy captured by 1 chlorophyll can be transferred to neighboring one
What is the chlorophyll special pair and where is it found?
Chlorophyll dimer that holds electrons at slightly lower energy than other chlorophyll molecules
If energy is accepted by a special pair then will be effectively trapped
Special pair is only found in REACTION CENTER
Explain photosystem II
1st photosystem
Absorbs light energy, reaction center passes electrons to mobile electron carrier PLASTOQUINONE which transfer high energy electron to H+ pump and uses electrochemical H+ gradient to drive production of ATP by ATP synthase in thylakoid
Explain photosystem I
2nd photosystem
Also captures light energy, reaction center passes its high-energy electron to a different mobile electron carrier (protein) called FERREDOXIN which brings them into an enzyme that used electrons to reduce NADP+ to NADPH
Where does photosystems II and I occur?
In the thylakoid membrane aka Stage 1 of photosyntehsis
What do the two photosystems produce?
Photosystem II = ATP
Photosystem I = NADPH
Both are required for carbon fixation in stage 2 of photosynthesis
What is the final electron acceptor of Stage 1 of photosynthesis?
NADP+ (instead of O2)
Where do stage 1 and 2 of photosynthesis occur?
Stage 1 occurs in the thylakoid membrane
Stage 2 occurs in the stroma (matrix) of the chloroplast
What is consumed, released, and synthesized in stage 1?
Light and H2O are consumed, O2 is released and ATP and NADPH are synthesized
What is consumed and synthesized in stage 2?
NADPH, ATP, CO2 are consumed to synthesize glyceraldehyde-3-phosphate
What does the porphyrin ring in the chlorophyll hold?
An Mg molecule
What surrounds the porphyrin ring of the chlorophyll?
Excitable electrons in cloud about the porphyrin ring of chlorophyll
Where does photosystem II get its electron from to restore the special pair in the reaction center?
From splitting a H2O molecule and generating 4 H+ and O2
Where does photosystem I get its electron from to restore the special pair in the reaction center?
From photosystem II via plastocyanin
What occurs in stage 1 of the Calvin cycle?
CO2 fixation
3 CO2 molecules with the Rubisco enzyme are added and make 6 of the 3-phosphoglycerate
What occurs in stage 2 of the Calvin cycle?
CO2 reduction
6 ATP is consumed, releasing 6 ADP and making 6 of the 1,3-biphosphoglycerate then 6 NADPH is consumed, releasing 6 NADP+ and 6 phosphate making 6 glyceraldehyde-3-phosphate
What occurs in stage 3 of the Calvin cycle?
Regeneration of Ribulose 1,5-Biphosphate (RuBP)
One of the 6 glyceraldehyde-3-phosphate is released for use elsewhere
5 glyceraldehyde-3-phosphate releases 2 phosphates and consumes 3 ATP which also releases 3 ADP making 3 of ribulose 1,3-bisphosphate
