Term
| What goes on inside the mitochondria? |
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Definition
| Pyruvate oxidation, krebs cycle, electron transport chain, chemiosmosis ATP synthase. |
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Term
| How do cells communicate? |
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Definition
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Term
| What happens in pyruvate oxidation? |
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Definition
| Pyruvate is converted into carbon dioxide and a two-carbon molecule called acetyl-CoA. For each molecule of pyruvate converted, one molecule of NAD+ is reduced to NADH, again to carry electrons that can be used to make ATP. Remember that two pyruvate molecules result from each glucose. |
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Term
| What, generally, happens during glycolysis and where does it occur? |
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Definition
| Glucose molecules are split during glycolysis and it occurs outside the mitochondria. It is a ten reaction biochemical pathway that produces ATP by substrate level phosphorylation. The enzymes that catalyze the glycolytic reactions are in the cytoplasm of the cell, not associated with any membrane or organelle. For each glucose molecule, two ATP molecules are used up early in the pathway, and four ATP molecules are produced by substrate-level phosphorylation. The net yield is two ATP molecules for each molecule of glucose catabolized. In addition, four electrons are harvested from the chemical bonds of glucose and carried by NADH for oxidative. Glycolysis yields two energy-rich pyruvate molecules for each glucose entering the pathway. |
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Term
What is fermentation and why is it preferred to respiration?
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Definition
| Cells that cannot utilize an alternative electron acceptor for respiration must rely exclusively on glycolysis to produce ATP. Under these conditions, the electrons generated by glycolysis are donated to organic molecules in a process called fermentation. This process recycles NAD+, the electron acceptor that allows glycolysis to proceed. Bacteria carry out more than a dozen kinds of fermentation reactions, with various organic molecules. Often the reduced organic compound is an organic acid. This process recycles NAD+ by the oxidation of NADH and reduction of an organic molecule. In yeast, pyruvate is decarboxylated, then reduced to ethanol as NADH is oxidized to NAD+. In animals, pyruvate is reduced to lactate as NADH is oxidized. |
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Term
| How to cells communicate with each other? |
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Definition
-Signals- which vary in typed based on the distance the signal travels from source to receptor.(direct contact, paracrine signaling, endocrine signaling, synaptic signaling)
-Signal Transduction Pathways-(intracellular events that result from a receptor binding to a signal molecule) are key and lead to cellular responses.
-Phosphoylation is crucial in controlling protein functions. (proteins can be controlled by phosphate added by kinase and removed by phophatase enzymes) |
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Term
| What broad types of receptors are there? |
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Definition
| Receptors proteins are classified by both function and location. Can be cell surface a.k.a membrane receptors, or they intracellular. |
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Term
| What types of membrane receptors are there and what traits do they share? |
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Definition
Membrane receptors are transmembrane proteins that transfer information across the membrane, but not the signal molecule.
Channel linked receptors
Enzymatic receptors
G protein coupled receptors |
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Term
| What are channel linked receptors? |
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Definition
| they are membrane receptors that are chemically gated ion channels and they allow specific ions to pass through a central pore. |
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Term
| What are enzymatic receptors? |
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Definition
| They are enzymes activated by binding a ligand; these enzymes are usually protein kinases. They are membrane receptors. |
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Term
| What are G protein coupled receptors? |
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Definition
| They interact with G proteins that control the function of effector proteins: enzymes or ion channels. They are membrane proteins. |
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Term
| What types of receptors produce second messengers, and what are second messengers? |
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Definition
| Most G coupled protein receptors and some enzymatic receptors produce second messengers-which relay messages in the cytoplasm. |
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Term
| How do G protein-coupled receptors transduct signals? |
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Definition
-G proteins are active bound to GTP and inactive bound to GDP. Receptors promote exchange of GDP for GTP.
-The activated G protein dissociates into two parts, Gα and Gβγ, each of which can act on effector proteins.
-Gα also hydrolyzes GTP to GDP to inactivate the G protein.
-Effector proteins can produce second messengers
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Term
| What are two common effector proteins and what second messengers do they produce? |
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Definition
| adenylyl cyclase and phospholipase C, and they produce the second messengers known as cAMP, and DAG and IP3, respectively. |
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Term
| Other than cAMP, and DAG and IP3, what is another second messenger and what does it bind to? |
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Definition
| Ca2+ is also a second messenger. It is released by IP3 binding to channel linked receptors in the ER. It can also bind to a cytoplasmic protein known as calmodulin, which in turn activates other proteins, producing a variety of responses. |
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Term
| Can different receptors produce the same response? |
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Definition
| Yes, different receptors can activate the same effector, which will produce the same second messenger leading to the same response. |
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Term
| When does a different receptor lead to a different effect? |
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Definition
| Different receptor subtypes or isoforms lead to different effects in different cells. |
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Term
| Different receptor types activate the same signaling pathways. Why and give an example |
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Definition
| Different receptor types such as G protein-coupled receptors and receptor tyrosine kinases can activate the same signaling pathways. |
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Term
| How can there be intracellular receptor proteins? |
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Definition
| Because many cells signals are lipid-soluble and readily pass through the plasma membrane and bind to receptors in the cytoplasm and nucleus. |
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Term
| Where do steroid hormones bind and what happens after they bind? |
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Definition
| They bind to cytoplasmic receptors and are then transported to the nucleus. These receptors are thus called nuclear receptors. |
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Term
| What are nuclear receptors? |
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Definition
| They are receptors which can directly affect gene expression, usually activating transcription of the genes they control. Nuclear receptors have three functional domains: hormone binding, DNA-binding, and transcription-activating domains. Ligand binding changes receptor shape, releasing an inhibiting inhibitor occupying the DNA-binding site. Some intracellular receptors activate cellular enzymes and do not affect gene expression. |
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Term
| Through what two types of receptors can signal transduction occur? |
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Definition
| Through G Protein-Coupled Receptors. or Receptors Kinases |
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Term
| What are receptor kinases? |
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Definition
Protein kinases phosphorylate proteins to alter protein function.
-The receptor tyrosine kinases (RTK) influence the cell cycle, cell migration, cell metabolism, and cell proliferation.
-Alterations to the function of these receptors and their signaling pathways can lead to cancers in humans and other animals.
-RTK's recognize hydrophilic ligands, and form a large class of membrane receptors in animal cells.
-Plant receptor kinases are similar in structure and function to receptor tyrosine kinases but they are serine-threonine kinases
-They have relatively simple structure consisting of a single transmembrane domain (anchors them in membrane), an extracellular ligand binding domain, and an intracellular kinase domain.
-Kinase domain contains the catalytic site of the receptor, and acts as a protein kinase that adds phosphate groups to tyrosines. |
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Term
| How are receptor kinases activated? |
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Definition
1. A hydrophilic ligand binds to the extracellular receptor.
2. Two receptors associate (dimerize, are next to each other) and phosphorylate each other (autophosphorylation)
3. Phosphorylated protein creates cellular response and binds to phosphotyrosine on receptor. Receptor can phosphorylate other response proteins.
4. Signal transduction pathway has begun, as response proteins have binded and because receptor phosphorylation of response proteins. |
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Term
| What is autophosphorylation? |
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Definition
| After a ligand has binded to the extracellular specific receptor, two of the receptor ligand complexes of RTK associate together (dimerization) and phosphorylate each other. This autophosphorylation creates binding domains for other proteins. |
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Term
| How is a signal propagated in the cytoplasm from a RTK? |
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Definition
| One way is via proteins that bind specifically to phophorylated tyrosines in the receptor. When the receptor is activated, regions of the protein outside the catalytic site are phophorylated. This creates docking sites for proteins that bind specifically to phosphotyrosine. These proteins can initiate intracellular events to convert the signal from the ligand into a response. |
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Term
| What is the structure of DNA? |
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Definition
1. A five carbon sugar
2. a phosphate (PO4) group
3. A nitrogen containing (nitrogenous) base. The base may be a purine (adenine, A, or guanine, G) a two ringed structure, or a pyrimidine (thymine, T, or cytosine C), a single-ringed structure.
4. They are in a double helix, two strands with phosphodiester backbone, and base pairing. (A-t or u) and C with G curvy with curvy |
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Term
| What is the structure of RNA? |
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Definition
| Same as DNA except RNA contains the pyrimidine uracil (U) in place of thymine. |
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Term
| What do you need to do to be a multicellular organism? |
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Definition
1. Division of Labor
2. Structure
3. Cell communication
4. energy-ATP so 1-3 can work
5. Lack of flexibility creativity in cells, i.e. brain cells do not change |
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Term
| In multicellular organism why are cells organized in specific ways with cell junctions? |
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Definition
| So that the cells can function as tissues |
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Term
| How long do cell junctions last? |
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Definition
| the last a long time or are permanent. |
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Term
| What are the three categories of cell junctions, and how does each enable a cell? |
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Definition
1. Anchoring Junction- connect adjacent cells, provide strength and flexibility
2. Communicating Junction-allow cytoplasm to move between cells.
3. Tight junction- connect the plasma membranes of adjacent cells into sheets and prevent small molecules from leaking out of the cells. |
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Term
| What is required for a multicellular organism to organize tissues? |
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Definition
1. Cells must have distinct identity
2. Cells must be connected |
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Term
| How is cell identity conversed in multicellular organisms? |
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Definition
Cell surface markers.
1. glycolipids
2. MHC (major histocompatibility complex) proteins. (self and non self) |
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Term
| What is the structure and function of tight junctions? |
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Definition
They are tightly bound, leakproof, fibrous protein seal that surrounds cell. Adjacent plasma membranes are connected by tight junction proteins.
It is an organizing junction; holds cells together such that materials pass through not between the cells. |
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Term
What is the structure and function of communicating junctions? And name two types.
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Definition
A Gap Junction, and a communicating junction (plasmodesmata)
A. Gap junction is six transmembrane connexon proteins creating a pore that connects cells. Communicating junction: allows passage of small molecules from cell to cell in a tissue.
B. Plasmodesmata- cytoplasmic connections between gaps in adjoining plant cell walls. Communicating junction between plant cells.
All cell junction have two adjacent connexons forming an open channel between cells/adjacent plasma membranes.
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Term
What is the structure and function of anchoring junctions? And name two types.
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Definition
A. Desmosome (can be spot two cells connected, hemi connected to noncellular material, or belt or cells connected with actin), intermediate filaments of cytoskeleton linked to adjoining cells through cadherins. Anchoring junction:binds cells together.
B. Adherens junction- transmembrane fibrous proteins. Anchoring junctionL connects extracellular matrix to cytoskeleton. |
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Term
| How can protein kinase cascades amplify a signal? |
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Definition
| mitogen activated protein (MAP) kinases are activated by a signaling module called a kinase(phosphorylation) cascade. This module is a series of protein kinases that phosphorylate each other in succession. This cascade can amplify a signal, producing a large response from a few original molecules. Usually MAP kinase ends in activation of gene expression (transcription factors). Ras activates the first kinases by exchanging GDP for GTP. |
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Term
| How and where does DNA replication begin? |
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Definition
| DNA replication begins at one or more sites called origins of replication. Initiator proteins recognize and bind to the origin, forming a complex that opens the helix to expose single-stranded templates used for the process of building a new strand. |
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Term
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Definition
| It is the enzyme that matches the existing DNA bases with complementary nucleotides and then links the nucleotides together to make the new strand. It adds bases to the 3' end of existing strands. All DNA polymerases need a primer to begin synthesis; they cannot begin without a strand of DNA base-paired to the template. The primers are usually synthesized by RNA. |
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Term
| How is the genetic code read? |
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Definition
| In groups of three (codons) bases. These three bases correspond to specific amino acids. |
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Term
| What happens during transcription? |
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Definition
| The enzyme RNA polymerase synthesizes an RNA strand using DNA as a template. Only one strand of the DNA, the template strand, is copied; the other strand, which has the same sequence as the transcribed RNA, is called the coding strand. RNA Polymerase is the enzyme complex used. |
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Term
| What happens during translation? |
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Definition
| mRNA strand is changed through ribosomes and transfer RNA into 20 essential amino acids which then make proteins |
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Term
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Definition
| The DNA that can be transcribed and translated. A sequence of DNA nucleotides on a chromosome that encodes a protein, tRNA, or rRNA molecule, or regulates the transcription of such a sequence. |
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Term
| When is an atom oxidized? |
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Definition
| When an atom loses electrons |
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Term
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Definition
| When it accepts electrons. |
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Term
| What reactions do cells use to take energy from food sources and convert it to ATP? |
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Definition
| redox reactions. Oxidation reactions coupled with reduction reactions. They are enzyme facilitated reactions. |
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Term
| Describe the two mechanisms that allow cells to make ATP from the oxidation of glucose. |
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Definition
1. Substrate-level phosphorylation, ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate, or substrate. During glycolysis, the initial breakdown of glucose, the chemical bonds of glucose are shifted around in reactions that provide the energy required to form ATP by substrate level phosphorylation.
2. In oxidative phosphorylation, ATP is synthesized by ATP synthase, using energy from a proton (H+) gradient. ATP synthase uses the energy from the photon gradient to catalyze the reaction (ADP + pi= ATP)
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Term
| How is the proton (H+) gradient formed? |
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Definition
| It is formed by high energy electrons from the oxidation of glucose passing down an electron transport chain. |
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Term
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Definition
| It is a series of chemical reactions that occur in the cell cytoplasm. Glucose yields 2 pyruvate, 2 NADH, and 2 ATP. Glucose is split. |
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Term
| How is a glucose molecule split? |
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Definition
Through glycolysis.
1. Glycolysis begins with the addition of energy. Two high energy phosphates from two molecules of ATP are added to the 6 carbon molecule glucose, producing a 6 carbon molecule with two phosphates.
2. Then, the 6 Carbon molecule with two phosphates is split in two, forming two 3-carbon sugar phosphates (G3P).
3. An additional inorganic phosphate is incorporated into each 3-carbon sugar phosphate. An Oxidation reaction converts the two sugar phosphates into intermediates that can transfer a phosphate to ADP to form ATP. The oxidation reactions also yield NADH giving a net energy yield of 2 ATP and 2 NADH and 2 pyruvate. |
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Term
| What reaction is links glycolysis and the reactions of the Krebs cycle? |
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Definition
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Term
| What happens when pyruvate is oxidized? |
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Definition
| In the mitochondria pyruvate is oxidized to produce acetyl-CoA and CO2. pyruvate + NAD+ + CoA-> acetyl-CoA + NADH + CO2 + H+. Acetyl-CoA feeds into the Krebs cycle. |
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Term
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Definition
pyruvate is oxidized in a series of nine reactions, in the matrix of mitochondria. This occurs in three segments
1. Acetyl-CoA plus oxalocetate- this reaction (condensation) produces the 6-Carbon citrate molecule.
2. Citrate Rearrangement and decarnoxylation-Five more steps (Isomerization twice, the frist oxidation, the second oxidation, substrate-level phosphorylation), reduce citrate to a 5-carbon intermediate and then to 4 carbon succinate. During these reaction, two NADH and one ATP are produced
3. Regeneration of oxaloacetate-Succinate undergoes three additional reactions (The third oxidation, Regneration of Oxaloacetate and the fourth oxidation) to become oxaloacetate. During these reactions, one NADH is produces; in addition, a molecule of flavin adenine dinucleotide (FAD), another cofactor, becomes reduced to FADH. |
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Term
| What happens in the electron transport chain? |
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Definition
NADH molecules carry their electrons to the inner mitochondrial membrane and they transfer the electrons to a series of membrane associated proteins collectively called the electron transport chain.
First proteins that receives NADH is enzyme called NADH dehydrogenase a mobile electron carrier (ubiquinone, and cytochrome) then transports the electrons to the other two enzymes/proteins (bc1 complez, and cytochrome oxidase complex).
The three protein complexes use portions of the electrons energy to pump protons out of the matrix and into the intermembrane space. The electrons are finally used to reduce oxygen forming water.
This chains produces a concentration gradient of protons across the inner membrane. This electrochemical gradient is a form of potential energy that can be used by ATP synthase (which is responsible for reentry of protons to the phosphorylation of ADP to form ATP.
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Term
| What is a light reaction? |
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Definition
| Light comes into the chlorophyll, pigments get energy from photons which go to reaction center that is two photosystems which produce nadph and atp. Proton gradient is then used to make ATP sythase work aka ATP. |
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Term
| What goes into the nucleus? |
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Definition
| Proteins, DNA and RNA polymerases, polymerase subunits, helicases, regulatory proteins (factose), some ligands (steroids), ATP, GTP..etc, histone proteins |
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Term
| What goes out of the nucleus? |
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Definition
| The messenger RNA, rRNAs, tRNAs, maybe some energy traffic like ATP, GTP..etc |
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Term
| What happens in the Calvin cycle? |
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Definition
Organic molecules are synthesized from inorganic carbon (CO2).
-CO2, ATP, and NADPH are required.
-It occurs in three stages: carbon fixation, reduction, and regeneration
a. Carbon fixation involves enzyme rubisco, combining CO2 and the five carbon ribulose 1,5 bisphosphate (RuBP). The resulting compound splits into two 3-carbon 3-phosphoglycerates (PGA)
b. Reduction converts the 3-carbon PGA to glyceraldehyde 3-phosphate (G3P) in a series of reactions that use ATP and NADPH.
c. Regeneration involves using G3P to synthesize more RuBP. |
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Term
| How many turns of the calvin cycle does it take to fix enough carbon to have two excess G3P's thats can be used to make one molecule of glucose? |
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Definition
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Term
| Eukaryotic genes contain introns and exons, when does splicing occur and how? |
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Definition
| It occurs after transcription, introns are splice by splicesomes which are snRNPs and recognizes introns. Introns all begin with the same 2-base sequence and end with another two that tag them for removal. |
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Term
| How many introns are in a gene? |
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Definition
| Some genes contain none, and some contain 50. So, it varies. |
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Term
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Definition
| A bifunctional molecule with one end that can form a bond to an amino acid and another end that can base-pair with mRNA. The tRNA charging reaction joins the carboxyl end of an amino acid to the 3' acceptor stem of its tRNA. |
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Term
| What is the function a ribosome? |
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Definition
| It decodes the transcribed message and forms peptide bonds. |
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