Biology 2060 Quiz Questions
What are the properties of neurons?
Neurons are specially adapted for the transmission of electrical signals. Cell body possesses the nucleus and organelles. Dendrites receive (and combine) signals. Axons conduct signals. Myelin sheath surrounds the axon in a discontinuous manner (form the nodes of Ranvier). Nerve cells can be very long (for example, a motor neuron's cell body in the spinal cord and the axon ends in your toes). An axon ends with terminal bulbs or synaptic knobs that transmit the signal through a specialized junction: the synapse.
What differences exist among bacterial and eukaryotic cells?
- Bacteria are small, eukaryotes are large - Bacteria do not have a nucleus or organelles, while eukaryotes do. - Bacteria have proteins similar to microtubules and microfilaments, but eukaryotes have proper microtubules and microfilaments. - Bacteria do not perform exocytosis or endocytosis, but eukaryotes do. - Bacteria have a cell wall made of peptidoglycan, while eukaryotes have varying cell walls (between plant and animal cells) - Bacteria divide via binary fission, while eukaryotes divide via mitosis and meiosis. - Bacteria have circular DNA, while eukaryotes have linear DNA. - Bacteria have minimal RNA processing, while eukaryotes have extensive RNA processing. - Bacteria have bacterial type transcription initiation, while eukaryotes have eukaryotic type transcription initiation. - Bacteria have bacterial type RNA polymerase, while eukaryotes have eukaryotic type RNA polymerase. - Bacteria have a 70S ribosome with 55 proteins, while eukaryotes have a 80S ribosome with 78 proteins. - Bacteria have bacterial type ribosomal RNAs, while eukaryotes have eukaryotic type ribosomal RNAs. - Bacteria have bacterial type translation initiation, while eukaryotes have eukaryotic type translation initiation.
How do channels function?
- Channel proteins form hydrophilic transmembrane channels across the membrane e.g. Ion channels are specific for one of the following: calcium ions, potassium ions, sodium ions, chloride ions moves 1 million ions per second! - Regulated by changes in voltage, ligand-binding, and mechanical forces (i.e. stretching) e.g. Nerve cells with BEST.
What are the properties of energetics?
- First Law of Thermodynamics: Energy is Conserved - Second Law of Thermodynamics: Reactions have Directionality - Entropy (randomness) - The change in the free energy is the maximum amount of work that a thermodynamic system can perform in a process at constant temperature, and its sign indicates whether a process is thermodynamically favorable or forbidden. - Exergonic reactions (spontaneous, energy is released, products have less energy than reactants) versus endergonic reactions (non-spontaneous, energy is absorbed from the environment, products have less energy than the reactants).
What differences exist among plant and animal cells?
- Plant cells have cell walls, animal cells do not. - Consequently, plant cells are usually rectangular and animal cells are typically round. - Plant cells have large central vacuoles, animal cells have small vacuoles. - Plant cells have chloroplasts, animal cells do not. - Plant cells do not have lysosomes, animal cells do.
What is the endosymbiotic theory of eukaryotic origin?
- Prokaryotic cell engulfs aerobic bacteria - Rather than digesting them, the bacteria remain, as symbionts, benefiting the host cell by removing harmful O2 and helping in the production of ATP. - As interdependence between the aerobic bacterium and the host cell grows, the bacterium becomes the mitochondrion. - To get plant cells, this happened twice. Some of these cells also engulf and keep blue-green algal cells which become chloroplasts.
What is the autogenous theory of eukaryotic origin?
- The eukaryotic cell evolved directly from a single prokaryote ancestor, likely archaea, through compartmentalization of functions arising from invaginations of the prokaryotic plasma membrane. - The endoplasmic reticulum (ER), Golgi, and the nuclear membrane, and of organelles enclosed by a single membrane - According to this theory, mitochondria and chloroplasts have evolved within by compartmentalizing plasmids within vesicles from the plasma membrane.
How does DNA proof-reading work?
If an incorrect base is inserted during DNA replication, the 3′→5′ exonuclease activity that is part of the DNA polymerase molecule catalyzes its removal so that the correct base can be inserted. When DNA polymerase makes an error during replication, the mismatch is detected, causing rotation of the daughter strand out of the polymerase active site and into the exonuclease site. After removal of the incorrect base, the daughter strand continues to be synthesized.
What six steps occurs in the function of the sodium potassium pump?
1) 3 Na+ from inside the cell bind to E1 2) Na+ binding triggers autophosphorylation of the α subunit using ATP and ADP is released 3) A conformational change to E2 expels 3 Na+ to the outside of the cell 4) 2 K+ from outside the cell bind to E2 5) K+ binding triggers dephosphorylation, cauing a conformational chnage back to E1. 6) K+ expelled to the inside as ATP binds and the pump returns to initial state.
What happens at a chemical synapse?
In a chemical synapse, the presynaptic and postsynaptic neurons are separated by a gap, the synaptic cleft. Neurotransmitter molecules that are kept in the terminal bulbs or synaptic knobs are secreted into the synaptic cleft and then bind to receptors on the postsynaptic neuron. This generates a signal to stimulate or inhibit a new action potential.
What are the major basic aspects of the chemical components of the cell?
1) Carbon has the ability to make four bonds (aka it has four valence electrons). 2) C can easily bond with H, N, or O. 3) Carbon can form double or triple bonds. 4) Carbon atom has tetrahedral structure, can form stereoisomers 5) There are L and D forms of compounds 6) Water molecules are polar 7) Water molecules form hydrogen bonds 8) Water molecules have high surface tension, a high boiling point, and a high heat of evaporation. 9) Membrane lipids and proteins are not simply hydrophilic or hydrophobic but have regions of both, making them amphipathic. Ex/ amphipathic phospholipids. 10) The hydrocarbon chains of phospholipids are non-polar + hydrophobic and the heads are polar + hydrophilic. 11) The lipid bilayer is (3 to 4 nm X 2) 7 to 8 nm thick and forms the basic structure of the membrane. 12) The lipid bilayer is semi-permeable.
What are the main features of the cell's organelles?
1) Cell Membranes: - Semi-permeable - about 7-8 nm thick - made up of a lipid bilayer 2) Extracellular Boundaries - Plasmodesmata in plant cells - Extracellular matrix in animal cells 3) Ribosomes - site of protein synthesis, translation (mRNA to protein) - Free or associated with membranes (Rough endoplasmic reticulum: rER) - eukaryotes: 30 nm diameter 4) Nucleus - compartmentalizes genetic material - site of DNA synthesis (S) - site of RNA synthesis (transcription) - Contains a double membrane, nuclear pores, chromatin, and nucleolus. 5) Endomembrane System - A series of internal membranes consisting of the endoplasmic reticulum, golgi apparatus, and vesicles. These are structurally and functionally related. - All these membranes synthesize and secrete proteins, carbohydrates, and/or lipids 6) Lysosomes - Hydrolases (biochemical catalysts that use water to break a chemical bond) are commonly located in lysosomes. - Digest and dispose of unwanted protein, DNA, RNA, carbohydrates, and lipids. This is why the lysosome is commonly known as the recycling center of the cell. 7) Peroxisomes - Generate hydrogen peroxide as a by-product - Catalase catalyzes the decomposition of hydrogen peroxide to water and oxygen. 8) Chloroplasts - site of photosynthesis 9) Mitochondria - The outer membrane is much smaller than the inner membrane, causing the inner membrane to fold up, increasing the surface area. This allows for the production of energy (ATP). 10) Cytoskeleton - A 3D interconnected array of protein-based filaments, including microtubules, microfilaments, and intermediate filaments. - Plays a role in cell shape, movement, cell signaling, endocytosis, and mitosis.
What are three roles for chaperones in the mitochondria?
1) Chaperones keep the polypeptide partially unfolded after synthesis in the cytosol so that binding of the transit sequence and translocation can occur. 2) Chaperones drive the translocation itself by binding to and releasing from the polypeptide within the matrix, an ATP-requiring process and 3) Chaperones often help the polypeptide fold into its final conformation. Polypeptides synthesized on cytosolic ribosomes but destined for either the intermembrane space or the inner membrane of the mitochondrion require two separate targeting sequences (both located at the N-terminus).
What are the roles of cellular membranes?
1) Define boundaries (permeability barrier) 2) Sites of specific functions 3) Regulation of solute transport 4) Signal detection and transmission 5) Cell to cell communication
Name the six model organisms in biology.
1) E. coli 2) S. cerevisiae 3) Drosphila 4) C. elegans 5) Mus musculus (mice) 6) Arabidopsis
What are the cell cycle phases? How long are they?
1) G1 Phase (8-10 hours) 2) S Phase (5-6 hours) 3) G2 Phase (4-6 hours) 4) M Phase (2 hours)
What are the five levels of eukaryotic gene expression?
1) Genome (amplification or rearrangement of DNA segments, chromatin decondensation/condensation and DNA methylation). 2) Transcription. 3) Processing (and nuclear export) of RNA. 4) Translation (and targeting) of protein. 5) Posttranslational events (folding and assembly, cleavage, chemical group modifications and organelle import/secretion).
What are the five steps in aerobic cellular respiration?
1) Glycolysis 2) Pyruvate Oxidation 3) Kreb's Cycle 4) Electron Transport Chain 5) ATP Synthesis
What are the steps in DNA synthesis?
1) Initiation 2) Elongation 3) Termination
How is the initiation of transcription controlled in prokaryotes?
1) RNA polymerase binds to −35 and −10 sequences in the promoter via the σ subunit. 2) While tightly bound to the promoter, the polymerase pulls additional DNA toward itself ("scrunching"). This creates a larger region of unwound DNA and a short piece of RNA, which is eventually released. This repeats. 3) Eventually, a sufficiently long RNA is produced that the polymerase escapes the promoter, releasing the σ subunit.
How do substances cross membranes?
1) Simple Diffusion 2) Facilitated Diffusion 3) Active Transport
How do enhancers work?
1) The activator proteins bind to the enhancer elements, forming an enhanceosome. 2) Bending of the DNA brings the enhanceosome closer to the core promoter. The general transcription factor TFIID is in the promoter's vicinity. For the purpose of this figure, two of the protein subunits of TFIID, which will function as coactivators in step 3, are distinguished from the rest of the factor. 3) The DNA-bound activators interact with specific coactivators that are part of TFIID. This interaction facilitates the correct positioning of TFIID on the promoter. 4) The other general transcription factors and RNA polymerase join the complex, and transcription is initiated.
What are five motifs found in transcription factors?
1) The helix-turn-helix motif contains two alpha helices are joined by a short flexible turn. 2)The zinc finger motif consists of an alpha helix and a two segment, antiparallel beta sheet, all held together by the interaction of four cysteine residues (or two cysteine & two histidine residues) with a zinc atom. Zinc finger proteins normally contain a number of zinc fingers. 3)The leucine zipper motif contains an alpha helix that has a regular arrangement of leucine residues that interacts with a similar region in a second polypeptide to coil around each other. 4) The helix-loop-helix motif contains a short a helix connected to a longer a helix by a polypeptide loop interacts with a similar region on another polypeptide to create a dimer. 5) The homeodomain motif is a helix-turn-helix DNA-binding domain containing three alpha helices encoded by a 180 base-pair homeobox
How do proteins enter the mitochondrial inner membrane & intermembrane space?
1) The polypeptide is directed to a contact (translocation) site on the mitochondrion by a positively charged or amphipathic transit sequence. 2) Cleavage of the transit sequence by a peptidase in the mitochondrial matrix uncovers a highly hydrophobic second signal sequence. 3) This second signal sequence causes the polypeptide to be inserted into the inner membrane in the same way that mitochondrial encoded polypeptides are targeted to this membrane. 4) The remainder of the polypeptide is then moved across the membrane into the intermembrane space (or into the inner membrane for integral inner membrane proteins). 5) Cleavage by a second peptidase can release the polypeptide into the intermembrane space leaving the signal sequence behind in the inner membrane.
What is the four step cycle behind muscle contraction?
1) myosin binds loosely to actin filament; 2) the power stroke, a trigger of the conformational change associated with move of thick versus thin filament 3) binding of ATP leads to change in myosin and weakening of bond to actin (no ATP leads to rigour or stiffness). 4) ATP hydrolysis returns myosin to high energy state, ready for the next round of movement.
What are the five main cell behaviours?
1. Cell-cell communication 2. Cell shape changes 3. Cell movement 4. Cell proliferation (as in, they multiply and become more cells) 5. Cell death (apoptosis)
What six standar cellular processes require energy?
1. Synthetic work 2. Mechanical work 3. Concentration work 4. Electrical work 5. Heat generation 6. Bioluminescence
What is active transport?
A method of moving substances across the membrane against the concentration gradient. It occurs via proteins and requires energy. It is endergonic and produces a thermodynamically unfavorable difference in concentrations. Enables a cell to maintain a constant intracellular non-equilibrium concentration of specific ions etc. There are two types of active transport: Direct and indirect. Direct active transport involves a transport system coupled to an exergonic chemical reaction. Examples include the hydrolysis of ATP and the sodium/potassium pump. Indirect active transport involves the coupled transport of a solute S and ions. Examples include cotransport, symport, and antiport.
What is "feedback regulation"?
A process that allows a system to adjust itself by responding to incoming information. This process is used to control the activity of allosteric enzymes by downstream products.
What four steps drive how actin-based cell migration works?
Actin microfilaments (MFs) drive cell migration through cycles of 1) protrusion; 2) attachment; 3) translocation; and 4) detachment.
What are microfilaments and what do they do?
Microfilaments are two intertwined chains of F-actin. They are the smallest element of the cytoskeleton. Microfilaments are responsible for muscle contraction and cell migration
What are microtubules and what do they do?
Microtubules are are hollow tubes with walls consisting of 13 protofilaments. They are the largest element of the cytoskeleton. Microtubules maintain axons; maintain shape; orient cellulose microfibrils (in plants); mitotic and meiotic spindles for chromosome movements; and vesicle movement.
What are the adhesive junctions?
Adhesive junctions link adjoining cells to one another and the extracellular matrix. There are three types of adhesive junctions: Desmosomes, hemidesmosomes, adherens junctions. Although the various adhesive junction types are similar in structure and function, they contain distinct: 1) intracellular attachment proteins; and 2) transmembrane linker proteins. Desmosomes form strong points of adhesion between cells in a tissue such that two adjoining cells are separated by a thin space of 25-35 nm, the desmosome core, in which cadherin molecules mediate cell-cell adhesion. The plaques on the inner surfaces of cells joined by desmosomes have a mixture of intracellular attachment proteins (desmoplakins and plakoglobin) which interact with the tonofilament intermediate filaments. Hemidesmosomes connect a cell, through a plaque, to the basal lamina (ECM) by integrins. Hemidesmosomes interact with tonofilament intermediate filaments. Adherens junctions resemble desmosomes except two adjoining cells are separated by a thin space of 20-25 nm and connect to actin microfilaments in the cytoplasm. Adherens junctions called focal contacts can join a cell to the ECM, primarily through fibronectin receptors.
What can happen post-translation?
After the amino chain is made, many proteins undergo posttranslational processing (including removal of stretches of amino acids). 1) In prokaryotes, the N-formyl group is always removed in the mature protein and often the methionine and, sometimes, a number of N-terminal amino acids are cleaved away from the final protein product. 2) The protein hormone insulin provides an example of posttranslational processing. Proinsulin is converted to the active hormone by the enzymatic removal of a long internal section of polypeptide. The two remaining chains continue to be covalently connected by disulfide bonds connecting cysteine residues in insulin. 3) Recently discovered, the process of protein splicing (analogous to RNA splicing) removes inteins and splices the exteins together to make a mature protein.
How do the three major types of RNA work together for protein synthesis?
All three major types of RNA are involved in directing the formation of protein. 1) mRNAs carry the message from the DNA to the ribosome. 2) rRNAs are major structural components of the protein-synthesizing ribosome. 3) tRNAs act as adaptor molecules in aligning the amino acids according to the sequence present in the mRNA.
What is alternative splicing of mRNA & what are the consequences?
Alternative splicing is the utilization of different combinations of intron/exon splice junctions in pre-mRNA to produce messenger RNAs that differ in exon composition, thereby allowing production of more than one type of polypeptide from the same gene.
How is the trp operon regulated?
An example of genetic control in prokaryotes: the trp operon The trp operon includes five structural genes (trpE, trpD, trpC, trpB, and trpA) as well as promoter (Ptrp), operator (O), and leader (L) sequences. The structural genes are transcribed and regulated as a unit. The repressor protein, encoded by the trpR gene is inactive (cannot recognize the operator site) in the free form when tryptophan is not abundant. The polycistronic mRNA encodes for the enzymes of the tryptophan biosynthetic pathway. When complexed with tryptophan, the repressor is active and binds tightly to the operator, blocking access of RNA polymerase to the promoter and keeping the operon repressed.
What are the components of the replicon?
At a replicon, one strand of DNA is made in a continuous manner (the leading strand) and the other in a discontinuous manner (the lagging strand). DNA is made in only the 5-prime to 3-prime direction and the replication bubble opens the original double stranded DNA to expose both a 3-prime to 5-prime template (Leading strand template) and it complement. The lagging strand must be synthesized as a series of discontinuous segments of DNA. These small fragments are called Okazaki fragments and they are joined together by an enzyme known as DNA ligase.
How does the unique 'trp ribo-switch' mechanism function?
Attenuation depends upon the ability of regions 1 and 2 and regions 3 and 4 of the trp leader sequence to base pair and form hairpin secondary structures. A part of the leader mRNA containing regions 3 and 4 and a string of eight U's is called the attenuator. The region 3+4 hairpin structure acts as a transcription termination signal; as soon as it forms, the RNA and the RNA polymerase are released from the DNA. During periods of tryptophan scarcity, a ribosome translating the coding sequence for the leader peptide may stall when it encounters the two tryptophan (trp) codons because of the shortage of tryptophan-carrying tRNA molecules. Because a stalled ribosome at this site blocks region 1, a region 1+2 hairpin cannot form and an alternative, region 2+3 hairpin is formed instead. The region 2+3 base pairing prevents formation of the region 3+4 transcription termination hairpin and therefore RNA polymerase can move on to transcribe the entire operon to produce enzymes that will synthesize tryptophan. When tryptophan is readily available, a ribosome can complete translation of the leader peptide without stalling. As it pauses at the stop codon, it blocks region 2, preventing it from base pairing. As a result, the region 3+4 structure forms and terminates transcription near the end of the leader sequence and the structural genes of the operon are not transcribed (nor translated). This is example of a riboswitch, a mechanism which can control transcription and translation through interactions of molecules with an mRNA
How is the structure of the mitochondria connected to function?
Mitochondria have three membrane systems: outer membrane, inner membrane, and the thylakoids. All components necessary for photosynthesis are contained on/in the thylakoid membranes.
How do cilia and flagella work?
Cilia and flagella share a common structure, known as the axoneme, that is about 0.25 μm in diameter. The axoneme is connected to a basal body and surrounded by an extension of the cell membrane. Between the axoneme and the basal body is a transition zone in which the arrangement of microtubules in the basal body takes on the pattern characteristic of the axoneme. The axonemes of propulsive cilia and flagella have a characteristic " 9 + 2" pattern, with nine outer doublets of tubules and two additional microtubules in the center, often called the central pair. Adjacent outer doublets slide relative to one another. This sliding movement is converted to a localized bending because the doublets of the axoneme are connected radially to the central pair and circumferentially to one another and therefore cannot slide past each other freely. Bends propagate along the length of cilia or flagella, leading to a wave-like undulation that begins at the base of the organelle and proceeds toward the tip. During the sliding process, the stalks of the dynein arms attach to and detach from the B tubule in a cyclic manner. Each cycle requires the hydrolysis of ATP and shifts the dynein arms of one doublet relative to the adjacent doublet. In this way, the dynein arms of one doublet move the neighboring doublet, resulting in a relative displacement of the two.
What are the classes and properties of membrane lipids (the 'fluid' part)?
Classes: 1) Phospholipids 2) Glycolipids 3) Sterols Properties: - Asymmetry: Little or no transverse diffusion (flip-flopping) from one lipid layer to the other. When this does occur, it is due to enzymes known as flippases. - Fluidity: Rotational movement and/or lateral diffusion within the lipid layer. - Temperature: Transition temperature (temperature at which a membrane changes between the fluid and gelled state) is affected by the length of the fatty acids (The longer the hydrocarbon chain is, the higher the melting point), the number of double bonds (the melting point decreases as the number of double bonds increases), and the proportion of sterols (moderate in both directions! Acts as a buffer up to 50% in mammalian cells, Less fluid at higher temps, More fluid at lower temps)
What are the classes and properties of membrane proteins (the 'mosaic' part)?
Classes: 1) integral membrane proteins: monotopic or transmembrane proteins cannot be readily removed, require detergents 2) peripheral membrane proteins: weak electrostatic forces 3) lipid anchored proteins: covalently bound Properties: - Mobility: Some proteins move freely, however, others are anchored in various places, like the cytoskeleton or extracellular matrix.
What is an operon?
Cluster of genes with related functions that is under the control of a single operator and promoter, thereby allowing transcription of these genes to be turned on and off together.
What differentiates competitive versus non-competitive inhibition?
Competitive Inhibition: Inhibitor and substrate both bind to the active site of the enzyme. Binding of an inhibitor prevents substrate binding, thereby inhibiting enzyme activity. Non-competitive Inhibition: Inhibitor and substrate bind to different sites. Binding of an inhibitor distorts the enzyme, inhibiting substrate binding, or reducing catalytic activity.
How does yeast switch mating type?
Depends upon the swapping of genetic cassettes to alter the DNA sequence. Saccharomyces cerevisiae has mating-types (sexes): alpha or a. Chromosome III contains three separate copies of the mating-type information. The HMLalpha and HMRa loci contain complete copies of the alpha and a forms of the gene but the transcription of these loci is inhibited by the products of the SIR gene. The cell's actual mating type is determined by the allele present at the MAT locus. When a cell switches mating types, the alpha or a DNA at the MAT locus is removed and replaced by a DNA "cassette" copy of the alternative mating type DNA.
What generates membrane potential?
Diffusion of K+ through K+ channels (made possible by sodium potassium pumps)
How is the transcript elongated?
During elongation, RNA polymerase binds to about 30 base pairs of DNA (each complete turn of the DNA double helix is about 10 base pairs). At any given time, about 18 base pairs of DNA are unwound, and the most recently synthesized RNA is still hydrogen-bonded to the DNA, forming a short RNA-DNA hybrid. This hybrid is probably about 12 base pairs long, but it may be shorter. The total length of growing RNA bound to the enzyme and/or DNA is about 25 nucleotides.
How is eukaryotic DNA packaged?
Eukaryotes package DNA in the nucleus into chromatin and chromosomes. Chromatin fibres are 10 to 30 nm in diameter which condense into much more compact (packaged) structure for cell division. The histones, a group of positive charged (lysine and arginine rich) proteins, which stabilize DNA (negatively charged). Chromatin contains equal amounts of H2A, H2B, H3 and H4 and ~ one-half the amount of H1 plus numerous non-histone proteins. Histones provide the basis for the nucleosome, the basic unit of chromatin structure, as seen as "beads-on-a-string" structures on electron micrographs. The nucleosome core consists of a histone octomer [(H2A-H2B)X2,(H3-H4)X2]. The DNA double helix is wrapped around (~1.7 times) the histone octomer. With nuclease digestion, 146 bps of DNA are tightly associated with the nucleosome but ~200 bps of DNA in total are associated with the nucleosome. The difference is the linker DNA. H1 is associated with the linker DNA between nucleosome cores. Nucleosomes are packed to form chromatin fibres and chromosomes The nucleosome is only the first level of packaging nuclear DNA. The "beads on a string" fibres are 10-nm in diameter. The next level of organization forms the 30-nm chromatin fibre. Looped (active?) domains (50 to 100 kilobases) of the 30-nm fibre are attached to the non-histone chromosomal scaffold. Heterochromatin is more compacted and mostly transcriptionally inactive. The most compact level of chromatin is, of course, the microscopically visible chromosomes (chromatids).
How is eukaryotic mRNA modified?
Eukaryotic mRNA undergoes three modifications: 1) Capping- To give the mRNA stability, a 5 prime "cap" (a guanosine nucleotide methylated at the 7th position) is joined to the 1st nucleotide in an unusual "5 prime to 5 prime" linkage [sort of "backwards"]. During the capping process, the first two nucleotides of the message may also become methylated. 2) Tailing- Transcription of eukaryotic pre-mRNAs often proceeds beyond the 3 prime end of the mature mRNA. An AAUAAA sequence located slightly upstream from the proper 3prime end then signals that the RNA chain should be cleaved about 10-35 nucleotides downstream from the signal site, followed by addition of a "poly-A tail" catalyzed by poly(A) polymerase. 3) Splicing- Spliceosomes remove introns from pre-mRNA
How is eukaryotic transcription controlled?
Eukaryotic nuclear genes have three classes of promoters which are individual for the three types of RNA polymerases RNA polymerase I: The promoter for RNA polymerase I has two components: 1) a core promoter (surrounding the start-point) and 2) an upstream control element. After the binding of appropriate transcription factors to both sites, RNA polymerase I binds to the core promoter. RNA polymerase II: The typical promoter for RNA polymerase II has a short initiator sequence, consisting mostly of pyrimidines and usually a TATA box about 25 bases upstream from the start-point. This type of promoter (with or without the TATA box) is often called a polymerase II core promoter, because for most genes a variety of upstream control elements also play important roles in the initiation of transcription. RNA polymerase III: The promoters for RNA polymerase III vary in structure but the ones for tRNA genes and 5S rRNA genes are located entirely downstream of the start-point, within the transcribed sequence. In tRNA genes, about 30-60 base-pairs of DNA separate promoter elements; in 5S rRNA genes, about 10-30 base-pairs separate promoter elements.
How are tRNAs made in eukaryotes?
Every tRNA gene is transcribed as a precursor that must be processed into a mature tRNA molecule by the removal, addition and chemical modification of nucleotides. Processing for some tRNA involves 1) removal of the leader sequence at the 5 prime end 2) replacement of two nucleotides at the 3 prime end by the sequence CCA (with which all mature tRNA molecules terminate) 3) chemical modification of certain bases and 4) excision of an intron. The mature tRNA is often diagrammed as a flattened cloverleaf which clearly shows the base pairing between self-complementary stretches in the molecule.
What are excision repair mechanisms?
Excision repair mechanisms remove abnormal nucleotides to correct mutations. Base excision repair mechanisms first remove a damaged base then causes excision of the remaining sugar-phosphate unit. DNA repair mechanism that recognizes and repairs damage involving major distortions of the DNA double helix, such as that caused by pyrimidine dimers. It causes two nicks which leads to the removal of a stretch of damaged single-stranded DNA. Mismatch repair corrects mutations of non-complementary bases that become included in DNA during replication that are not fixed by proof-reading
What do fibronectins do? How?
Fibronectins bind cells to the matrix and guide cellular movement. The RGD (arginine-glycine-aspartate) sequence binds to the integrin fibronectin receptor. The fibronectins bind cells to the ECM by bridging cell-surface receptors to the ECM
What are gap junctions?
Gap junctions separate cells by 2-3 nm and allow direct electrical and chemical communication.
How can DNA rearrangement influence antibody synthesis?
Genes coding for the human antibody heavy chains are created by DNA rearrangements involving multiple types of V, D and J segments. Initially, the DNA of the immune cells is arranged as tandem arrays of V, D and J regions DNA excision randomly removes several D and J segments to place individual D and J sequences side by side. A second random excision removes several V and D segments to join a V section to the others to form a VDJ segment. After transcription, the sequences separating the VDJ segment from the C segment are removed by RNA splicing.
How does the synthesis of ribosomes require nuclear pore transport?
The nucleolus is the intranuclear site where rRNA is made. Ribosomal proteins are imported into the nucleus and ribosomal subunits are made in the nucleolus. The ribosomal subunits are then exported through the nuclear pores to the cytoplasm.
How does co-translational import work?
In cotranslational import proteins to be targeted to the endoplasmic reticulum initially have an N-terminal peptide, the ER signal sequence, translated by a cytosolic ribosome. The ER signal sequence is bound by a signal-recognition particle (SRP), a ribonucleoprotein complex composed of 6 peptides and a 300 nucleotide RNA molecule. The SRP binds to the SRP receptor to dock the ribosome on the ER membrane. When the SRP receptor binds GTP, the nascent polypeptide enters the pore. The SRP is released with hydrolysis of the GTP. The growing polypeptide translocates through a hydrophilic pore created by one or more membrane proteins called the translocon. The most recent evidence suggests that the ribosome fits tightly across the cytoplasmic side of the pore and that the ER-lumen side is somehow closed off until the polypeptide is about 70 amino acids long. When the polypepide is complete, the signal peptidase cleave the signal to release the protein into the ER lumen while retaining the signal peptide, for a time, in the membrane. Afterwards the ribosome is released and the pore closes completely.
How do proteins enter the endomembrane system?
In the endoplasmic reticulum, folding of the newly-made proteins may also require molecular chaperones and other proteins involved in protein folding. Bip (binding protein), a member of the Hsp70 chaperone family, briefly binds to and stabilizes hydrophobic regions of proteins (especially rich in Trp, Phe, Leu) allowing proper folding instead of aggregation with other immature proteins. Protein disulfide isomerase catalyzes the formation and breakage of disulfide bonds between cysteine residues to produce a stable conformation.
How does translation initiate, elongate, & terminate?
Initiation: 1) Initiation factors (eIFs) bind to the 5' cap of mRNA. 2) 43S preinitiation complex binds 3) eIF2 hydrolyzes GTP; other eIFs dissociate; eIF58 binds 4) Small subunit scans for AUG (start codon); tRNA binds to start codon 5) Large ribosomal subunit binds; eIF58 hydrolyzes GTP; eIF58 and eLF1A dissociate Elongation: 1) An aminoacyl tRNA binds to the A site, escorted by EF-Tu bound to GTP. During tRNA binding, the GTP is hydrolyzed and EF-Tu is released. EF-Ts helps recycle EF-Tu. 2) A peptide bond is formed between the carboxyl group of fMet (or, in later cycles, of the terminal amino acid) at the P site and the amino group of the newly arrived amino acid at the A site. 3) The mRNA advances by three nucleotides, the peptidyl tRNA moves from the A site to the P site, and the empty tRNA moves from the P site to the E site, accompanied by the hydrolysis of GTP bound to EF-G. Termination: 1) Once a stop codon in the mRNA arrives at the ribosome's A site, a release factor recognizes it and binds to the stop codon. 2)After binding to the A site along with GTP, the release factors terminate translation by triggering release of the completed polypeptide from the peptidyl tRNA.
How do integrins connect ECM inside the cell?
Integrins act to integrate the cytoskeleton and the extracellular matrix. Integrins consist of two large non-covalently bound transmembrane proteins (alpha and beta subunits). A number of both alpha and beta subunits combine to produce a large variety of heterodimeric integrins. On the outer surface, the subunits interact to form a binding site for the adhesive glycoprotein, the RGD sequence of the ECM glycoprotein. Most of the binding specificity depend upon the alpha subunit. On the cytosolic side, the receptor binds components of the cytoskeleton to enable the ECM to communicate through the plasma membrane to the cytoskeleton
What are intermediate filaments and what do they do?
Intermediate Filaments are usually assembled coils of homodimers into protofilaments. They appear to play a structural or tension-bearing role.
How does intracellular microtubule-based movement act to move cargo?
Kinesin-1 uses the globular filament-binding domains of its heavy chains to bind to microtubules. Its light chains are involved in cargo binding. Steps: 1) Leading heavy chain binds ATP 2)ATP binding causes conformational change; trailing heavy chain swings forward 3) Trailing heavy chain finds new microtubule binding site 4) New leading heavy chain releases ADP; new trailing head hydrolyses ATP to ADP
What are the five levels of cell structure?
Level 1: small organic molecules (ex/ glucose, amino acids, nucleotides) Level 2: macromolecules (ex/ cellulose, protein, DNA) Level 3: supramolecular structures (ex/ Cell membrane, cell wall, chromosomes) Level 4: organelles & sub-cellular structures (ex/ chloroplast, mitochondrion, nucleus) Level 5: the cell
How are proteins targeted to organelles such as the mitochondria and chloroplast?
Like cotranslational import into the ER, posttranslational import into a mitochondrion (and chloroplast) involves a signal sequence (called a transit sequence), a membrane receptor, pore-forming membrane proteins, and a peptidase. Polypeptides being imported into the mitochondrion span both membranes at the same time. The transit sequence is cleaved by the transit peptidase present in the matrix, indicating that the N-terminus of the polypeptide is within the mitochondrion. At the same time, most of the polypeptide molecule is can be attacked by exogenously added proteolytic enzymes on the outside of the mitochondrion. Therefore, the polypeptide must span both membranes transiently during import at a contact site between the two membranes. However, in the mitochondria and chloroplasts, the membrane receptor recognizes the signal sequence directly without the intervention of a cytosolic SRP
What are the major classes of enzymes?
Major classes of enzymes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases.
What is the extracellular matrix?
Material secreted by animal cells that fills the spaces between neighboring cells; consists of a mixture of structural proteins (e.g., collagen, elastin) and adhesive glycoproteins (e.g., fibronectin, laminin) embedded in a matrix composed of protein-polysaccharide complexes called proteoglycans.
How does the nuclear pore function?
Nuclear pores are channels that pass through both nuclear membranes that join the cytosol with the nucleoplasm. The inner and outer membranes fuse to form a channel that is lined with the nuclear pore complex (diameter 120 nm). A mammalian nucleus may have 3000-4000 nuclear pores. Nuclear pores are site of molecular entry and exit both the passive transport of small molecules and the active transport of large proteins and RNA. Proteins that are required in the nucleus contain nuclear localization sequences (NLS) that target them through the nuclear pores. The NLS-containing proteins bind importin (a cytosolic receptor protein) which binds the protein to the nuclear pore. The nuclear pore transporter then passes the protein into the nucleoplasm.
How are ribosomal RNAs made?
Occurs in the nucleoli and involves cleavage of multiple rRNAs from a common precursor. The eukaryotic transcription unit that includes the genes for the three largest rRNAs occurs in multiple copies and arranged in tandem arrays with non-transcribed spacers separate the units. Each transcription unit includes the genes for the three rRNAs and transcribed spacer regions. The transcription unit is transcribed by RNA polymerase I into a single long transcript (pre-rRNA) with a sedimentation coefficient of about 45S. RNA processing yields mature rRNA molecules. RNA cleavage actually occurs in a series of steps which varies in order with the species and cell type but the final products are always the same three types of rRNA molecules.
How do RNA interference (RNAi) and microRNA (miRNA) work?
Produces mRNAs that are 21-22 nucleotides in length. The primary miRNAs are transcribed, form hair-pin structures and are cleaved by Drosha to make precursor microRNAs (roughly 70 nucleotides in length). The pre-miRNAs are exported to the cytoplam where they are cleaved by dicer into the 21-22 nucleotide mature microRNA's. The miRNA's form ribonucleoprotein complexes with mRNA's. If the match is exact, the mRNA is destroyed, similar to siRNA mechanisms. If the match is less-than-exact, then binding (usually of several miRNA's) inhibit translation. Genes for miRNA's seem to make up 0.5-1.0% of the total number of genes in multicellular organisms. i.e. 200-250 miRNA genes in humans.
How is prokaryotic DNA packaged?
Prokaryotes package DNA in bacterial chromosomes and plasmids. The bacterial chromosome is localized in the nucleoid region of the cell (no nucleus) and is looped into negative coils. The loops are 50,000 to 100,000 bps in length (similar to eukaryotic chromosomes) which are held in place by RNA and small basic (meaning positively charged) histone-like proteins. Plasmids, small negatively supercoiled circular DNA molecules, carry usually non-essential genes (often drug resistance).
What process drives protein breakdown and what is ubiquitin's role in this?
Proteins can be marked for destruction by the addition of ubiquitin. 1) A protein targeted for degradation is bound at its N-terminus by a ubiquitinating enzyme complex. 2) In an ATP-dependent series of reactions, ubiquitin molecules are sequentially attached to the protein's lysine residues. The ubiquitinating enzyme complex then detaches. 3) A proteasome degrades the ubiquitinated protein into short peptides
What are the differences and similarities between glycolysis and fermentation?
Similarities: - processes of converting complex molecules such as sugars and carbohydrates into simple forms. Differences: - In the presence of oxygen, glycolysis typically leads to aerobic respiration, while a lack of oxygen causes fermentation to occur. - Glycolysis produces ATP while fermentation does not - In aerobic respiration (glycolysis), an external, inorganic molecule (O2) oxidizes NADH. In fermentation, however, a molecule internal to the pathway (pyruvate) oxidizes NADH.
What are simple and facilitated diffusion?
Simple: - Occurs via lipid interaction - lipophilic/hydrophobic substances - Requires no cellular energy - Down the gradient towards equilibrium - Simple non-polar molecules, such as di-oxygen, carbon dioxide, carbon monoxide, and some drugs like nicotine, heroin, and anesthetics - The cell membranes are not (cannot be) selective in simple diffusion. Facilitated: - Requires no cellular energy - Down the gradient towards equilibrium - Occurs via proteins: lipophobic/hydrophilic - Types of proteins used include carrier proteins and ion channels - Very dependent upon the proteins present in the cell membrane. - This is a very specific process. The cell membranes are very selective in facilitated diffusion of certain solutes
What are the specialized motor proteins and how do they function?
Specialized motor proteins, also known as mechanoenzymes, convert chemical energy into mechanical energy, causing movement. Two main systems: 1) specialized motor proteins & microtubules; and 2) actin microfilaments and myosin motor molecules. Mechanoenzymes couple ATP hydrolysis to changes in shape and attachment of the motor to its associated cytoskeletal filament.
How is the eukaryotic genome organised?
The organization of the total sum of genetic information (or genome) of an organism is in the form of double-stranded DNA, except that viruses may have single-stranded DNA, single-stranded RNA or double-stranded RNA genomes. In eukaryotes, the nuclear genome consists of linear chromosomes (usually as a diploid set) and the mitochondrial and chloroplast (in plants) genomes are small circular DNA molecules
How does the spliceosome work?
Spliceosomes remove introns from pre-mRNA. In a stepwise fashion, the pre-mRNA assembles with the U1 snRNP, U2 snRNP, and U4/U6 and U5 snRNPs (along with some non-snRNP splicing factors), forming a mature spliceosome. The pre-mRNA is then cleaved at the 5 prime splice site and the newly released 5 prime end is linked to an adenine (A) nucleotide located at the branch-point sequence, creating a looped lariat structure. Next the 3 prime splice site is cleaved and the two ends of the exon are joined together, releasing the intron for subsequent degradation. Alternative results in alternate forms of mRNA and, often, proteins
How do tRNAs become charged?
Step 1: 1) The amino acid and a molecule of ATP enter the active site of the enzyme. 2) The ATP loses pyrophosphate and the resulting AMP bonds covalently to the amino acid. 3) The pyrophosphate is further hydrolyzed into two phosphate groups. Step 2: 4) The tRNA covalently bonds to the amino acid to displace the AMP. 5) The aminoacyl tRNA is then released from the enzyme.
How does telomerase function?
Telomerase, a special DNA polymerase, can add additional copies of the 5'-TTAGGG-3' to the end of a chromosome. The telomerase enzyme is actually a complex containing protein and RNA (a "ribozyme"). The RNA portion has a 5'-CCCTAA-3' region that acts as a template for adding the DNA repeat to the chromosome ends. In somatic cells, the absence of telomerase results in shorter chromosomal ends with each division and may be the limiting factor in an organism's life span.
How do you stop transcription?
Termination of transcription requires a termination sequence that triggers the end of transcription. Two classes exist, rho dependent and rho independent In rho independent termination, a short complementary GC-rich sequence (followed by several U residues) will form a "brake" that will help release the RNA polymerase from the template (at the weakly poly-U stretch). In rho dependent termination, binding of rho to the mRNA releases it from the template.
What are the properties of the "Fluid Mosaic Model"?
The Fluid Mosaic Model is universally accepted model for cell membrane structure. - Lipids are fluid and this fluidity can be regulated. - Proteins form a "mosaic", perform a variety of functions, and protein fluidity may be restricted. - Both are asymmetrically distributed in membranes. As in, the inner surface and the outer surface.
What is an action potential?
The action potential is a brief depolarization/repolarization that propagates from the site of origin. Action potentials involve rapid changes in the membrane potential of the axon
How can two different versions of the same protein, such as IgM, be made?
The antibody protein immunoglobulin M (IgM) exists in two forms, as secreted IgM and membrane-bound IgM. These molecules, encoded by a single gene, differ in their heavy chain's carboxyl ends. The IgM gene has two possible poly(A) addition (termination) sites and a number of exons that can produce two alternative forms. The plasma membrane-bound form contains a transmembrane anchor which is encoded by exons 5 and 6. If a splice junction within exon 4 is used, exons 5 and 6 (carrying the anchor) are added to generate the IgM heavy chain. The secreted product is produced when the exon 4 splice is not made and these transcripts are terminated just after exon 4.
Where and how is cellulose made?
The cellulose microfibrils are generated by cellulose-synthesizing enzyme complexes called rosettes that are localized within the plasma membrane. Because the microfibrils are anchored to other wall components, the rosettes must move in the plane of the membrane as they lengthen the growing cellulose microfibrils.
What is the Holliday Model of Recombination?
The current model of the mechanism of exchange of DNA between two homologous chromosomes explains gene conversion and genetic recombination. 1) A double-stranded DNA molecule undergoes a single-stranded break. 2) The single-stranded DNA invades the complementary region of the double-stranded homologue. 3) DNA repair (DNA synthesis) of the dsDNA (double stranded DNA) using the invading ssDNA (single stranded DNA) as template begins. 4) Reciprocal invasion results in the formation of the "double crossover" or Holliday Junction. 5) Branch migration (movement of the crossover structure) is the result of DNA unwinding and rewinding. 6) Resolution of the Holliday Junction will result in either a cross over event or gene conversion (without a cross over) event.
What are the physical properties of cytoskeleton components?
The cytoskeleton is composed of microtubules, microfilaments, and intermediate filaments. Microtubules: - 25 nm diameter - composed of alpha-beta tubulin heterodimers Microfilaments: - 7 nm diameter - Composed of G-actin monomers Intermediate filaments: - 8-12 nm - composed of six different proteins
How do codons code for amino acids?
The genetic code's "words" are three-letter codons present in the nucleotide sequence of mRNA, as read in the 5 prime to 3 prime direction. Each codon specifies either an amino acid or a stop signal.
What are the major aspects of lac operon regulation?
The lac operon includes 3 structural genes (lacZ, lacY and lacA) that are transcribed in unison. Located near the lac operon, is the lacI gene regulates the operon by producing the lac repressor protein. Both the regulatory gene and the lac operon itself contain... 1) promoters (Pl and Plac) at which RNA polymerase binds and 2) terminators at which transcription halts. Plac overlaps with the operator site (O) to which the active form of the repressor protein binds. The operon is transcribed into a single long molecule of mRNA that codes for all three polypeptides.
What are the basic properties of the main macromolecules of the cell?
The main macromolecules of the cell are proteins (amino acids), nucleic acids (DNA + RNA), lipids, and polysaccharides (starch, glycogen, cellulose). Proteins: - Proteins undergo a process of "self-assembly" - Denatured proteins can return to their native form via renaturation: spontaneous protein/peptide folding - Proteins are polymers of amino acids - While there are approximately 60 amino acids in the cell, only 20 are involved in protein synthesis. - Fun facts: The smallest R group is H, on Glycene. This makes Glycene the smallest and simplest amino acid. Prolene is actually not an amino acid, it's an imino acid. - After the proteins/peptides are made, the amino acid sub-units can be modified. - Amino acids have a central alpha-carbon, an amino group, a carboxyl group, and an R group. - R groups are different for each amino acid- some are hydrophobic while others are hydrophilic. - Proteins and peptides are made linearly in an "amino (N) to carboxyl (C)" direction, where the N-terminal end is the beginning and the C-terminal end is the end! - Polymerization is through formation of peptide bonds - Peptide bonds between two amino acids are stabilized by disulfide bonds, hydrogen bonds, ionic bonds, and van der Waals forces. - Protein structures depend upon the amino acid sequence and the many interactions among the amino acids. There are four levels of organization of protein structure: primary (amino acids linked together by peptide bonds to form a polypeptide), secondary (the polypeptide is then coiled into an alpha helix), tertiary (regions of the alpha helix associate with each other to form the tertiary structure), and quaternary (the association of two or more polypeptides as they interact to form the final protein). Nucleic Acids: - Nucleic acids are linear polymers of nucleotides - DNA and RNA differ in the 5 prime carbon sugar part of the nucleotide, as DNA has a H and RNA has an OH. - DNA is used to store genetic information and RNA is involved in utilizing the information - A nucleotide is made up of a nitrogenous base (purines or pyrimidines), a 5 prime carbon sugar and a phosphate group - Adenine and Guanine are purines (two rings) and Thymine, Uracil, and Cytosine are pyrimidines (one ring). - DNA is made in an "5 prime to 3 prime" direction, where the "5 prime" end is the beginning and the "3 prime" end is the end! - Nucleic acids are joined together by the "3 prime", while the "5 prime" end connects to the phosphodiester backbone. - DNA is a double-stranded helix, with each turn of the helix equalling 10 base pairs. - DNA has hydrogen bonds between A-T pairs and G-C pairs of opposite strands - Humans have more G-C pairs than A-T pairs. - G-C pairs are more stable than A-T pairs because they have three hydrogen bonds versus two. Polysaccharides: - Polysaccharides are polymers of simple sugars such as glucose. - Polysaccharides are for storage, such as starch (for plants) & glycogen (for animals) and structure such as cellulose (in plants). Lipids: - Lipids are polymers of various monomers, such as fatty acids. - Serve in energy storage, membrane structure, and specific biological functions.
What is eukaryotic organelle DNA like?
The mitochondria and chloroplasts also have a DNA genome (or chromosome). These resemble prokaryotic genomes (likely due to the endosymbiotic origin of these organelles) but are much smaller. The mitochondrial genome varies in size among eukaryotes (mammals =16.5 kb & 37 genes, yeast and plants are greater than 5X this). Chloroplasts are ~120 kb and have ~120 genes.
How do the major tools of translation work together for protein synthesis?
The model of ribosome structure shows the A (aminoacyl) and P (peptidyl) sites as cavities on the ribosome where charged tRNA (carrying an amino acid) molecules bind during polypeptide synthesis. The recently postulated E (exit) site is the site from which discharged tRNAs leave the ribosome. The mRNA-binding site binds a sequence near the 5 prime end of the mRNA, placing the mRNA in the proper position for the translation of its first codon The binding sites are all located at or near the interface between the large and small subunits.
How do action potentials propagate?
The passive spread of depolarization causes cations (mostly potassium) to spread to adjacent regions of the axon's cytoplasm. As the depolarization spreads, it loses its magnitude and MUST be actively generated (propagated) to move far. Propagation depends upon the passive spread of depolarization to induce the membrane potential in adjacent parts of the axon to reach the threshold potential which then triggers the intake of sodium ions and continuation of the cycle For example, signals move from the dendrites through the cell body to the base of the axon (the axon hillock) where sodium channels are concentrated. At the axon hillock, a great influx of sodium ions can occur which specify that action potentials initiated here are propagated down the axon. The propagated action potential is the nerve impulse. The rate of impulse transmission depends on electrical properties of the axon such as the electrical resistance of the cytosol and the ability to retain electric charge (capacitance) of the plasma membrane. The discontinuous myelin sheath acts like an electrical insulator surrounding the axon The neurons of the CNS have myelin sheath composed of oligodendrocytes and in the PNS the myelin sheath is composed of Schwann cells. In each case, the myelin cells wrap several layers of their plasma membranes around the axon. Each Schwann cell surrounds a stretch of 1 mm of axon, with many Schwann cells acting to insulate each axon. Myelination permits a depolarization of events to spread farther and faster than without because of saltatory propagation. This process depends upon the gathering of voltage-gated sodium channels at the nodes of Ranvier. Action potentials jump node to node (saltatory propagation) which is very rapid when compared to propagation in neurons that have the myelin removed.
What aspects of the structure of ATP are key to energy exchange?
The two energy-rich phosphate bonds that undergo hydrolysis to release energy.
How is repeated DNA ordered?
There are two types of repeated DNA: 1) Tandemly repeated DNA 2) Interspersed Repeated DNA Tandemly repeated DNA (10-15% of mammalian genomes) is made up of rows of many copies of the same sequence. The repeated unit ranges from 1 to 2000 base-pairs (bps) in length. Often the repeat is less than 10 bps and is referred to as simple-sequence repeated DNA or satellite DNA (due to centrifugation "satellite" bands). Interspersed repeated DNA make up 25 to 40% of most mammalian genomes that are hundreds to thousands of bps long. Many interspersed repeated DNA sequences are transposable elements.
How does the glucose transporter (in the RBC) work?
This is an example of facilitated diffusion using ion channels. - an integral membrane protein with 12 transmembrane segments - Glucose in blood plasma is about 3.6-5.0 mM. However, inside red blood cells, it is about 0.5-1.0 mM (=concentration gradient) because there is a glucose selective transporter in the RBC membrane. STEPS: - Glucose binds to a GLUT1 transporter protein that has its binding site open to the outside of the cell (T1 conformation) - Glucose binding cause the GLUT1 transporter to shift to its T2 conformation with the binding site open to the inside of the cell. - Glucose is released to the interior of the cell, initiating a second conformational change in GLUT1. - Loss of bound glucose causes GLUT1 to return to its original T1 conformation, ready for a further transport cycle.
What are tight junctions?
Tight junctions leave no space between plasma membranes of adjacent cells to prevent the movement of molecules across cell layers. The structure of tight junctions consists of fused ridges of tightly packed transmembrane junctional proteins. Tight junctions block lateral movement of lipids and membrane proteins to keep a cell polarized
How is 'wobble' related to the tRNA anticodon?
Twenty different aminoacyl-tRNA synthetases link amino acids to the correct tRNAs. Some recognize only one tRNA, some recognize a few because of the redundancy in the genetic code. Although there are 61 possible codons, there are far fewer tRNAs. A number of codons that encode the same amino acid differ only in the third position of the codon. A slight shift or "wobble" in the position of the base guanine in a tRNA anticodon would permit it to pair with uracil instead of its normal complementary base (cytosine) and other similar unusual pairings. Note that the base pairs permitted at the third position of a codon (by the wobble hypothesis) enable a single tRNA to pair with more than one codon which means that far fewer than 61 tRNAs are required.
How do voltage-gated channels work?
Voltage-gated ion channels respond to differences in voltage across the membrane (ligand-gated ion channels respond to ligands). Specific domains of voltage-gated channels act as sensors and inactivators. A specific transmembrane stretch of amino acids act as voltage sensor. Based upon the conformation of the voltage-gated channel, the channel can be closed but sensitive to a depolarizing signal (channel gating) or completely desensitized to the signal (channel inactivation) by the inactivating particle, a stopper-like part of the channel protein itself
How do proteins target cellular locations?
When the polypeptide is about 30 amino acids long, it enters one of two alternative pathways. 1) In cotranslational import, if the newly forming polypeptide is destined for any of the compartments of the endomembrane system, it becomes associated with the ER membrane and is transferred across the membrane into the lumen (cisternal space) of the ER as synthesis continues. The completed polypeptide then either remains in the ER or is transported via various vesicles and the Golgi complex to another final destination. Integral membrane proteins are inserted into the ER membrane as they are made, rather than into the lumen. 2) If the polypeptide is destined for the cytosol or for import into the nucleus, mitochondria, chloroplasts, or peroxisomes, its synthesis continues in the cytosol. When the polypeptide is complete, it is released from the ribosome and either remains in the cytosol or is transported into the appropriate organelle by posttranslational import. Polypeptide uptake by the nucleus occurs via the nuclear pores, using a mechanism different from that involved in posttranslational uptake by other organelles.
How do iron response elements work?
ferritin mRNA: Translation of ferritin is activated in the presence of iron. Translation is inhibited by binding of the IRE-binding protein to the hairpin structure of an iron response element in the 5 prime untranslated leader sequence of ferritin mRNA. When iron binds to IRE-binding protein, it contorts into a conformation that does not recognize the IRE. When iron is available, ribosomes can assemble on the mRNA and proceed to translate ferritin. The hairpin does not interfere with the ribosome activities. transferrin receptor mRNA: Degradation of the transferrin receptor mRNA (required for iron uptake) is also regulated by the allosteric IRE-binding protein. Transferrin receptor mRNA has an IRE in its 3 prime untranslated region. When intracellular [iron] is low, the IRE-binding protein remains bound to the IRE which 1) protects the mRNA from degradation and 2) allowing more transferrin receptor protein to be synthesized. When intracellular [iron] is high, iron binds to the IRE-binding protein, it releases the IRE and the mRNA can be degraded.
