Final Exam - Molecular & Cellular Biology PDF

Final exam - Sameinda og frumulíffræði | Bryndís Brynjúlfsdóttir...

Final exam - Sameinda og frumulíffræði | Bryndís Brynjúlfsdóttir Protein Protein amino acids are connected with synthesis : DNA GRNA - PROTEIN a peptide bond = 1. Transcription : in the nucleous RNA RNA polymerase an enzyme , will connect complementary stranded mRNA bases to the DNA form a single Chapter 1 – Cells: The Fundamental Units of Life Living cells contain an enormously diverse set of protein molecules, each made as a linear chain of amino acids linked together by covalent peptide Chapter 6 – DNA replication, repair and recombination ↓ MRNA tRNA iRNA) 2 Translation out of the nucleous and into cytoplasm (mRNA , bonds. ,. : Cells are the fundamental units of life. All present-day cells are believed to have evolved from an ancestral cell that existed more than 3 billion years Each type of protein has a unique amino acid sequence, which determines both its three-dimensional shape and its biological activity. And attatches made to aribosome Ribosomes make. protein. The ribosome is of rRNA ago. The folded structure of a protein is stabilized by multiple noncovalent interactions between different parts of the polypeptide chain. tRNA carrie an aminoaidson themand readsthebasesin Triplets On All cells are enclosed by a plasma membrane, which separates the inside of the cell from its environment. Hydrogen bonds between neighboring regions of the polypeptide backbone often give rise to regular folding patterns, known as α helicxes and β Before a cell divides, it must accurately replicate the vast quantity of genetic information carried in its DNA. All cells contain DNA as a store of genetic information and use it to guide the synthesis of RNA molecules and proteins. sheets. Because the two strands of a DNA double helix are complementary (viðbót) , each strand can act as a template for the synthesis (nýmyndun) of the Cells in a multicellular organism, though they all contain the same DNA, can be very different. They turn on different sets of genes according to their The structure of many proteins can be subdivided into smaller globular regions of compact three-dimensional structure, known as protein domains. other. Thus DNA replication produces two identical, double-helical DNA molecules, enabling genetic information to be copied and passed on from a developmental history and to signals they receive from their environment. The biological function of a protein depends on the detailed chemical properties of its surface and how it binds to other molecules, called ligands. cell to its daughter cells and from a parent to its offspring. Animal and plant cells are typically 5–20 μm in diameter and can be seen with a light microscope, which also reveals some of their internal When a protein catalyzes the formation or breakage of a specific covalent bond in a ligand, the protein is called an enzyme and the ligand is called a During replication, the two strands of a DNA double helix are pulled apart at a replication origin to form two Y-shaped replication forks. DNA components, including the larger organelles. substrate. polymerases at each fork produce a new complementary DNA strand on each parental strand. The electron microscope reveals even the smallest organelles, but specimens require elaborate preparation and cannot be viewed while alive. At the active site of an enzyme, the amino acid side chains of the folded protein are precisely positioned so that they favor the formation of the high- 7 DNA polymerase replicates a DNA template with remarkable fidelity, making only about one error in every 10 nucleotides copied. This accuracy is Specific large molecules can be located in fixed or living cells with a fluorescence microscope. energy transition states that the substrates must pass through to be converted to product. made possible, in part, by a proofreading process in which the enzyme corrects its own mistakes as it moves along the DNA. The simplest of present-day living cells are prokaryotes: although they contain DNA, they lack a nucleus and other organelles and probably resemble The three-dimensional structure of many proteins has evolved so that the binding of a small ligand can induce a significant change in protein shape. Because DNA polymerase synthesizes new DNA in only one direction, only the leading strand at the replication fork can be synthesized in a most closely the ancestral cell. Most enzymes are allosteric proteins that can exist in two conformations that differ in catalytic activity (hvatandi), and the enzyme can be turned on or continuous fashion. On the lagging strand, DNA is synthesized in a discontinuous backstitching process, producing short fragments of DNA that are Different species of prokaryotes are diverse in their chemical capabilities and inhabit an amazingly wide range of habitats. Two fundamental off by ligands that bind to a distinct regulatory site to stabilize either the active or the inactive conformation. later joined together by DNA ligase. evolutionary subdivisions are recognized: bacteria and archaea. The activities of most enzymes within the cell are strictly regulated. One of the most common forms of regulation is feedback inhibition, in which an DNA polymerase is incapable of starting a new DNA chain from scratch. Instead, DNA synthesis is primed by an RNA polymerase called primase, Eukaryotic cells possess a nucleus and other organelles not found in prokaryotes. They probably evolved in a series of stages, including the enzyme early in a metabolic pathway is inhibited by the binding of one of the pathway’s end products. which makes short lengths of RNA primers that are then elongated by DNA polymerase. These primers are subsequently erased and replaced with acquisition of mitochondria (hvatberar) by engulfment (gleypa) of aerobic bacteria and (for plant cells) the acquisition of chloroplasts (grænukorn) Enzyme Regulation: Enzymes can also be subject to positive regulation, in which the enzyme’s activity is stimulated by a regulatory molecule rather DNA. by engulfment of photosynthetic bacteria (ljóstillífunarbaktería). than being suppressed. Positive regulation occurs when a product in one branch of the metabolic maze stimulates the activity of an enzyme in another DNA replication requires the cooperation of many proteins that form a multienzyme replication machine that copies both DNA strands as it moves The nucleus contains the genetic information of the eukaryotic organism, stored in pathway. Allosteric enzymes have two or more binding sites that influence one another—most protein molecules are allosteric: they can adopt two or along the double helix. DNA molecules. more slightly different conformations, and their activity can be regulated by a shift from one to another. In eukaryotes, a special enzyme called telomerase replicates the DNA at the ends of the chromosomes. The cytoplasm (umfrymi) includes all of the cell’s contents outside the nucleus and Many thousands of proteins in a typical eukaryotic cell are regulated by cycles of phosphorylation and dephosphorylation. The rare copying mistakes that escape proofreading are dealt with by mismatch repair proteins, which increase the accuracy of DNA replication to one contains a variety of membrane-enclosed organelles with spe- cialized functions: GTP-binding proteins also regulate protein function in eukaryotes; they act as molecular switches that are active when GTP is bound and inactive 9 mitochondria carry out the final oxidation of food molecules; in plant cells, when GDP is bound; turning themselves off by hydrolyzing their bound GTP to GDP. mistake per 10 nucleotides copied. chloroplasts perform photosynthesis; the endoplasmic reticulum and the Golgi Motor proteins produce directed movement in eukaryotic cells through conformational changes linked to the hydrolysis of ATP to ADP. DNA Polymerase: Proofreading: Proofreading takes place at the same time as DNA synthesis. Before the enzyme adds the next nucleotide to a apparatus synthesize complex molecules for export from the cell and for insertion in Highly efficient protein machines are formed by assemblies of allosteric proteins in which the various conformational changes are coordinated to growing DNA strand, it checks whether the previously added nucleotide is correctly base-paired to the template strand. If so, the polymerase adds the cell membranes; lysosomes digest large molecules. perform complex functions. next nucleotide. If not, the polymerase clips off the mispaired nucleotide and tries again. This proofreading is carried out by a nuclease that cleaves Outside the membrane-enclosed organelles in the cytoplasm is the cytosol Covalent modifications added to a protein’s amino acid side chains can control the location and function of the protein and can serve as docking sites (klofnar) the phosphodiester backbone. Polymerization and proofreading are tightly coordinated (samræmd), and the two reactions are carried out by (frymisvökvi), a very concentrated mixture of large and small molecules that carry out for other proteins. different catalytic domains in the same polymerase molecule. many essential biochemical processes. Starting from crude cell or tissue homogenates, individual proteins can be obtained in pure form by using a series of chromatography steps. Damage to one of the two DNA strands, caused by unavoidable chemical reactions, is repaired by a variety of DNA repair enzymes that recognize The cytoskeleton is composed of protein filaments that extend throughout the The function of a purified protein can be discovered by biochemical analyses, and its exact three-dimensional structure can be determined by X-ray damaged DNA and excise a short stretch of the damaged strand. The missing DNA is then resynthesized by a repair DNA polymerase, using the cytoplasm and are responsible for cell shape and movement and for the transport of crystallography or NMR spectroscopy. undamaged strand as a template. organelles and other large molecular complexes from one location to another. Amyloid fibril formation in Alzheimer‘s disease: is a multiple state process, which starts with the cleavage of the amyloid fragments from the If both DNA strands are broken, the double-strand break can be rapidly repaired by nonhomologous end joining. Nucleotides are lost in the process, Free-living, single-celled eukaryotic microorganisms (örverur) are complex cells that transmembrane APP, misfolding of Amyloid beta (Aβ) monomers that form various structures, such as unfolded clusters, beta-sheet oligomers, altering the DNA sequence at the repair site. can swim, mate, hunt, and devour other microorganisms. larger fibrils and amyloid plaques. Homologous recombination can flawlessly repair double-strand breaks using an undamaged homologous double helix as a template. Animals, plants, and some fungi consist of diverse eukaryotic cell types, all derived Phosphorylation (fosfórun) can control protein activity by causing a conformational change: Another method that eukaryotic cells use to regulate Highly accurate DNA replication and DNA repair processes play a key role in protecting us from the uncontrolled growth of somatic cells known as from a single fertilized egg cell; the number of such cells cooperating to form a large protein activity involves attaching a phosphate group to one or more of the protein’s amino acid side chains. Because each phosphate group carries cancer. multicellular organism such as a human runs into thousands of billions. two negative charges, the enzyme-catalyzed addition can cause a major conformational change in a protein E.g. can attract a cluster of positively The pathway for repairing damage to DNA: Three basic steps: Biologists have chosen a small number of model organisms to study closely, charged amino acid side chains from somewhere else in the same protein! This conformational change can, in turn, affect the binding of ligands The damaged DNA is recognized and removed by one of a variety of mechanisms. These involve nucleases, which cleave the covalent bonds that including the bacterium E. coli, brewer’s yeast, a nematode worm, a fly, a small plant, elsewhere on the protein surface, thereby altering the protein’s activity. Removal of the phosphate group by a second enzyme will return the protein to join the damaged nucleotides to the rest of the DNA strand, leaving a small gap on one strand of the DNA double helix in the region. a fish, a mouse, and humans themselves. its original conformation and restore its initial activity. A repair DNA polymerase binds to the 3ʹ-hydroxyl end of the cut DNA strand. It then fills in the gap by making a complementary copy of the The simplest known cell is a bacterium with about 500 genes, but most cells contain significantly more. The human genome has about 25,000 genes, Protein phosphorylation from ATP: Reversible protein phosphorylation controls the activity of many types of proteins in eukaryotic cells. Indeed, it is information stored in the undamaged strand. Although different from the DNA polymerase that replicates DNA, repair DNA polymerases synthesize which is only about twice as many as a fly and six times as many as E. coli. so extensive that more than one-third of the ~10,000 proteins in a mammalian cell are phosphorylated at any one time!! Protein phosphorylation DNA strands in the same way. For example, they elongate chains in the 5ʹ-to-3ʹ direction and have the same type of proofreading activity to ensure involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of that the template strand is copied accurately. a protein, catalyzed by a protein kinase. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein When the repair DNA polymerase has filled in the gap, a break remains in the sugar–phosphate backbone of the repaired strand. This nick in the phosphatase. Cells contain hundreds of different protein kinases and phosphatases, each responsible for interacting with a different protein or set of helix is sealed by DNA ligase, the same enzyme that joins the Okazaki fragments during replication of the lagging DNA strand. Chapter 2 – Chemical Components of Cells proteins. Ionizing vs Non-Ionizing Radiation: When moving at relativistic speeds these particles have enough kinetic Motor Proteins: To make the conformational changes unidirectional—and force the entire cycle of movement to proceed in one direction—it is energy to be ionizing, but relativistic speeds are not required. For example, a typical alpha particle is enough to make any one of the steps irreversible. For most proteins that are able to move in a single direction for long distances, irreversibility is ionizing, but moves at about 5% c, and an electron with 33 eV (enough to ionize) moves at about 1% c. achieved by requiring the hydrolysis of an ATP molecule bound to the protein—which is why motor proteins are also ATPases. E.g. a great deal of Note: Neutron radiation consists of a free neutron, usually emitted as a result of spontaneous or induced nuclear fission. Able to travel hundreds or Living cells obey the same chemical and physical laws as nonliving things. Like all other forms of matter, they are made of atoms, which are the free energy is released when ATP is hydrolyzed, making it very unlikely that the protein will undergo a reverse shape change—as would be required even thousands of meters in air, they are however able to be effectively stopped if blocked by a hydrogen-rich material, such as concrete or water! smallest unit of a chemical element that retain the distinctive chemical properties of that element. for moving backward. Myosin walks along actin filaments at about 6 μm/sec during muscle contraction! Radiation Protection: Alpha (α) radiation consists of a fast-moving helium- 4 nucleus and is stopped by a sheet of paper. Beta (β) radiation, Cells are made up of a limited number of elements, four of which—C, H, N, O—make up about 96% of a cell’s mass. consisting of electrons, is halted by an aluminium plate.Gamma (γ) radiation, consisting of energetic photons, is eventually absorbed as it penetrates a Each atom has a positively charged nucleus, which is surrounded by a cloud of negatively charged electrons. The chemical properties of an atom are dense material. Neutron (n) radiation consists of free neutrons that are blocked by light elements, like hydrogen, which slow and/or capture them. determined by the number and arrangement of its electrons: it is most stable when its outer electron shell is completely filled. Linear No-Treshold Model of Radiation Dose: Alternative assumptions for the extrapolation of the DNA replication making more DNA : A covalent bond forms when a pair of outer-shell electrons is shared between two adjacent atoms; if two pairs of electrons are shared, a double bond Chapter 5 – DNA and chromosomes cancer risk vs. radiation dose to low-dose levels, given a known risk at a high dose: is formed. Clusters of two or more atoms held together by covalent bonds are known as molecules. (A) supra-linearity, (B) linear ineukaryotic cell: upthe usea When an electron jumps from one atom to another, two ions of opposite charge are generated; these ions are held together by mutual attraction forming (C) linear-quadratic, (D) hormesis beoa LNT: radiation is always considered harmful with no safety threshold, and the sum of several very small a noncovalent ionic bond. Happensin interphase : Living organisms contain a distinctive and restricted set of small carbonbased (organic) molecules, which are essentially the same for every living Life depends on the stable storage and inheritance of genetic information. exposures are considered to have the same effect as one larger exposure (response linearity). DNA Polymerase Thebuilder -> builds is new stand species. The main categories are sugars, fatty acids, amino acids, and nucleotides. Genetic information is carried by very long DNA molecules and is encoded in the linear sequence of four nucleotides: A, T, G, and C. Assessing the risk of radiation at low doses ( primes , membranes. The genetic material of a eukaryotic cell is contained in a set of chromosomes, each formed from a single, enormously long DNA molecule that (mean dose ~210 mSv), studies involving low doses are inconclusive for their influence on cancer rates. Ligase glues together - The vast majority of the dry mass of a cell consists of macromolecules—mainly polysaccharides, proteins, and nucleic acids (DNA and RNA); these contains many genes. Double-strand DNA breaks require a different stragety for repair: The repair mechanisms we have discussed thus far rely on the genetic redundancy macromolecules are formed as polymers of sugars, amino acids, or nucleotides, respectively. When a gene is expressed, part of its nucleotide sequence is transcribed into RNA molecules, many of which are translated into protein. built into every DNA double helix. E.g., if nucleotides on one strand are damaged, they can be repaired using the information present in the The most diverse and versatile class of macromolecules are proteins, which are formed from 20 types of amino acids that are covalently linked by Nucleotides: Nucleotides in nucleic acids are composed of three elements: complementary strand. But what happens when both strands of the double helix are damaged at the same time? Radiation, mishaps at the replication peptide bonds into long polypeptide chains. 1. a nitrogen-containing base fork, and various chemical assaults can all fracture the backbone of DNA. While especially hard to repair, cells have evolved two basic strategies: Nucleotides play a central part in energy-transfer reactions within cells; they are also joined together to form information-containing RNA and DNA 2. a five-carbon sugar 1. Rapidly sticking the broken ends back together before the DNA fragments drift apart and get lost—called nonhomologous end joining, carried out molecules, each of which is composed of only four types of nucleotides. 3. one or more phosphate groups by a specialized group of enzymes that “clean” the broken ends and rejoin them by DNA ligation, but this tends to remove nucleotides Protein, RNA, and DNA molecules are synthesized from subunits by repetitive condensation reactions, and it is the specific sequence of subunits that For DNA, the sugar is deoxyribose (hence the name deoxyribonucleic acid), and the base can be either adenine (A), cytosine (C), guanine (G), or 2. Homologous recombination—the preferred method for repairing double-strand breaks that arise shortly after the DNA has been replicated but determines their unique functions. thymine (T). A always pairs with T, and G always pairs with C. For RNA, the sugar is ribose and three of the four bases are the same—thymine is before the cell has divided. Four types of weak noncovalent bonds—hydrogen bonds, elec- trostatic attractions, van der Waals attractions, and hydrophobic interactions— replaced by uracil (U). Nucleotides are covalently linked together in a chain through their sugars and phosphates, which thus form an alternating enable macromolecules to bind specifically to other macromolecules or to selected small molecules. backbone of sugar–phosphate–sugar–phosphate. All nucleobases are hydrogen-bound on the inside of the double helix. The same four types of noncovalent bonds between different regions of a polypeptide or RNA chain allow these chains to fold into unique shapes The DNA that forms each eukaryotic chromosome contains, in addition to genes, many replication origins, one centromere, and two telomeres. These Chapter 7 – From DNA to Protein: How cells read the genome (conformations). special DNA sequences ensure that, before cell division, each chromosome can be duplicated efficiently, and that the resulting daughter chromosomes are parceled out equally to the two daughter cells. In eukaryotic chromosomes, the DNA is tightly folded by binding to a set of histone and nonhistone proteins. This complex of DNA and protein is called chromatin. The flow of genetic information in all living cells is DNA → RNA → protein. The Chapter 3 – Energy, Catalysis and Biosynthesis Histones pack the DNA into a repeating array of DNA–protein particles called nucleosomes, which further fold up into even more compact chromatin conversion of the genetic instructions in DNA into RNAs and proteins is termed gene structures. expression. Determining Nucleosome Structure: The structure of the nucleosome core particle was determined after first isolating nucleosomes by treating To express the genetic information carried in DNA, the nucleotide sequence of a gene is chromatin in its unfolded, “beads on a string” form with enzymes called nucleases, which break down DNA by cutting the phosphodiester bonds first transcribed into RNA. Transcription is catalyzed by the enzyme RNA polymerase, Living organisms are able to exist because of a continual input of energy. Part of this energy is used to carry out essential reactions that support cell between nucleotides. After digestion for a short period, only the exposed DNA between the core particles— the linker DNA—is degraded, allowing the which uses nucleotide sequences in the DNA molecule to determine which strand to use metabolism, growth, movement, and reproduction; the remainder is lost in the form of heat. core particles to be isolated. An individual nucleosome core particle consists of a complex of eight histone proteins—two molecules each of histones as a template, and where to start and stop transcribing. The ultimate source of energy for most living organisms is the sun. Plants, algae, and photosynthetic bacteria use solar energy to produce organic H2A, H2B, H3, and H4—and a stretch of double-stranded DNA 147 nucleotide pairs long that winds around this histone octamer. RNA! – The ribonucleic acid: The first step a cell takes in expressing one of its many molecules from carbon dioxide. Animals obtain food by eating plants or by eating animals that feed on plants. Chromosome Packing Occurs on Multiple Levels: Although long strings of nucleosomes form on most chromosomal DNA, chromatin in the living thousands of genes is called transcription—where the nucleotide sequence of a gene is copied into a RNA molecule. Each of the many hundreds of chemical reactions that occur in a cell is specifically catalyzed by an enzyme. Large numbers of different enzymes work cell rarely adopts the extended beads-on-a-string form. Instead, the nucleosomes are further packed on top of one another to generate a more compact Code is still written in essentially the same language—the language of nucleotides J Like DNA, RNA is a linear polymer made of four different in sequence to form chains of reactions, called metabolic pathways, each performing a different function in the cell. structure, such as chromatin fibers. This additional packing of nucleosomes into a chromatin fiber depends on a fifth histone called histone H1, which nucleotide subunits, linked together by phosphodiester bonds. Catabolic reactions release energy by breaking down organic molecules, including foods through oxidative pathways. Anabolic reactions generate the is thought to pull adjacent nucleosomes together into a regular repeating array.This changes the path DNA takes as it exits the nucleosome core, But!-–it differs from DNA chemically in two respects: (1) the nucleotides in RNA are ribonucleotides—they contain the sugar ribose (hence the name many complex organic molecules needed by the cell, and they require an energy input. In animal cells, both the building blocks and the energy required allowing it to form a more condensed chromatin fiber ribonucleic acid) (2) RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains uracil (U) instead of the thymine (T) for the anabolic reactions are obtained through catabolic reactions. A cell can regulate its chromatin structure—temporarily decondensing or condensing particular regions of its chromosomes—using chromatin- Cells produce various types of RNA: The vast majority of Enzymes catalyze reactions by binding to particular substrate molecules in a way that lowers the activation energy required for making and breaking remodeling complexes and enzymes that covalently modify histone tails in various ways. genes carried in a cell’s DNA specify the amino acid specific covalent bonds. The loosening of chromatin to a more decondensed state allows proteins involved in gene expression, DNA replication, and DNA repair to gain sequences of proteins—and the RNA molecules encoded by The rate at which an enzyme catalyzes a reaction depends on how rapidly it finds its substrates and how quickly the product forms and then diffuses access to the necessary DNA sequences. these genes are called messenger RNAs (mRNAs). In away. These rates vary widely from one enzyme to another. Some forms of chromatin have a pattern of histone tail modification that causes the DNA to become so highly condensed that its genes cannot be eukaryotes, each mRNA typically carries information expressed to produce RNA; such condensation occurs on all chromosomes during mitosis and in the heterochromatin of interphase chromosomes. transcribed from just one gene, which codes for a single The only chemical reactions possible are those that increase the total amount of disorder in the universe. The free-energy change for a reaction, ΔG, The regulation of chromosome structure: Another way of altering chromatin structure relies on the reversible chemical modification of the histones. protein. In bacteria, a set of adjacent genes is often measures this disorder, and it must be less than zero for a reaction to proceed spontaneously. The tails of all four of the core histones are particularly subject to these covalent modifications. For example, acetyl, phosphate, or methyl groups can transcribed as a single mRNA, which therefore carries the The ΔG for a chemical reaction depends on the concentrations of the reacting molecules, and it may be calculated from these concentrations if the be added to and removed from the tails by enzymes that reside in the nucleus.These and other modifications can have important consequences for the information for several different proteins. The final product of equilibrium constant (K) of the reaction (or the standard free-energy change, ΔG°, for the reactants) is known. stability of the chromatin fiber. Acetylation of lysines, for instance, can reduce the affinity of the tails for adjacent nucleosomes, thereby loosening other genes, however, is the RNA itself—these nonmessenger Equilibrium constants govern all of the associations (and dissociations) that occur between macromolecules and small molecules in the cell. The larger RNAs, like proteins, have various roles, serving as regulatory, the binding energy between two molecules, the larger the equilibrium constant and the more likely that these molecules will be found bound to each chromatin structure and allowing access to particular nuclear proteins. Most importantly, however, these modifications can serve as docking sites on the histone tails for a variety of regulatory proteins. E.g., different patterns of modifications attract different proteins to particular stretches of structural, and catalytic components of cells. other. chromatin.These patterns mean different things to the cell!--one pattern, for example, indicates that a particular stretch of chromatin has been newly RNA differs in several respects from DNA. It contains the By creating a reaction pathway that couples an energetically favorable reaction to an energetically unfavorable one, enzymes can make otherwise sugar ribose instead of deoxyribose and the base uracil (U) impossible chemical transformations occur. replicated, another indicates that the genes in that stretch of chromatin should be expressed; still others indicate that the nearby genes should be silenced instead of thymine (T). RNAs in cells are synthesized as single-stranded molecules, which often fold up into complex three-dimensional shapes. A small set of activated carriers, particularly ATP, NADH, and NADPH, plays a central part in these coupled reactions in cells. ATP carries high- Cells make several functional types of RNAs, including messenger RNAs (mRNAs), which carry the instructions for making proteins; ribosomal energy phosphate groups, whereas NADH and NADPH carry high-energy electrons. Most DNA that is permanently folded into heterochromatin in the cell does not contain genes: Because heterochromatin is so compact, genes that accidentally become packaged into heterochromatin usually fail to be expressed. Such inappropriate packaging of genes in heterochromatin can cause RNAs (rRNAs), which are the crucial components of ribosomes; and transfer RNAs (tRNAs), which act as adaptor molecules in protein synthesis. Food molecules provide the carbon skeletons for the formation of macromolecules. The covalent bonds of these larger molecules are produced by To begin transcription, RNA polymerase binds to specific DNA sites called promoters that lie immediately upstream of genes. To initiate disease: the gene that encodes β-globin—which forms part of the oxygen-carrying hemoglobin molecule—is situated next to a region of condensation reactions that are coupled to energetically favorable bond changes in activated carriers such as ATP and NADPH. transcription, eukaryotic RNA polymerases require the assembly of a complex of general transcription factors at the promoter, whereas bacterial RNA heterochromatin. If, because of an inherited DNA deletion (eyðing), that heterochromatin spreads, the β-globin gene is poorly expressed and the person develops a severe form of anemia. polymerase requires only an additional subunit, called sigma factor. intracellular : [K]i RNA Polymerase: Like DNA polymerase, RNA polymerases catalyzes the formation of the phosphodiester bonds that link the nucleotides together Calculate JG for the reactions and determine whether the and form the sugar–phosphate backbone of an RNA chain. RNA polymerase moves stepwise along DNA, unwinding the helix just ahead to expose a Chapter 4 – Protein Structure and Function Extracellular : [K]o jofnunum new region of the template strand for complementary base-pairing. Just like DNA synthesis, the growing RNA chain is extended by one nucleotide at a reactionwillcurTaahSee er hlitina Sinc Calculate the equilibrum potential , Un , and electric field RT = 0 616. Refraction example : In Still D i Ath!Hafa strength , E , across membrane (d =... ) and VEQ and Vop acting on 160 each species : Calculate equilibrium for tractive index K following reactions : constants 0 616 the - Va =n ind. K ATH ! e = cl : VEQ = 0 05 fyrir = 0 0581 160. 11/. - 0 616 In.. =.  Final exam - Sameinda og frumulíffræði | Bryndís Brynjúlfsdóttir time in the 5′-to-3′ direction. Also similar to DNA synthesis, incoming ribonucleoside triphosphates (ATP, CTP, UTP, and GTP) provide the energy Diffusion gradients—concentration differences between intra- and extracellular spaces, The inwardly-directed electric field generated by 5. What are the main secondary folding patterns in a protein's polypeptide backbone? a helices and B sheets needed to drive the reaction forward. ion flow, Membrane structure (availability of pores for passive transport), Active transport of ions against an established electrochemical 6. Which term describes smaller, compact three-dimensional regions within a protein? Protein domains RNA Splicing: How does the cell determine which parts of the RNA transcript to remove during splicing? Unlike the coding sequence of an exon, gradient. The general rules: Cations (positively charged): K+ ions can exit the cell easily, while it is more difficult for Na+ to enter. 7. What do we call a protein that catalyzes the formation or breakage of a covalent bond in a ligand? Enzyme most of the nucleotide sequence of an intron is unimportant. Although there is little overall resemblance between the nucleotide sequences of Anions (negatively charged): Cl- enters the cell easily, while large anions (protein molecules, organic phosphate compounds, sulfate 8. What is the primary role of amino acid side chains at the active site of an enzyme? Favor high-energy transition states in substrates different introns, each intron contains a few short nucleotide sequences that act as cues for its removal from the pre-mRNA. Guided by these compounds, etc.) cannot easily exit the cell. Na-K pump ejects Na+ more efficiently than injecting K+.Therefore, in resting state, outside 9. Which method of protein regulation involves the binding of multiple small ligands to specialized regulatory binding sites? Allosteric regulation sequences, an elaborate splicing machine cuts out the intron in the form of a “lariat” structure which is ultimately degraded. This machine is largely the cell there is an excess of positive charge, and the inside of the cell is conversely negatively charged 10. What is a common characteristic of allosteric proteins? They have multiple conformations. comprised of RNA molecules rather than proteins—called small nuclear RNAs (snRNAs), they are packaged with additional proteins to form small Na+ and K+ concentration gradient: The neuron cell membrane is super permeable to potassium ions, and so lots of potassium leaks out 11. What common form of enzyme regulation involves the interaction of reaction products with their own metabolic pathways? Feedback inhibiation nuclear ribonucleoproteins that recognize splice-site sequences through complementary base-pairing of the neuron through potassium leakage channels (holes in the cell wall). The neuron cell membrane is partially permeable to sodium 12. What do motor proteins use as the primary energy source for directed movement in eukaryotic cells? Hydrolysis of ATP to ADP Why do we splice? - Coding diversity: The transcripts of many eukaryotic genes can be spliced in different ways, each of which can produce a distinct ions, so sodium atoms slowly leak into the neuron through sodium leakage channels. The cell wants to maintain a negative resting 13. Which type of protein assembly features multiple different proteins that carry out complex functions together in an efficient, coordinated manner? protein. Such alternative splicing thereby allows many different proteins to be produced from the same gene—indeed, about 95% of human genes are membrane potential, so it has transporter proteins that pump potassium back into the cell and pumps sodium out of the cell at the same Protein machines thought to undergo alternative splicing! Thus RNA splicing enables eukaryotes to increase the already enormous coding potential of their genomes. time. During the resting state (before an action potential occurs) all of the gated sodium and potassium channels are closed. These gated 14. Which technique is used to obtain individual proteins in pure form from cell or tissue homogenates? Chromatography Evolutionarily, the intron–exon structure of genes is thought to have sped up the emergence of new and useful proteins: novel proteins appear to have channels are different from the leakage channels and only open once an action potential has been triggered. We say these channels are 15. Which of the following proteins is responsible for catalyzing the removal of a phosphate group? Phosphatase arisen by the mixing and matching of different exons of preexisting genes “voltage-gated” because they are open and closed depends on the voltage difference across the cell membrane. 16. Which of the following proteins is one of the canonical biomarkers in Alzheimer's disease? Amyloid B Most protein-coding genes in eukaryotic cells are composed of a number of coding regions, called exons, interspersed with larger noncoding regions, Action potential Treshold: An action potential will not occur until the initial rise in membrane potential is great enough to create the 17. Which of the following ways is NOT one of the ways that enzymes encourage reactions? Increasing substrate concentration. The ways that enzymes called introns. When a eukaryotic gene is transcribed from DNA into RNA, both the exons and introns are copied. positive feedback described in the preceding slide. This occurs when the number of Na+ ions entering the fiber becomes greater than the encourage reactions: Lowering activation energy, Providing an active site, Reducing reaction specificity, Regulatory binding at allosteric binding sites Introns are removed from the RNA transcripts in the nucleus by RNA splicing, a reaction catalyzed by small ribonucleoprotein complexes known number of K+ ions leaving the fiber. A sudden rise in membrane potential of 15 to 30 millivolts is usually required. E.g., a sudden increase 18. Which of the following macromolecules carries genetic information in cells and is encoded by the linear sequence of nucleotides A, T, G, and C? DNA as snRNPs. Splicing removes the introns from the RNA and joins together the exons—often in a variety of combinations, allowing multiple proteins in membrane potential in a large nerve fiber from -90 millivolts up to about -65 millivolts usually causes the explosive development of an 19. What type of bond holds the complementary DNA strands together in a double helix? Hydrogen bonds to be produced from the same gene. action potential. This level of -65 millivolts is said to be the threshold for stimulation. 20. What is the role of centromeres in eukaryotic chromosomes? Separation of sister chromatids during cell division Eukaryotic pre-mRNAs go through several additional RNA processing steps before they leave the nucleus as mRNAs, including 5′ RNA capping and Electrophysiology of Muscle: Muscle contraction due to a change in the relative sliding of thread-like molecules or filaments: Actin 21. Which molecule is transcribed from a gene and can be translated into a protein? RNA 3′ polyadenylation. These reactions, along with splicing, take place as the pre-mRNA is being transcribed. filaments (also known as microfilaments): helical polymers of the protein actin. Myosin filaments: a molecule of myosin-II contains two 22. What structures of the chromosome initiate the process of DNA replication during cell division? Replication origins Translation of the nucleotide sequence of an mRNA into a protein takes place in the cytoplasm on large ribonucleoprotein assemblies called identical heavy chains, each with a globular head and an extended tail, and two light chains bound to each head. Filament sliding is 23. In which direction does DNA polymerase add new nucleotides during DNA replication? 5' to 3' ribosomes. As the mRNA moves through the ribosome, its message is translated into protein. triggered by an Action Potential from a motor neuron. The myosin filament is like a double-headed arrow, with the two sets of myosin 24. What is the function of DNA helicase during DNA replication? Seperating DNA strands The Ribosome: Composed of one large subunit and one small subunit, which fit together to form a complete ribosome. The small ribosomal heads pointing in opposite directions, away from the middle. One set binds to actin filaments in one orientation and moves the filaments 25. What is the primary role of DNA ligase in DNA replication? Joining Okazaki fragments on the lagging strand subunit matches the tRNAs to the codons of the mRNA one way; the other set binds to other actin filaments in the opposite orientation and moves the filaments in the opposite direction. As a 26. Which complex of DNA and protein is formed when DNA is first folded in eukaryotic chromosomes? Nucleosome result, a myosin filament slides sets of oppositely oriented actin filaments past one another. 27. Which proteins are responsible for packing DNA into nucleosomes in eukaryotic cells? Histones The large subunit catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain. These two 28. What term describes the temporary decondensation or condensation of specific regions of chromosomes to regulate gene expression? Chromatin subunits come together on an mRNA molecule near its 5′ end to start the synthesis of a protein. The mRNA is then pulled through the ribosome like a Cerebral Cortex Structures: Frontal lobe: Concerned with reasoning, planning, parts of speech and movement (motor cortex), emotions, and problem-solving. Occipital lobe: Concerned with many aspects of vision. Parietal lobe: Concerned with perception of stimuli related remodeling long piece of tape. As the mRNA inches forward in a 5′-to-3′ direction, the ribosome translates its nucleotide sequence into an aminoacid sequence, to touch, pressure, temperature and pain. Temporal lobe: Concerned with perception and recognition of auditory stimuli (hearing) and 29. During which cell process does chromatin condense on all chromosomes, including the formation of heterochromatin in interphase chromosomes? one codon at a time, using the tRNAs as adaptors. memory (hippocampus). Mitosis How Ribosomes work: In addition to a binding site for an mRNA molecule, each ribosome contains three binding sites for tRNA molecules, called 30. Which structures are responsible for temporarily loosening chromatin to allow access to specific DNA sequences by proteins involved in gene the A site, the P site, and the E site. These are occupied in careful synchrony in the four-step translation cycle. The terms medial and lateral imply nearness and remoteness, respectively, to or from the central midline axis of the brain. Symbols: T (thalamus); HT (hypothalamus); MB (midbrain); SC (spinal cord); P pituitary gland). expression? Chromatin remodeling complexes The nucleotide sequence in mRNA is read in sets of three nucleotides called codons; each codon corresponds to one amino acid. 31. What is the role of telomeres in eukaryotic chromosomes? Preventing chromosome shortening The correspondence between amino acids and codons is specified by the genetic code. The possible combinations of the 4 different nucleotides in The Electroencephalogram: Pyramidal neurons make up the majority of the EEG signal. uniformly orientated with dendrites perpendicular to the surface, long enough to form dipoles. Synchronized neural activity produces larger signals. 32. Which of the following DNA base pairings features three stable hydrogen bonds? C-G RNA give 64 different codons in the genetic code. Most amino acids are specified by more than one codon. 33. Which term broadly describes the highly condensed, transcriptionally inactive regions of chromatin? Heterochromatin tRNAs act as adaptor molecules in protein synthesis. Enzymes called aminoacyl-tRNA synthetases covalently link amino acids to their appropriate Bioelectric Potentials in the Brain: Recorded potentials from the brain are called brain waves. Entire record is called 34. What is the primary function of euchromatin in the cell? Gene expression tRNAs. Each tRNA contains a sequence of three nucleotides, the anticodon, which recognizes a codon in an mRNA through complementary base- electroencephalogram (EEG). Brain recordings demonstrate continuous oscillating electrical activity. Intensity and pattern of recording 35. How many hydrogen bonds form between adenine (A) and thymine (T) base pairs in DNA? Two pairing. are determined by the overall excitation of the brain: Alpha Waves:8-13 Hz, occur when the subject is awake but rested. 36. Which of the following is the sugar molecule found in DNA nucleotides? Deoxyribose Protein synthesis begins when a ribosome assembles at an initiation codon (AUG) in an mRNA molecule, a process that depends on proteins called Beta Waves:14-30 Hz, occur during intense mental activity. Theta Waves:5-8 Hz, occurs during emotional stress, falling asleep. Delta 37. What is the primary purpose of DNA replication in a cell? To produce two identical DNA molecules translation initiation factors. The completed protein chain is released from the ribosome when a stop codon (UAA, UAG, or UGA) in the mRNA is Waves: 0.1-5 Hz, occur in deep sleep or in serious brain disease 38. During DNA replication, what structure forms at the replication origin? Replication fork reached. 39. What is the role of DNA polymerase during DNA replication? Synthesizing new DNA strands The stepwise linking of amino acids into a polypeptide chain is catalyzed by an rRNA molecule in the large ribosomal subunit, which thus acts as a 40. How does DNA polymerase achieve remarkable accuracy during DNA replication? By proofreading and correcting errors ribozyme. 41. Why is the synthesis of the lagging strand during DNA replication discontinuous? DNÀ polymerase can only synthesize DNA in the S' to 3' direction. The concentration of a protein in a cell depends on the rate at which the mRNA and protein are synthesized and degraded. Protein degradation in the Miðannapróf 1 – Introduction to cell biology, biochemistry of the cell and proteins (Chapters 1-3): 42. Which enzyme primes DNA synthesis by creating short lengths of RNA during replication? RNA polymerase cytosol and nucleus occurs inside large protein complexes called proteasomes. 43. What is responsible for the remarkable accuracy of DNA replication, making only one error per 107 nucleotides copied? DNA polymerase From our knowledge of present-day organisms and the molecules they contain, it seems likely that life on Earth began with the evolution of RNA 44. What enzyme is responsible for replicating the DNA at the ends of eukaryotic chromosomes? Telomerase molecules that could catalyze their own replication. 45. What is the consequence of a double-strand break in DNA if it is rapidly repaired by nonhomologous end joining? Nucleotides are lost, altering the