Biology 3030 Exam 1 Study Guide
Transcription in prokaryotes occurs in the cytosol. Transcription is the process by which DNA is transcribed into mRNA. In animal cells, this takes place in the nucleus. Translation is the process in which the mRNA is translated into a protein. This occurs simultaneously with transcription in bacteria. In animal cells, this process takes place in the ribosomes.
∙ Bacterial transcription
o RNA polymerase forms a complex with sigma called a holoenzyme.
o Sigma allows RNA Polymerase to recognize and bind to the promoter. This step is called initiation.
o There are two promoter sequences located upstream of the promoter: the 10 (TATAAT) box 10 base pairs from the beginning of the DNA strand and the 35 (TTGACA) box located 35 base pairs away.
o In Elongation, sigma leaves. RNA Polymerase continues to transcribe DNA and adding NTPs (ribonucleoside triphosphates).
o The holoenzyme consists of a core enzyme (RNA Polymerase) and proteins (sigma).
o At the transcription site the DNA copied is the template strand
o The DNA not copied is the nontemplate strand or coding stand.
o The area where DNA has been unzipped is called the transcription bubble. o RNA Polymerase moves along the DNA stand in the 3’5’ direction and synthesizes a complimentary mRNA in the 5’3’ direction. It adds NTPs to the growing mRNA on the 3’ end. Don't forget about the age old question of What are the sociological theories?
o During Termination, RNA Polymerase transcribes a sequence that makes the mRNA form a hairpin. This disrupts transcription and pulls the mRNA away from RNA Polymerase and the ribosomes and ends transcription.
∙ Eukaryotic Transcription
o Eukaryotes have three RNA Polymerases.
o RNA Polymerase II transcribes mRNA.
o Have basal transcriptions factors instead of sigma. They bind directly to the promoter (TATA box, which is 30 bp upstream) and help RNA Polymerase bind to the promoter.
o Termination occurs when the PolyA signal is transcribed.
o After transcription, mRNA needs to be processed before it is mature and is called premRNA. This involves splicing (cutting out introns) addition of 5’cap and polyA tail.
o SnRPs recognize the sequence GU and splices the 5’end. The premRNA forms a lariat. The 3’ end is cut and the exon ends join via phosphodiester bonds. The 5’ cap and 3’polyA tail protects the mRNA from degradation and allows the ribosomes to recognize it.
o The mRNA is translated 5’3’. The tRNA anticodon that binds to the mRNA codon is 3’5’(aka: antiparallel). If you want to learn more check out Who is hardy weinberg?
o A polyribosome is where more than one ribosome translates mRNA at one time. This occurs in both prokaryotes and eukaryotes.
o AminoacyltRNA Synthetase charges (adds amino acids) onto the 3’ end of tRNA.
o Charged tRNA is called aminoacyl tRNA.
o tRNA has three ribonucleosides called anicodons.
o There are 20 different amino acids, 61 different codons, 40 different tRNAs, and a specific aminoacyl tRNA synthetase for each amino acid. If you want to learn more check out What are sigmund freud's contributions to society?
o The Wobble Hypothesis states that the first two anticodons must match the mRNA codons, but the third anicodon could be any base.
o Translation occurs inside the ribosome.
o The ribosome has a small subunit and a large subunit.
o Translation begins with the start codon AUG.
o In bacteria, a special tRNA carriying fmet is required. In eukaryotes, only a tRNA carrying methionine is required.
o The tRNA binds to the P site on the small ribosomal subunit. Another tRNA binds in the A site. The amino acid on the tRNA in the P site is transferred to the amino acid in the A site. The ribosome moves down one codon. The tRNA in the P site is now in the E site and exits. The tRNA in the A site is now in the P site. A new tRNA binds to the open A site.
o Amino acids are attatched to tRNAs via hydrogen bonding.
o A special tRNA coded for by the sequence UAA, UAG, or UGA stops translation by binding to the A site and releases the polypeptide chain.
o Post mRNA processing include folding and chemical processing.
o Protein function is determined by the way a protein is folded.
o Molecular chaperones guide the folding.
∙ Gene expression: The process of translating the info in DNA into functional molecules. ∙ Translation: The process of converting nucleotide bases into protein. We also discuss several other topics like What is comparative physiology?
∙ The Triplet codon is:
o Redundant: some amino acids are coded by more than 1 triplet codon. o Unambiguous: 1 codon never codes for more than one amino acid.
o Universal: All codons specify the same amino acids in all organisms.
o Conservative: The first two bases are identical when multiple codons specify the same amino acid (remember the Wobble Hypothesis?)
o The ribosome is a ribozyme made of rRNA and catalyzes peptide bond formation between amino acids.If you want to learn more check out What are some ways that cells have modified (multicellular organisms)?
∙ Mutation: Any permanent change in an organism’s DNA, change in genotype, and ability to create new alleles.
o Point mutations: From a single base change. Can be missense ( change amino acid sequence) or silent ( does not change amino acid sequence). Results when the DNA repair system fails.
o Chromosomal mutations are visualized with a karyotype. Can result in polyploidy ( increase in the number of each type of chromosome), aneuploidy ( addition or deletion of a chromosome), Inversion ( A chromosome section breaks off, turns 180o and rejoins), or Translocation ( A broken section of one chromosome attaches to another chromosome). We also discuss several other topics like What is diorama for?
o Spinocerebellar ataxia (SCA13 is an autosomal dominant disease that affects the cerebellum caused by the KCNC3 gene that codes for K+ channel kv3.3 ( a tetramer).
o The adult form is caused by a base sequence change of CGC to CAC (arginine to histidine). Symptoms are progressive ataxia cerebellar degeneration. It is in the voltage sensor region of the channel.
o The infant form is caused by a base sequence change of TTC to CTC (phenylalanine to leucine). Symptoms include delayed development and
malformation of the cerebellum, delayed motor skills, and ataxia. It occurs in the pore region of the channel.
Before transcription and translation can take place, chromatin must be decondensed in a process called chromatin remodeling to all RNA polymerase to access the DNA.
∙ DNA is wrapped around 8 histone proteins and an H1 histone protein (glues DNA together) to form a structure called a nucleosome. It looks like beads on a string. ∙ The space between each nucleosome is called linker DNA.
∙ The nucleosomes are packed into a 30 nm fiber which is attached to scaffold/framework proteins inside the nucleus.
∙ The 30 nm fiber is then further condensed later during cell division.
∙ Chromatin remodeling involves altering chromatin by DNA methylation, histone modification, or chromatinremodeling complexes.
∙ DNA methylation is the process by which DNA methyltransferases add methyl groups to cytosine residues in DNA at the sequence CG or CpG.
o The methylated regions are recognized by proteins that trigger chromatin condensation, so actively transcribed regions have low levels of CpG methylation. ∙ Histone modification is the process in which histone acetyl transferase (HATs) add acetyl groups to (+) charged lysing residues in histones. The () charged acetyl groups neutralize the histones and they release the DNA.
o The histone code states that particular combinations of histone modifications set the state of chromatin condensation for a particular gene.
o Histone deacetylases (HDaCs remove acetyl groups to condense the DNA again. ∙ Chromatin remodeling complexes use energy from ATP to reshape the chromatin by sliding nucleosomes along the DNA strand or to knock off histones in order to decondense DNA.
∙ Chromatin Modifications can be inherited through epigenetic inheritance (inheritance from something other than DNA.
∙ Eukaryotes have regulatory sequences called the promoter/core promoter where RNA polymerase binds to, promotor proximal elements, enhancers, and silencers. o Regulatory TATAbinding proteins (TBP) are the basal transcription factors that bind to the promoter.
o Promoter Proximal Elements allows only certain genes to be expressed. o Enhancers enhance gene expression. They can be far away from the promoter and can be on introns, exons, UTRs (untranslated regions, upstream, downstream, on the 3’end, or on the 5’end. They can even be flipped around and placed somewhere else in on the gene. Transcription activator proteins bind to enhancers. Enhancers are like gas pedals in gene expression.
o Silencers are like brake pedals in gene expression. They are similar to enhancers except that they silence gene expression. Repressor proteins bind to them. ∙ Regulatory Transcription Factors are activator and repressor proteins, mediators and general transcription factors.
∙ Different cells express different genes because they have different transcription factors. ∙ Transcription factors recognize molecules in the major and minor grooves. o General transcription factors (TBP) can bind to any gene of any cell type. o Mediators are the bridge between regulatory transcription factors, general transcription factors, and RNA polymerase.
∙ After transcription, the primary transcript (premRNA) undergoes splicing. This splicing is actually called alternative splicing.
o Certain parts of mRNA need to be inhibited, destroyed or altered, or protein activity may need to be altered.
o Some introns or exons may be spliced out.
o Different splicing patterns result in different protein functions.
o Splicing is controlled by SnRPs
∙ Global regulation of translocation occurs when the process of translations is halted and is controlled by a proteins kinase called mTor. mTor phosphorylates translation initiation factors. mTor is regulated by RNA induced silencing.
∙ RNA induced silencing
o RNA polymerase transcribes genes that code for a hairpin structure (like bacterial transcription termination).
o In the nucleus, proteins bind to the hairpin to form a RNA processing complex that cuts the 5’ and 3’ ends.
o This premiRNA migrates to the cytoplasm and binds to a second RNA processing complex where the hairpin is trimmed, leaving a short double stranded premiRNA.
o The double stranded premiRNA is unwound by helicase, which digests one strand.
o The now mature single stranded miRNA binds to the RISC complex (RNA Induced Silencing Complex). RISC looks for complementary sequences in other target mRNA molecules that are complementary to the miRNA.
o If it finds a complimentary match, it cuts the mRNA in half. If the sequence is close but not quite complimentary, RISC inhibits translation.
∙ Posttranslation control includes:
o Protein activity is changed by enzymes that add sugars or cut off amino acids. o Proteins are phosphorylated by kinases (mTor) or cyclin –cdk complexes. o Proteins may be tagged with ubiquitin and digested by proteasomes.
o P53 is an example of a tumor suppressor gene. It turns off gene expression. o Protooncogenes turn on gene expression. They are called oncogenes if they mutate and continually tell the cell to replicate.
o Mutant P53 genes cannot bind to enhancers and the cell replicates continuously.
Kinetic energy is the energy of motion. Potential energy is the energy that is stored. Exothermic and endothermic reactions measure the energy or enthalpy in a system. Exergonic and Endergonic reactions measure the entropy or free energy of a system.
∙ In a reaction, if the products have shorter, stronger covalent bonds, potential energy decreases because more energy is required to break those bonds.
∙ First Law of Thermodynamics: Energy can’t be created or destroyed. Delta H = total energy of system=enthalpy.
o Enthalpy includes the potential energy of a molecule and effect on it by pressure and volume.
o Exothermic if reaction releases heat and products have decreased potential energy (H).
o Endothermic if reaction uses hear and products formed have increased potential energy (bonds that can easily be broken). Have +H.
∙ Second Law of Thermodynamics: Entropy always increases.
o Measures spontaneity of a reaction.
o Delta G=free energy. It measures the free energy available to do work: G=HTS, where H is the enthalpy, T is the temperature (in Kelvins) and S is the energy of the universe.
o () G= exergonic reaction. Releases energy and occurs spontaneously. Has high energy reactants and low energy products.
o (+) G= endergonic reaction. Uses energy. Has low energy reactants and high energy products.
o When G=0, the reaction is at equilibrium.
∙ Molecules must in the proper orientation to break bonds and bring electrons together in order to interact.
∙ The number of collisions in a reaction depends on the temperature and concentration of reactants.
o As temperature increases, molecules move faster and collide more frequently o As concentration of reactants increases, the number of collisions increases and the reaction process becomes faster.
∙ Phosphorylation couples exergonic and endergonic reactions.
o Exergonic reactions do not require an input of energy.
o Endergonic reactions do require an input of energy from ATP through a process called energetic coupling.
o Energetic coupling: energy released from exergonic reactions cleave 1 phosphate off of ATP to drive endergonic reactions. This occurs either through the transfer of electrons or phosphates.
∙ Energetic coupling through the transfer of electrons
o Redox reactions. One molecule is oxidized (loses electrons; loses hydrogens if there are any) and is called an electron donor. One molecule is reduced (gains electrons; gains hydrogens if there are any) and is called an electron acceptor.
o Electron acceptors gain energy as they are reduced because new weaker bonds new weaker bonds are formed.
o In a metabolic reaction, FAD is reduced to FADH2 and NAD is reduced to NADH.
o All reactions require a transfer of electrons but not always a transfer of hydrogen. o ATP has three () charged phosphates with strong repulsive forces that gives ATP is high potential energy.
o ADP has a lower potential energy, so the hydrolysis of ATP is exergonic. o ATP is a phosphate donor and phosphorylates a substrate to give it energy. ATP changes endergonic reactions into exergonic reactions.
∙ Reactions rates are increased by the help of enzymes.
o They are not used up in reactions.
o They bring the substrates together in the proper orientation instead allowing them to randomly collide.
o Enzymes have a depression where the substrates bind called the active site.
o There are two theories on how the enzyme and substrates bind together: Lock and Key model and the Induced Fit Model.
∙ Lock and Key enzyme model: Enzymes are fixed and can’t move. The substrates (example is glucose and ATP) fit perfectly in the active site.
∙ Induced Fit Model: Once the substrates bind the enzyme moves forward over the active site to bring the substrates closer together. The substrates are help in the active site via hydrogen bonding.
∙ Once the substrate is bound the enzymesubstrate enter the transition state. The transition state lowers the activation energy of a reaction. The free energy of the transition state is high because the bonds that exist the substrate are destabilized (broken in order to form new bonds).
o Reaction rates depend on both kinetic energy and the activation energy required to get to the transition state.
o Interactions with the amino acid residues in the active site stabilize the transition state and lowers the activation.
o Rgroups lining the active site form temporary covalent bonds to assist the transfer of atoms from atoms from one reactant to another.
o Lower activation energy does not decrease the free energy or change the energy of the reactants or the products.
o Enzymes only decrease the activation energy required to get to the transitions state.
∙ The process of substrate binding has three phases: initiations, transition state facilitation, and termination.
o Initiation: enzymes orient substrate at active site.
o Transition state: inside of the active site, the substrates enter the transition state which is stabilized by the enzymes’ shape. Interactions between the active site and Rgroups lower the activation energy and the catalyzed reaction proceeds faster.
o Termination: The products are released from the enzyme.
∙ Enzymes are proteins and are affected by temperature, pH, and interaction with other molecules.
o Cofactors (metal ions) and coenzymes (organic molecules like NADH or FADH2), and prosthetic groups ( nonamino acid molecules permanently attached to the protein Retinol) are part of the active site and stabilize the transition state.
o Temperature affects the way enzymes fold and their speed/kinetic energy. o pH affects the charge on amino acid residues.
o Enzymatic reactions rely on the concentration of substrate, concentration of enzyme, temperature, and pH.
∙ Enzymes are regulated in a variety of ways through inhibition of irreversible non covalent binding molecules and reversible covalent binding molecules. o Reversible inhibition:
Competitive inhibition: regulatory molecule is similar in shape and size to substrate and binds to the enzyme’s active site.
∙ Allosteric Activation: changes enzyme shape to activate enzyme.
∙ Allosteric Inhibition: changes enzyme shape to inactivate enzyme.
Phosphorylation: Enzyme is phosphorylated by ATP. This can alter the enzymes shape and either activate it or deactivate it.
o Irreversible inhibition: enzyme modifications that involve cleavage of peptide bonds.
o Feedback Inhibition
In a multistep reaction there are several enzymes.
Enzymes are not used up in the reaction.
In each subsequent reactions, the energy of the products is higher than the energy of the reactants.
If the concentration of products increases, some of the product will feed back and bind to the enzyme in an earlier step to deactivate it.
∙ ()G= A decrease in enthalpy and an increase in entropy.
∙ (+)G= An increase in enthalpy and an increase in entropy.
Cells have a plasma membrane that separates the outside world and the inside of the cell in order to regulate what goes into and out of the cell. Cells have a network of fibers that support the plant and allow for communication between cells.
∙ The ground substance is a cell’s first line of defense, affects cell shape, and allows it to adhere to surfaces and other cells.
∙ The extracellular matrix (ECM) is secreted by the animal cell and provides structural support. It is made in the Rough Endoplasmic Reticulum, modified in the Golgi, and then secreted. The amount of ECM and proteins it is made of varies depending on the particular kind of tissue it is in.
o Contains many proteins such as collagen and proteoglycan.
Collagen is elastic and supports the cell structure and attaches to the cell surface. It consists of three polypeptide chains twisted together and is the main component of the ECM
Proteoglycans surround collagen and secrete gel
∙ Integrins bind to ECM crosslinked proteins called laminins, which bind to other parts of the ECM skeleton to keep individual cells in place and aid in the adhesion to other cells.
∙ Plants have a primary cell wall made of bundled cellulose called microfibrils. It is cross linked to other polysaccharide filaments as well via hydrogen bonding. o The primary cell wall defines the shape of the plant through turgor pressure o Turgor Pressure: the process by which water flows into the cell via osmosis due to a higher concentration of solute. The increased volume of water pushes the plasma membrane up against the cell wall.
o Microfibrils are synthesized by enzymes.
o Spaces between microfibrils are filled with gelatin secreting proteins called pectin. They are hydrophilic.
o Pectins keep the cell moist and are made in the Rough ER and processed in the Golgi as well.
o Young plant cells have expansion proteins that disrupt hydrogen bonds in cross linked microfibrils in the cell wall allowing turgor pressure to elongate and expand the cell wall.
∙ Secondary cell walls is found in mature plants. It is Located between the plasma membrane and the primary cell wall.
o Function varies cellcell. Some are wax and aid in waterproofing and some have cellulose and support the plant’s stem.
o Trees have both lignin and cellulose to support their trunks and provide a very rigid structure.
∙ Multicellularity is the way cells connect to each other to communicate via the ECM.
o Epithelia tissues for external and internal surfaces and form a barrier between the cell and the outside world and separates organs with in the cell.
o The ECM between cells has a middle lamella that glue cells together. They are reinforced by collagen fibrils.
∙ Animal cells have membranes that allow for attachment to other cells like the secondary wall in plants.
o Junctions and desmosomes hold cells together.
o Gap junctions and plasmodesmata are involved in intercellular communication. o Tight junctions are made of special proteins in the plasma membrane. Long chains of these connect to other long chains of tight junctions on adjacent cells to prevent fluid from flowing in between the cells. Example: epithelial cells that line your stomach.
o Cadherin are proteins that link cells to desmosomes. Cells from different types of tissues have different cadherin, which can only bind to the same type of cadherin in the same type of tissue.
o Cadherins are the basis for selective adhesion (cells of the same type of tissue adhere).
∙ Cells can communicate via diffusion of cytosolic ions and small molecules. o Signals that regulate gene expression and alters which proteins should be produced.
o Signals that activate/inactivate proteins in the cell involved in metabolism, membrane support, secretions, and the cytoskeleton.
o Hormones are messengers secreted by the cell to act on distant targets and function in the cellular communication receptor.
o Lipid soluble molecules diffuse across the hydrophobic region of the membrane to enter the cytosol of target cells. The receptors for these molecules are inside the cell.
o Large/hydrophobic signal molecules cannot pass the plasma membrane are lipid insoluble. They are recognized by receptors in the plasma membrane.
∙ How lipid soluble signal proteins alter gene expression
o Lipid soluble signal proteins, like steroids, enter the cytosol and bind to a hormone receptor complex
o It is transported to the nucleus.
o The signal protein triggers a change in gene expression.
∙ How lipidinsoluble signal proteins enter the cell.
o Lipid insoluble hormones bind to the receptor on the plasma membrane. o A signal transduction is triggered and amplified. It causes ion channels to be opened.
Gprotein coupled receptors initiate the production of intracellular second messengers that amplify the signal.
Enzymelinked receptors amplify the signal by activating a series of proteins inside the cell by phosphorylating them.
o Are activated by signal receptors.
o Activate a second messenger
o Regulated by GDP and GTP.
o When a signal proteins binds to a receptor, the receptor activates the Gprotein by kicking out GDP and allowing GTP to bind.
o The Gprotein activates an enzyme that catalyzes the production of a second messenger.
o Second messengers are small so they can work quickly.
∙ Enzymelinked receptors
o Catalyze a reaction inside a cell triggered by a hormone signal molecule. o An example is the RTKs (receptor tyrosine kinases).
o A hormone binds to the two RTK subunits causing them to form a dimer. o RTK is activated and phosphorylates itself.
o Proteins bind to RTK and connect it to the Peripheral Membrane Protein, RAS. RAS is a type of Gprotein.
o RAS exchanges GDP for GTP and triggers the phosphorylation and activation of a protein kinase.
o This first protein kinase phosphorylates and activates a second protein kinase. o This second protein kinase phosphorylates and activates a third protein kinase. o This third protein kinase phosphorylates other proteins.
o This process of phosphorylation is called the “Phosphorylation Cascade.” o The cascade is initiated by mitogen –activated protein kinases (MAPKs). o Scaffold proteins hold proteins involved in the cascade close together to speed up the process.
∙ Signal deactivation
o In signal transduction the process is terminated when the GTP loses a phosphate and becomes GDP. The Gprotein is then inactivated and the process stops. o In phosphorylation cascades, if the receptor tyrosine kinase stimulation ends, phosphatases remove phosphates from the components in the cascade and stops the process.
o When the smooth ER returns calcium ions to storage and phosphodiesterase converts cAMP and cGMP back to AMP and GMP, the second messengers stop.