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Bio Test 3 Study Set
| Question | Answer |
|---|---|
| What are mutations? | Changes to the DNA sequence in an organism |
| How does one get a mutation (2 ways)? | Mutations are either inherited or acquired during one's lifetime |
| What causes one to acquire a mutation? | Mutations could be caused by errors during DNA synthesis or exposure to substances that increase the rate of mutation |
| T or F: Mutations are harmful | False, mutations could be harmful, helpful, or neutral |
| What is one reason that individuals vary in traits and was a source of variation for natural selection during evolution? | Mutations |
| Allele | Different forms of a gene with slightly different DNA sequences |
| What is a silent mutation? | One nucleotide change that has no effect on the protein sequence |
| Why does a silent mutation have no effect on the protein sequence? | Due to the redundancy in the genetic code |
| What is a wild-type DNA sequence? | The form of a DNA sequence that is most common in the population |
| What is a missense mutation? | One nucleotide change results in one amino acid change in the protein |
| What is a nonsense mutation? | One nucleotide change converts a codon into an early stop codon in the mRNA, creating a shorter protein |
| What is a frameshift mutation? | An insertion or deletion of nucleotides changes the reading frame, making all amino acids beyond the shift different and a new stop codon may be created (close or far from the change) |
| What does the effect of missense mutations depend on? | The specific site in the protein that it occurs and the specific amino acid substitution |
| What is the usual/typical result of a nonsense mutation and why? | It usually results in "loss of function" mutations, since the shorted protein is usually non-functional |
| What insertions or deletions may or may not have an effect depending on what is gained or lost and where? | Insertions/deletions that are multiples of 3 (3, 6, 9, etc.) |
| T or F: Mutations in other DNA locations have less predictable effects. | True |
| What is a possible effect of a mutation to a DNA promoter? | It could affect how much transctiption occurs...or have no effect |
| What is a possible effect of a mutation to the introns in a DNA strand? | It could affect whether splicing works properly...or have no effect |
| What process must DNA replication occur before? | Before cell division |
| What is the process of cell division called? | Mitosis |
| What occurs during mitosis? | Each new cell will receive an identical double-stranded DNA molecule with one original (parental) strand and one newly synthesized strand |
| What are the similarities between DNA replication and trancription of RNA? | A polymerase can read a DNA template from 3' to 5' to build a new nucleic acid strand 5' to 3' |
| What makes DNA replication different from transcription of RNA? (4) | Makes exactly one copy of the full length of every chromosome; Both strands of DNA serve as templates; synth. begins at origins of rep. and end when DNA pol. runs into double stranded regions; DNA pol. can't begin synthesis without an RNA primer |
| What makes transcription of RNA different from DNA replication? (4) | Makes many copies of small segments of a chromosome; One of the DNA strands in the double-helix serve as the template; Synth. terminates at a specific sequence; Once RNA pol. binds to the promoter region, it is ready to start bonding the nucleotides |
| What are origins of replication and where are they located? | Origins of replication are DNA sites where DNA replication begins, and they are located in the middle of each replciation bubble |
| What is DNA helicase? | Enzyme (protein) that breaks H-bonds between the 2 DNA strands in the double-helix. Important to expose each strand as a template for replication |
| What are single strand DNA binding proteins? | Single strand binding proteins keep the two DNA strands from coming back together |
| How many origins of replication do prokaryotic chromosomes have? | 1 origin of replication |
| How many origins of replication do eukaryotic chromosomes have? | Eukaryotic chromosomes could have many origins of replication |
| What do DNA polymerases need in order to begin the process of nucleotide polymerization? | A primer |
| What is a primer and what is it composed of? | A primer is a short nucleic acid sequence that acts as a starting point for DNA synthesis by providing a free 3' OH. Primers are composed of RNA nucleotides |
| What type of nucleotides do DNA polymerases use? | DNA polymerases use dNTPs (dATP, d,CTP, dGTP, dTTP) |
| How are DNA polymerases similar to RNA polymerases? | Both enzymes read a DNA template strand and build/synthesize in the 5' to 3' direction |
| What do primers provide that DNA polymerase needs to begin synthesizing the new strand? | A free 3' OH to build onto |
| What is primase? | The enzyme that builds RNA primers |
| What happens after the short RNA primer is synthesized by primase? | The DNA polymerase will elongate the nucleic acid chain |
| Where does the synthesis of the copied strands initiate? | At the origin of replication |
| What is a replication bubble and what is it composed of? | the bubble of space between the two strands of DNA after being separated by DNA helicase (with an origin of replication in the middle of the bubble). The replication bubble is composed of two replication forks |
| T or F: Replication is one directional. | False, replication is bidirectional, meaning both strands are being copied in both directions at the same time |
| What does each replication fork consist of? (2) | A leading strand and a lagging strand |
| What type of synthesis is asscoiated with the leading strand? | Continuous synthesis |
| What type of synthesis is associated with the lagging strand? | Discontinuous synthesis |
| What are Okazaki fragments? | The discontinuous pieces of DNA that make up the lagging strand (does not include the RNA primers) |
| T or F: Each Okazaki fragment can use the same RNA primer. | False, each Okazaki fragment requires its own RNA primer |
| Why is the lagging strand considered discontinuous? | Because each Okazaki fragment is independently synthesized |
| What does DNA Polymerase III do at the DNA replication fork? | It extends from the primer to synthesize a complementary DNA strand |
| What do single-strand binding proteins do in the replication fork? | They keep the template strands of DNA separated |
| What does the sliding clamp do in the DNA replication process? | Sliding clamp proteins attach to DNA polymerase and keep it secured to the DNA strand, ultimately allowing DNA polymerase to be processive without releasing the template |
| What does DNA polymerase I do? | It degrades the RNA primer and fills in with DNA |
| What does DNA ligase do? | It seals the remaining gap (forming a phosphodiester bond) |
| T or F: DNA polymerase III has proofreading activity. | True, it can sesne the addition of the wrong nucleotide, back up and cut it out, and then move forward again re-synthesizing using the correct nucleotide |
| What is mismatch repair? | Mismatch repair removes mismatched nucleotides by cutting out the error, filling by DNA polymerase I, and sealing with DNA ligase |
| What is excision repair? | Removes chemically damaged nucleotide by cutting out the error, filling with DNA polymerase I, and sealing by ligase |
| What 3 macromolecules are included in membranes? | Membranes include lipids, proteins, and carbohydrates |
| T or F: Eukaryotic cells are surrounded by a plasma membrane and contain membrane-bound organelles. | True |
| What are some important features of the membrane system? (4) | 1) Allows for the compartmentalization of processes 2) Allows for est. of conc. gradients that can store + harness energy 3) Acts as a gatekeeper to separate internal and external enviros. 4) Serves as a communication center to receive and send signals |
| What is the name for proteins that are noncovalently attached to either membrane surface? | Peripheral membrane proteins |
| What is the name for proteins emebedded in the phospholipid bilayer? | Intergral membrane proteins |
| What is the name of the protein that spans the entire membrane and what branch of the two main classes of membrane proteins does it fall under? | Transmembrane proteins span the entire phospholipid bilayer and they are a type of integral membrane protein |
| What type of lipid makes up the membrane? | Phospholipids |
| What makes up a phospholipid (its groups) and indicate whether that group contributes to its hydrophilic head or its hydrophobic tail? | Phospholipids consist of hydrocarbon chains (hydrophobic tail), glycerol (hydrophilic head), a negatively charged phophate group (hydrophilic head), and a positively charged group that can vary (hydrophilic head) |
| When the phopholipids form a bilayer membrane, how are they oriented? | The hydrophilic heads are positioned towards the cytoplasm of the cell or towards water while the tales are positioned towards each other in the middle |
| Can the two leaflets of the bilayer itself differ from one another in exact lipid components? | Yes, membranes can be different even to such a degree as this! |
| What is a glycoprotein? | A protein with a covalent addition of a carbohydrate |
| What is a glycolipid? | A lipid with covalent addition of carbohydrate |
| What are the general functions of glycoproteins and glycolipids? | Cell recognition and cell adhesion |
| T or F: Membranes are rigid and its components rarely move laterally within the membrane. | False, membranes are fluid anf can bend and stretch without braking. Membrane components also readily move laterally within the membrane |
| What are 3 favorable movements for phospholipids? | Lateral diffusion, rotation, and the flexing of their tails |
| What is an unfavorable movement for phospholids and why? | A phospholipid flipping from one leaflet to the other because it requires the hydrophilic head to go through the hydrophobic tails in the middle of the membrane which would repel it |
| Are membranes more fluid with unsaturated phospholipids or saturated phospholipids and why? | Unsaturated phospholipids because saturated phospholipids are straight, can pack more tightly together and can form more van der Waal interactions, however, the bends at the double bonds of unsaturated tails disrupts this to increase fluidity |
| What does amphipathic mean? | A molecule that consists of both hydrophilic and hydrophobic components |
| Is cholesterol hydrophilic, hydrophobic, or amphipathic? | Cholesterol is amphipathic |
| What components make up cholesterol and indicate whether they are hydrophilic or hydrophobic? | Cholesterol is made up of an OH polar head group (hydrophilic), a rigid steroid ring structure (hydrophobic), and a nonpolar hydrocarbon tail (hydrophobic) |
| How does cholesterol orient itself in the membrane? | Its polar OH head interacts with the polar head of the phospholipid and its rings and tail interact with the phospholipid tails |
| At normal temps/circumstances, does the addition of cholesterol make the membrane more or less fluid and why? | Less fluid because it holds adjacent phospholipids together by interacting with them both |
| At very low temps, does the addition of cholesterol make the membrane more or less fluid and why? | More fluid because at low temps it prevents the membrane's transition to a rigid crystaline-like state that would otherwise make it very tightly packed |
| T or F: Membranes include many proteins with a variety of functions. | True |
| T or F: The lipid bilayer is completely permeable. | False, the lipid bilayer has limited permeability as only small, hydrophoib molecules can readily diffuse across the membrane, while others require membrane proteins to cross |
| T or F: The membrane helps set up and maintain gradients. | True |
| What is a gradient? | Different concentrations or net charges on either side of the membrane |
| What creates gradients? | The limited permeability of membranes and the function of transporters creates gradients |
| What do gradients store? | Gradients store potential energy |
| What is passive diffusion? | Crossing the membrane without the input of external energy |
| What does it mean to move down a gradient? | To move from a side of high concentration to low concentration |
| Which direction of particle movement classifies as passive diffusion? | Net movement of particles from an area of high concentration to low concentration (moving down a gradient) is a form of passive diffusion |
| What is simple diffusion and what molecules can do it? | Very small, hydrophobic (nonpolar) molecules can readily diffuse across the lipid portion of the membrane down their concentration gradients without the need of a transporter |
| How do all molecules that aren't small and hydrophobic move across the membrane? | By facilitated diffusion |
| What is facilitated diffusion? | Facilitated diffusion allows small uncharged polar molecules, large uncharged polar molecules, and ions to cross the membrane via protein transporters or channels |
| How does water corss the membrane? (be specific) | Water crosses the membrane by facilitated diffusion through proteins called aquaporins |
| What is osmosis? | The diffusion of water across a semi-permeable membrane (like a cell membrane) |
| What do aquaporins have inside them that allows water to travel through the protein? | Inside the aquaporin are positively charged R-groups that attract the slightly negative charge of the oxygen in water. The positively charged R-groups are spaced throughout the protein and pull the water through due to this attraction |
| What is free water? | Water that is not bound or interacting with any solute and can move through the membrane |
| Can water-solute particles pass through the aquaporins? | No only free water can |
| What is the trend in osmosis for water moving down its gradient? | Free water moves from area of high concentration of free water to area low concentration of free water... or free water moves from area of low concentration of solute to area of high concentration of solute |
| What is a hypotonic solution (in terms of comparing to another side of a gradient)? | The side with the relatively lower concetration of solute (would have higher concentration of free water) |
| What is a hypertonic solution (in terms of comparing to another side of a gradient)? | The side with relatively higher concentration of solute (would have lower concentration of free water) |
| What is an isotonic solution? | Occurs if the solute concentrations are the same on both sides of the gradient |
| Do covalent bonds break in water? | No, they remain intact |
| Do ionic bonds break in water? | Yes, they dissociate into two separate ions |
| What is osmolarity? | The concentration of particles in solution that allows us to know which direction water will move down its concentration gradient |
| What does Osmolarity equal? | # particles solute/L |
| What are the units of Osmolarity? | Osmoles / L (Osmol) |
| When are the terms hypotonic, hypertonic, and isotonic used? | When comparing the osmolarity of two things (like a cell and the solution/environment its in) |
| Can ions pass through the lipid protion of the membrane? | No |
| What is the chemical driving force? | For ions or other molecules, it refers to the energy associated with moving down the concentration gradient, from an area of high concentration to an area of low concentration |
| What is the electrical (charged) driving force? | For ions, it refers to the energy associated with moving towards an opposite charge |
| If the chemical driving force and electrical driving force are in the same direction it is... | Stronger (more energy) |
| If the chemical driving force and electrical driving force are in opposite directions it is... | weaker (less energy) |
| What is free energy (or Gibbs free energy)? | The energy that is available to do work, specifically to facilitate some chemical, mechanical, or transport process in the cell that requires energy |
| Do spontaneous processes require or release energy? | Release energy |
| What is the free energy equation? | Delta G = Gfinal - Ginitial |
| Do spontaneous processes have a positive, negative, or zero value for delta G? | Negative delta G |
| Do spontaneous process allow work to be done or they themselves work? | They allow work to be done |
| Do non-spontaneous processes require or release energy? | Require energy |
| Do non-spontaneous processes have a positive, negative, or zero value for delta G? | Positive delta G |
| Do non-spontaneous processes allow work to be done or are they themselves work? | They themselves are work |
| What is equilibrium in terms of free energy? | A state at which the total free energy is 0 |
| Whta is the microstate of a gradient system? | The individual particles |
| What is the macrostate of a gradient system? | The whole system |
| What is the delta G a measure of? | The change in free energy of the macrostate |
| Is diffusion (both simple and facilitated) a spontaneous process or a non-spontaneous process? | Diffusion is associated with a negative delta G and is thus spontaneous, providing energy available to do work |
| At equilibrium, what is occurring in the macrostate? | There is no change in the macrostate, no net change in the concentration in any region (delta G = 0, so no energy to do work) |
| At equilibrium, what is occuring in the microstate? | The microstate is still changing, as particles are always moving, even at equilibrium, just no net movement across the membrane |
| T or F: At equilibrium, as many particles move in one direction as the other. | True |
| What is the Gibbs-Donnan Equilibrium Effect for ions? | It describes the movement of ions across membranes as reaching equilibrium when the force of the chemical gradient is equal and opposite to the force of the charge gradient |
| At equilibrium is there any net movement of ions? What about in terms of the macrostate? | At equilibrium, there is no net movement of the ions and the macrostate is not changing |
| T of F: At equilibrium, the concentration of ions on either side of the membrane is equal. | False, the concentration of ions on either side is not equal, rather the force of the charge gradient must be equal and opposite to the force of the chemical gradient |
| What is osmotic equilibrium? | The energy available in concentration gradient of free water is equal and opposite to the energy available in the pressure. gradient. Here, net movement of water will cease and free energy will be zero |
| What is osmotic pressure? | The pressure that would need to be applied to prevent water from moving across the membrane by osmosis |
| Why do we care about the Gibbs-Donnan equilibrium? (3) | -Fundamental for cell biology -Allows neurons to fire action potentials (electrical signals) -It's considered in biomedicine |
| What is the difference between passive and active transport? | Passive transport moves solute from high to low concentration and no additional energy iput is needed, whereas active transport moves solute from low to high concentration and energy is required |
| What are the 2 types of proteins that participate in membrane transport? | Carrier proteins and channel proteins |
| What do carrier proteins do to transport, how much do they transport, and what kind of transport can they support? | Carrier proteins bind solute and undergo allosteric (shape) change to deliver a small number of molecules across the membrane. They can support passive or active transport. |
| What do channel proteins do to transport, how much do they transport, and what kind of transport can they support? | Channel proteins don't bind solute, rather they have a single shape change (opening) that allows many ions to pass. Channels are always passive transport, never active |
| What is required to move particles against their gradient? | The input of external energy |
| Where does the energy for passive transport come from? | The energy is in the gradient itself |
| Is moving a substance up/against its gradient thermodynamically favorable or unfavorable? | Thermodynamically unfavorable |
| In order to harness energy that will drive a thermodynamically unfavorable transport, what must be done? | It must be coupled with a thermodynamically favorable process |
| What are the 2 places energy for active transport can come from? | 1) ATP 2) From another molecule's gradient |
| What is primary active transport? | When the energy to perform active transport comes directly from coupling the unfavorable movement of the molecule with ATP hydrolysis |
| What does ATP hydrolysis do? | Water is added to remove a negatively charged phosphate from the ATP (making it ADP) and the breaking of this high energy bond between phosphates releases energy which can be used by the transport protein |
| Not only are primary active transport proteins transporters, but they're also... | ATPase enzymes |
| What does the primary active transport proteins' ATPase enzyme role? | To catalyze the hydrolysis of ATP |
| After the transporter catalyzes the hydrolysis of ATP into ADP, what happens? | The removed phosphate is covalently linked to the transporter |
| What does the covalent addition of phophate onto the transport protein cause? | The transport protein to change its conformation (shape), allowing the transport of the molecules against their gradient |
| What is another name for active transport proteins? | Pumps |
| What thermodynamic coupling occurs in primary active transport? | The energy from ATP hydrolysis (thermo. fav) is coupled with the work of moving a substance against its gradient (thermo. unfav) |
| What is secondary active transport? | When the energy to perform active transport comes indirectly, by harnessing the energy of another gradient that is moving down its gradient |
| Does secondary active transport require primary active transport to be present somewhere in the system? | Yes, in order to actively transport a substance it needs a gradient to be established by primary active transport first |
| What are the 3 types of active transport protein pumps called? | Symport, antiport, and uniport |
| What is a symport protein? | An active transport protein in which two different solutes move across the membrane in the same direction |
| What is an antiport protein? | An active transport protein in which two different solutes move across the membrane in opposite directions |
| What is a uniport protein? | A protein in which one solute moves in one direction across the membrane |
| What is an example of primary active transport? | The Na+ / K+ Pump (look at notes and be able to explain this process) |
| Why is the Na+ / K+ pump important for cell function? | It establishes and maintains gradients that contribute to osmotic balance and the resting electrical potential |
| T or F: Many cells use couple transporters, one being the primary active transport of the Na+ /K+ pump to privde energy for secondary active transport | True |
| What is an example of secondary active transport? | Na+ / glucose co-transporter (see notes) |
| How do larger molecules, like proteins, enter and exit cells? | Through endocytosis and exocytosis |
| What is endocytosis? | A way for large molecules to enter the cell, in which the plasma membrane surrounds the molecule and pinches off a vesicle to send to another cell location |
| What is exocytosis? | A way for large molecules to exit the cell in which materials packed in vesicles can be secreted from inside to outside the cell (transmembrane proteins, like transporters, can be delivered to the plasma membrane via a vesicle) |
| What are the steps of vesicle trafficking (exocytosis direction)? | -Secreted proteins and transmembrane proteins must be synthesized by ribosomes on the rough ER -Vesicles leave ER-->fuse to Golgi -New vesicles leave golgi-->fuse to plasma membrane -transmembrane proteins delivered; vesicle contents released outside |
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