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Biol 190 Unit 2 Study Guide

by: Amy Rice

Biol 190 Unit 2 Study Guide Biol 190, Intr biology health profession

Amy Rice

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Study guide covering: DNA Functions Protein Structure and Function Mutations Cell Membrane Structure & Function
Joanna M. Paterson
Study Guide
Science, Biology
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This 13 page Study Guide was uploaded by Amy Rice on Tuesday March 1, 2016. The Study Guide belongs to Biol 190, Intr biology health profession at Towson University taught by Joanna M. Paterson in Spring 2016. Since its upload, it has received 36 views. For similar materials see Biology in Biology at Towson University.

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Date Created: 03/01/16
UNIT 2 STUDY GUIDE 1. DNA roles: transmission of genetic information and control of cell structure a. What DNA role involves replication? – genetic information What role involves transcription and translation? – Control of cell structure and form b. How are genes expressed through transcription and translation?  What are the basic steps of transcription and translation?  What are the three types of RNA involved? – messenger, transfer, and ribosomal  How are RNA molecules made/created?  Describe each type of RNA mRNA- created in the nucleus from a DNA template strand, is a long coding sequence with a cap and tail to escort the coding to its destination in the cytoplasm. Carrying the genetic code for protein. tRNA- Picks up appropriate amino acids w/ amino acid attachment site in order to create a polypeptide chain. As well as recognizes the appropriate coding codons in mRNA with anticodon rRNA- Binds to each other in order to create ribosomes that are the binding sites for mRNA and tRNA. Also connects amino acids to the growing polypeptide chain.  What enzymes are involved in transcription and translation? – RNA polymerase c. What does complementary base pairing do? – CBP is important to copy the correct coding sequence to mRNA so that the correct proteins are being translated d. What is the difference between an error in replication vs an error in transcription and translation? How does this effect cellular function? How does it affect the passing of genetic instruction? 2. Protein Structure and Function a. Four levels of protein structure: Primary- a specific, linear chain of amino acids; not a protein, only a polypeptide chain Secondary- hydrogen bonding holds the backbone together as its composed of helices and pleated sheets with connecting segments Tertiary- Covalent, ionic, and hydrogen bonds holds the structure together between R-groups, stabilizing the structure. Folds into (generally globular) 3D shape; functional polypeptide chain. Quaternary- Held together by ionic, covalent, and hydrogen bonds. Composed of two or more polypeptide chains creating a functional protein. b. Hydrolysis vs Protein Denaturation Hydrolysis- Water and an enzyme is required in order for a protein to lose its primary structure. Is nonreversible. Breaks strong covalent bonds that holds amino acids together. Protein denaturation- loss of higher structures; when a protein returns to primary structure in response to a change in physical environment (temperature, pH level, and/or salt), because H-bonds, ionic, van der Waals and hydrophobic interaction are disrupted. Does not require an enzyme. Can be reversed when the outside influence is removed (renaturation), returning the protein to its natural environment.  What can you conclude from this about the relationship between protein structure and function?  How does this relate to the difference between the chemical bond strength in primary structure opposed to a higher level structure? c. 3 Functional Categories of Proteins? - Storage; Ferratin; stores mineral ions in the body - Hormone; steroids; chemical-based proteins secreted by endocrine cells - Transport; Hemoglobin; carries vital materials to the cells 3. Mutation a. What is a gene mutation? – Any permanent change in the base nucleotide chain of DNA b. How? When? Likelihood? – Likely to occur during the DNA synthesis phase c. Substitution- Replacement of one nucleotide pair with a different set of nucleotide complementary base pairs; has a possibility that it may not change the amino acid at all Insertion/Deletion- when a nucleotide is added or removed, causing the following nucleotides to be regrouped into different amino acids; may have a disastrous effect, possibly ending in a nonfunctional polypeptide. d. Mutations Silent- base substitutions; no change in protein Missense- slight mistake; 1 nucleotide changed, causes amino acid to change Nonsense- creates stop codon; shortens protein, therefore cannot complete its job Frameshift- shifts the reading frame due to inserted nucleotides; (FAT CAT ATE THE RAT); 3 nucleotides adds whole amino acid e. The first three levels of proteins structure include primary, secondary, and tertiary. Primary structure is a chain of amino acids, a missense mutation would affect this by changing the codon sequence. In secondary structure, the hydrogen bonding along the backbone would be affected if the nucleotides were to change, causing a kink in the structure. The tertiary structure is when the protein folds upon its self so that the hydrophobic portions are on the inside of the cell, protected by the hydrophilic parts. If 1 nucleotide was substituted, that could cause the protein to be nonfunctional. f. SICKLE CELL ANEMIA If someone contracts sickle cell anemia, one amino acid is changed from GLU to VAL, a hydrophobic R-group. Symptoms include sickle hemoglobin that have a different shape and cannot absorb oxygen as well and sickle red blood cells that clog capillaries and block blood flow, causing pain and organ degeneration. g. Glucose monomers are linked using protein enzymes. The coding of DNA effects the protein, causing the protein to be unable to make the carbohydrate and lipid, because the one component cannot complete the function. (1 broken section of car factory causes car not to fully function, making it useless) 4. Cell Membrane Structure and Function a. phospholipids belong to the lipid class with fatty acid + glycerol subunit (monomer). Different from triglycerides in that triglycerides have 3 fatty acid tails instead of only 2 b. A steroid is a lipid because it supports the membrane structure with four fused rings in the carbon skeleton and 3 fatty acid tails, making it a triglyceride. c. The structure of a phospholipid has a polar head with 2 hydrophobic tails due to the phosphate group in the head and C, H and a little O in the fatty acid tails. Creates phospholipid bilayer in order for the hydrophobic tails to be protected by the polar heads from the water. d. lipid synthesis occurs in the smooth ER where g. Passive transport  Simple diffusion- when oxygen, carbon dioxide, and/or water cross the phospholipid bilayer from a high level of concentration, to low concentration  Facilitated diffusion- when a transport protein is required to move ions, amino acids, and monosaccharides across the phospholipid bilayer (into/out of cells) Active transport- When cell energy and a transport protein is required to pump anything from a low concentration to high. Transport protein is inserted into bilayer. It is easier for small, uncharged particles to cross the bilayer Small section of HBB (hemoglobin B) is transcribed from a single strand copy of DNA into mRNA. mRNA is then processed into mature mRNA, a shorter strand with a cap and tail. Finally sent through a nuclear pore out of the nucleus, into the cytoplasm to carry out translation. Structure: mRNA- Long coding sequence with cap and tail tRNA- Single strand molecule of 80 bases with amino acid attachment site on one end and anticodon on opposite end rRNA- 2-3 rRNAs and about 50 proteins make up the large subunit of a ribosome and 1 rRNA and ~30 proteins construct the small subunit of a ribosome Role in Translation: mRNA- 1 important ingredient required for translation; carries genetic code for protein tRNA- 1) Pick up appropriate amino acids 2) Recognize appropriate codons in the mRNA rRNA- Creates the binding site for mRNA and tRNA and connects amino acids to the growing polypeptide chain. messengerRNA:  Transcripted from DNA in order to carry genetic coding to be translated in the cytoplasm  The cap (single G nucleotide) and tail (chain of 50-250 nucleotides) facilitate the export of the mRNA from the nucleus, and protects the mRNA from being attacked by cellular enzymes (like the mRNAs own personally secret service body guards, escorting the mRNA to its destination in the cytoplasm), as well as helping bind ribosomes to the mRNA  Introns- internal non-coding regions  Exons- the part of the gene that is expressed (coding region)  Before leaving the nucleus, introns are removed and exons are added to produce a continuing coding sequence  RNA Splicing- the cutting and pasting processes of introns and exons Codons: coding units; sequence of 3 DNA/RNA nucleotides that correspond with specific amino acids Anticodon: The special triplet of bases at one end of the folded molecule AUG is the start of the genetic message; start codon UAA, UAG, UGA are all stop codons The Triplet Code:  3:1 code- 3 nucleotides code for 1 amino acid  Protein language has 20 letters/amino acids transferRNA:  Single-stranded molecule of 80 bases  Amino acid attachment site- where amino acids attach, passed from another tRNA attachment site  3 base sequence that is hydrogen-bonds to codon in mRNA BY complementary base pairing rules  Made in nucleus but functions in cytoplasm  Each tRNA has its own specific loading enzyme  Anticodon- special triplet of bases at one end of the folding molecule (humans not have anticodons) ribosomalRNA:  Made by DNA transcription from particular rRNA coding genes in nucleolus  Large subunit- catalyzes formation of covalent bond between amino acid in protein synthesis (contains peptidyl transferase, an RNA enzyme)  Small subunit- place where mRNA hydrongenly-bonds with tRNA  Small and large pass through nuclear pore separately Ribosome- cytoplasmic structure or organelle; cellular component that is directed by the nucleus in order to carry out protein synthesis Free and bound ribosomes are structurally identical. They can alternate between being suspended in the cytoplasm (free) or attaching to the outside of the nuclear envelope/endoplasmic reticulum (bound) TRANSLATION – When codons and anticodons bind together to create somewhere for tRNA to latch onto in order for amino acids to add onto and grow the polypeptide chain. The tRNA ‘reads’ the coding on mRNA to then be translated into amino acids, while rRNA catalyzes the process. Initiation:  tRNA binds to small subunit  mRNA binds to tRNA and small subunit  small subunit and tRNA travel along mRNA, searching for AUG to start coding  large subunit joins complex Elongation:  tRNA diffuses w/ amino acids to dock at next codon  Correct tRNA comes in because of complementary anticodon  Amino acid breaks off tRNA then covalently links to next amino acid  Old tRNA diffuses away  Translocation- Ribosome moves along mRNA, looking for next codon  Repeat Elongation cycle: o Codon recognition o Bond formation o Translocation Termination:  tRNA comes in contact with stop codon  no further tRNA binds  release factor binds to stop codon  complex disassembles: o finished protein is released into the cell o empty tRNA falls out of complex o ribosomal subunit (small and large) break apart Protein- biomolecule composed of amino acids; structure enables to carry out function Structures:  Globular- irregular spherical shape; contains many bumps and grooves (many) [helixcase, ligase]  Fibrous- long and narrow; cable like (few); aka STRUCTURAL Function:  Transport- moving material into or out of cells [potassium channels, hemoglobin]  Hormones- chemical signaling [insulin, glucagon]  Contractile- contraction [actin, myosin]  Structural- support, toughness [collagen, keratin]  Protection- defend against harm [antibodies]  Enzyme- carry out every reaction within the cell or body (-ase)  Storage- nutrient storage for growing embryo [endosperm proteins, albumin] There are 4 different nucleotides in RNA and 20 amino acids in protein  Bonded to amino group  Carboxyl group  R-group R-group aka side chain differs between each different amino acid R Group:  Size  Charge (+ or -)  Polarity (hydrophilic) o “partial” charge o Unequal sharing of electrons (polar covalent bond) Bending of amino acid chain; small R group allows the bending of the chain; large R groups are more stiff and do not allow for bending Dehydration Synthesis:  Removal of –OH from one amino acid and –H from a different amino acid, in order to release H2O  Allows direct covalent bond between the two amino acids  Water is taken out in order for the amino acids to combine and create one big molecule Polypeptide to protein structure:  Chain of amino acids, produced by dehydration synthesis or translation Primary structure- specific chain of amino acids A linear chain of amino acids cannot function; not a protein, only a polypeptide chain Secondary- coils (helices) and folds (pleated sheets) w/ connecting segments o Due to Hydrogen bonding along the backbone o H-bonds between parts of polypeptide backbone Tertiary- structure folds into 3D shape; generally globular; bonds between R groups  Hydrophobic amino acids huddle together on the inside (non-polar)  Hydrophilic position on outside (polar and charged)  Large loops are hydrophobic  Bonds between R groups stabilize the tertiary structure  Covalent, ionic, and hydrogen bonds hold the tertiary structure together between the R groups Quaternary- functional protein consisting of 2+ individual polypeptide chain  Not all proteins have a quaternary structure  Covalent, ionic, and hydrogen bonds hold the quaternary structure together Mutation- any change in the nucleotide sequence of DNA; permanent change in the base sequence of DNA Errors in cell cycle are likely to occur during DNA synthesis (‘S’ phase)  Nucleotide substitution- replacement of one nucleotide and its base-pairing partner with another pair of nucleotides; because genetic code is redundant, some substitution mutations have no effect at all  Nucleotide insertion/deletion- when a nucleotide is added or removed to the coding sequence; often has disastrous effects; all nucleotides “downstream” of the insertion/deletion will be regrouped into different codons, possibly resulting in a nonfunctional polypeptide Silent mutation- when a mutation causes an RNA codon to change, but the original and mutated codon code for the same amino acid; one nucleotide is substituted for another, however it does not change the protein Missense mutation- changes amino acid coding; some have little or no effect on shape or function on resulting protein, but others prevent the protein from performing its normal function (sickle-cell disease) EX: mutated hemoglobin in DNA can cause sickle-cell disease (substitutes TA in DNA to AU in RNA) SICKLE CELL ANEMIA  Change in one amino acid (glu to val) [missense mutation]  Sickle hemoglobin has different 3D shape; less efficient in binding oxygen; distorts shape from round to flat and spikey Nonsense mutations- changes an amino acid codon into a stop codon, resulting in a prematurely terminated protein (truncated protein) that probably won’t be able to function properly Frameshift mutation- one nucleotide is inserted, altering the reading framed Amino acid insertion (3 base insertion)- adds extra codon; one amino acid is inserted in the protein Mutagenesis- production of mutation Mutagens- chemical or physical agent that causes mutations; physical mutagens includes high-energy radiation (x-rays or ultraviolet light); chemical mutagens may be similar to DNAs chemical compositions, but incorrectly pairs (anti-AIDS drug AZT) Evolution by natural selection is made possible by gene mutations, causing such a wide diversity of genes in the living world. Protein Structure Amylase- salivary enzyme that hydrolyzes starch; single polypeptide chain (1), has alpha helices and beta pleated sheets (2), 3D structure (3) Glucagon- regulate blood sugar levels; (1), has helix (2) Hexokinase- catalyzes first reaction in glycolysis; (4) globular Hemoglobin- carries oxygen through the body via red blood cells; composed of four polypeptides; transport protein K+ (potassium ion)- membrane transport protein; quaternary structure Collagen- a fibrous protein; common 3D structure in structural proteins; 3 different polypeptides, therefore has a quaternary structure Quaternary structure is identified via color coding (more than one color) POLYPEPTIDE VS PROTEIN Polypeptide  Linear chain of amino acids or an amino acid chain with helices and pleated sheets, but does not have 3D structure  Cannot perform a function Protein  A polypeptide with a tertiary or quaternary structure in order to make it function  Native conformation- normal/functional structure Dehydration synthesis- Formation of primary structure, structure drives formation of higher levels Denaturation- loss of higher structures (4,3,2) and remains a linear chain of amino acids (1); no enzyme required; in response to change in physical environment; Can be changed with temperature, pH level, and/or salt Hydrolysis- loss of primary structure; water and an enzyme is required LIPIDS Lipids- diverse compounds that are grouped together because they all do not mix well with water (hydrophobic); They are not huge macromolecules, nor polymers built from monomers (Fats, oils, phospholipids, steroids, waxes); Atoms include C, H, O; always a lot more C and H than oxygen  Fats and Oils- 3 fatty acids & 1 glycerol  Phospholipids- 2 fatty acids, phosphate group (PO4), & 1 glycerol Lipid functions  Fats and Oils- long term energy storage; insulation and cushioning  Phospholipids- membrane structure; separation of water-filled cell from watery environment  Steroids- hormones; membrane structure; triglyceride  Waxes- protection; prevent dehydration Fat- a large lipid, made from glycerol and fatty acids; linking 3 fatty acids to glycerol produces a fat Unsaturated fatty acid- Has one fewer hydrogen atom on each carbon of the double bond; liquid at room temp; healthier in diet; kinks at double bonds of fatty acids; loose packing In animal cell membranes, the steroid cholesterol stabilizes the membrane at warm temperatures while also keeping the membrane fluid at lower temperatures. Different types of cells have different membrane proteins. Saturated Fatty Acid- a fatty acid with no double bonds in their hydrocarbon chain; has the maximum number of hydrogen atoms (“hydrogenated vegetable oil” has been converted from unsaturated fat, to saturated fat); closely packed fatty acids; vascular damage, stroke, heart attack; solid at room temp Trans Fats- A form of fat associated with health risks; H are on opposite sides of C-C double bond; form of Saturated Fat Phospholipids- The major component of cell membranes; structurally similar to fats, but contains only 2 fatty acids; Phospholipids made in the smooth ER are inserted in the ER membrane The hydrophilic and hydrophobic ends of multiple molecules assemble in a bilayer of phospholipids to form a membrane Steroids- lipids in which the carbon skeleton contains four fused rings Cholesterol- Starting material for making other steroids, including sex hormones; common component in animal cell membranes Endoplasmic Reticulum- one of the major manufacturing sites in a cell Smooth ER- lacks attached ribosomes; enzymes of this are important in the synthesis of lipids, oils, phospholipids, and steroids; stores calcium ions (in muscles cells); Our liver cells has large amounts of smooth ER, these enzymes aide in processing drugs, alcohol, and other potentially harmful substances Rough ER- has ribosomes attached to the outer surface of the membrane with other important functions; makes more membrane As the endoplasmic reticulum membrane grows, portions of it are transferred to other components of the endomembrane system as vesicles. The bound ribosomes attached produce proteins to be inserted into the growing ER membrane, transported to other organelles, or secreted by the cell Fluid mosaic- A bilayer of phospholipids with embedded and attached proteins Some proteins help maintain cell shape and coordinate changes inside and outside the cell through their attachment to the cytoskeleton and extra cellular matrix. Other proteins function as receptors for chemical messengers (signaling molecules from other cells) from other cells. Signal Transduction- The binding of a signaling molecule triggers a change in the protein, which relays the message into the cell, activating molecules that perform specific functions. Some membrane proteins are enzymes, which may be grouped in a membrane to carry out sequential steps for a metabolic pathway. Membrane proteins also participate in intercellular junctions that attach adjacent cells. Selective permeability- When membranes allow some substances to cross more easily than others A membrane can enclose a solution that is different in composition from its surroundings. A plasma membrane that allows cells to regulate their chemical exchanges with the environment is a basic requirement for life. Diffusion- The movement of molecules from an area of high concentration to an area of low concentration, until the space reaches equilibrium There is a net movement from the side of the membrane where the dye molecules are more concentrated to the side where they are less concentrated Concentration gradient- the region along which the density of a chemical substance increases or decreases Active Transport- a cell has to give off energy in order to move a solute across its concentration gradient; allows a cell to maintain internal concentrations of small molecules and ions that are different from the concentrations in its surroundings; moving anything Passive Transport- When molecules diffuse across a membrane Both oxygen and carbon dioxide are small nonpolar molecules that diffuse easily across the phospholipid bilayer of a membrane. Facilitated Diffusion- When polar or changed substances can move across a membrane with the help of specific transport proteins; a type of passive transport because it does not require energy Nonpolar hydrophobic molecules can dissolve in the lipid bilayer of a membrane and cross it with ease. Without the transport protein, the substance cannot cross the membrane, or it diffuses too slowly to be useful. The transport protein is specific for the substance it aids in movement across the membrane. The more transport proteins, the faster the solute diffuses. Exocytosis- When a cell exports bulky materials (proteins/polysaccharides) [fibroblast releasing collagen fibers into extra-cellular space for incorporation into the ECM] out of cell A transport vesicle (containing macromolecules) excretes from the Golgi apparatus, moving to the plasma membrane. Then it fuses with the plasma membrane. Once fused, the macromolecules are released into the new fusion of vesicle and plasma membranes. Endocytosis- opposite of exocytosis; when large molecules are consumed by the cell; A depression in the plasma membrane pinches in and forms a vesicle enclosing material, that was previously outside the cell  Phagocytosis- “cellular eating”; cell wraps pseudopodia around a particle, packaging it in a vacuole. The vacuole then fuses with a lysosome, whose hydrolytic enzymes digest the contents of the vacuole.  Pinocytosis- “cellular drinking”; the cell consumes large amounts of fluid into small vesicles, taking in any and all solutes dissolved in the droplets  Receptor-mediated endocytosis- highly selective; Receptor proteins for specific molecules are embedded in regions of the membrane, lined by a coating of proteins Cells use receptor-mediated endocytosis to take in cholesterol from the blood for synthesis of membranes and as a precursor for other steroids Phospholipid Bilayer Phospholipids have a polar head group with fatty acid tail (nonpolar) Micelle- many phospholipids collect together with the head on the outside, creating a vesicle to protect the hydrophobic tails on the inside Bilayer- two layers of phospholipids, top layer head up, bottom layer head down, creating hydrophobic core. This is the barrier between two layers of water Amphipathic- can survive in and out of water (phospholipids) Water is the most abundant molecule inside and outside the cell. Cytoplasm is 70-90% water. LARGE AND CHARGED CANNOT CROSS THE BILAYER Small and uncharged can cross the P-L tails Materials cross into/out of cells either through the membrane or via membrane vesicles Plasma membrane- membrane that surrounds the cell; phospholipid bilayer & other associated proteins and biomolecule


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