BIO Chapter 1 - Molecules and Fundamentals of Biology

Matter
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Terms in this set (79)
Matter
Anything that has mass and takes up space
Element
A pure substance that has specific physical/chemical properties and can't be broken down into a simpler substance
Atom
The smallest unit of matter that still retains the chemical properties of the element
Molecule
Two or more atoms joined together
Intramolecular Forces
Attractive forces that act on atoms within a molecule
Intermolecular Forces
Forces that exist between molecules and affect physical properties of the substance
Monomers
Single molecules that can potentially polymerize
Polymers
Substances made up of many monomers together in chains
Carbohydrates
- Contain carbon, hydrogen, and oxygen atoms
- Monosaccharides, disaccharides, and polysaccharides
Monosaccharides
- Empirical formula of (CH2O)n, where n represents the number of carbons
- Ribose (5 carbons)
- Fructose (6 carbons)
- Glucose (6 carbons)
- Glucose and fructose are isomers (same chemical formula, but different arrangement of atoms)
Disaccharides- Contain two monosaccharides joined together by a glycosidic bond - It is the result of a dehydration (condensation) reaction, where a water molecule leaves and a covalent bond forms - Sucrose (disaccharide made of glucose + fructose) - Lactose (disaccharide made of galactose + glucose) - Maltose (disaccharide made of glucose + glucose)Polysaccharides- Contain multiple monosaccharides connected by glycosidic bonds to form long polymers - Starch (form of energy storage for plants and is an alpha (α) bonded polysaccharide) - Linear starch is called amylose; the branched form is amylopectin - Glycogen (form of energy storage in animals and is an alpha (α) bonded polysaccharide) - It has much more branching than starch.Hydrolysis Reaction- A covalent bond is broken by the addition of water - Break peptide bondsCellulose- Structural component in plant cell walls, and is a beta (β) bonded polysaccharide - Linear strands packed rigidly in parallelChitin- Structural component in fungi cell walls and insect exoskeletons - It is a beta (β) bonded polysaccharide with nitrogen added to each monomerProteins- Contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON) - These atoms combine to form amino acids, which link together to build polypeptides (or proteins)ProteomeA proteome refers to all the proteins expressed by one type of cell under one set of conditions.Amino Acids- The monomers of proteins that contain an amino group, hydrogen group, carboxyl group, and R group - There are twenty different kinds of amino acids that each have a different R groupPolypeptides- Polypeptides are polymers of amino acids and are joined by peptide bonds through dehydration (condensation) reactions - The polypeptide becomes an amino acid chain that contains two end terminals on opposite sidesN-terminus (amino terminus)The side that ends with the last amino acid's amino groupC-terminus (carboxyl terminus)The side that ends with the last amino acid's carboxyl groupConjugated Proteins- Proteins that are composed of amino acids and non-protein components - Metalloproteins (ex. hemoglobin) - proteins that contain a metal ion cofactor - Glycoprotein (ex. mucin) - proteins that contain a carbohydrate groupPrimary StructureSequence of amino acids connected through peptide bondsSecondary Structure- Intermolecular forces between the polypeptide backbone (not R groups) due to hydrogen bonding - Forms α-helices or β-pleated sheets.Tertiary Structure- Three-dimensional structure due to interactions between R-groups - Can create hydrophobic interactions based on the R-groups - Hydrogen bonding and ionic bonding between R groups also hold together the tertiary structure.Disulfide bondsCreated by covalent bonding between the R-groups of two cysteine amino acidsQuaternary Structure- Multiple polypeptide chains come together to form one proteinProtein Denaturation- Describes the loss of protein function and higher order structures - Only the primary structure is unaffected - Proteins will denature as a result of high or low temperatures, pH changes, and salt concentrations - For example, cooking an egg in high heat will disrupt the intermolecular forces in the egg's proteins, causing it to coagulateProtein Function - StorageReserve of amino acidsProtein Function - HormonesSignaling molecules that regulate physiological processesProtein Function - ReceptorsProteins in cell membranes, which bind to signal molecules to trigger changes inside cellsProtein Function - StructureProvide strength and support to tissues (hair, spider silk)Protein Function - ImmunityAntibodies that protect against foreign substancesProtein Function - EnzymesRegulate the rate of chemical reactionsCatalysts- Increase reaction rates by lowering the activation energy of a reaction - The transition state is the unstable conformation between the reactants and the products - Catalysts reduce the energy of the transition state - Catalysts do not shift a chemical reaction or affect spontaneityEnzymes- Act as biological catalysts by binding to substrates (reactants) and converting them into products - Enzymes bind to substrates at an active site, which is specific for the substrate that it acts upon - Most enzymes are proteins - Protein enzymes are susceptible to denaturation and they require optimal temperatures and pH for functionSpecificity Constant- Measures how efficient an enzyme is at binding to the substrate and converting it to a product.Induced Fit Theory- Describes how the active site molds itself and changes shape to fit the substrate when it binds - The "lock and key" model is an outdated theory of how substrates bindRibozyme- An RNA molecule that can act as an enzyme (a non-protein enzyme)Cofactor- A non-protein molecule that helps enzymes perform reactionsCoenzyme- An organic cofactor (i.e. vitamins) - Inorganic cofactors are usually metal ionsHoloenzymesEnzymes that are bound to their cofactorsApoenzymesEnzymes that are not bound to their cofactorsProsthetic GroupsCofactors that are tightly or covalently bonded to their enzymesPhosphorylaseDirectly adds a phosphate group to a substrate molecule by breaking bonds within a substrate moleculeEnzyme catalyze reactions in the following ways:- Conformational changes that bring reactive groups closer - The presence of acidic or basic groups - Induced fit of the enzyme-substrate complex - Electrostatic attractions between the enzyme and substratePhosphataseCleaves a phosphate group off of a substrate moleculeKinaseIndirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from an ATP molecule - These enzymes do not break bonds to add the phosphate groupFeedback Regulation of EnzymesThe end product of an enzyme-catalyzed reaction inhibits the enzyme's activity by binding to an allosteric siteCompetitive Inhibition- Occurs when a competitive inhibitor competes directly with the substrate for active site binding - Adding more substrate can increase enzyme action - KM increases, while Vmax stays the sameNoncompetitive Inhibition- Occurs when the noncompetitive inhibitor binds to an allosteric site (a location on an enzyme that is different from the active site) that modifies the active site - In noncompetitive inhibition, the rate of enzyme action cannot be increased by adding more substrate - KM stays the same, while Vmax decreasesEnzyme Kinetics Plot- Can be used to visualize how inhibitors affect enzymes - The x-axis represents substrate concentration [X] while the y-axis represents reaction rate or velocity (V) - Vmax is the maximum reaction velocity - Michaelis Constant (KM) is the substrate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax) - Saturation occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus)Lipids- Contain carbon, hydrogen, and oxygen atoms (CHO), like carbohydrates - They have long hydrocarbon tails that make them very hydrophobicTriaclyglycerol/Triglyceride- A lipid molecule with a glycerol backbone (three carbons and three hydroxyl groups) and three fatty acids (long hydrocarbon tails) - Glycerol and the three fatty acids are connected by ester linkagesSaturated Fatty Acids- Have no double bonds and as a result pack tightly (solid at room temperature)Unsaturated Fatty Acids- Have double bonds - They can be divided into monounsaturated fatty acids (one double bond) and polyunsaturated fatty acids (two or more double bonds) - Cis-unsaturated fatty acids have kinks that cause the hydrocarbon tails to bend. As a result, they do not pack tightly - Trans-unsaturated fatty acids have straighter hydrocarbon tails, so they pack tightlyPhospholipids- Phospholipids are lipid molecules that have a glycerol backbone, one phosphate group, and two fatty acid tails - The phosphate group is polar, while the fatty acids are nonpolar - As a result, they are amphipathic (both hydrophobic and hydrophilic) - Furthermore, they spontaneously assemble to form lipid bilayersCholesterol- An amphipathic lipid molecule that is a component of the cell membranes - It is the most common precursor to steroid hormones (lipids with four hydrocarbon rings) - It is also the starting material for vitamin D and bile acidsFactors that influence membrane fluidity:1. Temperature - higher temperatures increase fluidity while lower temperatures decrease it 2. Cholesterol - holds membrane together at high temperatures and keeps membrane fluid at low temperatures 3. Degrees of unsaturation - saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinksLipoproteins- Allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins - Low-density lipoproteins (LDLs) have low protein density and work to deliver cholesterol to peripheral tissues (considered bad cholesterol) - High-density lipoproteins (HDLs) have high protein density and take cholesterol away from peripheral tissues (considered good cholesterol because they deliver cholesterol to the liver to make bile, which reduces blood lipid levels) - No role in glucose breakdownWaxes- Simple lipids with long fatty acid chains connected to monohydroxy alcohols (contain a single hydroxyl group) through ester linkages - Used mainly as hydrophobic protective coatingsCarotenoids- Lipid derivatives containing long carbon chains with conjugated double bonds and six-membered rings at each end - They function mainly as pigmentsSphingolipids- Have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognitionGlycolipids- Lipids found in the cell membrane with a carbohydrate group attached instead of a phosphate group in phospholipids - Like phospholipids, they are amphipathic and contain a polar head and a fatty acid chainNucleic Acids- Nucleic acids contain carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms (CHONP) - They contain nucleotide monomers that build into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) polymersNucleosides- Contain a five-carbon sugar and a nitrogenous baseNucleotides- Contain a five-carbon sugar, a nitrogenous base, and a phosphate groupDeoxyribose vs Ribose Sugars- Deoxyribose sugars (in DNA) have a hydrogen at the 2' carbon while ribose five-carbon sugars (in RNA) have a hydroxyl group at the 2' carbonNitrogenous Bases- Adenine, Thymine, Cytosine, Guanine - Uracil replaces thymine in RNA - A and G are purines that have a two-ringed structure (PUR As Gold = purines are adenine and guanine) - C, U, and T are pyrimidines that have a one-ringed structurePhosphodiester Bonds- Bonds formed through a condensation reaction where the phosphate group of one nucleotide (at the 5' carbon) connects to the hydroxyl group of another nucleotide (at the 3' carbon) and releases a water molecule as a by-product - A series of phosphodiester bonds create the sugar-phosphate backbone, with a 5' end (free phosphate) and a 3' end (free hydroxyl) - Nucleic acid polymerization proceeds as nucleoside triphosphates are added to the 3' end of the sugar-phosphate backboneDNA- Antiparallel double helix, in which two complementary strands with opposite directionalities (positioning of 5' ends and 3' ends) twist around each other - Furthermore, adenine can only H-bond to thymine (using two hydrogen bonds) and guanine can only H-bond to cytosine (using three hydrogen bonds)mRNASingle-stranded after being copied from DNA during transcription - In RNA, uracil binds to adenine, replacing thyminemiRNA- MicroRNA - Small RNA molecules that can silence gene expression by base pairing to complementary sequences in mRNArRNA- Ribosomal RNA - It is formed in the nucleolus of the cell and helps ribosomes translate mRNAdsRNA- Double stranded RNA - Some viruses carry their code as double stranded RNA - dsRNA must pair its nucleotides, so it must have equal amounts of A/U, and C/GtRNA- Transfer RNA - Small RNA molecule that participates in protein synthesisModern Cell Theory1. All lifeforms have one or more cells 2. The cell is the basic structural, functional, and organizational unit of life 3. All cells come from other cells (cell division) 4. Genetic information is stored and passed down through DNA 5. An organism's activity is dependent on the total activity of its independent cells 6. Metabolism and biochemistry (energy flow) occurs within cells 7. All cells have the same chemical composition within organisms of similar speciesCentral Dogma of GeneticsDNA -> RNA -> Protein - exception is reverse transcriptase and prionsRNA World Hypothesis- States that RNA dominated Earth's primordial soup before there was life - RNA developed self-replicating mechanisms and later could catalyze reactions, such as protein synthesis, to make more complex macromolecules - Since RNA is reactive and unstable, DNA eventually became a better way of reliably storing genetic information