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Biological Molecules

Biology Unit 1

QuestionAnswer
Biological molecules mcs organisms need to build their bodies & carry out life processes -organic, carbon based compounds -make up majority of the dry weight of a cell. (Water, a small mc, makes up the majority of the wet weight)
Nucleic acids purpose -AKA condensation polymers store genetic information & pass it from generation to generation EX: DNA & RNA (these provide instructions for making proteins) -has the sequence that provides the coding for the amino acids that make up proteins
monomers of each of the four biological molecules Nucleic acids: nucleotides Protein: Amino Acids Lipids: NOT MADE UP OF MONOMERS Carbohydrates: glucose or monosaccharides (simple sugars)
Nucleotides molecular structure phosphate + 5-carbon sugar + nitrogenous base
Proteins function makes up almost everything: enzymes, structure, transport, signaling, movement little machines that carry out specific jobs in a cell, such as catalyzing metabolic reactions or receiving and transmitting signals. EX: Anzymes, antibodies, hemogoblin
Amino Acids structure central carbon, amino group (-NH2), Carboxyl group: (-COOH), R group (makes every amino acid different), hydrogen atom
lipids function -waterproof plants/animals -oxidation of fat givevs E & metabolic H2o -insilation -cushoning -LONG-TERM/concentrated E storage -generally nonpolar but certain part of certain lipids can be polar -main structural components of cell membranes.
Why are lipids not made up of monomers they are not tecnically polymers because they are not made of long chains of repeating monomers they're one big monomer mainly glycerol + fatty acids
Carbohydrates function short-term/quick energy as glucose -structural components of cells (cell walls) -attached to proteins or lipids on the outside of cell membrane (helps with cell communication/recognition) -end in "ose"
monomers building blocks that make up biological molecules
monosacarides -simplest carbs (single sugar molecules) - they are the monomers of carbs -multiples of CH2O -sugars end in "ose" -used to make glucose, fructose, galactose -2 joined by covalent bonds = disaccharide -many = polysaccharide
Monomers VS polymers -a monomer is a small building block while a polymer is a large molecules made by connecting many monomers
How monomers are connected dehydration synthesis -one monomer forms a covalent bond to another monomer (or growing chain of monomers), releasing a water molecule in the process
dehydration synthesis -joins two molecules by forming a covalent band & removes water in the process -the process is used to build monomers into polymers -take an OH from 1 mc and a H from another to form water -requires energy
How polymers are broken apart hydrolysis
hydrolysis polymers turn back into monomers (EX: body needs to recycle 1 mc to build a different one) - cell adds H2O to break a covalent bond & one of the new mcs gains a H atom, while the other gains a hydroxyl (-OH) group -releases energy
polymers VS macromolecules VS biological molecules Polymers are a specific type of biological molecule All polymers are macromolecules but not all macromolecules are polymers
Specific bonds for each biomolecule - what it forms carbohydrates: glycosidic bond - disaccharides & polysaccharides proteins: peptide bond - polypeptides nucleic acids: phosphodiester bond - DNA/RNA lipids: ester bond - triglycerides & phosphilipids NOTE: these are all covalent bonds
what holds together two strands of DNA Along the vertical backbone of a single strand --> phosphodiester bonds between complementary strands--> HB horizontally across the center between 2 nitrogenous bases
ester bonds fatty acid chains attach to gycerol through ester bonds & through dehydration synthesis
triglyceride glycerol molecule + 3 fatty acid chains -primary type of fat found in food -main form of long-term stored energy -fat & oil
Dehydration synthesis VS peptide/glycosidic/ester/etc. 1. the process that connect molecules --> it forms covalent bonds, but the but the name of that bond depends on what molecules you are creating 2. the type of bond that the process creates -hydrolysis uses water to break those bonds in #2
if dehydration synthesis connects ___(1), the bond formed is ___ (2) two monosaccharides --> glycosidic bond two amino acids --> peptide bond nucleotides --> phosphodiester bond glycerol + fatty acid --> ester bond
how different R groups affect the amino acids
how many different types of amino acids are there 20
macromolecules very large molecules composed of thousands of covalently connected atoms
Because lipids are the smallest of the four, are they considered macromolecules?
enzymes catalysts : speed up chemical rxns in living organisms without being used up in the process -don't affect ∆G, only hasten favorable rxns -speed up synthesis & hydrolysis -lower the AE -protein -end in "ase"
how to identify different types of enzymes ones involved in breaking bonds end with -ase
directionality in macromolecules joined monomers have specific ends ( 2 chemically differ. ends), so new monomers are only added in particular ways (gives molecules directionality) - orientation & order monomers connect give mcs specific structures & therefore different functions
directionality: proteins -they have a structural backbone direction -starts at the amino side and ends with the carboxyl side -this makes it possible for ribosomes to create a chain of amino acids
directionality: Nucleic acids -acids always flow/synthesize 5' to 3' -starts at 3 o' clock & moves clockwise (5-carbon sugar) --> 1' to 5' -complementary DNA strands of a double helix run antiparallel - 1 strand's 5' end is beside the other's 3' -new nucliatides attach to 3'
5-carbon sugar -one of the componets of a nucleotide -sugar in DNA (Deoxyribonucleic) is deoxyribose (H at the 2' C) while in RNA (ribonucleic) it's called ribose (OH at the 2' C)
Sugar phosphate backbone -alternating phosphate groups and 5-carbon sugars create a rigid outer framework -within DNA & RNA -gives mcs asymmetrical structure (one side ends in 3' and the other with 5') which gives strand direction
Nucleobases stick off the backbone DNA: Cytosine, Guanine, Adenine, Thymine → A goes with T & C goes with G (how bases pair) RNA: cytosine (C), Guanine (G), adenine (A), Uracil (U) → A goes with U
antiparallel two molecular strands run side by side in opposite directional orientations
why do complementary strands have to be antiparallel nucleobases only form stable HB w/ each other when the backbones are antiparallel -otherwise, bases won't property align or lock together to form those stable bonds
Four major lipid types Cholesterol Free Fatty Acid Triglyceride phospholipid (all nonpolar except this!)
Cholesterol -provides structural stability to cell membranes -belongs to steroid class (which have four fused carbon rings, hormones that influence growth and development, metabolism and homeostasis.) CHO
Fatty Acids - long hydrocarbon tail w/ an even # of C atoms attached to a carboxyl group (-COOH makes them a carboxylic acid) CHO -saturated or unsaturated -major components of neutral fats & phospholipids -provide energy storage and sometimes insulation
Triglyceride made of three fatty acid chains bound to glycerol (long term energy storage) -AKA neutral fats (uncharged/nonpolar)(although steroids are NP they are not called neutral fats) CHO -fat or oil -
phospholipid 1 glycerol + 2 fatty acids + phosphate group + most have N containing group - cell membranes (phospholipid bilayer) -amphipathic (P/hydrophillic head - phosphate- facing aqu outside & NP tail - fatty acid - faces inward) CHOP
Transfat -specific type of unstaurated fat where the H atoms around a double bond are flipped to opposite sides of the carbon chain--hydrogen atoms sit on opposite sides of the double bond, balancing the mc out & making the C chain stay straight
hydrocarbon tails long chains made primarily of carbon and hydrogen atoms -nonpolar -store and release large amounts of energy -present in fatty acids, triglycerides, and phospholipids (not in steroids)
saturated fatty acids single bonds only -maximum number of hydrogen atoms -considered "unhealthy" -tail shape: straight molecule -packed tightly together --> solid at room temperature
unsaturated fatty acids -one or more double bonds -fewer hydrogens due to double bonds -kinks/bends in the chain at double bonds -double bonds prevent tight packing --> liquid at room temperature
Cis fats (natural unsaturated fats) H atoms sit on the same side of the double bond. forcing the C chain to bend/kink
Are transfats naturally occuring? -yes, in small amounts -artificial transfats are created through industrial hydrogenation (REALLY bad for you)
practice identifying what each molecule looks like
Alpha -when a glucose is in a 6-membered ring, it can occur in 2 different forms. 1. Alpha: -OH points down relative to the CH2OH 2. Beta: -OH points up (on the same side as the CH2OH)
What happens when linear monosaccharides form rings the oxygen from the carbonyl group (C=O) becomes a hydroxyl group
Phosphodiester bond covalent bonds that connect the 3' C (has terminal hydroxl group) one 1 sugar to 5' (terminal phosphate group) phosphate group of adjacent nucleotide (sugar-phosphate-sugar-etc) creating a sugar-phosphate backbone of DNA & RNA
glycerol alcohol w/ 3 C (each C bonded to a hydroxyl) -backbone for certain lipids (base fatty acids attach to) 1 glycerol + 3 fatty acids = triglyceride (3 condensation rxns create ester bonds) 1 glycerol + 2 fatty acids + phosphate group = phospholipids
molecular structure of nucleic acids CHONP
molecular structure of proteins CHONSP
peptide bond -bonds between amino acids -dehydration synthesis connects the amino group of 1 acid to the carboxyl group of another
lipids structure CHO
carbohydrates structure CHO -rings
polypeptides or peptide chains a chain of amino acids connected by peptide bonds they fold into functional proteins
glycosidic bond bonds between monosaccharides that from disaccharides and polysaccharides (carbohydrates)
How are proteins denatured -proteins (including enzymes) have ideal conditions (EX: stomach = very acidic ideal pH) like PH & TEMP ranges -when outside these conditions, it's interactions are disrupted, shape is distorted -unfolds & enzymes can't bind to substrate
active sites areas on an enzyme where items (called substrates) bind -these cites are specially shaped for the items that bind there
induced fit model (newer model) active site changes shape to bind substrates (makes it more likely the substrate will change) -enzyme can break down or build up substrates to make the product -active site is flexible, not rigid
lactose -sugar -disaccharide (contains 2 sugar molecules bound together) -we can't digest it well, so the enzyme lactase breaks it down into smaller pieces (people without much lactase are lactose intolerant) -it's a subtrate
lipase enzyme that breaks down lipids
Amylase enxyme that breaks down starch
Protease enzyme that breaks down protein
Cofactors & Coenzymes cofactors = broader group including organic coenzymes & inorganic metal ions. EX: Mg+ 2, Zn2+ coenzymes = organic molecule EX: NAD+, FAD they bind to the substrate or active site to help the enzyme build up or break down substrates into products
Lock and Key model An older idea. It shows the enzyme as a rigid lock. The substrate is a rigid key that fits right in.
what type of bond is an enzyme-substrate bond -After an enzyme turns a substrate into a product, it releases the it & returns to its og state. Therefore, interactions require weak, non-covalent interactions. EX: HB, ionic forces, hydrophobic interactions, Van der Waals forces
Primary Structure -sequence of AA -straight, unbranched chains of AA -peptide/covalent (stronger than non-covalent --> last to break in denaturing) 2 + charged AA = repel each other during folding 2 - charged AA = attract each other (determine final shape)
secondary structure sequence of amino acids folds different ways (alpha helix & beta pleated sheet) -both shapes are due to hydrogen bonding between CO & NH (in backbone of the AA structure) -the chain folds & amino acids that were far apart comes closer & form HB
Chain VS Backbone Chain: the whole polypeptide/chain of amino acids (included the R groups and entire structure Backbone: the central repeating part of the chain, it is just a small part of the chain that repeats throughout the chain
Tertiary Structure -overall #D shape of ONE polypeptide chain -determined by the R groups -globular -distant parts of chain interact -Forces: hydrophobic/hydrophilic, ionic (stronger for non-covalent), hydrogen bonding, disulfide bridges, van der waals
Describe the hydrophobic/hydrophilic interactions in the Tertiary structure -acids with hydrophobic r groups orientate towards the inside of the protein while hydrophilic R groups orientate towards the outside -there is water outside the protein
describe the hydrogen bonds within the Tertiary structure -between polar R groups (or sometimes between R groups and the backbone) -only polar because HB requires partial charges - FON pull e- unevenly creating polarity (the positively charged H is attrached to the negative FON)
Describe the ionic bonds within the Tertiary structure -R-groups are positively or negatively charged at a given pH -basic R = accepts H+ & becomes + -acidic R = donates H+ & becomes - - opposites attract creating an ionic interaction (salt bridge) -brings the two R groups together increasing folding
Describe the disulfide bridges within the tertiary structure -strong covalent bond between the R groups of 2 cysteine amino acids -they both have sulfur within them & when they are close their S atoms form a covalent bond (the bridge) -
Describe the van der waal forces within the tertiary structure Van der Waals: very weak attractions between atoms caused by temporary, uneven distributions of e- -even w/ NP R groups, the e- are constantly moving & if they are concentrated on 1 side it can polarize a nearby atom
Quartary structure two or more polypeptide chains come together to make 1 functional protein EX: hemogoblin -each chain is a subunit & interactions between them (same as tertiary but between DIFFERENT mcs instead)
catalase an enzyme found in almost all living things -breaks down H2O2 (hydrogen peroxide) into water and some oxygen bubbles -found is yeast
how to convert data into a rate?
As the concentration of enzymes increases, the rate of the reaction increases. However, eventually this plateaus. Explain why After a certain point, the number of enzyme molecules available to bind substrate is no longer the limiting factor. The amount of substrate becomes limiting. All the available substrate molecules are already being acted on by enzymes.
Four variables that affect the rate of enzyme activity Temperature (higher temp = more frequent collisions, too high temp = protein denatures) Enzyme Substrate (increasing - more substrate to break down, faster rxn) pH (it has an optimum pH & denatures at any other pH)
chaperonins proteins that help proteins fold into the tertiary structure (sometimes Quaternary) -barrel-shaped; proteins go inside; protected environments where proteins can fold without sticking to other proteins or folding incorrectly -they are reusable
helical shapes -shaped like a spiral -DNA - double helix RNA - short helical regions
which enzyme breaks down lipids lipase -small intestine
which enzyme breaks down proteins pepsine -stomache
which enzyme breaks down carbs amylase -mouth
When something is denatured, which interactions are specially being distorted? Quaternary tertiary secondary RARELY primary
effect of temperature on protein function higher temperatures increase KE leading to more frequent collisions -if the temp is too high, the energy breaks the bonds/denatures the protein
In a graph with substrate concentration on the x-axis and the rxn rate on the y-axis, why does the graph eventually plateau? -the actives sites of the enzymes are already full -the substrates are no longer the limiting factor, the enzyme concentration is -the pt when the graph starts to plateau is called the saturation point
which of the four structures of proteins determines the final shape primary structure
How does a denatured protein regain its shape (refold) Chaperone proteins can help proteins fold correctly by preventing incorrect interactions & giving them a protected environment to fold -unfolded proteins have exposed hydrophobic regions that can accidentally stick to other proteins. Chap. shield them
When is denaturation not reversible extreme changes -unfolded proteins stick together & become difficult to separate & refold -the proteins structure is permanently altered
Properties of water high specific heat cohesion & adhesion high bp high latent heat of fusion high latent heat of vaporization ice is less dense than liquid water thermal good solvent
why is water essential to life Due to its polarity & ability to form hydrogen bonds (weak individually but collectively strong) with other polar molecules, it has many properties essential for sustaining life
Why is ice less dense than water HBs are constantly breaking, reforming & moving around, letting H2O mcs move closer - H2O freezes = bonds slow down & are less flexible, causing it to expand (creates empty space between mcs) -floating ice on oceans insulates underlying water
How does water keep solute dissolved charged water mcs are attracted to & surround charged ions -the formation of inter-molecular bonds between H2O & ions keeps the ions dissolved -thats why polar mcs (amino acids & carbs) dissolve in water -
Cohesive property of water -water mcs stick to each other because HBs form between them -allows water to form droplets -SURFACE TENSION -cohesion allows water to form an unbroken column while moving through the xylem of plants (water uptake from soil)
Adhesive properties of water -water is attracted to other mcs because of its polarity -enables capillary action (ability of a liquid to flow against gravity in a narrow space) -meniscus of liquid in a tube -helps h2O mcs stick to xylem walls in capillary action
why might water be able to flow against gravity -if adhesive forces (H2O & surface) are stronger than cohesive forces, H2O spreads along & climbs the surface -adhesion pulls H2O up the sides while cohesion carries other water mcs along -only in narrow spaces (more surface area compared to water)
solvent properties of water -polarity lets it dissociate ions in salts & bond w/ P mcs (alcohols/acids) dissolving them -metabolic processes depend on solutes coming into contact -blood plasma is largely water & transports water-soluable substances (glucose, AA) around the body
specific heat -highest specific heat capacity of all liquids (takes a lot of energy before it changes temp) -caused by cohesion -large bodies of water will maintain stable temps -
high heat latent of vaporization -it takes a lot of energy to break the HB & change from liquid to gas -makes sweating a very effective cooling mechanism (the water takes the energy it needs to evaporate from your skin) -change from liquid to gas absorbs a lot of E
is water acidic or basic amphoteric -it can donate an H or rieceve an H in chemical reactions
how does specific heat and cohesion relate -cohesive = many HB = when you + heat the E is used not only to make mcs move faster but to disrupt HBs (temporarily breaking & reforming) -because some added E goes into disrupting them the mcs temp (average kinetic energy) doesn't rise as quickly -
How does water have a buffering effect on the climate when the environment warms, oceans & lakes absorb heat without their temp increasing much -when it environ. cools, water slowly releases the stroed heat, preventing temps from dropping fast
water's transparency -high transmission of visible light -light penetrates aquatic environments, allowing photosynthesis to occur
Starch -storage carb for PLANT cells made of two alpha glucose polymers -plants make & store it inside amyloplasts (unpigmented organelles) -made of amylose (long & unbranced) & amylopectin (has many branches)
cellulose -unbranched structural beta glucose polymer bonded by stable glycosidic bonds -unbranded structure produces parallel chains that become cross-linked w/ HBs to form strong microfibrils
glucose -type of monosaccaride (monomer of carbohydrates) -
maltose --two glucose mcs
glycogen -many glucose molecules (alpha glucose) -VERY branched -polysacciride -stores energy in the form of glucose for ANIMAL cells
microfibrils -cell walls in plants are made from cellulose microfibrils (40-70 cellulose chains joined by HBs) which provide the cell with strength & ridgidity
amylose -made of thousands of alpha glucose monomers -simplest form of starch -linear molecule (forms a helix spiral cauz of the angle its glucose mcs are connected by glycosidic bonds)
cellulose Vs starch -molecular structures starch: alpha glucose = coiled/helix Cellulose: beta glucose = straight, unbranched chains (each glucose unit is flipped relative to its neighbor = balanced chain)
neutral fats/oils -most abundant lipids in living things -non-polar (no overall charge) -consists of glycerol attached to one (mono-), two (di-) or three (tri) fatty acids by ester bonds
esterification a condensation rxn of an alcohol (like glycerol) w/ an acid (like fatty acid) to produce an ester & water
Lipolysis the breakdown of lipids -it involves hydrolysis of triglycerides into glycerol mcs & free fatty acids
monosaturated a chain with only one double bond
How does the proportion of saturated VS unsaturated fatty acids affect the fluidity of the phospholipid bilayer? -fatty acid tails can be unsaturated or saturated -more double bonds in the tail = more fluidity in the membrane less -more double bonds means the mcs are less compact = fewer IMF between them = lower mp & phospholipids are help together less lightly
How the saturation of an Arctic fish's cell membrane would differ from those of a tropical fish Arctic: more unsaturated tails, maintains fluidity in cold temperatures tropical: more saturated, prevents membrane from becoming too fluid
How do enzymes know when to stop working? -end product can control and stop the initial step -When in excess, the final product can bond to the enzyme, changing its shape and ultimately function
Fuels that are produced from a biological source that was recently living Biodiesel Syngas Ethanol from starches/sugars Cellulosic ethanol
Cellulose breakdown heat, acid, ammonia, Enzyme mixtures (cellulases hydrolyze the bonds)
transpiration the evaporation of water from plant leaves -because water mcs have strong cohesion, the loss of H2O from the leaves draws a continuous column of water upward through the xylem from the roots
how to find the number of water mcs produced during dehydration synthesis the number of monomers being connected minus one
globular proteins spherical, 3D shapes -tertiary & Quaternary structures -includes Enzymes -compact -soluble in water -hydrophobic R groups inside -metabolism, transport, signaling, regularion, defense
fibrous proteins keratin, collagen -provide structural support rather than dynamic biological roles
messenger RNA transcribed from DNA carries a copy of the genetic instructions from DNA to ribosomes in the cytoplasm, where it is translated into a polypeptide chain
Transfer RNA carries amino acids to the growing polypeptide chain. One end of the tRNA carries the genetic code in a 3-nucleotide sequence called the anticodon. The amino acid links to the 3' end of the tRNA
Ribosomal RNA -associated with proteins that make up ribosomal componets (the large and small subunits) assemble amino acidsin to a polypeptide chain
Types of proteins fibrous, globular
Fibrous proteins long & structural -long, strong, structural -physically tough -insoluable in water -repetitive AA sequences -keratin, collegian -strength, support, protection (not chemical rxns) -form fibers, cables, sheets, or other strong structures
Isomerism -same molecular formula but different structures -sugars (carbs) with the same molecular structure but different structures changes how they function (glucose VS fructose) (glucose VS galactose)
Why are lipids such good sources of energy -they are highly reduced (a mc is more reduced when its carbon atoms have more C-H bonds & fewer oxygen) -they are anhydrous
intracellular enzymes -function inside the cell that produced them -catalyze metabolic pathways essential for cellular survival -EX: catalase (catalase converts hydrogen peroxide produced by metabolic processes into water and oxygen gas) -most common
extracellular enzymes --enzyme that functions outside the cell from which it originates (produced in one location but active in another) -
Enzyme inhibitors chemicals that stop or slow enzyme activity either temporarily, or permanently -reversible inhibitors: easily diconnect from the enzyme -irreversible: bind tighlty (often act as poisons) and can't be removed -phyically blocks subtrate from binding
Competitive inhibition - inhibitor directly competes w/ substrate for active site -overcome it by increasing subtrate conc. (more likely for subtrate mc to reach active site before inhibitor) -reaches same max rate but requires higher substrate conc. to get there
non-competitive inhibition -Allosteric regulation -inhibitor (oftentime the product in the rxn) binds to a different site on enzyme -alters shape of the enzyme so it can't bond with substrate -can't be overcome by adding more substrate -lower max rate despite subtrate conc. -
Allosteric Site binding location on an enzyme distinct from the active site used for regulatory mcs (inhibitors or activators) -
Feedback inhibition neg. feedback: prevents cells from overproducing substances -when the cell uses up the product, the product detaches from the allosteric site so the enzyme can make more -when the product concentration is high, the inhibtor/product attaches
How to nucleic acids bond the phosphate group of one and the sugar (pentose) of the other -phosphodiester bond forms -3' C atom of one neucleotide to the 5' of another -3' --- phosphate -- 5'
RNA folding complementary bases can HB with each other helping stabilize the folded structure
Bonds within DNA & RNA glycodsidic bonds = nucelobase to sugar (base to backbone) phosphodiester = sugar + phosphate (within the backbone) hydrogen bonds = complementary bases + bases (holds the 2 strands tg in DNA)
Of all the interactions within the tertiary and quarternary structure, which is strongest? disulfide bond
What determines the properties of an active site? -tertiary structure (3D shape)
explain why an extracellular enzyme would be secreted (released) in an inactive form? -it would start breaking down mcs within the cell or in the wrong place -they are activated only after they reach their correct location
How do enzymes increase the reaction rate? -provide a site where reactants come tg w/ proper speed & orientation (reactive regions on reactants come tg) -destabilize bonds within the reactants; formation of ES complex strains substrate bonds & lower AE needed to reach transition state
intermediate enzyme product complex -the stage after the chemical rxn has occurred but before the products leave the enzyme -the substrate becomes the newly formed product
active complex once the substrate enters the active site, the shape of the active site changes to form an active complex.
irreversible VS reversible inhibitors irreversible inhibitors: bind tightly to the enzyme and are not easily displaced reversible: used for regulation in metabolic pathways (as more inhibitor is produced the rxn slows down & when less is produced the rxn speeds up)
allosteric site the place on the enzyme where a mc that is not a subtrate may bind. It is never the active site -where non-compeitive inhibitors bond
cellobiose -broken down by the enzyme B-glucosidase (cellobiase), but rxn is colorless, so use pNPG (yellow in basic) as an artificial substrate -made of 2 glucose mcs
Chitin structural polysaccharide, is found in the exoskeleton of arthropods -structural support for the cell walls of many fungi
DNA function instructions for making proteins -contains the genertifc info that determines the AA sequence of protiens
RNA function uses info in DNA to make proteins -mRNA carries instructiona from RNA to ribosomes tRNA & rRNA help assemble proteins
 

 



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