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Unit 1: Biochemistry 1. 1 atomic number: #of protons (equal to number of electrons) atomic mass: sum of protons and neutrons in nucleus. isoto...

Unit 1: Biochemistry 1. 1 atomic number: #of protons (equal to number of electrons) atomic mass: sum of protons and neutrons in nucleus. isotopes: atoms of an element with the same atomic number but different mass number (then on the periodic table) electronegativity: atom's ability to attract/ hold on to electrons (increases → ↑) 0 0.4 1. 7 iii.in Iii, ionic hydrogen bonding: hydrogen atom is covalently bonded to electronegative atom (oxygen, nitrogen, etc.) acids: increase the concentration of H 30 + can, when dissolved in water (donate Ht) bases: increase the concentration of OH- ions (release 0H] buffer: solution that resists changes in pH when small amounts of acid or base is added. OH 1. 2 OH OH macromolecules: carbohydrates, lipids, proteins, nucleic acids. OH OH OH OH OH condensation / dehydration synthesis reaction: covalently link subunits of macromolecules together by having +120. OH OH H2O t OH 0H + OH OH OH OH At B → H, O + AB (2 glucose → H2o t maltose) OH OH hydrolysis: polymers are broken down into monomers by adding H2O. energy HO - C - C- C - C - H HO - C - C - C - H t HO - C - H H2O polymers: molecule consisting of smaller subunits (many) Monomer: subunit of polymer (single) Making → anabolic /endothermic and condensation /dehydration synthesis reactions. ↳ reality; ↳ energy ↳ mass stored buildup breaking → hydrolysis (catabolism / endothermic) ciriiiii.is" sugars short - term energy storage contain C, H , and 0 (1: 2:11. " monosaccharides : simplest form of carbohydrates. ↳ structure → has hydroxyl (OH) groups attached to each carbon except one , which has a double banded oxygen (1=0). ↳ glucose , fructose , galactose functional groups (found on amino sucrose : glucose t fructose H acids) lactose : glucose t galactose R Hydroxyl Maltose : glucose + glucose R \o/%- OH \ disaccharides : double sugar of 2 Monosaccharides, Joined by glycosidic linkages. OH 0 ↳ formed from condensation reactions. Phosphate Oligosaccharides: 2 - 3 monosaccharides. R- ! R' Polysaccharides: few hundred / thousand monosaccharides. R -S \, carbonyl (Ketone) ↳ functions as energy storage or structural support. ↳ starch: plant storage of energy. Sulfhydrl cellulose: tough fiber- live structural material (insoluble) found in plant cell walls. i glycogen: highly branched chain of glucose used in the muscles and liver of animals. H R /'i H chitin: structural material in exoskeletons. R-N (aldehyde) H lipids Amino hydrophobic molecules (non polar compounds). composed of C, H, O. : functions: \ energy storage OH R carboxylcarboxylic / acid insulation against cold regulating cell activities through hormone actions. protection against desication (drying out). i ♀ "I_or k: " C R has a phospholipid bilayer membrane. / - NH} R R fatty acids: long hydrocarbon chains with a - coott at one end. amide ester anhydride saturated: unsaturated: no! _ 'c- 'c - & 1 1 I C 1 - 1 C I - I. C i-i - i- I , 1 Ho! - I - I - & I I - id- i' = i-i-i. phospholipid bilayer (solid) ◦ liquid at room temp. releases energy by breaking hydrocarbon bonds. plant fats. animal fats. t"rigFly"iserides: most common fat composed of glycerol and 3 fatty acids. ↑ H C - O - 'c - R l H - O - É - R H- - o - % - R H 2) phospholipids - head (hydrophilic) cell membranes - tail (hydrophobic) O 3) steroids: cholesterol, estrogen , testosterone. 4) waxes proteins consists of polypeptide chains (sequence of amino acids I which have peptide bonds between 20 possible amino acids. functions: a enzymes: speed up specific chemical reactions. structural materials: keratin (hair/nails) and collagin (connective tissue). specific binding : antibodies bind to specific foreign substances. specific carriers: membrane transport proteins , blood proteins (hemoglobin). contractions : actin and myosin interact in muscle tissues. signaling: hormones, such as insulin , which regulate blood sugar levels. structure of amino acid monomers: central carbon ↳ attatched to amino group ↳ a carboxyl group H, N -[ - Iii: ↳ a hydrogen atom mi:p ½ group ↳ a variable R group, specific to each amino acid. structural levels of protein: 1) primary : sequence of amino acids (covalent bonding) 2) secondary : - helix & or β -pleated sheet (hydrogen bonds) 3) tertiary: complex folding folds again 4) quaternary: several polypeptides interact /with"" [0th " """""""). (R - group - R - group "" cractions betweens globular polypeptide chains). denature: change in the three - dimensional shape of protein through temperature, pH or ionic concentration (cannot carry out biological functions). Nucleic acids - informational macromolecule composed of nucleotide polymers (sugar, phosphate group, and nitrogenous base) DNA and RNA protein synthesis and gene regulation. ↳ genetic info. 1.3 1. 4 Metabolism enzymes free energy → useful work biological catalysts that increase biochemical reaction rates. Kinetic energy → moving objects energy activation: the energy used to break bonds in the reactants so they can be potential energy → stored by position reformed in the products. anabolic reactions: build more complex molecules from simpler subunits. characteristics: catabolic reactions: break down more complex molecules into simpler subunits. Made of proteins (RNA) ends in "ase" Metabolism: sum of all anabolic and catabolic reactions in a cell or organism. % specific and only work with a certain set of substances that fit in the active site. induced fit: enzyme - substrate interaction causes the enzyme to change shape. laws of thermodynamics: 1) energy cannot be created nor destroyed, only converted. This allows the chemical reaction to occur. 2) when energy is transfered from one form to another, some energy is always "lost" as heat. competitive inhibitor: enter the enzy"'s """ site , blocking the substrate main types of reactions: from binding. "EEEE inhibitor 1) endergonic: building bonds / putting energy into molecules. 2) exergonic: breaking bonds / releasing energy. noncompetitive inhibitor: attatch to another site on the enzyme, causing a change shape of the enzyme's active site. ""EE" allosteric sites: specific regions that are distinct from the active site , where molecules can bind, inducing changes that affect the enzyme's activity (control it). % feedback inhibition: end product inhibits an earlier stop (allosteric), stopping overproduction.  unit 2 Photosynthesis Cellular Respiration Hyo ytoplasm) Glycolysis pyruvate oxidation (Mitochondrial Matrix): Light → ② Glucose →('" 2 ½ Pyruvate looses a Co2 molecule and becomes C 000000 000-P 000-P In Joins with CoA (enzyme) to form acetyl - COA : Reactants Products Reactants products light dependant reactions (takes place in thylakoid membranes): glucose 2 pyruvate 2 pyruvate 2 acetyl - COA ZAT P 4 ATP 2N AD + 2 NADH 1) Photo excitation: 4 AOP ZAUP 2 CoA 2H t 2 NAD t ZNAUH Photon is absorbed by the antenna complex (contains chlorophyll and accessory pigments). 2202 Energy is passed to the reaction centre with chlorophyll a. ZP, 2 COA Chlorophyll in photosystem# absorbs sunlight 2H + 2) Electron transport: Net 2 ATP produces ATP NADPH, and 02 Non cyclic electron flow (linear movement from PSII to PSI) Krebs / citric Acid cycle (Mitochondrial matrix and inner membrane). The energy from the ETC is used to pump protons across the thylakoid membrane. ◦ series of enzymes oxidize acetyl- CoA , creating 4 Cuz molecules (2 cycles from 2 acetyl- CoA) More photons are absorbed by PSI , and the excited electrons are passed through a second ETC. ◦ Purpose: to create high -energy electron carriers (NADH and FAOH,) and produce some ATP At the second ETC , NAD Pt is reduced to NADPH. while regenerating oxyloacetate to continue the cycle z protein associated with PSII splits (oxidizes) H2o into 02 Cyclic flow: only uses PSI Reactants Products Electrons are returned to chlorophyll and not passed on to NADP + zacctyl.co#­ 2oxyloacctatc­ ZADP GNAD+­ 2 COA Generates ATP, but not NADPH or 02. 4202 20×410 acetate 3) chemiosmosis: ◦ Proton gradient (accumulation of Ht) builds up in the thylakoid. 6 NADH 2P: Proton - motive force drives ATP synthase enzyme to produce ATP. 3170+12 4H + is used for each ATP produced. IFAD 2 ATP Thylakoid Interior Space TATP 1 photons 102+2 Ht photons Ht +l t Ht H2O Ht ETC Oxidative Phosphorylation (inner mitochondrial membrane and intermembrane space) 2e PS PSI 1) Electron Transport Chain (ETC): 1J?those Electrons are dropped off from electron carriers and are passed through a ETC Ht + NADP +. series of complexes that results in proton (Ht) pumping with the formed proton gradient. Stroma Light Independent: Oxygen is the last Electron carriers: The Calvin cycle ATP → Powers photosynthesis acceptor which bonds with parts: NADPH → Reduces Coz some of the pumped hydrogens NFAADO ++ ⊖⊖ 1) carbon fixation FNAADOHHZ 4 Reduction reactions to make H2O. 3) RuBp regeneration. (02 → organic molecules, then uses ATP and NADPH to further reduce it to carbohydrates ((641200). 2) chemi osmosis: - Reverse of Kret cycle and pyruvate oxidation. The pumped protons drive the ATP synthase enzyme, which converts ADP to ATP. ↳ Potential energy push 1) Carbon dioxide fixation: 36oz + 3RUBP → GPE# (3 - phosphoglycerate) b o - o - o - p Reactants Products RUBP P-o-o-o o-c-P 6 NADH (Krebs) 8 NADT 2 NADH (pyroxi) 4 FAO" 2) Reduction reactions: Z FA DHL (Krebs) 24 Ht 46,AµTpP → 1, 3 BEP Phosphorylate 2 FADHIL 32 ATP P - O - u-o - p 6H20 (take out 6 phosphates / 32 ADP 6 NADPH 32 P: ↳ GNA opt → 66,3 P 602 l is used to make sugars (glucose) 12 Ht other 5 is used to regenerate 3 RuBP 3) RuBP Regeneration: 5 ESP macules (15 carbons) undergoes reactions requiring 3 ATP to regenerate RuBP for the next cycle. Calvin Cycle (takes place in stroma): 3602 = carbon 3 RUB P Itis:- area-p 37- 0 O - P Can601 6 3-PGA Fixation :-p 3 ADD - G ATP 3 ATP + 6 AOP + GP; Regeneration Reduction 5 - P G3P 6 P G3P - ::*:P# are recycled to make RuBP l - P G3P to make glucose. Alternative Mechanisms of Carbon Fixation: Photorespiration: Rubisco enzyme catalyzes reaction of RUBP with 02, instead of CO2. ↳ results in the loss of fixed carbon, reducing the efficiency OF photosynthesis. (3 plants in higher temperatures increase photorcspiration, negatively impacting its growth. In - methyl guanosine (5" cap) is added to the s' end of the mRNA, protects from degradation and helps ribosome binding in translation. string of 200 to 300 adenine nucleotides are added to the 3' tail by the enzyme poly-A polymerase (known as poly - A tail). Introns (noncoding): cut out by splicosomes. ↳ &:p: Exons (coding regions): splicosomes rejoin the remaining exons. MRNA is ready to exit the ruckus  c o n t a in s 2 s it e s , t h e A ( a cc e p t o r ) a nd p ( p e p t id e ). T r a n s l a t i o n 1) I n it i a t i o n M R N A b in d in g : th e t r a n s c rib e d m R N A s ' c a p b in d s t o r ib o s o m e s u b u n its ( la r g e an d s m a ll) a t th e ir b in d i n g s it e. R ib o s o m e s ca n s f o r m R N A s t a r t co d o n ( A U G ) , c o rre s p o n d i n g t o m e t h i o n in e. t R N A : t r a n s f e r R N A ( t R N A - c a r r ie s m e t h io n i n e ) b in d s to st a r t c o d o n t h rou g h it s a n ti c o do n LÉ É ). 2 ) E lo n g a t i o n R ib o s o m e m o v e s a lo ng m R N A r e a d i n g e a c h c o d on ( s e q u en ce o f 3 n u c le o t i d e s ). R ib o so m e s c a t a ly z e th e f o r m a t io n o f p e p t id e bo nd s be t w een t h e a m in o a c id s , c r e a t i n g a p o ly p e p t id e ch a i n. t R N A a t t h e P s i te t r a n sf e r s it s a m in o a c id s to t h e A s it e. T r a n s lo c a t io n : r ib o s o m e s h if t s , y y j g s e t y g.t t ? N I. f r o n t h e A t o P s it a. T h e e m pt y t R N A in th e P s ite m ov e s ↳ T h is p r oce ss r e p e a ts t o e lo n g a t e t h e p o ly p e p t i d e c h a in. 3 ) T e r m in a t i o n : s t o p c o d o n s t o p s t r a n s l a t io n. A r e le a se f a c to r pr ote in b in d s to t h e s t o p co d o n , m a k in g th e r ib o so m e r e le a s e t h e s y n t h e s iz e d p o ly p e p t id e c h a in. pr o t e i n is f o ld e d , m o d i f ie d an d d ir e c t e d t o w h ere it is n ee d e d in t h e c a l! 5.5 ( L a c / t r p o p e r o n s ) O p e r o n s : g e n e r e g u la t i o n m e c h a n is m in pr o k a r y o t e s. T h e se g e n e s co d e f o r pr otei n s p r e se n t in th e s a m e m e t a b o li c p a th w a y s. ↳ A l lo w s for s y n t h e s is le v e l r e g u la t io n. L a c o p e r o n ( in d u c t io n - t r ig g e r s s y n t h e s is ) : r e g u la t e s p r o d u c t io n o f β - g a la c t o s i d a s e a n d o th e r prot e in s i n v o lv e d in th e m e t a b o li s m o f la c t o s e. → = la c t o s e ^ (N O M RN A r ate) (M R N A r a t e ) L a c 't r e p r es s o r pr o tein t o op e r a to r w h e n la c t o s e : b in d s is lo w. T u n s o n w h e n Opera tor : la c t o se r u n s o u t. A → + ( P ( t ryp top h an ) o p e r a t o r : r e g u la t e s p ro du c t i o n of a m in o a c id tr y p t op h a n. ↳ o p p o s ite o f L u c k t r p ( c o r e p r es s o r - t o g e t h er t h ey ca u se r e p re ss io n ) ( M R N A is m a d e ) ( M R N A n ot m a de ) ↳ b in d s t o t r p r ep re ss o r w h ic h b in d s t o th e op e r a to r w h en t r p le v e ls are h ig h. 5. 6 ( M u t a t io n s ) M is s e n s e : n o n s e n s e : E t j j a n g e in a m in o a ci d ↳ on e s u b s t it u t io n o f a m i n o a c id in ↳ c o d o n fo r a m in o a c id t h e r e s u l t i n g p o ly p e p t i d e. b e c o m e s a t e r m in a t io n co do n. A T T H E A A A ± : : ✓ A A ÷ : :: : : : : ph e : Ley s t o p o r g. m u ta te d Or g. m u ta te d S u b s t it u t io n : D e le t i o n : I n s e r t io n : P o in t : ↳ R e p la c e m en t o f on e ↳ E x t r a u s ted n u c le o ti d e ↳ sp e c if i c to one ba se p a ir. ↳ e li m i n a t i on o f a b a s e * AG.. ÷.. b a se f or a n oth er in a DN A s e q u e nce. p a ir or g rou p of b a se p a ir s o rg. C I G G E E o r g. C T ∈ ⊛ A G r a n s lo c a t io n : ↳ tr a n sf e r of a f ra g m en t of DN A "A c c UA E U A - TC E A T C A T C T A G C T A A A G ⇐ G E f r o m o n e s it e t o a n o th e r lo c a tio n. C a u s e s : s p o n t a n io n s m u t a t io n s : e r ro r in r e p li c a t io n. m u t a g e n ic a g en t s c a u se m u t a t io n. I n d u ced m u t a t io n s : ch e m ic a l a g en t or r a d i a t io n 6. 1 ( B i o t e c h n o lo g i c a l t o o ls ) 1) R e s t r i c t io n E n d on u cle a s e s R e s t r i c t io n e n z y m e B lu s t E n d : # E )E F c le a v e s ( c u t s ) d o u b le - s tr a n d e d DN A in to f r a g m en t s a t s p e c if ic s e q u e n c e s. R e c o g n i t io n s i t e : t ic k y E n d s : s p e c if ic s e q u e n c e o f d ou b le - s t r a n d e d D N A ( 4 t o 8 n u c le o t i d e s ) , w h ic h f it s in t o th e a c t iv e s it e.. ↳ p a lin d r o m i c : S m c f or w ard s / ba ck w ard s. E C O R I : s ca n s DN A m o le c u le f or r e c o g n it io n s it e a n d cr e a t es 2 f r a g m en ts w it h c o m p le m e n t a r y en d s. 2 ) M e t h y la s e : e n z y m e t h a t a d d s a m e th y l g r oup , w h ic h p r otec t s t h in g s yo u d o n 't w a n t t o cu t o u t. 3 ) D N A L ig a s e : r e co n n ec ts t h e p h o s p h o d ie s t e r lin k a g e of O N A ba c k b o n e. 4 ) P la s m id s : Lo o p s of do u b le - s t r a n d e d D N A. P C R - p o ly m e r c h a in R e a c tio n ↳ T e m p e r a t u r e cy c lin g D N A to d e n a t u r e D N A a n n e a l p r im e r s , a n d s y n t h e s iz e s n e w D N A s t r a nd s f r o m a t e m p la t e. 1) D e n a tu r e 2 ) A n n e a li n g : t e m p , lo w e r e d to a ll o w p r im e r s to b in d. 3 ) E lo n g a t io n : T a q D N A p o ly m e r a s e (h e a t r es is t a n t ) , s y n t h e s iz e s n e w s t r a n d a d d i ng d N T P s ( S ' - 3 ' ) ↳ J A T P R F L P ( c u t ON A a t s p e c if ic s e q u en c e s , c r e a t in g v a r ia t i o n s in le n g t h (D N A f r a g m e n ts ) ). J T T P R e s t r i c t io n (e n z y m e ) I C T P F r a g m en t S F T P L e n g t h P o ly m o r p h is m ↳ D N A f r a g m e n t s a t S e p a r a te d in y e t e le c t r o p h o r e s is ( t h r o u g h s o u th e r n b lo t t i n g - t r a n sf e r r e d to a n y lo n m e m b ra ne , m a in t a i n in g t h e p o s iti o n o f DN A f rog + i ↑ ↑ - g e t D N A s e q u en c in g :  C h a p te r 7 - H o m e o s t a s is 7. I o m e o s ta s is : a co n s ta n t in te r n a l e n v ir o n m e n t m a i n ta i n e d d e s p ite ch a n ge s in th e e x te r n a l e n v ir o n m e n t. h ◦ C h a ng e s in b lo o d g lu c o s e , t e m p e r a tu r e , s y s t o li c b lo o d p r e ss u r e , o r b lo o d p H. y n a m ic e q u i l ib r iu m : c o n d it i o n th a t r e m a in s s ta b le w ith f lu c tu a t i o n li m i t s. d B lo o d G lu c o s e T e m p e r a tu r e s y s t o li c B lo o d p r e ss u re B lo o d pH b e c o m e s m o r e a c id i c 1 d u r in g e x e r c is e d u e to e x e r cise s le e p exercise s it e p la c t i c a c id b u i ld u p. m ea l e a te n e x er cise i i i.i n e x e r c ise M e c h a n is m is th e ir o r ig in a l s t a t e. 1 e g a t iv e f e e d b a c k : p r o c e ss w h ere a a c t iv a te d to re s to re c o n d it io n s to e g. T h e r m o s ta t O s it iv e fe e d b a c k : p r ocess w h er e a s m a ll ef f e c t is a m p li f i e d. p 7. 3 E x c r e t in g w a s te s d e a m in a t i o n : re m o v a l o f a m in o g r o u p fro m a n o r g a n ic c o m p o u n d. ( 2 N H , + 1 C O 2 ). u r e a : n i tr og e n w a s te f o rm ed fro m tw o m o le c u l e s of a m m o n ia a n d o n e m o le c u l e o f c a r b o n d io x id e u r ic a c id : w a s te p r o du c t fo rm e d fr om th e br ea k d ow n o f n u c le i c a c id s. m e t a b o li c w a s te s : a m m o n ia , u r e a , u r ic a c id , c a r b o n d i o x id e , b ile p ig m e n t s , la c t i c a c id , s o li d w a st e. K id n e y f i lt e r s w a ste f r o m b lo o d. ◦ L iv e r h e lp s e lim in a te to x ic n itr o g e n g r o u p s f r o m th e b o d y b y d e a m in a t io n. L a nd a n im a ls produ c e u re a la rg e r / m o r e c o m p le x a n i m a ls p r od u c e m o r e w ast es ; h a ve s p e c i a li z e d c e lls th a t a l lo w fo r m o re e ffic ien t w a ste r e m o v a l. 7. 4 T h e U r in a r y s y s te m S tr u c tu r e s : 1) 2 k i dn e y s 2 ) 2 u r e te r 3 ) 1 b la d d e r 4 ) R e n a l v e in / a r te r y u r e te r s : tu be s th a t c o nd u ct w in e fr o m th e k id n e y s to th e b la d d e r u r e t h r a : tu b e s th a t ca rr y u r in e f r o m th e b la d d e r to th e e x te r i o r o f th e b o d y. c o r te x : o u te r la y e r o