Biochemistry Lecture 2 - Bonding, Water, & Thermodynamics PDF

Biochemistry lecture 2 Chemical review: Bonding, water, & thermodynamics note: Fig 1-14 pg 15 is a reference for the common functional groups used in biochemistry. continue Types of molecules interactions. 2. Ionic interactions - it is the interactions o...

Biochemistry lecture 2 Chemical review: Bonding, water, & thermodynamics note: Fig 1-14 pg 15 is a reference for the common functional groups used in biochemistry. continue Types of molecules interactions. 2. Ionic interactions - it is the interactions of 2 charged atoms based on the columb law. Leave 2 atoms with formal charge (Q) on the atom separated by a distance (r). Then the force of that interaction is equal to the charge on the first atom × the charge on the second atom, divided by ∑ r 2 Force (F) = 91.92 Σr² where Σ is the dielectric constant. ☆ Σ takes into account the medium the atoms are in. - In chemistry , ionic interactions can be as strong or stronger than covalent interactions, but not the case in biological system in biological system,ionic interactions are usually weaker, and we classify them one level down why ? Ionic interactions occur in water, and water has high dieletric constant, reducing/ weaking the strength of the interaction between charges. - second strongest interaction - electrostatic can be both the attraction and repulsion. ex: DNA- Ionic interaction is affecting the shape of DNA by repulsion.  3. Hydrogen Interactions. a hydrogen atom is partly shared by 2 electronegative atoms : a hydrogen donor (which the H is covalently bond to) and a H acceptor - both are usually oxygen or nitrogen (sometimes sulfur). - This is a special form of an electrostatic interaction. H donor H acceptor - is electronegative - is electronegative - pull e- away from the H - develop a 5 resulting in electronegative donor becoming partly negatively charged, and - it has to have a lone pair of e- H becomes 1st, partly positively charged - The sc harged H is attracted 8- 8T. &; to the s-a cceptor and a H bond is formed. N - H ¼ at H bond not e: An g s t r o ms - H-bonds are weak 14-13 (KJ/mole) and longer - 10 o i s 10 m. 1. 5- 2.6 A (angstroms) then covalent bonds. Fig 2-4 Pg 45 shows H-bonding in bases pairing in DNA.  4. van d e r W aa ls. In te ra c tio n s. - a ttra c tio n o f a ny 2 m o le c u le s - a lso a s p e c ia lize s form o f e le c tro sta tic in te ra c tio n - T h e id e a b e h in d V an d e r w a lls is th a t th e c h a rg e a ro u n d a n u c le u s is n o t p e rfec tly s y m m e tric a ny t g iven tim e i. yo u c o u ld h ave for a s p lit s e c o n d m o re e le c tro n d e n sity o ver o n o n e s id e o f th a t a to m. If th is is b ro u g h t in p roxim ity to a n o th e r a to m , it w ill in d u c e a c o m p le m e n ta ry a sy m m e trsy.. c a u sin g th e a ttra c tio n b e tw e e n 2 a to m s. & ♂ + 8- - at any given time, the charge distribution around an atom is not symmetric. - This assymetry causes complimentary assymetric on another atom. resulting in the z atom being attracted to each other vinaigrette - As we decrease the distance, the &: attraction increases, and suddenly α it greatly decreases because Distance ¾ §:{ distance the negative electron clouds decrease are repelling each other = Van der Waals contact distance - Van der Waals is the is the distance of maximal attraction Weakest bond type as it has of the 2 atoms. small energies of 2-4 KJ/mole. ☐ The attraction increases until the electron clouds start to overlap and repel.  - D N A d o u b le h e li x w it h b a s e p a irs f o rm in g lik e a la d d e r. It t u rn s ou t t h a t t h e d is t a n c e b e t w e e n t h e b a s e p a ir s is t h e v a n d e r W a a ls c o n t a c t d is t a n c e ( t o m a x im iz e t h e v a n d e r w a a l in t e r a c t i o n b e t w e e n e a c h o f th o se p a ir s ). 5. H y d r o p h o b ic in t e r a c t io n / e f f e c t. - s p e c ia l t y p e o f in t e r a c t io n - w i ll d is c u s s m o re s h o rt ly B. w a t e r - a lm o s t a l l b i o c h e m i c a l r a in s ( r e a c t i o n s ) o c c u r in a q u e o u s s o l v e n t ( i.e H 2 o ) - w a te r h a s a b i g e f f e c t on th e s e r a in s a n d in t e r a c t i o n s. - w a te r h a s a b e n t s h a p e , m a k in g t h e m o le c u le p o la r a n d c a p a b le o f f o rm i n g m u l t i p le H b o n d s. b e c a u s e o f t h is w a t e r is v e ry c o h e s iv e t h a t is w a t e r m o le c u l es c a n f o rm H - b onds ea ch o th er as can be s e e n in f i g u r e o n lef t ( ic e ). → a " → w a t e r is a n e x c e ll e n t s o l v e n t f o r a H E Y p o la r o r c h a rg e d m o le c u l es → h y d r o p h o b i c. ( w a t e r f e a r in g ) m o le c u l e s o r g r o u p s t h a t a r e n o t s o lu b le in w a t e r. h y d r o p h il i c : ( w a t e r l o v in g ) m o le c u le s o r g ro u p s t h a t A R E s o l u b le in w a t e r → a m p h i p a t h i c : c o n t a in s b o t h h y d r o p h i l ic a n d h y d r o p h o b ic H ow w a t e r c a n in t e r f e r e in w a t e r. w it h H -b o n d in g. → W a t e r m o le c u l e s c a n w e a k e n e l e c t r o s t a t ic in t e r a c t i o n s b y c o m p e t in g fo r t h e ir c h a rg e C o r p a r t ia l c h a rg e ). ↳ W a t e r re d u c e s e l e c t r o s t a t ic in t e r a c t i o n s b y 8 0 ✗ ( it h a s a h ig h d ie le c t r i c c o n s t a n t )  This can have serious consequences for biological systems..- water often needs to be excluded or manipulated to allow the various electrostatic interactions to occur. - water is a "double edged sword". we needs it to dissolve things but it interferes electrostatic interactions. C. Thermodynamic - all biological events are governed by a series of physical laws. Law ① The total energy of a system (matter in a defined space) and its surroundings is constant - you can't create or destroy energy energy can change its form. ex: burning wood or dropping a ball of a roof. Enthalpy: H: heat content of the system Law ② : The total entropy of a system and its surrounding always increases for a spontaneous process → For a system to be spontaneous, either the system has to get more random the universe must get more random. entropy: s: Randomness. - ¾) ^