BioChem Notes Dr Karen Hoober PDF

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Extensive Biochem Notes taught by professor Karen Hoober...

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8/31/17 Scope for this class: looking at organic molecules that are bio molecules  contain C, O, and N    

Will learn about proteins, how amino acids build to make a protein, what they look like, etc. Carbohydrates Breaking down carbohydrates through metabolic processes / metabolism Lipids

Lecture 1: Water -

All macromolecules that we will discuss will be housed in a water based environment Water has unusual physical properties o Is a polar molecule…Hydrogens don’t have much electronegativity o Water is the most abundant in living cell

Hydrogen bonding: answers question of why water  Weak electrostatic interacts btwn a H attached to an electronegative atom and its interaction with another electronegative atom  Why does hydrogen bonding contribute to water having unusual physical properties?  Hydrogen bonding is represented by a dashed line  It doesn’t take much energy to break a hydrogen bond  Electronegative atoms: O, N, S  One water molecule can have up 4 hydrogen bonds/ 4 other water molecules  Water has a higher MP and BP, higher heat of vaporization, surface tension, etc  because of the mutual attraction of H2O molecules = hydrogen bonding

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Oxygen has a greater capacity to attract electrons because of electronegativity Amount of energy needed to break a hydrogen bond = 4.5 kcal/mol Amount of energy needed to break R-OH = 110 kcal/mol ^^ Just goes to show how weak hydrogen bonding is However, the accumulation of hydrogen bonding in water makes it an important force biochemically

Comparing Water to CH4 Water and methane have similar molecular weight If you compared water to methane at room temperature, methane would be gas If water had similar physical properties, at room temperature it would also be a liquid and we would all be vaporized and life would be unlikely The point: these unusual physical properties of water are extremely important for our environment

Noncovalent Forces -

There are 4 major types of noncovalent forces o 1. Charge-Charge Interactions o 2. Hydrogen Bonds o 3. Vander Waals forces o 4. Hydrophobic interactions

^^ Structure of Ice Why does Ice Float? -

Water expands near the freezing point to an open lattice This makes ice less dense than liquid water 15% This causes ice to float and water to freeze from top down o Ice is less dense  What happens in the crystal structure?  In liquid water, the water molecules are very mobile and they are packed closer together and are more dense…in doing that, they actually have less hydrogen bonding  water has 15% less hydrogen bonding when they are in liquid form  When water moves to the solid state, it actually pushed those 2 molecules apart and freezes in the lattice structure and then you have the maximum amount of hydrogen bonding in the frozen form

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Think about how this applies to life…in a lake, the ice floats to the top. If ice was more dense, a lake would freeze from the bottom up and it would push all the fish to the surface and would kill off a lot

Like dissolves like. Non polar compounds such as hydrocarbons are not soluble in water For next class: Review Functional Groups + draw in Hydrogen bonding between water and each functional group

Hydrogen bonding Between carboxylic acid How many different water molecules are being used?  maximum of 5 -

That’s why a carboxylic acid is soluble in water, because of the hydrogen bonding

9/15 Hydrogen bonds with functional groups -

Secondary Amine  Max H bonds = 2 o Why can’t hydrogen bonds occur on the hydrogens attached to carbons?  The carbons are not electronegative! There is no pulling! Common mistake

Definitions 1. Hydrophobic: water hating such as non-polar compounds 2. Hydrophilic: water loving  such as polar and ionic compounds 3. Partitioning: molecules partition between oil and water according to hydrophobicity

Where will these partition/accumulate in oil or water? 1. Benzene  oil because it’s all hydrocarbons 2. Urea  water because it’s very polar, has 2 nitrogen &&& an oxygen 3. NaCl-  water because it is an ionic compound

Our body has general partitioning environments in it  urine is water based, adipose fat is made up of more oil layers (not polar)

Where will the following partition? Benzopyrene  Is a major carcinogen in cigarette smoke …where would it go, your urine or fat?  Oil.....it will accumulate in your adimose tissue over time Vitamin A Can be toxic if too much accumulates in the body, majority of it is hydrocarbons

Amphipathic : hydrophobic and hydrophilic Vitamin A is amphipathic So, what do amphipathic molecules do in water?  Sodium dodecyl sulfate = SDA, is amphipathic and has a very polar head **know structure*  This is what we see happening  You have the long R group and the polar head….amphipathic molecules will have the hydrophobic tail buried in the interior and around the outside is the polar head  water is pushed out of the hydrophobic interior  called “Micelle” Micelle: will be formed in amphipathic molecules that are in contact with water  Water is solubilizing the polar head through hydrogen bonds  Micelles have a very hydrophobic interior and a charged exterior and that allows the amphipathic molecule to be soluble in a water based environment Hydrophobic bonding/binding: The hydrophobic parts will segregate and form a core for which water is excluded ….non-covalent association of hydrophobic species with exclusion of H 2O Hydrophobic binding is important to proteins! -

Carry a negative surface charge Are found in the formation of our lipid membranes/biological membranes Allow proteins to be soluble It is one of the major driving forces in protein folding

Amino acids are the building blocks of proteins and proteins have the N end and C end to them -

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As a protein folds at the end of Endoplasmic Reticulum, at the ribosomes, you have amino acids inside the ER which come together and link by peptide bonds, then the backbone of the AA’s come together as the protein is synthesizes  that is the protein folding process/synthesis/transcription Once it is fully synthesized, we have this protein and it folds Proteins are soluble in a water based environment like int eh cell o They are soluble based off of hydrophobic binding in that in the interior of a protein, it’s very hydrophobic, the exterior of a protein can be hydrophilic  similar to what we see in micelles o Water is pushed out of the interior of a protein o There is no room in the interior of protein for water to be there because it is so compact

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Future lecture: learning about the R groups for each amino acid and where it would be in a protein

We have

partitioning here.  

oil water

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 a membrane o

We have an amphipathic molecule…what will it do in the test tube? Where would vitamin A go?  the polar head would be associated with the water, the hydrophobic tail would be associated with the oil Lipid membranes: amphipathic membranes that create a hydrophobic environment and the polar heads are towards the exterior and is in contact with water Later we will see proteins that are embedded in

 shows that we cant have charged proteins in the hydrophobic center

SDS is a detergent  what do detergents do? What is some of the chemistry behind Lysol acting as a detergent?  It emulsifies the stains  It allows that grease to be in the bucket of water and to be soluble…it makes micelles!  It takes the grease and it traps the hydrophobic tails in the interior/hydrophobic head on the exterior, traps the hydrocarbon and allows it to be soluble in water Remember you can make a monolayer or a bilayer o

Hydrophobic interactions are very weak

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4. Charge-Charge is the strongest non-covalent interaction and takes place over the largest distance BECAUSE it is a charge (pos or neg) so this will make a stronger interaction  opposites attract  Like charges repel  We will see some charges AAs  We will see some charges R groups If you take 2 lysines [pos charges] and place them close enough together in the interior of a protein, they will repel each other, but if you have 2 OPPOSITE charges, they will have attractive forces

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Basically, we are saying that we have a protein with a lysine on the backbone somewhere with its positive charge. If that is found on the interior of the protein then there must be something that is stabilizing that charge because of the hydrophobic environment The stabilization is called a  “SALT BRIDGE”  2 opp charged AAs found in a protein  The reason why this takes place over the largest distance, because there’s 2 full blown charges and is the strongest of the interactions

VAN DER WAALS FORCE -

These are weak electrostatic interactions  takes place over a shorter distance because it’s with partial charges, not full blown charges Basically, one end if partially positive, one end is partially negative

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The van der waals radii  The distance that the force exists is called the Van der waals radii  If the carbonyls are too far apart, there won’t be an VDW force at all

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Which is the strongest of noncovalent interactions?  charge to charge interactions

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Which is the driving force of protein folding?  Hydrophobic interactions

The reason why we talk about the physical properties of water is because our cells are made up of water! We need to look at strong acids and strong bases and look at how they dissociate in a water based environment -

For review, recall that water can act as an acid or a base!

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H2O  H+ + OH[H2O]pure water = constant = 55.5M(mol/L)  fixed number

Recall Equilibrium

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Keq = 1.8 x 10-16 M for water  fixed number Keq = [Products] / [Reactants]  [H+] [OH-] / [H2O] Kw = [H+] [OH-] = 1 x 10-14 M2  need to memorize this number!!  It essentially refers to the ration in solution of hydroxide vs hydronium ions…if you have more H in a solution, is it more acidic or basic?  acidic  If you have equal amounts of H and OH, what is it?  Neutral  pH equation  pH= -log [H+]

Practice problems 1. 2. 3. -

pH of 0.06M HCL? pH of 5mM KOH? If pH = 2.3, What is the [H+]? Hint: using anti log of -2.3 to get H+ Make sure you can convert mililmolar to micromolar to molar Make sure you can get the answers 1 = 1.22 2 = 11.7 H+ = 5.0 x 10-3M

^^ To answer these equations, really all you need is the pH equation or the K w equation 1. What are the units of molar?  mol/L 2. 65 mM [milimolar] is how many molar?  move the decimal 3 places to the left .065M

Acid Dissociation Constants of Weak Acids 1. Strong acids and bases dissociate completely in water

Cyclopropane, where does it partition, oil or water? -

In oil, it is very hydrophobic, it is the major ingredient in anesthesia  When you are going into surgery, you have to weighed to see how much adipose tissue you have  If you tell them that you are 15lbs lighter or heavier  you might wake up or not wake up in surgery!

9/12/17 Titration of Weak Acid with Strong Base -

After displacing 0.3 mol of KOH, what is the pH of the solution using 1 mo l of acetic acid? o pKa acetic acid = 4.8 o We don’t have the A- because in this example, we are adding a strong base and the pH is changing and the number of protons being removed is changing

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The point is that proton can keep coming off and the ratio HA: A can change based on how much KOH is added But you don’t plug KOH into Henderson-hasselbach equation because that’s a STRONG base need to find the ratio of HA and A- to get the pH If you start out at no KOH, you have a very low pH As you increase KOH, you slowly convert your HA to A- because protons are being donated and pH is increasing Before any KOH is added, you have 1 mol of the weak acid and you have 0 moles of the conjugate/weak base then we add 0.3 moles of KOH pH = 4.8 + log[0.3] = 4.8 - .37  pH = 4.4

At Half equivalence? -

I have equal concentrations of my acid and my conjugate base  equal ratio What happens then? You end up with 0.5 M of this and 0.5 M of that and if you take the log of . 5/.5 you get 0 At half equivalence, the pH is equal to the pKa That is a point that you can always graph on a titration curve

PRACTICE PROBLEM

You start with a solution of 0.6mol of acetic acid and then add 0.1 mol of NaOH. What is the pH of the new solution? (1L of solution and pKa = 4.8) Answer: pH = 4.1 This can be graphed! Half equivalence pH = pKa = 4.75

1. Strong acids and bases completely dissociate in water o When you are dealing with a weak acid, these do not completely dissociate in water, so that proton doesn’t completely come off. How strong the acid is will determine how much of that proton is removed o The nomenclature is saying that you have the weak acid which would be the proton ON,  Represented at HA o Ka = acid dissociation constant = measures strength of acid - Ka = [H+]{A-] / [HA] The STRONGER the weak acid, the higher the Ka The higher Ka, the smaller/lower the pKa is -

pKa is something fixed and known about every weak acid and is based off of a log scale

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pKa = -log [Ka] Larger Ka = lower pka = stronger the acid = lower pH = higher [H+] concentration

**Clicker Question** Which is the stronger weak Acid? A. Acidic Acid pKa = 4.76 B. Bicarbonate pKa = 10.25 ANSWER: Acidic acid has the lower pKa

The Henderson- Hasselbach equation links the pKa with the pH of a solution pH = pKa + log ([A] / [HA]) -

Need to be able to solve for any variable in this equation and be able to convert units, etc.

If you mix 0.3mol of Acetic acid and 0.2mol of sodium acetate in 1L of H2O. pKa of acetic acid is 4.8. What is the pH?

pH= 4.6 Take moles of acetic acid and moles of sodium acetate  Sodium acetate is acetic acid with the proton off so that is A Acetic acid is HA  Just plug it into the equation and solve

We don’t always know the weak acid and its conjugate base so you must know how to solve. Buffer: maintain a constant pH We can have changes in the acid or base concentration and the buffer work dot maintin a relatively constant pH

Equivalence: amount of OH- needed to completely neutralize the acid -

Neutralize doesn’t mean pH 7…we mean you’ve taken the proton off, it no longer can act as an acid and it cannot be a proton donor anymore If you’re starting out at 0.4 mols of the proton on. It will take .4 moles of base to completely neutralize that acid and pull the proton off

**Clicker Question** If you have 0.6 moles of acetic acid, how many moles of NaOH would you need to completely neutralize CH3OOH? Meaning pull off all the protons? A. 0.3 moles NaOH B. 0.9 moles NaOH C. 0.6 moles NaOH  correct

Titrations Continued -

At half equivalence, you can plot the pKa If you take another weak acid that has 1 ionizable proton but its pKa is 12…how is that titration curve going to look?  It will take 1 equivalence of base because there is 1 H…what will be different about that curve? o If pKa = 12  it is very weak o If it is weaker, it will take a lot of OH to remove the H o Where will that be on the curve?  At half equivalent you plat the pKa….12  It will have the same shape, but it will be displaced up and down the pH scale based off of the pKa  it will be very high up on the titration curve

Different acids will have the same titration curve shape but displace up and down the pH acix based off of their pKa Buffered Solutions -

A solution is considered buffered if addition of small amounts of strong acid/base do not change the pH of the solution Most effective region by buffer is ± 1 of the pKa

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In other words, a pH that will be buffered is ± 1 of the pKa so the pH range at which formic acid will have a buffering capacity would be 2.8-4.8  within this range, formic acid is acting as a buffer

Buffers in your blood -

pH in blood is 7.35-7.45 Changes to pH below 6.8 and above 8.0 may result in death Major buffer system in blood is H2CO3 [ Carbonic acid] & HCO3- [bicarbonate] Our bodies make CO2 during metabolism…some of this is carried to the lungs for elimination...the rest is dissolved in body fluids to make carbonic acid Weak Acid with more than 1 ionizable group

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Example: phosphoric acid with 3 protons….meaning there is 3 pkas associated with phosphoric acid 1 pka = 1 proton to be removed

Amino Acids -

Alanine Has 2 pkas

- All amino acids have a carboxylic acid and an amine on the ends and each of them have associated pKas…the carboxylic acid end has a pKa of 2.3 and the amine end has a pKa of 9.7 Titration curve of alanine -

If we are doing a titration and all protons are on, which proton will be removed? The carboxylic acid will be removed first if we start at a low pH and get to a higher pH  the carboxylic acid will come off first because it has a lower pka and is a lower acid…the lower pka is stronger, it will remove its proton first. It will come off and be donated

Proton on = low pH Proton off = high pH What would we have in solution in 1.5 equivalence?  pH = pKa + log ([A-]/[HA]) you have half the proton on and half the proton on Whats the pH at 1.5 equivalence? pH = pKa Zwitterion: an amino acid with a net neutral charge -

You can calculate the pH at the zwitterion and this is called the PI The pI = pH at which you have a net neutral charge

How do you do this?  PI = Pka1 +pKa 2 / 2 -

The pKas are what are used to make the zwitterion Remember, if pH is below the pKa, the proton is ON

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If pH is above the pKa, the proton is Off

Amino Acids -

In general, amino acids have a general backbone, an amine terminus, and an carboxyl group Carboxyl pKa = 2.3 Amine pKa = 9.7 The pH of your cellular environment is 7.4 therefore amine and carboxylic acids are ionized at physiological pH Know 3 letter abbreviation for amino acids Amino Acid structures to know: Glycine, phenylalanine, tryptophan, cysteine, proline, histidine

Aliphatic Amino acids -

Simplest aa and the only ones without a chiral center 4 AA’s have saturated side chains : alanine, leucine, valine, isoleucine Leucine: in the aliphatic group! Proline: 3 carbon chain connects C to N, its R group comes back and attaches to the backbone … what kind of an amine does that make this? Secondary!

Which is the most hydrophobic amino acid of valine, Glycine, leucine

 Leucine Proline: because that R group swings back and attaches to itself, it generates steric hindrance in proteins, the ring restricts the geometry of polypeptides

Myoglobin: the first globular protein whose structure was worked out from x-ray diffraction by protein crystals. The periodic repeats characteristic of alpha helix were recognized, and this helped determine the structure shown, in which 70% of the polypeptide is alpha-helical

Protein Folding and Unfolding -

Reversible Forces that are involved in the folding process rely on non-covalent interactions Cooperative Folded proteins most stable

Our body generated over 20-30 different DNA transcripts that then code proteins, -

Modifications to those proteins can generate up to a million different proteins

Cooperative Folding Process

2. Denaturation- disrup...