MCAT Study Guide Ochem Ch. 8 – Bio-Chemistry 2017-08-15T06:45:06+00:00

I.          8.1:  AMINO ACIDS – 20 AAs

A.     AMINO ACID STRUCTURE AND NOMENCLATURE

1.     Side chain (R-group) is what makes each AA unique

2.     Glycine is the only AA whose R-group is a hydrogen (only non-chiral AA)

B.     L- AND D-AMINO ACIDS – enantiomeric isomers

1.     L-configuration – All AAs have this configuration!! (left)

a)     All AAs derive from glyceraldehyde

2.     D-configuration – right

C.    ASSIGNING THE CONFIGURATION TO A CHIRAL CENTER

1.     There may be multiple chiral centers, but when we assign L- and D- configuration, we are referring to one specific chiral carbon, the penultimate carbon (last chiral carbon)

2.     L-glyceraldehyde – the smallest carbohydrate, all amino acids derive from this (and are ∴ all L- configuration)

3.     D-glyceraldehyde – all animal carbohydrates are derived from this

4.     Classification system:

a)     (+) and (-) describe optical activity

b)     R and S describe actual structure or absolute configuration

c)     D and L tell use what the precursor molecule was

D.    AMINO ACID REACTIVITY

1.     Acidic group – carboxylic acid

2.     Basic group – amine

E.     REVIEWING THE FUNDAMENTALS OF ACID/BASE CHEMISTRY

1.     Amphoteric – has both acidic and basic activities (AAs)

2.     Acid dissociation constant (Ka) – ⇋ constant for acid dissociation

3.     pH – -log

[H+]

4.     Henderson-Hasselbach equation:  describes the relationship between pH and pKa

5.     ↓ pKa = ↑Ka = stronger acid (if pH = pKa, the acid/base ratio = 1)

 

F.     APPLICATION OF FUNDAMENTAL ACID/BASE CHEMISTRY TO AMINO ACIDS

1.     Amino group – pKa ≈ 9

2.     Carboxylic acid group – pKa ≈ 2

3.     If pH < pKa, then protonation occurs

a)     ↓ pH means basic solution, so it will try to put H+s back on the AA, out of solution

4.     If pH > pKa, then deprotonation occurs

a)     ↑ pH means basic solution, so it will try to steal all the H+s and deprotonate

G.    ISOELECTRIC POINT OF AMINO ACIDS

1.     Zwitterion – the (+) and (-) charges on the carboxylate and amino group cancel each other out

2.     Isoelectric point (pI)– the pH at which the molecule is a zwitterion

a)     pI is the average pKas of the functional groups

H.    CLASSIFICATION OF AMINO ACIDS

1.     Hydrophobic (nonpolar) AAs – determined by R-group

a)     R-group – either alkyl or aromatic side chains

(1)   Alkyl – glycine, alanine, valine, leucine, isoleucine

(2)   Aromatic – phenylalanine, tyrosine, triptophan

2.     Hydrophilic AAs (3 categories)

a)     Acidic AAs

(1)   R-group = carboxylic acid (glutamate and aspartate)

b)     Basic AAs

(1)   R-group = basic (has an N, is proton acceptor)

(2)   Histidine can be acidic or basic (“His goes both ways”)

c)     Polar AAs – polar enough to form H-bonds with water, but not polar enough to be acid/base

(1)   Serine, threonine, tyrosine often have phosphate groups attached (very polar)

3.     Sulfur-containing AAs – says nothing about polarity

a)     Cysteine (polar) and methionine (nonpolar)

4.     Proline – unique in that the side  chain is essentially a second AA forming a ring

SUMMARY TABLE OF AMINO ACIDS

HYDROPHOBIC HYDROPHILIC
Nonpolar Polar Acidic Basic
Valine*Isoleucine*Phenylalanine*GlycineAlanine

Leucine*

Proline

Tryptophan*

Methionine*

 

She is a VIP GAL who is a Pro at Trypping on Meth

SerineCysteineTyrosineThreonine*Asparagine

Glutamine

 

 

See the Three Asparagus Cysts on Tyrone’s Glutes?

Aspartic acidGlutamic acidAsparaGus makes acidic pee Lysine*ArginineHistidineBasically Lick ArseHole

*Denotes one of eight essential amino acids (PVT TIM HALL is mnemonic)

I.       AA SEPARATION – gel electrophoresis

1.     Gel electrophoresis – separates AAs based on their charge; AAs are put into a gel then exposed to the electric field; the AAs will migrate through the get based on their charge and external electric field

2.     Think about this:  when pH < pI, that means there are lots of H+s floating around and some are bound to attach to the AA, making the net charges more (+), more attracted to the (-) electrode

3.     When pH > pI, that means there are few H+s floating around, so more will be pulled off the AA, making the net charge more (-), and more attracted to (+) electrode

 

II.         8.2:  PROTEINS

AAs hooked together by peptide bonds or disulfide bridges (only between cysteine R-groups)

A.     THE PEPTIDE BOND

1.     Between carboxyl group of one AA and the α-amino group of another AA through hydrolysis

2.     Peptide = amide (N–C=O)

3.     Not thermodynamically favorable; requires energy

B.     DCC COUPLING

1.     Used to artificially synthesize peptides in labs

2.     Pattern of backbone is N–C–C–N–C–C

3.     In naming, 1st AA named is the amino terminus; last one named is the carboxy terminus AA

4.     Residue – AAs in peptides are referred to as residues

C.    PLANARITY OF THE PEPTIDE BOND

1.     No rotation around a peptide bond because of double-bond character between carbonyl C and N

2.     This results in a rigid, planar structure

D.    HYDROLYSIS OF THE PEPTIDE BOND

1.     Thermodynamically favored (see image above), but kinetically slow

2.     Can be sped up with:

a)     Strong acids (and heat)

b)     Proteolytic enzymes (protease); many cleave bonds at specific AAs

E.     THE DISULFIDE BOND

Only formed between R groups of 2 cysteine AA side groups

1.     Important in stabilizing tertiary protein structure

2.     Cysteine–cysteine → becomes cystine when bound together

F.     PROTEIN STRUCTURE IN 3D

1.     Primary Structure:  The AA sequence

a)     Referred to as sequence

b)     Peptide bond determines sequence

2.     Secondary Structure:  Hydrogen bonds between backbone groups

a)     Refers to initial folding of a polypeptide chain into shapes stabilized by H-bonds (between N-H and C-O groups)

b)     α-helixes

(1)   Formed by backbone spiral where H-bonding occurs between residues in the same chain that line up in the coil (N-H and C-O groups)

(2)   Proline never appears within α-helix

(3)   α-helixes are used in transmembrane proteins; all the partially charged areas are interacting with each other, and ∴ don’t interact with the hydrophobic membrane

c)     β-pleated sheets

(1)   β-pleated sheets have H-bonding between N-H and C-O groups, but they are often on separate chains

(2)   Backbone is stretched out with side groups above and below the side chains

3.     Tertiary Structure:  Hydrophobic/Hydrophilic Interactions

a)     Further folding of the secondary structure; usually driven by R-groups and their interactions with the solvent

b)     H-bonding and hydrophobic interactions often cause a protein to spontaneously fold into the correct conformation

4.     Quarternary Structure:  Various Bonds between separate chains

a)     Non-covalent interactions (H-bond, hydrophobic interatction, van der Waals)

b)     Covalent also, but no peptide bonds!

III.          8.3:  CARBOHYDRATES

A.     STRUCTURE AND NOMENCLATURE OF MONOSACCHARIDES

1.     Oligosaccharide – bigger than disaccharide, smaller than polysaccharide

2.     Strong acids hydrolize polysaccharides into monosaccharides

3.     Naming:

a)     1st –  aldo vs keto:  depends on whether aldehyde or ketone is present

b)     2nd – number in chain

c)     C numbering – begins w/most oxidized end of chain (aldehyde/ketone end)

d)     Most are referred to by their common name

4.     EX

a)     6C monosaccharides: glucose, galactose, fructose (but frutose forms 5-C ring!)

b)     Others:  ribose, glyceraldehyde

 

 

B.     ABSOLUTE CONFIGURATION OF MONOSACCHARIDES

1.     D- configuration – the direction the OH is pointing on the last chiral C in the chain (right)

a)     All sugars in our body exist in D- configuration (think D for dessert)

2.     L- configuration – opposite of D-configuration

a)     All proteins (but no sugars) in our body exist in L-configuration! (L for lamb)

3.     Number of stereoisomers – 2n, where n = # of chiral carbons

C.    CYCLIC STRUCTURES OF MONOSACCHARIDES

1.     In solution, 5-6 C sugars spontaneously form rings (thermodynamically favored)

a)     6 C = pyranose

b)     5 C = furanose

2.     The OH- on the C5 attacks C1 forming a ring (C1 is now anomeric carbon)

a)     α-configuration – if OH- on carbonyl C (1st C) faces down

b)     β-configuration – if OH- on carbonyl C (1st C) faces up

3.     Haworth notation – way to draw sugar; can convert from Fischer to Haworth

D.    STRUCTURE AND NOMENCLATURE OF DISACCHARIDES

1.     Glycosidic linkage – the bond between 2 sugar molecules (covalent, formed in dehydration rxn that requires enzyme)

a)     Usually C1 joins C4 (sometimes C2 or C6)

b)     Once joined, the sugar is no longer free to mutarotate to α or β configuration!

2.     Naming

a)     Named according to which C in each sugar comprises linkage

b)     α- or β- configuration is specified

3.     Memorize:

a)     Sucrose – Glu-α-1,2-Fru

b)     Lactose – Gal-β-1,4-Glu

c)     Maltose – Glu-α-1,4-Glu

d)     Cellobiose – Glu-β-1,4-Glu

4.     Polysaccharides

a)     Glycogen – thousands of glucose stored in α-1,4 linkages (sometimes α-1,6 branches)

b)     Cellulose – polymer of cellobiose

E.     HYDROLYSIS OF GLYCOSIDIC LINKAGES

1.     Enzymatic hydrolysis breaks di- and polysaccharides down into monosaccharides

2.     Hydrolysis is thermodynamically favored (ΔG < 0, releases energy) but is kinetically slow

a)     Catalysts ↓ Ea and ↑ rate of reaction, but do not Δ final conc of reactants and products

F.     REDUCING SUGARS

1.     Benedict’s test – chemical assay that detects the carbonyl units of sugars; distinguishes hemiacetals from acetals (hemiacetals are reducing sugars)

2.     Only hemiacetals are at ⇋ with carbonyl (open chain), only in monosaccharide form

3.     Positive Benedict’s test – means lots of carbonyls ∴ hemiacetals ∴ monosaccharide form

4.     Negative Benedict’s test – means few carbonyls ∴ few hemiacetals ∴ polysaccharide (glycogen) form

a)     All aldehydes, ketones, and hemiacetals will result in (+) Benedict’s test

 

 IV.          8.4:  LIPIDS

3 roles:  cellular membranes fat storage, cholesterol as building block for steroid

A.     FATTY ACID STRUCTURE

1.     Long unsubstituted C-chain that ends in carboxylic acid

a)     Usually 14-18 C long

b)     Synthesized from acetate (CH3-COO), so always even # of carbons

c)     Unsaturated almost always in Z (or cis-) formation

(1)   (Z)-Δ3 ([cis]-Δ7) – fatty acid with = between C3 and C4, with Z-formation

B.     TRIACYLGLYCEROLS (TG)

1.     Triacylglycerol (triglyceride) – technical name for fat; storage form of fatty acid

2.     Glycerol is HOCH2–CHOH–CH2OH; the fatty acids are esterified to glycerol molecule

3.     Saponification – base-catalyzed hydrolysis of triglycerides from animal fat into fatty acid salts

4.     Lipases – enzymes that hydrolyze fat

C.    INTRODUCTION TO BILAYER MEMBRANE

1.     Phospholipids – membrane lipid derived from DGP (looks like triglyceride, but 1 fatty acid is replaced by phosphate group)

2.     Lipid bilayer:

a)     Double bonds (unsaturation) ↑ fluidity

b)     ↓ length of fatty acid tail ↑ fluidity

c)     Cholesterol stabilizes membrane fluidity at different temperatures

3.     Lipid bilayer is impermeable to charged molecules

 

V.          8.5:  STEROIDS

A.     Structure

All steroids have tetracyclic ring, has both hydrophilic and hydrophobic tendencies (amphipath)

B.     Transportation

Carried in the blood packaged with fats and proteins into lipoproteins

 

VI.          8.6:  NUCLEIC ACIDS

A.     PHOSPHORUS-CONTAINING COMPOUNDS

1.     Phosphates (aka orthophosphates) are bound via anhydride linkage and is high energy bond (ΔG very negative)

2.     3 reasons why they are so high energy:

a)     Negative charges repel each other

b)     Orthophosphate has more resonance (↑ stable, ↓ free energy) than linked phosphates

c)     Orthophosphate has ↑ favorable interaction with water than linked phosphates

B.     NUCLEOTIDES

1.     ATP – used in cellular metabolism in addition to being RNA precursor

CHAPTER 8 SUMMARY:

○       AAs consist of tetrahedral α-C connected to an amino group, a carboxyl group, and a variable R group which determines AA’s properties

○       The isoelectric point of an AA is the pH at which the net charge on the molecule is zero; this structure is referred to as the zwitterion

○       Electrophoresis separates mixtures of AAs and is contuced at buffered pH; (+) AAs move to the (-) end of the gel, and (-) AAs move to the (+) end’Proteins consist of AAs linked by peptide bonds, which have partial ⚌ characteristics, lack rotation, and are very stable

○       The 2° structure of proteins (α-helices and β-sheets) is formed through H-bonding between atoms in the backbone of the molecule

○       The most stable 3° protein structure generally places polar AAs on the exterior and nonpolar AAs on the interior of the protein; this minimizes interactions between nonpolar AAs and sater, while optimizing interactions between side chains inside the protein

○       All animal AAs are L-configuration (amine group in L position) and all animal sugars are D-configuration

○       Carbohydrates are chains of hydrated C atoms with the molecular formula CnH2nOn

○       Sugars in solution exist in ⇋ between the straight chain form and either the furanose or pyranose cyclic forms

○       The anomeric forms of a sugar differ by the position of the OH group on the anomeric C

■       OH- down = α

■       OH- up = β

○       All monosaccharides will give a positive result in a Benedict’s test because they contain an aldehyde, ketone or hemiacetal, and are ∴ reducing sugars

○       The glycosidic linkages in a disaccharide is named based on which anomer is present for the sugar containing the acetal and the number of the C linked to the bridging O

○       Saponification (base-mediated hydrolysis) of a triglyceride produces 3 equivalent fatty acid carboxylates

■       These amphipathic molecules form micells in solution

○       The building blocks of nucleic acids (DNA and RNA) are nucleotides, which are comprised of a pentose sugar, a purine or pyrimidine base, and 2-3 phosphate units

MCAT Study Guide Ochem - Kim Matsumoto


More MCAT Study Guide Ochem

1.

Ch. 2 Basics of Organic Chemistry

2.

Ch. 3 Bonds + Isomers

3.

Ch. 4 Alkane Reactions

4.

Ch. 5 Alkenes and Alkynes

5.

Ch. 6 Aldehydes and Ketones

6.

Ch. 7 Lab Techniques

7.

Ch. 8 Amino Acids + Carbohydrates

← View Full MCAT Study Guide Directory