MCAT - Biochemistry

D vs L amino acids

L amino acids = all chiral acids in eukaryotes, D = Prokaryotes

Glycine

Only amino acid that isn’t chiral(hydrogen for R group)

Nonpolar, nonaromatic Amino Acids

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Aromatic Amino Acids

Tryptophan, phenylalanine, tyrosine

Polar Amino Acids

Serine, threonine, asparagine, glutamine, cysteine

Cystine

All chiral amino acids except cystine(R) have S configuration

Acidic Amino Acids(Negative)

aspartate, glutamate

Basic Amino Acids(Positive)

Lysine, arginine, histidine

Amino Acids are amphoteric

can accept or donate electrons

pKa Group

The pH at which half the species are deprotonated, HA = A-

Isoelectric Point(PI)

An amino acid without a charged side chain can be calculated by averaging the two pKa values - at pH near PI = neutral zwitterion

Titration Curve of Amino Acids

• Titration curve is nearly flat at pKa values of amino acid

• Titration curve is nearly vertical at pI of amino acid

pKA of charged amino acids

Amino acids with charged side chains have an additional pKa value, calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitterion

• Amino acids without charged side chains have pI around 6, acidic = below 6, basic = above 6

Peptide Bond Formation

condensation or dehydration reaction(releases 1 molecule of water)

* The nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid

* Amide bonds are rigid because of resonance

Primary Structure

Linear sequence of amino acids in a peptide, stabilized by peptide bonds

Secondary Structure

Local structure of neighboring amino acids, stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups

• Alpha helices: clockwise coils around a central axis

• Beta-pleated sheets: Rippled strands that can be parallel or antiparallel, prefer anti because of more optimal bonding

• Proline can interrupt secondary structure because of its rigid cyclic structure

Tertiary Structure

Three dimensional shape of a single polypeptide chain, stabilized by hydrophobic interactions, acid-base interactions(salt bridge), hydrogen bonding, disulfide bonds

• Hydrophobic interactions push hydrophobic R groups to the interior of protein, increases entropy of surrounding water, creates a negative Gibbs free energy

• Disulfide bonds occur when two cystine molecules are oxidized and create a covalent bond to form cystine

Quaternary Structure

Interaction between peptides in proteins that contain multiple subunits

Conjugated Proteins

Interaction between peptides in proteins that contain multiple subunits

Proteins with covalently attached molecules between are termed conjugated proteins, attached molecule is Prosthetic Group, may be a metal ion, vitamin, lipid, carb, nucleic acid

Enzymes

Biological catalysts that are unchanged by reactions they catalyze and are reusable

Each enzyme catalyzes a single reaction or type of reaction with high specificity

Enzymes do not alter free energy, or enthalpy(delta H) that accompanies the reaction nor the equilibrium position, they simply change the rate at which equilibrium is reached

Enzymes act by stabilizing the transition state

Enzymes have an active site which is the site of catalysis

Binding to the active site is explained by lock and key theory or induced fit model

* Lock and key: Enzyme and substrate are exactly complementary

* Induced Fit: Enzyme and substrate undergo conformational changes to interact fully

Some enzymes need metal cation cofactors or small organic coenzymes to be active

Oxidoreductase

Catalyze oxidation-reduction reactions that involve transfer of electrons

Transferase

Move functional group from one molecule to another

Hydrolase

Catalyze cleavage with addition of water(hydrolysis)

Lyases

Catalyze cleavage without addition of water, without transfer of electrons

Isomerases

Catalyze the interconversion of isomers, both constitutional isomers and stereoisomers

Ligases

Joining two large biomolecules, often of same type

Exergonic vs Endergonic

Exergonic reactions = Release energy, Delta G is negative

Opposite for Endergonic

Negative Feedback

Where the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway

Positive Feedback

High levels of product activate the reaction

Competitive Inhibition

Inhibitor is similar to the substrate and binds at active site, can be overcome by adding more substrate. Vmax is unchanged, Km increases(decrease in affinity)

Noncompetitive Inhibition

Inhibitor binds with equal affinity to the enzyme and the enzyme-substrate complex. Vmax is decreased, Km is unchanged

Mixed Inhibition

Inhibitor binds with unequal affinity to the enzyme and the complex. Vmax is decreased, Km is increased or decreased depending on if the inhibitor has higher affinity for the enzyme or the complex

Uncompetitive Inhibtion

Inhibitor binds only with the enzyme-substrate complex. Km and Vmax both decrease

Irreversible Inhibition

Alters the enzyme in a way that the active site is unavailable for a prolonged duration or permanently

Enzymes can experience Activate or Inhibition

• Allosteric sites can be occupied by activators, which increase either affinity or enzymatic turnover

• Phosphorylation or glycosylation can alter activity or selectivity of enzymes

• Zymogens are secreted in an inactive form and are activated by cleavage

Structural Proteins(cytoskeleton, anchoring proteins, and extracellular matrix)

Most common: Collagen, Elastin, Keratin, Actin, Tubulin

Motor Proteins

one or more heads capable of force generation through a conformational change

• Catalytic activity, acting as ATPase to power movement

• Muscle contraction, vesicle movement, cell motility are most common application of motor proteins

• Common examples: Myosin, Kinesin, dynein

Function of Binding Proteins

Bind to a specific substrate, either to sequester it in the body or hold its concentration at a steady state

Cell Adhesion Molecule(CAM)

Allow cells to bind to other cells or surfaces

• Cadherin is a calcium dependent glycoprotein that hold similar cells together

• Integrins have two membrane spanning chains and permit cells to adhere to proteins in the extracellular matrix, some have signaling capabilities

• Selectins allow cells to adhere to carbs on surfaces of other cells, most commonly used in immune system

Antibodies(Immunoglobulins)

Are used by the immune system to target a specific antigen, which may be a protein on the surface of a pathogen or a toxin

* Immunoglobulins contain a constant region and a variable region, the variable region is responsible for antigen binding

* Two identical heavy chains and two identical light chains form the antibody, held together by disulfide linkages and noncovalent interactions

Ion Channels(3 types)

Can be used for regulating ion flow into or out of a cell, 3 main types

• Ungated channels - Always open

• Voltage-gated channels - Open within a range of membrane potentials

• Ligand-gated channels - Open in presence of a specific binding substance(hormone or neurotransmitter)

Enzyme Linked Receptors

Participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades

G Protein Coupled Receptors

Have a membrane bound protein associated with a trimeric G protein, they also initiate second messenger systems

• Ligand binding engages the G protein

• GDP is replaced with GTP, alpha subunit dissociates from the beta and y subunits

• Activated alpha alters the activity of [[adenylate cyclase]](phospholipase C)

• GTP is dephosphorylated to GDP, alpha subunit rebinds to the beta and y subunits

• Gs stimulates adenylate cyclase, Gi inhibits, Gq activates phospholipase C

Electrophoresis

Uses a gel matrix to observe the migration of proteins in response to an electric field

Native PAGE

Maintains proteins shape, results are difficult to compare because mass to charge ratio differs for each proteins, measures mass(small amounts of protein)

SDS PAGE

Denatures proteins and masks native charge so that comparison of size is more accurate but functional protein cannot be recaptured from gel

Isoelectric Focusing

Separates proteins by their isoelectric point(pI), the protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein

Chromatography

Separates protein mixtures on the basis of their affinity for a stationary phase or a mobile phase - Can filter large amounts of protein

Column Chromatography

Uses beads of a polar compound like silica or alumina(stationary phase), with a nonpolar solvent(mobile phase

Ion Exchange Chromatography

Uses a charged column and a variably saline eluent

Size Exclusion Chromatography

Relies on porous beads, larger molecules elute first because they are not trapped in the small pores

Affinity Chromatography

Uses a bound receptor or ligand and an eluent with free ligand or receptor for the protein of interest

X Ray Crystallography

Shows protein structure(NMR can also be used)

Amino Acid Composition

can be determined by a simple hydrolysis, but amino acid sequencing requires sequential degradation, such as the Edman degradation

BCA Assay, Lowry Reagent Assay, Bradford Assay

Each test for protein and have different advantages and disadvantages

• The Bradford protein assay which uses a color change from brown/green to blue is most common

Enantiomers

D and L forms of same sugar(Highest numbered chiral carbon with OH group to the right are D-sugars, left = L-sugars)

Diastereomers

Nonsuperimposable configurations of molecules with similar connectivity, differ at at least one but not all chiral carbons

Epimers

Subtype of diastereomers that differ at exactly one chiral carbon

Anomers

Differ at the anomeric carbon(carbon where aldehyde or ketone is or when in cyclic form the carbon that is bonded to 2 oxygens)

Anomeric Carbon for Cyclic Sugar Molecules

The anomeric carbon is the new chiral center formed in ring closure, it was the carbon containing the carbonyl in the straight chain form(carbon where aldehyde or ketone is or when in cyclic form the carbon that is bonded to 2 oxygens)

• Alpha anomers have the OH on the anomeric carbon trans to the free CH2OH group

• Beta anomers have OH cis to CH2OH

Haworth Projections

Good way to represent three dimensional structure(shows core of molecule and shows groups as axial)

Mutarotation

Cyclic compounds can undergo this, in which they shift from one anomeric form to another with the straight chain form as an intermediate

Common Disaccharides

Sucrose(glucose, fructose), lactose(galactose, glucose), maltose(glucose, glucose)

Cellulose

Main structural component for plant cell walls and is a main source of fiber in human diet

Starch

Amylose and amylopectin function as a main energy storage form for plants

Glycogen

Main energy storage for animals

Phospholipids

Amphipathic(hydrophilic head, hydrophobic tail) and form the bilayer of membranes

Saturation of fatty acid tails determines fluidity of membrane, saturated = less fluid than unsaturated(double bonds)

Glycerophospholipids

Phospholipids that contain a glycerol backbone

Sphingolipids

Contain a sphingosine or spingoid backbone

* Many sphingolipids are also phospholipids, containing a phosphodiester bond = sphingophospholipid

Sphingomyelin

Major class of sphingophospholipids and contain a phosphatidylcholine or phosphatidylethanolamine head group, Major component of myelin sheath

Glycosphingolipids

Attach to sugar molecules instead of phosphate group, cerebrosides = one sugar connected to sphingosine, globosides = two or more

Gangliosides

Contain oligosaccharides with at least one terminal N-acetylneuraminic acid(sialic acid)

Wax

Long chain fatty acids esterified to long chain alcohols, used as protection against evaporation and parasites in plant and animals

Terpenes

Odiferous steroid precursors made from isoprene - 5 carbon molecule

• One terpene unit(monoterpene) contains two isoprene units

• Terpenoids - Derived from terpenes via oxygenation or backbone rearrangement, similar odorous characteristics

Steroids

Contain 3 cyclohexane rings and one cyclopentane ring, oxidation state and functional groups may vary

Steroid Hormones

High affinity receptors(work at low concentration), affect gene expression and metabolism

Cholesterol

Important to membrane fluidity and stability, precursor to a host of other molecules(steroid)

Prostaglandins

Autocrine and paracrine signaling molecules that regulate cAMP levels, powerful effects on smooth muscle contraction, body temp, circadian rhythm, fever, and pain

Fat Soluble Vitamins

• Vitamin A(carotene) - Metabolized to retinal for vision and retinoic acid for gene expression in epithelial development

• Vitamin D(cholecalciferol) - Metabolized to calcitriol in kidneys and regulates calcium and phosphorus homeostasis in the intestines(increasing absorption), promoting bone formation, deficiency = rickets

• Vitamin E(tocopherols) - Biological antioxidants, aromatic rings destroy free radicals preventing oxidative damage

• Vitamin K(phylloquinon and menaquinones) - Important for formation of prothrombin, clotting factor, performs posttranslational modifications on a number of proteins, creating calcium-binding sites

Triacylglycerols

Preferred method of storing energy for long-term use

• Contain one glycerol attached to three fatty acids by ester bonds

• Carbon atoms in lipids are more reduced than carbs giving twice as much energy per gram during oxidation

• Very hydrophobic so they are not hydrated by body water and do not carry additional water weight

Adipocytes

Storage in animal cells for triacylglycerol

Saponification

Ester hydrolysis of triacylglycerols using a strong base like sodium or potassium hydroxide

Soaps act as surfactants, forming micelles, A micelle can dissolve a lipid soluble molecule in its fatty acid core, washes away with water because of its shell of carboxylate head groups

Nucleosides

Five carbon sugar bonded to a nitrogenous base

Nucleotides

Five carbon sugar bonded to a nitrogenous base(nucleosides) with one to three phosphate groups added

Watson and Crick Model of DNA

• The backbone is composed of alternating sugar and phosphate groups, always read from 5' to 3'

• Two strands with antiparallel polarity, wound into double helix

Purines

A,G - double ringed, pair with pyrimidines

Pyrimidines

C,U,T - single ringed

G - C

3 hydrogen bonds, stronger bonds

Huckels Rule

4n + 2pi electrons for aromatic cyclic molecules(purines and pyrimidines)

Chargaff’s Rule

States that purines and pyrimidines are equal in number in a DNA molecule, A=T, C=G

DNA(Right handed/left handed)

Most DNA is B-DNA(right handed helix), very little of Z-DNA(zig zag left handed helix) may be seen with high GC content or high salt concentration

Histones

DNA is wound around histone proteins(H2A,H2B,H3,H4) to form nucleosomes(can be stabilized by H1 protein)

Heterochromatin

Dense, transcriptionally silent DNA that appears dark, is also organized towards outer parts of nucleus

Euchromatin

Less dense, transcriptionally active DNA that appears light

Telomeres

Ends of chromosomes, high GC content to prevent unraveling of DNA, during each replication telomeres are shortened, can be partially reversed by telomerase

Centromeres

Middle of chromosomes, hold sister chromatids together until they are separated during anaphase in mitosis, Also have high GC content to maintain strong bond between chromatids

Replisome

Set of specialized proteins that assist the DNA Polymerase

Helicase

DNA is unwound at origin of replication by helicase, makes two replication forks

Origin of Replication difference between Prokaryotes and Eukaryotes

• Prokaryotes: Circular chromosomes that contain only one origin of replication

• Eukaryotes: Linear chromosomes that contain many origins of replication

Single Stranded DNA Binding Proteins

Unwound strands are kept from reannealing or being degraded by these binding proteins