Biochemistry Exam 1

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83 Terms

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Trace Elements Purposes

Many aid as catalyst for biochemical reactions

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Carbon

Most stable bonds

Abundant element

Can form bonds with up to 4 other atoms

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Enthalpy

Making and breaking covalent bonds or ionic interactions

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Entropy

Changes in organization, disorganization, chaos

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ΔG

Determines the speed at which equilibrium is approached

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Thermodynamics

Tells us a reaction should proceed if the products are more stable than the reactants

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Kinetics

Tells us how fast the reaction will go, though doesn’t tell us anything about the final state of things

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-ΔH and +ΔS

-ΔG

Spontaneous at all temperatures

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+ΔH and -ΔS

+ΔG

Nonspontaneous at all temperatures

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Nucleophile

Attacks molecule for its proton (H)

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Electrophile

Gives proton (H) to other molecule

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Polarity

Unequal sharing of electrons in covalent bonds

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Hydrophobic

Nonpolar molecules

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Hydrophilic

Polar molecules

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Non-polarity

Equal sharing of electrons in covalent bonds

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Amphipathic

Polar and nonpolar parts in the same molecule

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Electrostatic Interactions

Charges interacting with each other

Charge can interact with partial or full charges

Decrease in strength when distance increases

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Van der Waals

Induces dipole-dipole interaction

Very weak compared to charge or polar forces

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Hydrogen Bonds

Part electrostatic, part covalent

Donor Hydrogen is the H in polar covalent bond (X-H)

C-H bonds cannot be donor hydrogens because they are nonpolar

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Strongest Bond Angle

180°

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Hydrophobic Effect

Strength of hydrophobic effect depends on surface area

Clustered lipids to form bigger clathrate cage is stronger than individual hydrophobic lipids

Entropy is increased with clustered hydrophobic lipids

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Clathrate Cage

Highly ordered H2O molecules formed around a hydrophobic molecule

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Self-Ionization of Water

H2O disassociates and reacts with itself

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Bronsted-Lowry Acid

Proton Donors

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Bronsted-Lowry Base

Proton Acceptors

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pka low and the protons go

pka high and they stand by

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When pka = pH

Concentration of acid and base are the same

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Buffers

Resists the change in pH when additional acid or base is added

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Amino Acid Stereochemistry

Every amino acid is in the L-stereoisomer configuration

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<p>Gibbs Free Energy Equation</p>

Gibbs Free Energy Equation

Finding ΔG from only products and reactants

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pH Equation

pH = -log10[H+]

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Henderson-Hasselbalch Equation

pH = pKa + log[A]/[HA]

<p>pH = pKa + log[A]/[HA]</p>
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Fischer Projections

Carbon backbone is vertical with most oxidized carbon at the top

Vertical bonds go away from you

Horizontal bonds reach out and hug you

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Hydrolysis

Adding H2O to break a peptide bond

Thermodynamically favorable

Must be catalyzed to break peptide bond

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Condensation

Removing H2O to form a peptide bond

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Peptide Bond

Using a ribosome to make an NH2 makes the NH2 nucleophilic attack the C to make a peptide bond

Has resonance

Rigid and planar

Trans conformation

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Central Dogma

DNA is transcribed into RNA, which is translated by ribosomes into amino acids that then code into proteins

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Amino Terminal End

NH3+ end of peptide chain

Synthesize from amino terminal to carboxyl terminal

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\
Carboxyl Terminal End

COO- end of peptide chain

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Protein Purification

To understand the properties of individual proteins

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Analytical Techniques

Usually takes a small amount of protein that is modified or destroyed in analysis

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Preparative Techniques

Produces a large amount of protein and maintains native protein activity

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Precipitation

After homogenization of material and removal of insoluble components, differential retention of proteins and other components in a soluble or insoluble phase

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Solubility

Affected by pH or ionic strength of solution

pI = 0 when proteins are aggregated (positive charges are equally connected to negative charges)

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Salting In

Proteins are insoluble at low ionic strength

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Salting Out

Proteins are insoluble at high ionic strength

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Column Chromatography

Differential retention of proteins and other components of cells using size exclusion, ion exchange, or affinity methods

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Size Exclusion Chromatography

Using discs with holes to separate proteins by size

Largest proteins should sink to the bottom

Smallest proteins should stick to the top discs

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Affinity Based Chromatography

Using chemicals to separate proteins of interest

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Ion Exchange Chromatography

Using discs that are negatively charged to separate proteins by charge

Negative charges should sink to the bottom

Positive charges should stick to the top discs

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SDS-PAGE Gel Electrophoresis

Denatured proteins are run through an electrically charged gel

Must break disulfide bonds to have a linear polypeptide chain

Smaller, faster proteins will run along the gel further than other proteins

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Two Dimensional Electrophoresis

Columnar tube of decreasing pH

Broken disulfide polypeptides are dropped into tube with decreasing pH

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Sanger’s Method

Used to determine identity of N-terminal residue

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Edman Degradation

Used to sequence 20-30 N-terminal residues

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Mass Spectrometry

Modern method for sequencing proteins and characterizing complex mixtures

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Peptide Backbone

C and N make up backbone

Steric constraints on protein backbone angles

Trans conformation, bond angle = 180°

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<p>Ramachandran Plot</p>

Ramachandran Plot

Map of allowed conformations

Pro and Gly side chains give off different conformations and plots from other amino acids

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Secondary Structures

Repeating patterns of backbones

Must satisfy all H-bonds

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Alpha Helix

Backbone carbonyl of amino acid forms H-bond to amine

Nearly all are right handed

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Rise Per Turn Equation

p = n * d

d = 1.5

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Antiparallel Beta Sheet

Side chains are on alternating sides

Interact favorably

H-bonds are 180°

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Parallel Beta Sheet

Side chains are on same side

Width between H-bonded side chains = 4

Length between R Groups on same side = 7

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Beta Turns

Gly and Pro chains are in this conformation because they are in cis

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Fibrous Protein Structure

Repeating protein structures

All secondary structures

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Keratin

Fibrous

Rich in AVLIMF

Nonpolar and hydrophobic

Coiled coil

Right handed

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Coiled Coil

Left handed

Reduces overall turns in each alpha helix to 3.5 (originally 3.6) residues per turn

Leads to a repeating pattern of hydrophobic side chains

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Collagen

Triple helical cable

Repeats of Gly and Pro

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Fibroin Protein

Aligned, stacked, packed antiparallel beta sheets

Gly and Ala

Knobs and holes of Gly and Ala align

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Energetics of Protein Folding

Disfavorable entropy (-ΔS) change due to many possible conformations (+ΔG)

Favorable entropy (+ΔS) change due to hydrophobic effect (-ΔG)

Favorable enthalpy (+ΔH) change due to stronger H-bonds (-ΔG)

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Hydrophobic Core

Most proteins have hydrophobic, nonpolar R Groups LIVMF

Optimizes density and packing

Large negative effects for hydrophobicity on surface

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Hydrophilic Surface

Most proteins have hydrophilic, polar R Groups RHKDE

Large negative effects for hydrophilicity in core

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Side Chain Hydrogen and Salt Bridge Bonding

When hydrophilic surface is in the core

Buried H-bonds don’t give full benefits because they were already partially satisfied by water in unfolded state

Buried salt bridges are stronger, more likely to bond to each other than to H2O

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Domain Tertiary Pattern

Independently folding segment of protein sequence

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Motif Tertiary Pattern

Commonly recurring structural element found in domains with different overall folds

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Quaternary Structure

Interactions between separately folded protein subunits to form an overall complex

Stabilized by non-covalent interactions or disulfide bonds

May include one or several polypeptides

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Levinthal’s Paradox

10^143 conformations for a 100 amino acid protein

There is not enough history in the universe to randomly sample every combo of amino acids to find a native

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Denature a Protein

Heat

Chemical Denaturants

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Pathway Dependent Folding

Steps must be taken before protein refolds to native state

Heat and chemical denaturation could interrupt beginning steps of protein folding

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Energy Landscapes

Proteins follow favorable paths in conformation space that funnel them towards a native state

Ideally, protein only has a few errors and step backs to get to native state

In reality, protein takes many steps and errors to get to native state, may not reach it at all

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Disulfide Isomerases

Speed up exchange of incorrect with correct disulfide bonds to get to native state

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Prolyl Cis-Trans Isomerases

Flip proline between cis and trans isomers to affect backbone to get protein to native state

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Molecular Chaperones

Uses ATP to bind misfolded and partially unfolded proteins

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Misfolding Diseases

Ultra stable fibers and aggregates are formed that are more stable than native state

Form amyloid plaques that cause neurodegeneration