Basic Concepts, Amino Acids, Proteins Flashcards Preview

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Flashcards in Basic Concepts, Amino Acids, Proteins Deck (88):
1

Milli-

10__

2

Micro-

10__

3

Nano-

10__

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M

mol/L

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%

weight/volume (usually g/dL)

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Equivalent

available charges of the particular ion

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Units of activity

Defined in terms of some effect

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Osmolarity

moles of solute particles in a solution

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Henderson-Hasselbach

pH= pKa + log ([A_]/[HA])

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α-amino acids

  • Carboxylic acid with amine group on the α-carbon
  • R-groups change (most are L-amino acids)

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Non Polar Aliphatic Amino Acids

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine

(GAP, LIV)

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Glycine

Gly

Non Polar aliphatic

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Alanine

Ala

Non polar Aliphatic

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Proline

Pro

Non Polar Aliphatic

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Valine

Val

Non Polar Aliphatic

Branched Chain

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Leucine

Leu

Non polar Aliphatic

Branched Chain

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Isoleucine

Ile

Non polar Aliphatic

Branched chain

most hydrophobic (charges are very balanced)

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Aromatic Amino Acids

Phenylalanine, Tyrosine, Tryptophan

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Phenylalanine

Phe

Aromatic

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Tyrosine

Tyr

Aromatic

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Tryptophan

Trp

Aromatic

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Polar, Uncharged Amino Acids

Asparagine, Glutamine, Serine, Threonine

Typically found on the surface

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Asparagine

Asn

Polar/Uncharged

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Glutamine

Gln

Polar, uncharged

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Serine

Ser

Polar, uncharged

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Threonine

Thr

Polar, uncharged

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Sulfur-containing Amino Acids

Methionine, Cysteine

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Methionine

Met

Sulfur-containing

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Cysteine

Cys

Sulfur-containing, so can form disulfide bonds

Cystine = 2 cysteines bound by disulfide bond

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Negatively charged Amino Acids

Aspartate, Glutamate

Acidic Amino Acids

 

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Positively Charged Amino Acids

Arginine, lysine, histidine

Basic amino acid

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Aspartate

Asp

Negatively charged (acidic)

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Glutamate

Glu

Negatively charged (acidic)

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Arginine

Arg

Positively charged (basic)

Most hydrophilic (very polar)

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Lysine

Lys

Positive charge (basic)

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Histidine

His

Positively charged (basic)

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Hydropathy

How hydrophilic/phobic an anima acid is

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pI

The pH at which the net charge on an amino acid is 0

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Selenocysteine

  • Modification fo a serine bound to a unique tRNA to selenocycteine
  • Found in a few enzymes, where it is essential for activity

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Types of amino acid modifications

  • Carbohydrate addition
  • Lipid addition (can anchor to protein membrane or be involved in regulation)
  • Regulation

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O-glycosylation

Occurs on the OH of ser, thr, tyr

Carbohydrate addition

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N-glycosylation

Occurs on the NH2 of asn

Carbohydrate addition

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Palmitoylation

Occurs on the internal SH of cys

Lipid addition

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Myristolation

Occurs on the NH of the N-terminal of gly

Lipid addition

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Prenylation

Occurs on the Sh of cys

Lipid addition

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Phosphorylation

Occurs on the OH of ser, thr, tyr

is reversible

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Acetylation

Occurs on the NH2 of lys (N-terminus)

Reversible

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ADP-ribosylation

Occurs on the N of arg, gln, cys

Reversible

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Carboxylation

Turns gutamyl residues into Ɣ-carboxylglutamyl residues

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Oxidation

Pro/lys into hydroxylpro/hydroxylys

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Peptide bond

  • Bond b/t the α-carboxyl grp of 1 AA and the α-amino group of another AA
  • Is planar
  • Adjacent R-groups are almost always trans

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Proteins

linear polymers of α-amino acids bound together by peptide bonds

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Primary structure of proteins

  • Amino acyl sequence of proteins
  • N-terminal = amino 
  • C-terminal = carboxyl

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Polymorphism

  • genetic variation with a species
  • Can produce a variation in phenotype which could be deleterious

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Developmental variaion

  • Different protein isoforms/isozymes may be expressed at different developmental stages of an organism
  • Ex: HbF, HbA, and other hemoglobins

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Tissue-specific Isoforms

  • Different protein isoforms/isozymes are expressed simulteneously in one organism, but are restricted to different tissues
  • Ex: creatine kinase isozymes and lactate dehydrogenase isozymes

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Secondary Structures

Recurring, localized structures found within regions of a poly peptide chain

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Alpha – Helix

  • Helical structure stabilized by hydrogen bonds (b/t amino and carboxyl O atom of 2nd AA 4 residues down the chain)
  • AA R-group projects outward from the axis of the helix
  • Proline cannot be a part of a α-helix

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Beta-Pleated Sheet

  • somewhat planar surface stabilized by H-bonds b/t amide hydrograns and carboxyl Os
  • AA R-groups are perpendicular to the plane of the sheet
  • surfaces formed by β-sheets are often twisted

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Parallel β-pleated sheets

2 polypeptide chains are oriented in the same direction relative to the N/C termini

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Anti-Parallel β-pleated Sheets

2 polypeptide cains are oriented in opposite directions relative to their N/C termini

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Domain

Part of a secondary structure that can exist on its own

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Motif

  • Type of supersecondary structure that is found in an array of different proteins (can make up a domain)
  • Ex: helix-turn-helix motifs are found in many DNA-binding proteins

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Teriary Structures

The folding pattern of the secondary structural elements into a 3D conformation

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Forces involved in 3º structures

H-bonds, Salt bridges, Hydrophobic interactions, Van der Wall forces, Disulfide bridges

 

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Globular protein properties

  • Core is usually hydrophobic AA
  • Surface is usually charged/polar AA (so hydrophilic) that interacts w/ a polar/aqueous environment and forms salt bridges to stabilize the structure

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Transmembrane proteins typically have what types of 2º and 3º structures?

  • 2º: usually α-helices that have hydrophobic residues that are embedded in the lipid/hydrophobic layer of the membrane
  • 3º: hydrophilic residues interact extra/intracellularly

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Quaternary structure

The individual subunits form a functional protein

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What determines the protein type?

The number of subunits determines what about the protein?

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Forces in 4º structure in globular proteins

H-bonding, Hydrophobic interactions, salt bridges/ionic bonds, rarely disulfide bonds (no covalent bonds)

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Forces in 4º structure in fiborus/structural proteins

Extensive covalent bonds

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What are the functional aspects of 4º structure

  1. Increased stability (bc increased # of interactions b/t AA)
  2. Cooperativity b/t subunits (Ex: hemoglobin-O2 binding)
  3. Different subunits may have different activities

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Protein folding

  • 1º structure of protein determines folding
  • Some fold spontaneously while others require specific cellular processes to promote proper folding

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Heat Shock Proteins

  • Some prevent improper folding
  • Others requires ATP energy to promote folding

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Cis-trans isomerases and disulfide isomerases promote what?

What non HSP function to promote proper protein folding?

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Size Exclusion Chromatography

  • Uses porous beads
  • Larger proteins elude 1st bc smaller proteins get caught in the pores of the beads

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Ion Exchange Chromatography (Cation)

  • bound chemicals have a negative charge
  • Cations adhere to the negatively charged column
  • charges on proteins are pH dependent

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Ion Exchange Chromatography (Anion)

  • bound chemicals have positive charge
  • Anions adhere to the positively charged column
  • Charges on proteins are pH dependent

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Hydrophobic Interaction Chromatography

  • Medium contains hydrophobic groups
  • Proteins w/ hydrophobic groups adhere to the column

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Affinity Chromatography

  • Medium has a bound, protein specific ligand
  • Proteins that bind to the ligand adhere to the column

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High-Pressure Liquid Chromatography (HPLC)

  • Eluent pumped thru column under high pressure
  • Typically looking for hydrophobic interaction chromatography (aka reversed phase)
  • Separation is faster and at higher resolution

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Electrophoresis

Separation based on mirgration of charged molecules applied in an electrical field

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Native electrophoresis

  • Separates by differences in charges due to the 1º structure
  • Ex: hemoglobin isoforms, some isozymes (LDH, CK)

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SDS-PAGE

  • Protein molecules interact with the detergent (SDS) to produce proteins of about = charge-to-mass ratios
  • SDS disrupts 4º structures (proteins become monomers
  • migration thru the gel is based on size: smaller proteins go faster

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Iso-Electric Focusing (IEF)

  • Buffers generate a pH gradients within a PA gel
  • Proteins migrate to pI=pH of gel

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2D Electrophoresis

Uses both IEF and SDS-PAGE

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Western blot

  • Proteins are separated via electrophoresis and transferred to synthetic membrane (incubated w/ antibodies for specific protein
  • 2nd antibody conjugated w/ reporter molecule to help visualize the specific protein

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Mass Spect

  • Separates molecules based on their mass
  • Can identify proteins thru determination of masses of peptides produced thru tryptic digestion of proteins
  • detects covalent modifications of a protein