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Med Chem > Biochem 1-4 > Flashcards

Biochem 1-4 Flashcards

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1
Q

Macromolecules

A

Made of monomers or residues

Kinds:
proteins
polysaccharides 
nucleic acids 
lipids and membranes
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2
Q

Gibbs free energy change

A

deltaG = deltaH - TdeltaS

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3
Q

Protein purification techniques

A 
1. Crystallize
  separate proteins from other molecules
2. column chromatography (interactions between matrix and proteins) 
ion exchange chromatography
   positive and negative charges 
Gel-filtrate 
  porous matrix separate based on size 
Affinity 
  covalently bound small molecule, separate based on interaction with the molecule
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4
Q

Saccharides

A

monomer. Also called a carbohydrate
carbon, hydrogen and oxygen
5-6 carbons
Fisher, Haworth, Envelope

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5
Q

Polysaccharides

A

covalently bonded saccharide monomers

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6
Q

glycosidic bond

A

acetal–two OR groups and two R groups on one carbon

dehydration reaction

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7
Q

Nucleic acids

A 
(polynucleotides)
composed of monomers called nucleotides:
1. 5 carbon sugar
2. heterocyclic nitrogen containing base
3. a phosphate or P containing group

ATP is an example

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8
Q

nucleic acid structure

A

In DNA and RNA nucleotides are connected via a 3’,5’ phosphodiester linkage

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9
Q

Lipids

A

rich in carbon and hydrogen few oxygen
simplest lipids are fatty acids
when combined with glycerol-3-phosphate they form glycerophospholipids which make up biological membranes!

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10
Q

Metabolism

A 
2 parts:
Catabolism 
breakdown to release energy 
Anabolism  
use energy to construct
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11
Q

Euks versus Proks

A

complex differentiated organisms versus single cell
proks have no nucleus rather nucleoid region
prok no internal membrane compartments euks have organelles
prok pili or flagella, high surface area to volume

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12
Q

Cytosol complexity

A

Stew of things!
Selectivity becomes important
highly organized

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13
Q

Biological functions of proteins

A
  1. enzymes
  2. storage, transport
  3. structural support
  4. mechanical work
  5. decode and regulate genetics
  6. hormones
  7. Abs, toxins and other fun things
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14
Q

Amino Acids

A

20 kinds (common ones)
amino group and a carby acid on the same carbon (called the alpha carbon)
R sidechain
chiral at alpha, some have extra chirality :D

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15
Q

Aminos and pH

A

at body pH (7.1 - 7.4): amino group protonated pKa 9, carby acid deprotonated pKa

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16
Q

Amino Stereochemistry

A

L-aminos are bae
a few D exist but they are rare
L is carby at top, amino is on the left
D is carby at top, amino on the right

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17
Q

Types of aminos

A 
Aliphatic (hydrophobic)
Aromatic (hydrophobic)
Sulfur containing
alcohol containing 
Basic 
Acidic
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18
Q

Aliphatic Aminos

A

Hydrophobic sidechains
Glycine [G] (Gly) exception! not very hydrophobic, also only AA with no chiral carbon.
Alanine [A] (Ala)
Valine [V] (Val)
Leucine [L] (Leu)
Isoleucine [I] (Iso) has second chiral center

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19
Q

Aliphatic Aminos with rings

A

My fav amino: Proline [P] (Pro).
Sidechain is cyclized on the alpha amino group (less nucleophilic)
pyrrolidine ring restricts geometry GETTIN’ KINKY
less hydrophobic than other aliphatic aminos

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20
Q

Aromatic Aminos

A

Phenylalanine [F] (Phe)
Tyrosine [Y] (Tyr) Can be ionized but not at body pH 280 nm
Tryptophan [W] (Trp) 280 nm
nm absorbance Can be used to find the conc of proteins in a solution

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21
Q

Sulfur containing aminos

A

Methionine [M] (Met) nonpolar methyl thioether

Cysteine [C] (Cys) dimerize to form cystine pKa = 8.4

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22
Q

Alcoholic Aminos

A

Serine [S] (Ser)
Threonine [T] (Thr) second chiral center
uncharged polar side chains with beta hydroxyl groups
weakly ionizable pKa ~16
nucleophiles (especially in active sites)

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23
Q

Basic Aminos

A

Histidine [H] (His)
Lysine [K] (Lys)
Arginine [R] (Arg)
nitrogenous bases
at body pH they are protonated and polar
histidine pKa is near body at 6–often transiently protonated, used in active sites

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24
Q

Acidic Aminos

A

Aspartate [D] (Asp)
Glutamate [E] (Glu)
Aspargine [N] (Asn)
Glutamine [Q] (Gln)
asp and glu have carby acids in the sidechain
deprotonated at body pH, negative charge
asn and gln are primary amide derivatives of the other two–highly polar but uncharged

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25
Q

Biosynthetic Aminos

A

More than 200!
sometimes made in biological pathways
employ decarboxylation and deamination enzymes:
adrenaline, thyroxine
sometimes chemically modded once inside a protein

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26
Q

Ionization of Aminos

A

2 Pkas–the one from the carby and also the amino
Ionization influences:
3D shape of proteins
enzyme catalysis

27
Q

Henderson-Hasselbalch

A

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

28
Q

Amino Titration

A

Cation–>zwitterion–>Anion

29
Q

Isoelectric Point

A

The pH where a molecule is electronically neutral

30
Q

Amino Titration Histidine

A

Special because side chain can be ionized

3 pKas

31
Q

Peptide bond

A

linear sequence is called the primary structure
amino acids are linked through an amide bond also called the peptide bond
dehydration reaction
N terminus to C terminus

32
Q

Peptide nomenclature

A

amino residues change their –ine or –ate to –yl
glutamine becomes glutamyl
name from N to C

33
Q

Sodium Dodecylsulfate Polyacrylamimde Gel Electrophoresis

A

SDS-PAGE
separate small mixes of proteins
migration in electric field
SDS detergent overwhelms the native charge on a protein

34
Q

Mass spectrometry

A

determine mol weight and amino sequence in protein s
-Electrospray Ionization (ESI) and MAtrix assisted desorption ionization (MALDI) MALDI can be used to find post transcriptional mods as well

35
Q

Percent composition of proteins

A

Acid hydrolysis followed by PITC treatment and detection

36
Q

Edman degradation procedure

A

identity of each a.a. starting from the N terminus

  1. treat with PITC at pH 9
  2. Treat PTC peptide with anhydrous acid like TFA
  3. extract anilinothiazoline product, treat with aqueous acid to make phenylthiohydantoin derivative
  4. identify with chromatography
  5. repeat sequentially

Puts limits on the number of sequential aminos you can detect

37
Q

Cyanogen Bromide BrCN

A

cleaves polypeptide chains on the C terminus side of methionine residues

38
Q

Proteases

A

Trypsin catalyzes cleavage on the C terminus side of Lys and Arg
Chymotrypsin catalyzes cleavage on C terminus side of aromatic hydrophobs like Phe, Trp, Tyr

39
Q

Polypeptide sequencing

A
  1. treat with hydrolytic enzymes
  2. analyze fragments via Edman degradation
  3. deduce structure
40
Q

Proteomics

A

study of large sets of proteins

41
Q

native conformation

A

a protein’s natural shape at physiological pH

42
Q

Four levels of protein structure

A 
1. primary 
linear structure of aminos 
2. Secondary 
regularities due to H bonding and other interactions 
3. Tertiary 
folded and compacted polypeptide chain. interactions between secondary structure  
4. Quaternary 
Domain interactions
43
Q

Primary

A

linear sequence along the polypeptide backbone

44
Q

Secondary

A

alpha helix

beta sheet

45
Q

Tertiary

A

interactions between secondary. Side chains in helix to helix or sheet to sheet

46
Q

Quaternary

A

Domains of the protein interacting

47
Q

3D structure depictions

A

Space filling models–radii to illustrate overall shape and surface
Ribbon structure–simplifies backbone and shows secondary structure
Ball and Stick–highly detailed show H bonding and other molecular interactions

48
Q

NMR

A

used to determine protein structure

Proteins do not have static immovable structures!

49
Q

Peptide bond conformations

A

phi N–Ca bond
trans or cis. restricted for proline
psi Ca–C bond
trans and cis

+ is clockwise
- is counter

the Carby–N bond doesn’t rotate very much. Its called omega

50
Q

Ramachandran Plot

A

Way to tell where the bonds can be rotated/are sterically permissible
alpha helix or beta sheet is what is liked

51
Q

Alpha Helix

A

right or left handed
Pitch–how many nm peptide advances per turn
Rise–nm advance per a.a.
3.6 AA residues, 13 atoms per turn so 3.6 sub 13 helix
psi and phi for the bond angles
side chains oriented outward
a.a sequence confers stability
Ala is fine. Tyr or Asn not fine. Gly destabilizes. Pro won’t allow for H bonding
FACIAL DIRECTIONALITY

52
Q

Beta Sheet

A

Parallel–R groups line up on top and bottom
Anti-parallel perfectly straight bonds, the R groups and the h alternate
Right hand twist but mostly flat
side chains above and below
technically is a 2 and 3 structure
more flexibility in bond angles
Amphiphatic

53
Q

Loops and Turns

A

Loops usually have hydrophilic residues at or near surface
~10% of Aminos
short loops called turns (

54
Q

Common motifs

A
  • helix-loop-helix
  • coiled coil
  • helix bundle
  • beta-alpha-beta
  • hairpin
  • beta meander
  • greek key
  • beta sandwich
55
Q

Protein Domain

A

25-300+ AA residues

covalently connected to other domains by noncovalent interactions

56
Q

Common domain folds

A

different functions in protein

  • enzymatic activities
  • surface recognition elements
  • ligand binding
57
Q

Quaternary structure

A
  • subunits in an oligomeric protein have a set stoichiometry
  • greek letters to describe subunits
  • weak covalent reactions hold subunits
  • (4 structure creates active site)
58
Q

Protein Denaturation

A
  • Altering the native conformation will result in denaturation
  • loss of normal activity
  • energy can be small to accomplish this
  • many ways to denature–heat and chemicals
  • characteristic mel temp (50-60 C)
59
Q

Chemical denaturation

A
  • Disrupt the hydrophobic interactions
  • Chaotrophic (urea and guanidinium salts)
  • Detergents
60
Q

Denaturation and Disulfide

A

Example: Native ribonuclease + urea and beta mercaptoethanol denatures the protein, reduces disulfide bonds. Take away ME randomly reforms bonds . Some small proteins can reform

61
Q

Protein Folding

A
  • can be assisted by molecular chaperones!
  • uses n ATP
    example: heat shock proteins
62
Q

Case Study: Collagen

A
  • connective tissue and structural protein
  • molecule of collagen contains three left-handed helical polypeptide chains coiled around each other to form right-handed supercoil
  • inter-chain hydrogen bonds
  • polypeptide sequence has pattern Gly-X-Y
  • X is often Pro
  • Y is often modified Pro
  • high proline content makes collagen rigid
63
Q

Case Study: Collagen

A
  • Individual collagen triple-helices are crosslinked via Schiff bases
  • Allysine residues are chemically-modified from Lys
64
Q

Case Study: Antibodies

A
  • Ab are integral to the immune system
  • Abs recognize epitopes on antigens
  • most abundant are the immunoglobulin G (IgG) class.
  • tetramers with two heavy chains and a light chain.
  • linked by disulfide bridge. heavy chains have 4 domains and light have 2 domains.
  • Common motif: immunoglobulin fold–sandwich of two antiparallel beta sheets
  • high affinity for antigen. Heavy chain is specific to organism of origin

Med Chem (3 decks)

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