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Biochem 1-4 Flashcards

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
Biosynthetic Aminos
More than 200! sometimes made in biological pathways employ decarboxylation and deamination enzymes: adrenaline, thyroxine sometimes chemically modded once inside a protein
26
Ionization of Aminos
2 Pkas--the one from the carby and also the amino Ionization influences: 3D shape of proteins enzyme catalysis
27
Henderson-Hasselbalch
pH = pKa + log[A]/[HA]
28
Amino Titration
Cation-->zwitterion-->Anion
29
Isoelectric Point
The pH where a molecule is electronically neutral
30
Amino Titration Histidine
Special because side chain can be ionized | 3 pKas
31
Peptide bond
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
Peptide nomenclature
amino residues change their --ine or --ate to --yl glutamine becomes glutamyl name from N to C
33
Sodium Dodecylsulfate Polyacrylamimde Gel Electrophoresis
SDS-PAGE separate small mixes of proteins migration in electric field SDS detergent overwhelms the native charge on a protein
34
Mass spectrometry
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
Percent composition of proteins
Acid hydrolysis followed by PITC treatment and detection
36
Edman degradation procedure
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
Cyanogen Bromide BrCN
cleaves polypeptide chains on the C terminus side of methionine residues
38
Proteases
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
Polypeptide sequencing
1. treat with hydrolytic enzymes 2. analyze fragments via Edman degradation 3. deduce structure
40
Proteomics
study of large sets of proteins
41
native conformation
a protein's natural shape at physiological pH
42
Four levels of protein structure
``` 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
Primary
linear sequence along the polypeptide backbone
44
Secondary
alpha helix | beta sheet
45
Tertiary
interactions between secondary. Side chains in helix to helix or sheet to sheet
46
Quaternary
Domains of the protein interacting
47
3D structure depictions
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
NMR
used to determine protein structure | Proteins do not have static immovable structures!
49
Peptide bond conformations
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
Ramachandran Plot
Way to tell where the bonds can be rotated/are sterically permissible alpha helix or beta sheet is what is liked
51
Alpha Helix
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
Beta Sheet
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
Loops and Turns
Loops usually have hydrophilic residues at or near surface ~10% of Aminos short loops called turns (
54
Common motifs
- helix-loop-helix - coiled coil - helix bundle - beta-alpha-beta - hairpin - beta meander - greek key - beta sandwich
55
Protein Domain
25-300+ AA residues | covalently connected to other domains by noncovalent interactions
56
Common domain folds
different functions in protein - enzymatic activities - surface recognition elements - ligand binding
57
Quaternary structure
- 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
Protein Denaturation
- 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
Chemical denaturation
- Disrupt the hydrophobic interactions - Chaotrophic (urea and guanidinium salts) - Detergents
60
Denaturation and Disulfide
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
Protein Folding
- can be assisted by molecular chaperones! - uses n ATP example: heat shock proteins
62
Case Study: Collagen
- 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
Case Study: Collagen
- Individual collagen triple-helices are crosslinked via Schiff bases - Allysine residues are chemically-modified from Lys
64
Case Study: Antibodies
- 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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