Test 1 Flashcards
Aliphatic AAs
Valine V Leu L Ile I Ala A Gly G
Polar OH and SH AAs
Serine S Tyr Y Thr T Cys C Met M
Acidic AAs
Glu E
Asp D
Asn N
Gln Q
Basic AAs
Lys K
Arg R
His H
Aromatic AAs
Tyr Y Phe F His H Trp W Pro P
Characteristics of water
Nucleophile
70% body mass
Regulated by ADH
Important for metabolic rxns and enzymatic rxns
Amphoteric (donates OH- or H+)
PH >7.45 alkalosis (vomiting with loss of HCl)
Dissolves biomolecules
PH<7.35 acidosis (diabetic ketones or lactic acidosis)
H-bonds
Most important property of water High BP Viscosity High surface tension H-bonds to 4 other water molecules
PKa
-log ka
Keq
=pdct/reactant=ka
When HA=A-
PH=pKa
Henderson Hasselbach
PH=pka+log [A-]/[Ha] (base/acid)
Must be at peak protonation to go through lipid membrane
When pH is lower than the pka…
AA is protonated (more H+ in solution at low pH)
When pH>pka
AA is deprotonated
Carbonic acid
H2C03, very important acid
Bicarbonate buffer system most important inorganic buffer
H20 C02–H2C03—-H+ HC03
Water and carbon dioxide–Carbonic acid—Protons and Bicarbonate
Carbonic anhydrase
Converts H2C03—H+ HC03-
More carbonic anhydrase means more H+ ions excreted in urine, leaving blood more basic (higher pH)
Needs zinc ion and catalyst
Lungs and kidneys
Most important for controlling pH
Lungs decrease pC02 by
Hyperventilation (higher HC03-/C02 ratio), increases pH since bicarbonate is more basic than carbon dioxide
Kidneys control pH
retain HC03-, make more of it, and eliminate H+ in urine as NaH2PO4 + NH4+
Most C02 transported as
HC03-, bicarbonate buffer used for Isohydric transport
Hb binds 02 and takes it to tissues (acidic) where 02 is released Then H+ binds to Hb
HC03- goes to lungs and binds H+ from H+Hb
02 from air binds Hb again and takes to tissues
C02 released at lungs; chloride exchange…
low Cl-, high HC03- venous
maintains electrical neutrality during bicarbonate passage
02 released at tissues;
high Cl-, low HC03- in lung plasma (arterial)
Phosphate buffer is important (like bicarbonate buffer)
H2P04- – HP042-
pka 6.7
Close to pH of our body (7.4)
PH >pka means it’s deprotonated since there’s less H+ in solution at higher pH
To determine good buffer, look for
High molar concentration
PKa closest to desired pH
OH+AH–>
A- + H20
[gas]~partial pressure
Multiply pC02 x
0.03 mM/mmHg
PH is measurement of
Acidity/alkalinity
PH concentration
Strong acids dissociated completely, H+ concentration equal to
Concentration of strong acid
Weak acids are good buffers depending on pH of desired buffering zone, ions partially dissociate, H+ concentration
Isn’t equal to concentration of weak acid and is dependent on ka and weak acid concentration
Salt results when
You put acid and base together
Buffer
Keeps pH relatively constant
Effective range of buffer
Near pka of weak acid, so small amount of acid or base won’t change pH much
Ka=products/reactant
=[H+] [Ac-]/[HAc]
10-5=x2/0.1
X=.001~10-3
PH=-log [H+]
H+=Ac=X
PH=-log [10-3]
Alkalosis with high pH means there’s more H+ being excreted, leaving blood
more basic
The runner decreased pC02 by
Hyperventilation (increases HC03-/C02 ratio) by blowing off C02, also decreasing H+ by pushing rxn to left and increasing pH
Hypoventilation is first aid treatment to
Breathe into bag and increase C02, thereby decreasing HC03-/C02 ratio
20 AAs
1 Imino
The physical and chemical characteristics of R group determine
The characteristics of a particular AA
Zwitterion
+ and - charges in AA, overall neutral
Amphoteric
Protonated amino group (pH
PH near pka
Mixture of 2 forms will exist
PI
Isoelectric point
Average of 2 pkas
Or average of acidic pkas if AA is acidic
Or average of basic pkas if AA is basic
Post translational modifications of proteins by enzymes
Histone modification for epigenetics
Side chains modified for blood coagulation
Defects in AA degradation cause
genetic disorders like PKU (phenylalanine can’t get converted to tyrosine)
All AAs (except glycerol)
Are optically active
L isomers active in animals
D isomers of AAs in bacteria and used as drugs and antibiotics to inhibit AIDS virus (HIV-1)
Geometry of protein is important for reactivity
Substrate binding by enzymes can affect shape
Peptide bond
Covalent bond, made by removal of water, planar,free rotation around alpha carbon (amide bond/peptide bond is rigid, partial DB due to e- on N, sp2 confirmation and 120 degree angle)
Naming peptides
Start with free amine
Add -yl endings to all AAs except last one
Be sure the AAs are connected by alpha carbons (not beta, delta, or gamma carbons)
Covalent bonds
Peptide and disulfide bonds with oxidation of SH for conformational changes
50 kcal/M
Noncovalent bonds
Ionic/electrostatic between oppositely charged molecules
H-bonds for protein folding, very strong if many are together (3-4 kcal/M)
Van der walls interactions between atoms forming induced dipole but repulsed at close distances
Hydrophobic interactions between nonpolar side chains that come together due to high entropy of water
Glutathione
Antioxidant, prevents DNA and protein damage from free radicals and peroxides
Peptide hormones
Glucagon, oxytocin, vasopressin
Factors determining protein activity
PH with side chain protonation states
Enzymes (protease, peptides, phosphatase)
Temperature
Thiol groups prevent disulfide bond formation (important for protein folding)
Air/water exposure, unstable with 02, water can help folding to an extent but can dilute and deactivate protein
Isolate protein based on
Charge: ion exchange, electrophoresis, isoelectric focusing
Size: dialysis and centrifugation, gel electrophoresis, gel filtration chromatography
Polarity: adsorption paper, reverse phase or hydrophobic chromatography
Specificity/affinity: affinity chromatography
Solubility
Must purify protein first before you can
Determine primary structure
Western blot
If you have a specific antibody to bind to
2D gel electrophoresis
Uses isoelectric focusing with pI
Then SDS page horizontally to get more bands of protein
Primary structure of protein
AA sequence, backbone determines structure and function of protein
Edman degradation
Edman reagent binds and reacts with amino groups–hydrolysis residue while protein stays intact–label and analyze AAs one at a time ~20 max–Run HPLC and look at rxn time to determine primary structure
Better than Sanger sequencing since it doesn’t destroy proteins
Mass spectrometry
Best method of determining 1° structure
High specificity
Doesn’t require protein purification
Highly sensitive and quantitative
High coverage
Identifies PT modifications that Edman and DNA sequencing cannot
Breaks down protein into very small pieces for accurate readings of all side chains
PT modifications influence function and fate of protein
Side chain modifications and cleavage regulate activity and transport and secretion
can’t be predicted with just DNA sequence
May involve complex enzyme systems
Dynamic since phosphorylation and acetylation are reversible
Can cause disease (by activating kinases)
PT modifications detected by changes in AA side chain masses with
Mass spectrometry
Look for increase in mass due to phosphorylation (activation), acetylation, myristylation, palmitoylation, glycosylation for labeling, or methylation for destruction
2° structure examples and stabilization
H-bond stabilization of secondary structural elements
Alpha helical (right handed)
B-pleated sheets
B-turns
2° structure disruptions
Proline, bulky AAs, or like charged AAs close together, 3.6 AA/turn
3° structure
3D shape of polypeptide, how secondary structures interact
Side chain interactions
Stabilized by hydrophobic, hydrophilic, salt bridges, H-bonds, and disulfide bonds
4° structure
Quaternary structure is arrangement of multiple subunits into complex
2+ tertiary units
Stabilized by hydrophobic/hydrophilic, salt bridges, H-bonds, disulfide bonds
2ndary structures continued
B-pleated sheets with chains side by side, R groups above and below, parallel is more stable with angled bonds
B turns change direction of globular proteins, often with proline and glycine
Disrupted by proline, bulky, or like charged AAs
Proline cis-trans-isomerases/cyclophillins
Fold proteins that cause disease/infections, often target for treatments
Proline in cis configuration can form B-turn
Protein life cycle
Synthesis–leaves ribosome for folding into secondary structure–processing–covalent modification to be tagged to go to membrane or processed by Golgi body–translocation–activation at site–catalysis (does its job)–aging/oxidation/deamination–ubiquitination to be tagged for death/degradation
Endosome-lysosome pathway
Degrades extra cellular and cell surface proteins and transports proteins
Ubiquitin-proteasome pathway
Degrades proteins from cytoplasm, nucleus, and ER
Mitochondria and chloroplasts from bacterial origin have separate
Proteolytic system for degradation
Ubiquitin-proteasome pathway enzymes
E1 with ATP activates ubiquitinproteasome
E2 accepts ubiquitin
E3 transfers ubiquitin to NH2 group of lysin on damaged/misfiled protein that needs degraded
Chaperons
Segregate hydrophobic regions to help form 2° structure of proteins
Protein disulfide isomerase
Stabilizes 3° and 4° structures
X ray crystallography determines 2ndary and tertiary structures
Purify protein–crystallize–diffract and collect x-rays–use computer to make electron density map and get model of protein
For all sizes of proteins but can’t see hydrogens or membrane proteins and the protein must be crystallized
NMR for seeing 2ndary and tertiary structures
Purify and dissolve protein, collect NMR data and assign NMR signals, calculate structure
Allows for looking at dynamic proteins that must be soluble
Good for smaller proteins, can see hydrogens
Improperly folded proteins make aggregates/occlusions/tangles/fibrils causing disease
Alzheimer’s and dementia from Tau phosphorylation
Parkinson’s
Lewis body dementia
Amyotropic lateral sclerosis
ECM functions
Structural (collagen, proteoglycans, fibrillin)
Adhesive (fibronectin, laminin)
Tells things where to go, keeps things attached, lots in connective tissues
Collagen 1 defect
Causes osteogenesis imperfecta and brittle bones
Normally gives strength to tissue, bone, cartilage like plywood, gly XY repeats and lots of proline
Most abundant fibrous protein made of 3 tropocollagen with disulfide bonds–triple helix
Forms fibrils
Lysyl oxidase forms crosslinks
Lysol oxidase in collagen
Adds cross linking for strength
PT modifications of collagen
Lysol hydroxylase Cu and prolly hydroxylase Fe add OH groups in ER and require iron for activity
Collagen 4 defect
Alport syndrome affecting kidneys and hearing
Has breaks in triple helix for flexibility and N and C-terminal domains
Basal laminae
Network forming mesh for filtration
Collagen 7 defect
Causes dystrophic epidermolysis bullosa
Collagen 7 has N and C-terminal domains, no breaks
Keeps basement membrane in tact and anchors fibrils
Anchors fibrils
Glycosaminoglycans (ECM)
Have - charged sulfates
GAG+ protein=proteoglycan with negative charge that binds Na+ and draws water to lubricate joints
Fibroblast growth factor
Must bind to proteoglycan to activate its cell surface receptor
Angiogenesis
Blood vessel secretes heparanase that clips heparin sulfate, releasing GFs that bind to blood vessel for growth
Fibrillin deficiency (ECM)
Marfan syndrome with abnormally long bones (lots of GFs), myopic vision, aneurism, death
Allows elasticity in blood vessels, skin, and eye, suppresses GFs
Associates with elastic fibers in ECM
Fibronectin (ECM)
Has 2 large multiple domain chains with sulfide bonds
Adhesive, functions as glue, high levels can indicate premature delivery
Has 1 gene but can make different forms of fibronectin with RNA alternative splicing
Used for blood clotting, wound healing, platelets, and cell adhesion
Integrin (junctions)
Receptor for fibronectin
Binds ECM proteins and senses environment
Dimer of A (specificity) and B (binds cytoskeleton) subunits
Requires Mg++ or Mn++
No enzymatic activity, attaches indirectly to cytoskeleton via Talin or alpha action in bundles
Velcro effect with lots of integrin together
Stabilizes underlying matrix, forms signaling complexes, and activates proteins
Integrin B2 defect
Decreases WBCs
Integrin B3 defect
Decreases platelets, affects blood clotting
Laminin 5 (ECM) defect
Causes junctional epidermolysis bullosa in basement membrane
Connects epidermis to dermis
Has 3 chains (alpha, beta, gamma)
Connects basal lamina
Multiple different laminin genes
Can form network and interact with collagen 4 and proteoglycans
Tumor cells and matrix metaloproteinases affecting ECM
MMPs degrade ECM, decrease GFs, remove cell surface receptors, and destroys ECM if activity is excessive
ECM and heparanases/MMPs and turnover
Heparanases (clip heparin sulfate to release GF for angiogenesis) and MMPs remodel dynamic ECM
ECM turnover important for wound healing, bone remodeling, WBC migration, and reproduction
MMPs
ECM degradation enzymes
Require Zn or Ca
Inhibited by TIMPS
G-actin formation (cytoskeleton)
Monomers assemble and form dimers and trimmed during nucleation with ATP–elongation when monomers are added to make F-actin filaments
Requires ATP and cations (MG, K, Na)
G actin ATP binds + end
G actin ADP is released on - end
Formin (cytoskeleton)
Forms filaments, attaches to positive end of actin filament to make long unbranched filaments.
Arp 2/3 (Cytoskeleton))
Binds near branched end of actin to form branches
ADF/Cofilin
Binds - end. (ADP actin) and sticks to severed monomers so they can’t bind to filaments
Causes actin disassembly
Profilin (cytoskeleton)
Stimulates filament formation, replaces ADP with ATP on G actin Monomer
Steady state treadmilling
With no caps, adding monomers to + barbed end and removing from - pointed end of actin, leaving length unchanged
CapZ
Binds + end of actin and inhibits polymerization (reduces length) and gets actin past steady state
Tropomodulin
Cap that binds - end and prevents dissociation of actin monomers to increase length
Wasp (Ctsk)
Activates Arp 2/3 to create branching in actin
Filamen
Cross links actin filaments to form networks that support cell surface
Alpha actinin
Cross links actin filaments in bundle that contracts
Fimbrin
Cross links actin filaments in parallel to support plasma membrane projections
Cell movement Requires 2 things
Branching and filament polymerization