Test 1 Flashcards
1
Q
Aliphatic AAs
A
Valine V Leu L Ile I Ala A Gly G
2
Q
Polar OH and SH AAs
A
Serine S Tyr Y Thr T Cys C Met M
3
Q
Acidic AAs
A
Glu E
Asp D
Asn N
Gln Q
4
Q
Basic AAs
A
Lys K
Arg R
His H
5
Q
Aromatic AAs
A
Tyr Y Phe F His H Trp W Pro P
6
Q
Characteristics of water
A
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)
7
Q
H-bonds
A
Most important property of water High BP Viscosity High surface tension H-bonds to 4 other water molecules
8
Q
PKa
A
-log ka
9
Q
Keq
A
=pdct/reactant=ka
10
Q
When HA=A-
A
PH=pKa
11
Q
Henderson Hasselbach
A
PH=pka+log [A-]/[Ha] (base/acid)
12
Q
Must be at peak protonation to go through lipid membrane
When pH is lower than the pka…
A
AA is protonated (more H+ in solution at low pH)
13
Q
When pH>pka
A
AA is deprotonated
14
Q
Carbonic acid
A
H2C03, very important acid
15
Q
Bicarbonate buffer system most important inorganic buffer
A
H20 C02–H2C03—-H+ HC03
Water and carbon dioxide–Carbonic acid—Protons and Bicarbonate
16
Q
Carbonic anhydrase
A
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
17
Q
Lungs and kidneys
A
Most important for controlling pH
18
Q
Lungs decrease pC02 by
A
Hyperventilation (higher HC03-/C02 ratio), increases pH since bicarbonate is more basic than carbon dioxide
19
Q
Kidneys control pH
A
retain HC03-, make more of it, and eliminate H+ in urine as NaH2PO4 + NH4+
20
Q
Most C02 transported as
A
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
21
Q
C02 released at lungs; chloride exchange…
A
low Cl-, high HC03- venous
maintains electrical neutrality during bicarbonate passage
22
Q
02 released at tissues;
A
high Cl-, low HC03- in lung plasma (arterial)
23
Q
Phosphate buffer is important (like bicarbonate buffer)
A
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
24
Q
To determine good buffer, look for
A
High molar concentration
PKa closest to desired pH
25
OH+AH-->
A- + H20
26
[gas]~partial pressure
| Multiply pC02 x
0.03 mM/mmHg
27
PH is measurement of
Acidity/alkalinity
| PH concentration
28
Strong acids dissociated completely, H+ concentration equal to
Concentration of strong acid
29
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
30
Salt results when
You put acid and base together
31
Buffer
Keeps pH relatively constant
32
Effective range of buffer
Near pka of weak acid, so small amount of acid or base won't change pH much
33
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]
34
Alkalosis with high pH means there's more H+ being excreted, leaving blood
more basic
35
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
36
Hypoventilation is first aid treatment to
Breathe into bag and increase C02, thereby decreasing HC03-/C02 ratio
37
20 AAs
1 Imino
The physical and chemical characteristics of R group determine
The characteristics of a particular AA
38
Zwitterion
+ and - charges in AA, overall neutral
Amphoteric
Protonated amino group (pH
39
PH near pka
Mixture of 2 forms will exist
40
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
41
Post translational modifications of proteins by enzymes
Histone modification for epigenetics
| Side chains modified for blood coagulation
42
Defects in AA degradation cause
genetic disorders like PKU (phenylalanine can't get converted to tyrosine)
43
All AAs (except glycerol)
Are optically active
44
L isomers active in animals
D isomers of AAs in bacteria and used as drugs and antibiotics to inhibit AIDS virus (HIV-1)
45
Geometry of protein is important for reactivity
Substrate binding by enzymes can affect shape
46
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)
47
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)
48
Covalent bonds
Peptide and disulfide bonds with oxidation of SH for conformational changes
50 kcal/M
49
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
50
Glutathione
Antioxidant, prevents DNA and protein damage from free radicals and peroxides
51
Peptide hormones
Glucagon, oxytocin, vasopressin
52
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
53
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
54
Must purify protein first before you can
Determine primary structure
55
Western blot
If you have a specific antibody to bind to
56
2D gel electrophoresis
Uses isoelectric focusing with pI
| Then SDS page horizontally to get more bands of protein
57
Primary structure of protein
AA sequence, backbone determines structure and function of protein
58
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
59
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
60
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)
61
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
62
2° structure examples and stabilization
H-bond stabilization of secondary structural elements
Alpha helical (right handed)
B-pleated sheets
B-turns
63
2° structure disruptions
Proline, bulky AAs, or like charged AAs close together, 3.6 AA/turn
64
3° structure
3D shape of polypeptide, how secondary structures interact
Side chain interactions
Stabilized by hydrophobic, hydrophilic, salt bridges, H-bonds, and disulfide bonds
65
4° structure
Quaternary structure is arrangement of multiple subunits into complex
2+ tertiary units
Stabilized by hydrophobic/hydrophilic, salt bridges, H-bonds, disulfide bonds
66
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
67
Proline cis-trans-isomerases/cyclophillins
Fold proteins that cause disease/infections, often target for treatments
Proline in cis configuration can form B-turn
68
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
69
Endosome-lysosome pathway
Degrades extra cellular and cell surface proteins and transports proteins
70
Ubiquitin-proteasome pathway
Degrades proteins from cytoplasm, nucleus, and ER
71
Mitochondria and chloroplasts from bacterial origin have separate
Proteolytic system for degradation
72
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
73
Chaperons
Segregate hydrophobic regions to help form 2° structure of proteins
74
Protein disulfide isomerase
Stabilizes 3° and 4° structures
75
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
76
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
77
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
78
ECM functions
Structural (collagen, proteoglycans, fibrillin)
Adhesive (fibronectin, laminin)
Tells things where to go, keeps things attached, lots in connective tissues
79
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
80
Lysol oxidase in collagen
Adds cross linking for strength
81
PT modifications of collagen
Lysol hydroxylase Cu and prolly hydroxylase Fe add OH groups in ER and require iron for activity
82
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
83
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
84
Glycosaminoglycans (ECM)
Have - charged sulfates
| GAG+ protein=proteoglycan with negative charge that binds Na+ and draws water to lubricate joints
85
Fibroblast growth factor
Must bind to proteoglycan to activate its cell surface receptor
86
Angiogenesis
Blood vessel secretes heparanase that clips heparin sulfate, releasing GFs that bind to blood vessel for growth
87
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
88
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
89
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
90
Integrin B2 defect
Decreases WBCs
91
Integrin B3 defect
Decreases platelets, affects blood clotting
92
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
93
Tumor cells and matrix metaloproteinases affecting ECM
MMPs degrade ECM, decrease GFs, remove cell surface receptors, and destroys ECM if activity is excessive
94
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
95
MMPs
ECM degradation enzymes
Require Zn or Ca
Inhibited by TIMPS
96
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
97
Formin (cytoskeleton)
Forms filaments, attaches to positive end of actin filament to make long unbranched filaments.
98
Arp 2/3 (Cytoskeleton))
Binds near branched end of actin to form branches
99
ADF/Cofilin
Binds - end. (ADP actin) and sticks to severed monomers so they can't bind to filaments
Causes actin disassembly
100
Profilin (cytoskeleton)
Stimulates filament formation, replaces ADP with ATP on G actin Monomer
101
Steady state treadmilling
With no caps, adding monomers to + barbed end and removing from - pointed end of actin, leaving length unchanged
102
CapZ
Binds + end of actin and inhibits polymerization (reduces length) and gets actin past steady state
103
Tropomodulin
Cap that binds - end and prevents dissociation of actin monomers to increase length
104
Wasp (Ctsk)
Activates Arp 2/3 to create branching in actin
105
Filamen
Cross links actin filaments to form networks that support cell surface
106
Alpha actinin
Cross links actin filaments in bundle that contracts
107
Fimbrin
Cross links actin filaments in parallel to support plasma membrane projections
108
Cell movement Requires 2 things
Branching and filament polymerization
109
Cytoskeleton components
Actin
Intermediate filaments
Microtubules
110
Actin assembly
G-actin ATP-->polymerization to F-actin ATP-->cleavage to F-actin ADP-->depolymerization to G-actin ADP-->exchange so it can polymerize again as G-actin ATP
111
Many actin binding proteins are present
To regulate steps of actin assembly
| Can stabilize, cross link, sever, or cause polymerization
112
Cell movement
Extend leading edge, attach to substratum, and retract rear of cell
Filopodia and fimbrin with actin filaments extend out first followed by lammellopodia with actin bundles---filamen crosslinks filaments to form Networks
Branching and polymerization with Arp /3 and WASP/SCAR complex while. Barbed end connects growing filaments to plasma membrane
Move cell membrane with generated force
Cofilin//ADF. Disassembles - end
Monomer taken to + end by. Twinkling
Reactivated by profilin
113
Wiskott-Aldrich syndrome
Mutation in gene coding for WASP protein
| Bleed easily, WBC function disrupted, immunodeficiency disease, affects actin cytoskeleton in immune and blood cells
114
Movement along actin filament
Myosins get energy from ATP to move along actin filaments carrying cargoes
115
Intermediate filaments (ctsk)
Central rod domain
N and C Terminals
Size between actin and microtubules
Tissue Specific (keratin at epithelium Only)
Attach cells to each other and underlying matrix, give tensile strength, cell and tissue integrity
unpolarized
not dynamic
Monomer--tetramer--8 protofilaments--intermediate filament
116
Defective keratin (Intermediate Filament) in epithelial cells
Epidermolysis bullosa simplex, less severe than other forms, blisters where rubbed
117
Microtubules (ctsk)
Largest, dynamic, unstable, move material long distances
Alpha and beta tubulin dimers attached to gamma tubulin, 13 protofilaments around hollow core
MAPs regulate growth and assembly
GTP for assembly, GTP cleaved on Beta Tubulin
Polarity like actin
Remove GTP B tubulin from negative end to shrink/catastrophe
Add GTP B tubulin to + End to grow microtubules
Grow from centrosome (not centrioles)
Shrinks and grows rapidly Unless Stabilized
118
Polymerases on MTs
| Depolymerases on MTs
Increase assembly
Prevent GTP Tubulin from binding so GTP is cleaved With shrinkage
119
CLASP
Stops shrinking MTs So GTP Can bind and Grow MT
120
Tau and MTs
| Map2 and MTs
Tau in axon stabilizes MT with + end toward cell body
| MAP2 binds in dendrites with + end in either direction to crosslink MTs to IF
121
Tau coming off MTs
Can aggregate into tangles and cause Alzheimer's disease and frontotemporal dementia
122
MTs have tracks for dynein that walks inward and kinesin that walks outward to + end
Long range organelle transport
Dynein grabs alpha at its light chains and beta tubules at its head group and bends microtubules causing beating of flagella and cilia
123
Smoking damages MTs
Cilia lose function, can't keep particulate matter out of lungs
124
Microfilaments (ctsk)actin
```
Actin binds ATP
Has + and - ends
Polarized, dynamic
Has tracks for myosins
Forms rigid gels, networks, and bundles
```
125
Selectins on endothelium (junctions)
Attract WBCs with integrin and create weak adhesion between WBC and endothelium--activates integrin--ICAM on endothelium strongly binds integrin (on WBC surface) to trap WBC to site of inflammation
126
Cadherins (junctions)
Bind like cells to each other (all cells have cadherins)
Attach to actin cytoskeleton via catering and stabilizing P120
Requires Ca++
127
Wnt signal in undifferentiated cells
Can cause cancer
APC and other proteins can't destruction complex, binds on membrane with disheveled, B-catenin isn't destroyed and translocation to nucleus to activate Tcf to transcribe target genes that increase cell division
128
APC mutation (B-catenin)
Causes FAP with lots of colon polyps
129
No Wnt signal in differentiated cells
APC forms destruction complex with other proteins that phosphorylate B-catenin that gets marked for destruction, so Tcf continues to repress gene transcription
130
Desmosome (junction)
Connects cells via cadherin like molecules and Intermediate filaments, joins heart cells
Provides stability for cells subject to shearing
131
Pemphigus and desmosomes
Autoimmune disease against desmosomes that causes oral and mucosal and skin lesions
132
Hemi desmosomes
Connects cells to basal lamina of ECM via Integrin and IFs
| Attach cells to basement membrane
133
Adherens junction (zonulae adherens)
Connects cells via cadherin--P120 and catenin--actin
| Adhesion between cells
134
Focal adhesion
Connects cells to matrix via integrin and actin
135
Tight junction (zonulae occludentes)
Seal to prevent entrance of material
Determines polarity for protein distribution in cells
Acts as barrier in endothelial and epithelial cells
Goes around entire cell
Links cells to actin
136
Gap junctions
Form channel for electrical and metabolic activities
Can be regulated, modified, and gated (connexons)
Ions, sugars, AAs, nucleotides, and vitamins can be shared
Large macromolecules can't pass through connected cytoplasms
Selective diffusion of molecules between cells
Rapid communication
137
Charcot-Marie-Tooth disease
Defect of gap junctions causes it
| Deafness, cataracts, arrhythmia, loss of muscle control, muscle degeneration
138
Fibrous proteins
Collagen, elastin, keratin, axial ratio >10
Insoluble in water
Threadlike structure
139
Globular proteins
Myoglobin, hemoglobin, enzymes, ratio < or equal to 3
| Soluble in water and acids and bases
140
Elastin
Fibrous for elasticity of organs
| Lysine cross linking with Lysyl oxidase adds crosslinking for strength--allysine aldehyde--desmosome crosslinking
141
Myoglobin and hemoglobin
Store and Deliver O2 to muscle and tissues
Best understood globular proteins
Proteins and metals can't bind O2--oxidizes proteins and metals create free radicals
142
Myoglobin vs. hemoglobin
Mb: 1 heme group, 02 storage in muscle, 153 AAs
Strong O2 affinity with hyperbolic curve to deliver oxygen to starved muscles
Hb: 4 heme group carrying 4 O2s, 2 alpha (141 AAs) and 2 beta subunits (146 AAs)
Completely different primary structure but similar 2° and 3° structures
Sigmoidal curve with positive coopertivity of multiple subunits
143
Hb mutation HbS
Sickle cell anemia: Glu 6-->valine (alipathic) that is on outside of B-subunits and causes it to get sticky so Hb molecules stick to each other and form fibers--> distorts RBC shape so that it's a sickle-->prevents proper blood flow
144
Alpha-1 antitrypsin and elastin inhibit
Proteases, protect from emphysema and protect alveolar walls of lungs
Smoking inactivates alpha-1 antitrypsin
145
Hemoglobin structure
4 subunits, prosthetic group of protoporphyrin 9 with tetrapyrroles (4 Nitrogens and Fe attached to distil histidine) Fe for 02 binding
146
T-R state
02 binding of heme brings heme closer to porphyria ring with histidine and distorts alpha helix shape
Positive Cooperative binding, so binding of 1st O2 changes Hb to R state and increases likelihood of other 02s binding
Can therefore reach saturation at low p02 in R state
147
Positive coopertivity
Affinity for 02 changes due to this quality, has multiple binding sites that interact, 1st binding site increases affinity at remaining sites (sigmoidal curve of R state)
148
T state
Tense state when 02 isn't bound, histidine is away from central heme group
More interactions and more stable
149
R state
Relaxed state after 02 binds, Histidine pulled closer to distort alpha helix
Fewer interactions and more flexible
150
Allosteric effects
H+, C02, low pH, and 2,3-BPG (especially at high altitudes) decrease affinity of 02 for binding to Hb and stabilizes T state, releasing 02 to tissues
151
Difference in pH between tissues and lungs increases 02 transport efficiency
Bohr effect: C02 decreases Hb affinity for 02 so more 02 is dropped off to tissues
C02 from tissues goes through cycle (C02 H20--carbonic anhydrase--H2C03--H+ HC03-
H+s bind deoxy Hb at tissues and go to lungs, where 02 is taken up by Hb after deoxy Hb releases H+ that join with HC03 and go through cycle to form C02 that's exhaled
152
2,3-BPG
By product of glycolysis, in RBCs and placenta (allows mom to release more 02 that binds to baby's Hb)
153
C02 transport
By bicarbonate predominantly (HC03)
| Also by carbamate (Hb-N-C00-) that stabilizes T state with salt bridges
154
RBCs and 02 transport
Lack mitochondria, no oxidative phosphorylation so they don't generate C02, gets energy from glycolysis
If C02 were generated, they wouldn't hold onto 02 for transport to tissues
155
Carbon monoxide and 02
C0 is toxic (blocks function of Mb, Hb, and cytochromes in oxidative phosphorylation) and binds to heme better than 02 (20,000x better) due to its ability to donate electrons to d-orbitals of Fe++
Side chains and histidine residue sterically hinder CO's binding (can't bind linearly), while 02 can
156
Nitrous oxide
NO relaxes smooth muscles
Facilitates O2 release to tissues
Binds to Hb so O2 can't
157
Globin genes (of Hb)
Protein part of Hb
Chromosome 16: expression of alpha globin gene family
Chromosome 11: expression of beta globin gene family
158
HbA=normal adult
Alpha2 Beta2
159
HbS=sickle cell
Alpha2 Beta2S
160
Infant Hb=HbF
Alpha2 Gamma2
161
HbF and HbA 02 affinity
HbF has higher 02 affinity to get 02 from mom's blood
Lower P50 to reach saturation at lower O2 concentrations
Only beneficial up to birth
After that high HbF limits ability to deliver O2 to tissues
HbA increases after birth, however
162
HbA1c
Binds glucose and is increased in people with diabetes mellitis since their HbA comes into contact with higher concentrations of glucose during 120 day half life of RBCs
163
HbC
Mild hemolytic anemia
| Converts Glu-->Lysine (instead of valine)
164
Methemoglobinemias
Hb with Fe+++ instead of Fe2+
Reduces ability to release O2 to tissues
Nitrate exacerbate this problem
Methylene blue can reduce Fe3+ to Fe2+ and save patients
165
Epithelium locations
External surfaces of body
Lining internal cavities and organs
Form organs and glands and line ducts
166
Epithelium functions
```
Protection/barrier to desiccation, abrasion, and infection
Absorption/secretion
Gas exchange
Filtration
Remove particulate matter
Transport fluids
```
167
Epithelium gets nutrients?
Avascular
Gets metabolites, 02, and nutrients by diffusion from blood in adjacent capillaries located in underlying connective tissue
168
Parenchyma
Functional unit of organ in lobule, does work
169
Stroma
Supportive connective tissue of organ
170
Exocrine subcategories
Unicellular enteroendocrine and goblet cells
| Multicellular simple or compound (branched) ducts with secretory and ductal portion
171
Duct structure of exocrine gland
Simple or compound (branched ducts~pink portion)
172
Secretory shapes of exocrine gland
Tubular
| Acinar
173
Type of secretion of exocrine gland
Serous, mucus (light colored), or mixed
174
Mechanism of secretion of exocrine glands
Merocrine-most common-exocytosis of product from vesicles in membrane (salivary/sweat/acinar cells of pancreas)
Holocrine-cell becomes secretion, gland gets full of lipid droplets shed into lumen (sebaceous gland)
Apocrine-has some lipid droplets like in breast milk, some of cytoplasm and plasma membrane comes with secretion (mammary gland)
175
Cilia
Motile
Microtubules 9+2, ordered arrangement, basal body, longer than other surface specializations for motility
In reproductive and respiratory tracts
176
Microvilli
Increase SA for absorption, shorter than cilia
Made of actin
Nonmotile
Cover absorptive cell surface in small intestine (GI tract) and kidney
177
Sterocilia
Nonmotile
Made of actin, branched, increases absorptive SA
Line surfaces in epididymis and vas deferens
178
Basal surface specializations
Basal unfolding of plasma membrane for lots of transport
Associated with mitochondria for ATP
Found in proximal convoluted tubule of kidney and ducts of salivary glands
179
Nonkeratinized epithelium
Live
Surface cells
Covers moist cavities like mouth, vagina, anal canal, pharynx, and esophagus
180
Keratinized epithelium
Nonliving cells filled with keratin granules
Often loses nucleus
External body surfaces like palms of hand and soles of feet with thick layers for protection against abrasion, infection, and desiccation
181
Endocrine glands
Lack ducts, highly vascularized near bloodstream, loses connection to surface, products delivered into surrounding capillary networks
Can be individual cells of digestive organs, endocrine tissue of pancreas and reproductive organs, or endocrine organs like pituitary, thyroid, parathyroid, and adrenal glands
182
Acinar/alveolar
Sphere like in shape
| Field of flowers
183
Hilum
Doorway for ducts, nerves, blood, and lymph vessels, goes. Through CT trabeculae to parenchyma
184
Simple columnar epithelium
Small intestine with microvilli and goblet cells and basal body
Uterine tube with cilia and basal body
185
Simple cuboidal epithelium
Kidneys, thyroid, and lining ducts
| Taller cells=more activity
186
Simple squamous epithelium: 2 types
Endothelium lining internal surfaces of heart and blood vessels for transport of fluids and gas exchange
Mesothelium lining external surfaces of internal organs, secretes fluid that reduce friction between organs
187
Pseudostratified epithelium
Respiratory tract with goblet cells and cilia
Pseudostratified columnar in epididymus with stereocilia
Has basal cells
188
Transitional epithelium
In bladder and urinary tract, plaques pull it into dome shape with rounded cells at top that may be binuclear, provides osmotic barrier
189
Stratified epithelium
Always named based on most apical layer
190
L-AAs
Only L-amino acids are manufactured in cells and incorporated into proteins
NH3 group on left (L AA means right handed helix)
191
AA light absorbance
Aromatic amino acids are relatively nonpolar and absorb ultraviolet light
Especially tyrosine and tryptophan (280nm)
192
Bradykinin (biologically active peptide)
Released in blood for smooth muscle contraction and dilation of blood vessels
Inflammatory mediator
Drops BP
ACE inhibitors increase bradykinin to lower BP further
193
Bacitracin
Polypeptide Antibiotic
| Topical treatment of skin and eye infections
194
Nucleoproteins (conjugated protein with non-AA components)
Ribosomes, nucleosides
| Protein with nuclei acid
195
Lipoprotein (conjugated)
plasma lipoprotein particles such as HDL, LDL, IDL, VLDL, and ULDL (chylomicrons)
196
Glycoprotein
| Mucoprotein
Glucose, mannose cell surface proteins
Protein with carbohydrate
Mucoprotein has large polysaccharide associated with glycoprotein like type 1 and 2 globulins in serum
197
Chromoprotein
Hemoglobin, carotenoids, flavoproteins
| Protein with pigmented prosthetic group or cofactor
198
Metalloproteins
Hemoglobin, zinc fingers, cytochrome
| Protein with metal ion cofactor
199
Gel electrophoresis and use in western blots to determine molecular weights
SDS PAGE detergent denatures proteins and masks charged groups to neutralize charges so they migrate according to size in electrical field
Using polyacrylamide gel, load samples, apply current, proteins migrate to positive end since SDS is -, separates proteins by size with smallest ones traveling farthest, look at marker to determine weight of unknown protein by looking at its migration
This separates the proteins
Transfer proteins to a PVDF membrane
Block non specific binding (prevent interactions between membrane and antibody used for detection of protein)
Probe for protein of interest with specific antibody linked to reporter enzyme
Labeled Primary and secondary antibodies are bound and detected
200
Scurvy
Vitamin C deficiency
Vitamin C normally supports stability of collagen
Therefore it leads to impaired collagen formation
201
Collagen and elastin
Structural proteins
Collagen is found in tendons, ligaments, and CT of skin, blood vessels, and lungs
Elastin is in artery walls, lungs, intestines, and skin
202
Alpha 1 antitrypsin deficiency
Causes liver and lung diseases
Brought on by elastin degradation
Normally protects the lungs from emphysema
Protease inhibitor
203
Repulsive interactions in protein structure
Van der Waals forces assist in stabilization of protein structure
Pertains to attractive and repulsive forces between molecules that become polarized
Contribute to binding between molecules
204
Random coil (secondary structure)
Monomer subunits are oriented randomly while bonded to adjacent units
Statistical distribution of shapes for all the chains in a population of macromolecules
Not one specific shape
205
Denaturants of proteins
Involves disruption or destruction of secondary and tertiary structures
Can't break peptide bonds of primary structure
Disrupts alpha helix/B sheets and uncoils it into random shape
Heat and organic compounds disrupt H-bonds and hydrophobic interactions (increases KE and disrupts bonds)
Alcohol disrupts H-bonding between amide groups in secondary structure and between side chains in tertiary structure
Acids and bases disrupt salt bridges and ionic interactions between R groups
Heavy metal salts disrupt disulfide bonds and salt bridges and forms aggregates
Agitation breaks bonds
Reducing agents disrupt disulfide bonds (normally formed by oxidation of SH groups)
206
Enzymes
```
-ase
Catalyze reversible reactions
High specificity for attaching substrate
For synthesis, degradation, transport, replication, motility, communication
Kinetic analysis to analyze behaviors
```
207
Enzymes trump inorganic catalysts
Enzymes are highly specific in body (but not in vitro), avoids side products
Normal rxn conditions (body temp, pH 7, except in stomach pH 1.5)
Higher rxn rates
Can be regulated (side chain modifications)
208
6 classes of protein enzymes
| 2 classes of RNA enzymes (ribozymes)
Oxidoreductases for redox rxns
Transferases (move phosphate from ATP--substrate)
Hydrolases transfer functional groups to water
Lyases for breaking C-C, C-N, C-O bonds, elimination + addition
Isomeraes transfer groups within molecules
Ligases for forming C-C, C-N, C-O, C-S by condensation rxn, uses ATP
Ribosomes with catalytic peptidyl transferase
Hammerhead, hepatitis delta virus RNA, group 1 intron ribozymes
209
IUB rule for EC number 2.7.1.1
2 denotes transferase class
210
1,3-BPG-->2,3-BPG
Uses isomerase called BPG mutase
211
Fe3+ e- --> Fe2+
Uses Methemoglobin reductase
Redox rxn, Fe3+ causes Hb to be darker
Use NADH to reduce Fe3+ to Fe2+
NADH gives up electron to become NAD+
212
Enzymes often require prosthetic groups/coenzymes or cofactors
Prosthetic groups/coenzymes bind covalently, tightly associated with protein part of enzyme
Cofactors bind transiently to enzyme or substrate like ATP, often metal ions and vitamins (containing metal)
213
Important cofactors
Fe2+ and Fe3+ ions serve as cofactors for cytochrome oxidase, catalase, and peroxidase
Mg++ serves as cofactor for hexokinase, glucose-6-phosphatase, and private kinase (kinases often use Mg++ to stabilize ATP and prevent hydrolysis of phosphate groups in water)
Fe-Su center in oxidative phosphorylation
Fe-Cu center in heme group of Complex IV of ETC to reduce O2 to water
214
Apoenzyme
Protein part by itself without cofactor/prosthetic group to activate it, inactive state
Can stop protein production
215
Holoenzyme
Enzyme with prosthetic group/cofactors or enzyme that's active by itself
216
Nicotinamide adenine denuclearize (NAD)
Transfers H- groups (hydride ions)
Used by dehydrogenase (redox enzyme)
Niacin precursor
Oxidized NAD has absorbance at 260 nm
When it's reduced it has 2 absorbances at 260 and 340 nm
Its absorbance is used to measure enzyme kinematics
217
PDH converts pyruvate-->acetyl CoA
Uses 5 coenzymes: TPP, lipoamide, CoA, NAD+, FAD
For binding acetyl group, transferring it, generating acetyl CoA, transferring H- ions to FAD covalently bound to enzyme, and giving H+ to NAD as mobile energy source
3 enzymes in complex: E1, E2, E3
218
Niacin deficiency
Pellagra
Decreased activity of lactate dehydrogenase since it's a redox enzyme that uses NAD as coenzyme (contains niacin)
Skin condition that affects neurological systems
Alcoholics are prone to it due to decreased niacin absorption
Tryptophan can be converted to niacin
Nixtamalization of corn to reach niacin requirements
219
Connective tissue components
Has Cells (fibroblasts, blood cells, adipocytes)
ECM (proteoglycans, GAGs, glycoproteins, tissue fluid from cellular metabolism waste products) that support and connect other tissues in organs
Fibers (primarily collagen, reticular, elastic)
Includes bone, blood, and cartilage
220
CT function
Sits under and supports avascular epithelium through diffusion
Medium for gas exchange, nutrients, and metabolites
Immune system cells function if epithelial barrier breaks down
Gives strength and flexibility depending on type of CT
221
Fibroblasts of CT
Produce fibers and matrix, spindle shaped with small nucleus
222
Mast cells of CT
Larger with dark staining basophils granules
Close to blood vessels
Secrete vasoactive compounds (histamine, heparin, chemoattractants) for response to allergens and irritants
223
Macrophages (histiocytes in CT)
Derived from monocytes in blood that move from blood differentiate into macrophages
Respond to foreign matter
Release cytokines to stimulate immune response
Speckled watermelon shape with large nucleus
224
leukocytes (WBCs) cells in CT
Plasma cells
Adipocytes
WBCs=Neutrophil with many lobes, eosinophils with red hue and bilobed, lymphocytes with prominent nucleus
Defense against infection
Plasma cells=derived from lymphocytes, clock face appearance
Produce antibodies for defense
Adipocytes=unilocular white fat or multilocular brown fat
225
ECM (matrix) function in CT
Contains GAGs that hold water to make supportive gel like matrix, still fluid enough for diffusion
Gel with things imbedded
Compressible for supple skin and flexible cartilage for joint surfaces
226
Collagen 1 in CT
Primary collagen for tensile strength, pink to orange stain
Collagen lacks nuclei and organelles (secreted extracellularly), unlike skeletal muscle but both have parallel fibers running side by side
227
Collagen 2 in CT
Resists pressure, in hyaline and elastic cartilage and vitreous of eye
228
Type 3 collagen
Branching collagen forms networks (reticulum)
provides network for free flowing cells
Holds together lymphoid organs
229
Type 4 collagen in CT
Holds together basement membrane as attachment point for epithelial cells
230
Elastin vs. collagen CT fibers
Elastin (made of elastin synthesized by fibroblasts, chondrocytes, and smooth muscle cells) is thinner with angular projections
Collagen is thicker, maintained by fibroblasts
231
Elastic lamellae form of elastic fibers
Wavy surface on sides of smooth muscle
| Relaxed elastic fibers appear wavy
232
Loose irregular CT
Close to epithelial with capillary beds
Medium for diffusion of waste and nutrients between epithelium and capillaries
Holds together organs
Attaches epithelium to underlying tissues
Includes areolar, reticular, and adipose tissue
Few fibers (elastin/collagen)
Lots of matrix and cells (red mast cells, fibrocytes, lymphocytes with dark staining nuclei; macrophages with prominent nucleoli and speckled watermelon appearance; eosinophils with red granules and bilobed nucleus; plasma cells with clock face and pale pink cytoplasm beside it, differentiate from lymphocytes and secrete antibodies)
233
Dense irregular CT
Thicker fibers for resisting pulling forces in all directions, flexible
Less matrix, fewer cells
Found in fascia and dermis of skin, capsules and septa of glands and organs, periosteum, perichondrium, epimysium, epineurium, dura, GI and respiratory tract submucosa
Plantar fascia
234
Dense regular CT
```
Primarily collagen type 1, runs parallel for strength along long axis
Minimal matrix
In tendons
In ligaments (have more elastic fibers)
```
235
Adipose tissue CT (brown and white)
Derived from mesenchymal cells
Adipose is undifferentiated
Surrounded by loose CT
Storage for triglycerides
White=large, unilocular with 1 lipid droplet free in cytoplasm, chicken wire appearance, increased with estrogen changes and caloric excess
Brown fat=smaller, multiple fat droplets in neck, back, around organs to maintain core temperature, massive blood supply with mitochondria and high metabolic capacity for no shiver in thermogenesis in infants and hibernation
236
Composition and structure of cellular membranes
Fluid mosaic model of 1972 by Singer and Nicholson
Phospholipid bilayerwith embedded proteins, polar heads on outside, hydrophobic tails towards inside
RBCs that lack organelles provided easy membrane preparation for freeze fracture with e- microscope that strikes frozen cell to split layers of membrane
Has proteins (peripheral and integral)
Carbs linked to lipids/proteins
Proportions of proteins/lipids depends on function of membrane
237
How lipids promote structure and function of membranes
Lipids are hydrophobic and can associate with the hydrophobic tails
Lipids make up most of myelin sheath that wraps axons for insulation (pseudopod of glial cell wraps around axon to form thick layer of plasma membrane with very little cytoplasm)
238
3 Amphipathic lipids suitable for forming membranes:
Phospholipids for membrane structure
Cholesterol for fluidity at lower temperatures
Neutral Glycolipids with sugars, ABO system blood group determinant, contributes to glycocalyx (carbs on glycolipids and glycoproteins that looks like fuzzy coat on plasma membrane and protects GI tract membranes from digestion), has variable pattern of sugar residues, in outer leaflet of cell membrane but inner leaflet of organelles
Glycolipids can be gangliosides with sialic acid residues (- charge)
239
Ganglioside accumulation on brain
Contributes to lysosomal storage diseases (Tay-Sachs and Gaucher)
Occurs when enzymes are defective and sugars aren't metabolized--> gangliosides accumulate on brain
240
Selectins and cellular recognition
Selectins are receptors that recognize sugar residues on glycoproteins in membranes of another cell type
Moves blood cells from inside capillary to ECM to fight infection
241
Glycolipids
Neutral Glycolipids with sugars, ABO system blood group determinant,
Contributes to glycocalyx (carbs on glycolipids and glycoproteins that looks like fuzzy coat on plasma membrane and protects GI tract membranes from digestion)
Has variable pattern of sugar residues, in outer leaflet of cell membrane but inner leaflet of organelles
Glycolipids can be gangliosides with sialic acid residues (- charge) and defects in enzymes can lead to their accumulation on the brain
242
Peripheral proteins
No covalent bonds with proteins or lipids
Ionic or H-bond interactions
Removed by high salt or extreme pH
243
Integral membrane proteins
Embedded in bilayer: single leaflet, single pass transmembrane, or multiple pass transmembrane
Removed by detergent that binds and protects hydrophobic domains (sequesters lipids) and denatures protein while giving it a charge (SDS removes lipid from protein to isolate protein for further analysis)
244
Single leaflet integral proteins
Lipid covalently bound to 1 AA
Outer leaflet has GPI anchor
Inner leaflet has fatty acid and long chain hydrocarbons (phenyl groups added to C-terminal cysteine)
245
Alpha helical transmembrane proteins
Has glycosylated extracellular domain and cytoplasmic domain
| Single or multipass transmembrane proteins
246
Alpha helical single pass transmembrane
Has polar domain in extracellular and cytoplasmic environments and hydrophobic alpha helix in membrane (Glycophorin)
247
Alpha helical multiple pass transmembrane proteins
```
Have alternating hydrophobic domain interacting with lipid part of membrane and hydrophilic AAs that stick out to external environment/cytoplasm
Hydropathy plot shows hydrophobic and hydrophilic regions
Band 3 (Integral multipass transmembrane protein example)
Can make aqueous channels with hydrophilic regions in center
```
248
B-barrel transmembrane proteins
Alternating side chains
Hydrophobic and hydrophilic side chains on opposite sides
Can form porins
249
Membrane protein asymmetry, fluidity, and specialized domains
Distributed on opposite sides of membrane according to function
Proteins and lipids can move
Proteins have specific orientations
Different in the 2 halves of bilayer
250
Asymmetrical lipid distribution on bilayer
Internal leaflet has more phosphatidylserine and phosphatidylinositol for signal transduction inside bilayer
251
Asymmetrical transmembrane protein distribution on bilayer
Ligand binding domains are on outside of membrane (like GF ligand)
Functional domain/effector portion is on inside/cytoplasmic side to transmit signal to cell
252
Endocytosis: Ligand binding site starts on extracellular/outside surface with signaling component on cytosolic/internal side
The ligand binding site switches to the inside of vesicle during endocytosis
253
Lipid and protein movement
Lipids can rotate, flex tails, laterally move, but rarely flip flop
Proteins can rotate and move laterally (so 2 receptors can get closer together to function)
Cell fusion experiment with mouse and human cells tagged with different dyes and fused-->eventually colors diffused evenly, showing ability of proteins to move in membrane
254
Fluidity depends on 2 things
```
Temperature (warmer=more fluid)
Lipid composition (shorter chains=more fluid, unsaturated phospholipids with bend=more fluid)
```
Cholesterol content makes more fluid at lower temperatures to prevent freezing
255
Apical domain
Faces lumen of organ or external surface in case of skin
Maintained by tight junctions
Restricts proteins to certain regions
256
Basolateral domain
Faces internal side of tissues (CT) and adjacent cells
Maintained by tight junctions
Restricts proteins to specific regions
H+ ATPase is stuck in apical surface
Cl-/HC03- exchanger stuck in basal surface
To help with exchange of ions in urine of kidneys
257
Membrane domains restricted by
Junctional complexes
Bound to each other
Bound to cytoskeleton in cell
Bound to proteins of ECM
258
Lipid rafts
Microdomains enriched in sphingolipids with long chain FAs, cholesterol, GPI linked and acylated proteins
Restricts protein movement
Brings together parts of signaling pathways
Rafts are less fluid
259
Protein misfolding diseases
```
Alzheimer's
Parkinson's
Creutzfeldt Jakob
Gaucher's
Cystic fibrosis
```
260
Protein folding
Stabilized by finding lowest energy state, most stable form, hydrophobic interactions, disulfide bridges
261
PDH
Pyruvate--acetyl CoA
E1 TPP carries aldehyde; E2 lipoate and CoA to transfer acyl group; FAD bound to E3 accepts H+s and transfers to NAD+ (better carrier)
262
Tetrahydrofolate contains folic acid
Deficiency of Vitamin B9 folic acid causes spine bifida
263
Wound healing
Inflammatory: fibronectin to form blood clot and MMPs to facilitate migration of cells to wound
Proliferative: MMPs upregulated for ECM degradation, GAGs to facilitate cell migration, proteoglycans to release GFs, and new epidermis forms when fibroblasts make collagen 3 and fibronectin matrix
Remodeling: more organized phase, collagen 3 converted to collagen 1, MMPs, proteoglycan, hyaluron, and GAGs degraded, normal constituents of skin are made
264
Vitamin B3 (niacin)
Deficiency causes pellagra skin condition that leads to neurological disorders if left untreated, NAD+ and NADH e- carriers involved
265
Tau phosphorylation diseases
Alzheimer's and frontotemporal dementia
266
Alpha 1 antitrypsin deficiency
Causes emphysema since it usually synthesizes elastin. Without elastin, you're prone to get COPD/emphysema, exacerbated by smoking
267
Errors in glycolipid metabolism
Causes lysosomal storage diseases such as Tay Sachs and Gaucher's diseases (especially in Jews)
268
3 types of epidermolysis diseases
Simplex in epidermis caused by keratin (IF)
Junctional in basement membrane by laminin 5
Dystrophic in dermis by collagen VII
269
Cell to cell junctions
Desmosomes: cadherin-like molecule and IF
| Adherens junction: cadherin and actin
270
Cell to matrix junctions
Hemidesmosome: integrin and IF
| Focal adhesion: integrin and actin
271
HbA has 120 day RBC life
HbS has 20 day RBC life
272
Zwitterion pH
7.4
