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Flashcards in Test 1 Deck (272):
1

Aliphatic AAs

Valine V
Leu L
Ile I
Ala A
Gly G

2

Polar OH and SH AAs

Serine S
Tyr Y
Thr T
Cys C
Met M

3

Acidic AAs

Glu E
Asp D
Asn N
Gln Q

4

Basic AAs

Lys K
Arg R
His H

5

Aromatic AAs

Tyr Y
Phe F
His H
Trp W
Pro P

6

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)

7

H-bonds

Most important property of water
High BP
Viscosity
High surface tension
H-bonds to 4 other water molecules

8

PKa

-log ka

9

Keq

=pdct/reactant=ka

10

When HA=A-

PH=pKa

11

Henderson Hasselbach

PH=pka+log [A-]/[Ha] (base/acid)

12

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)

13

When pH>pka

AA is deprotonated

14

Carbonic acid

H2C03, very important acid

15

Bicarbonate buffer system most important inorganic buffer

H20 C02--H2C03----H+ HC03
Water and carbon dioxide--Carbonic acid---Protons and Bicarbonate

16

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

17

Lungs and kidneys

Most important for controlling pH

18

Lungs decrease pC02 by

Hyperventilation (higher HC03-/C02 ratio), increases pH since bicarbonate is more basic than carbon dioxide

19

Kidneys control pH

retain HC03-, make more of it, and eliminate H+ in urine as NaH2PO4 + NH4+

20

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

21

C02 released at lungs; chloride exchange...

low Cl-, high HC03- venous

maintains electrical neutrality during bicarbonate passage

22

02 released at tissues;

high Cl-, low HC03- in lung plasma (arterial)

23

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

24

To determine good buffer, look for

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