EXAM II Material Flashcards
1
Q
Ribonuclease/Deoxyribonuclease
A
Converts long RNA/DNA chain to short RNA/DNA oligomer
2
Q
Phosphodiesterase
A
Converts RNA/DNA oligomers into nucleotide monophosphates (NMPs) or deoxynucleoside monophosphate (dNMPs)
3
Q
Nucleotidase*
A
Converts NMPs and dNMPs to nucleosides and deoxynucleosides
Nucleotide –> Nucleoside
4
Q
Nucleosidase
A
Removes the base from the ribose or deoxyribose
5
Q
Xanthine oxidase
A
Converts Hypoxanthine (precursor of something that the body can get rid of) to Xanthine
And Xanthine to Uric acid
Drug target for treatment of gout
Contains 2FADs, 2Mo atoms, 8Fe atoms per molecule of enzyme
6
Q
Allopurinol
A
Inhibits the action of Xanthine Oxidase
Prevents the build up of uric acid which can lead to gout
7
Q
Urate Oxidase
A
Catalyzes the oxidation of uric acid into Allantoin - a soluble compound
8
Q
Gout symptoms
A
Painful, inflammed joints; mainly effects big toe (metatarsal pharangeal joint); can form cystals bc nonsoluble
9
Q
Causes of Gout
A
Over production of uric acid; primary hyperuricemia
Underexcretion of uric acid; secondary hyperuricemia
Sodium urate crystals precipitate in synovial fluid of joints; deposits in kidney; acute inflammatory response via phagocytic cells engulfing crystals and releasing factors that initiate this
Diet rich in beans, lentils, spinach w/ meat, seafood, OH
10
Q
Types of organic solvents that lipids are soluble in
A
Ethanol (alcohols)
Oils
11
Q
What is the greatest biologically significant property of lipids, contributed by ____?
A
Hydrophobicity, contributed from FA (hydrocarbon tails); ability to form the bilayers and michelles
12
Q
What does it means to be ionized?
A
When a atom/molecule gains or loses electrons; FA at ionized at physiological pH and have a (-) charge at the carboxy end
Palmitic acid –> Palmitate (16:0)
Oleic acid –> Oleate (18:1)
13
Q
Structure of Triacylglycerols (TAGs)
A
Glycerol backbone with 3 acetyl acid goups
14
Q
Derivatives of TAGs can serve as:
A
Hormones, Signal Molecules, and Intracellular Messengers
15
Q
How would you name this from both ends? assume n=4
A
- From omega end: omega-3
- From carboxy end: cis-delta7
16
Q
What are the EFAs?
A
Omega-3 = Linoleate (18:2)
Omega-6 = Linolenate (18:3) Octadecatrienoic; Veggie oils
Omega-6 Arachidonate (20:4) Hemp oil
17
Q
Which FA configuation is most common in the body?
A
Cis (always)
Ex: oleic acid - non ionized
Oletate = ionized
18
Q
What are the major 3 functional classes of FA?
A
NEFAs
Omega-3s and Omega-6 Essential FA
19
Q
What are the 2 NEFAs?
A
Palmitic acid (16:0) Hexadecanoic - ionized = palm oil
Stearic acid (18:0) Octadecanoic - ionized = several uses
20
Q
What enzyme converts RNA to DNA?
A
Ribonucleotide reductase
oxy –> deoxy
21
Q
List common:
Disaccharides
Oligosaccharides
Polysaccharides
A
Di = sucrose, maltose, lactose
Oligo = glycoprotein, glycolipid
Poly = Glycogen, starch, cellulose
22
Q
Special features of the archaeon
A
Single-celled organism
- Avoids hydrolysis bc it has an ether bond b/w Phosphate head group and glyerol backbone (ROR)
- Branched and Saturated (linear) = more resistant to oxidation
- Inverted stereochemistry of central C in glycerol backbone
23
Q
3 major membrane lipids
A
Phospholipids = PGs
Glycolipids = cerebroside
Cholesterol
24
Q
Components of Phospholipid?
A
- Glycerol backbone
- 2 FAs (hydrophobic)
- Phosphate group = philic
- Alcohol = philic
25
Phosphoglycerol components:
1. Glycerol backbone
2. 2 Acyl groups (FA) (RCOO)
Unsaturated FA usually occupy C2, Sat = C1
3. Phosphate + Alcohol
26
What is the intermediate in forming a number of phospholycerides?
**Phosphatidate/Diacylglycerol 3-P**
Glycerol backbone, 2 acyl/FA, P
Small amounts present in membrane
27
What are the 5 Phosphoglycerides that are derived from Phosphotidase? What type of bond is formed?
**Ester bond;** Carb. acid & OH **DSACI**
1. Diphosphatidylglycerol - Inner mito membrane
2. Phosphatidylserine - memory & cognition
3. Phosphatidylamine - nervous tissue
4. Phosphatidylcholine - cell membrane, pulmonary surfactant
5. Phosphatidylinositol - signaling
28
Components of Sphingolipids
1. Sphingosine backbone
2. Long, **unsaturated** hydrocarbon chain bound with double bond
3. Amino OH (NH3+, 2 OH = all diff Cs on backbone)
29
Sphingomyelin components
A Sphingosine = Phospholipid; membranous myelin sheath
1. Sphingosine backbone
2. Phosphotidase-derived group **(Phosphotidylcholine)**
3. FA bound with amino group via **Amide bond**
4. **Unsaturated Hydrocarbon Chain**
30
Glycolipid components
1. Sphingosine backbone
2. Unsaturated hydrocarbon chain
3. Amino group
4. Sugar residue linked to OH (ECM = polar)
31
Cerebroside Components:
Complex Glycosphingolipid in **muscles and nerve cell membranes** (Monoglycosylceramides)
1. Sphingosine backbone
2. Long, unsaturated hydrocarbon chain
3. **Glucose or Galactose** bound to OH
4. FA bound to amino group
32
Why is cholesterol considered a sterol?
Contains branched aliphatic side chain of 8-10 C atoms
Contains an OH goup
33
What type of bonds are associated with the bilayer?
Noncovalent
34
What are the charge distributions along a bilayer membrane?
Phobic = negative (ICM)
Philic = positive (ECM)
Membrane is **electrically polarized**
35
What are the driving forces of lipid bilayer formation?
1. **Hydrophobic Interactions** (predominate)
2. VDW (b/w lipid tails)
3. Electrostatic (b/w polar heads and water)
36
List the 3 things that occur due to the hydrophobic interactions of membranes
1. **Extensive membranes** are usually formed
2. **Self-sealing** occurs bc it is energetically favorable = thermodynamic stability
3. The bilayers close on themselves forming **closed compartments** maintaining its integrity
37
Lipid bilayers have low permeability for:
Ions and polar molecules
i.e. Glucose (+)
38
What type of interactions are peripheral proteins involved with in the lipid bilayer and how can they be removed?
H-bonds and Electrostatic
Can be removed via salt or pH changes
39
List 2 examples of integral membrane proteins?
1. **Bacteriorhodopsin (BR)**
light-driven proton pump; mainly alpha-helices (most common transmembrane structure bc flexible)
2. **COX 1/PGHS 1** integral protein but not membrane spanning
40
Function of lipids on lipid bilayer and how are they attached?
Consitute/mediate protein-protein interactions and covalently associated with proteins
41
What 3 modifications do lipid-linked proteins perform on the lipid bilayer?
1. Palmitoylation
2. Farnesylation
3. GPI
42
Palmitoylation
One of the lipid-protein modifications
Covalent attachment via **thioester bond** of FA to a cys residue
43
Farnesylation
Covalent attachment of a farnesyl unit **(C15)** to C-terminal tetrapeptide (CAAX) with the further addition of a thioether linkage w/ Cys residue
## Footnote
**Anchors protein to membrane & protein-protein interaction**
44
GPI Anchor
Anchors proteins to outer leaflet of plasma membrane
Common with cell-surface hydrolytic enzyme and adhesions, tethered to cells via GPI
45
What are the 2 compartments of the mito membrane?
1. **Intermembrane space** = Oxidative Phosphorylation
2. **Matrix** = TCA and FA oxidation
46
Inner mito membrane is impermeable to:
Nearly all ions and polar molecules
47
What is Tm defined as?
**Rigidity** = determined by saturation levels (length)
Tm is also effected by cis/trans bonds; cis = more fluidity (harder to pack together)
48
What determines membrane fluidity?
FA composition
Cholesterol content
49
The rate of recovery of fluorescence when using the FRAP technique depends on:
The lateral mobility of the labeled component
50
T/F: Cholesterol is found only on the outer leaflet of the membrane lipid bilayer
False; present on both inner and outer leaflet
51
Glycocalyx
Glycoprotein polysaccharide that lines the cellular membrane
Important for cell adhesion, lymphocyte homing
i.e. vascular cells adhere to blood vessels
52
Glycosylation
The addition of carbohydrate to another group on a molecule; usually done on the ECM of the plasma membrane
53
Receptor-mediated endocytosis is done by:
Invagination of the membrane which folds in and breaks off forming a vesicle "budding"
54
Another form of receptor-mediated endocytosis is
"fusion"
55
What is the postulated mechanism for mito proliferation?
Fission; via oligomers; more extensive than "pinching" done by bacteria due to the inner and outer membranes
56
Name the salvage process that occurs in mitochondria
Fusion
57
In order for fusion to occur, what type of environment must the mito be in?
High GTP levels (high energy)
A large electrochemical gradient across the inner membrane
58
Protein import into mitochondria is done through what type of signal?
N-terminal signal sequence = "matrix targeting signal"
Proteins are usually unfolded before entering
59
Under what conditions will ATP be required when a protein needs to be imported into a mito?
When being tranported into the matrix (crossing the inner membrane)
60
Example of a polytopic membrane protein
GPCR = multiple domains/transmembrane
61
Ionic composition of plasma membranes is determined by \_\_\_\_
Protein transporters
62
Types of molecules that can undergo passive diffusion
Small
Nonpolar
Uncharged
63
Cells have \_\_\_\_\_\_\_high or low energy when the ionic [gradient] is equal?
Low Energy
64
What type of transport is occurring when you have a positive/negative free energy value?
Positive = active = not ideal so requires energy
Negative = facilitated = doesn't require energy
65
What are the Primary Type ATPases?
1. Na+/K+ pump
2. SERCA
3. Plasma membrane Ca2+-ATPase (PMCA)
4. H+/K+ ATPase
All form Aspartate Phosphorus Intermediates
66
What are the differences b/w the P-type ATPases and ABC Transporters
In P-type, the phosphate that's liberated forms a **covalent bond** on the enzyme and creates an **enzyme-phosphorylated intermediate**
67
Enzyme of importance in P-type ATPases
Aspartate
During ATP hydrolysis, the rxn occurs on its residue
68
What is the mechanism of action of plant steroids/cardiotonic steriods on Na+/K+ pump & what are these inhibitors called?
Inhibits dephosphorylation of the enzyme-phosphate intermediate
**Digitoxigenin** (clinical)
**Ouabain** (lab)
Involved w/ treatment of congestive heart failure by increasing contractile force of heart by increasing ICM [Ca2+] via inhibiting Na+/Ca+ **exchanger** indirectly
69
Difference between PMCA and SERCA
PMCA contains a C-terminal domain (Zaidi's study)
Both have 10 TM domains
70
What's the main driving force during the transport of K+ ions in the K+ channel?
Repulsion of like charges
71
While most ion channels are tetramers, which channel is a pentamer?
Ligand gated channels; ACh receptor; the 5 subunits = pore
72
What type of molecules can pass through gap junctions?
Small and hydrophilic (less than 1kDa; sugars, aa, nucleotides) NOT proteins, polysaccharides, nucleic acids
73
What interactions stabilize the double helix of DNA?
H-bonds
VDW
Hydrophobic effect
74
What type of bonds are associated with a nucleotide?
Beta-glycosidic bond (C1 of sugar and a base)
Ester bond (reduction of the OH on C3 of sugar linked to phosphate)
75
Important feature of creatine phosphate
Stored in the brain and quickly releases energy; within seconds
76
ATP features in metabolism
Immediate energy source via carbon fuels/breakdown via carbon oxidation
Body houses about 100g
77
Which molecule has the most energy potential? (releases the most amount of energy by its oxidation)
Formaldehyde; more reduced, less oxidation, more negative deltaG
78
Which metabolic cycle produces the most ATP?
Oxidative Phosphorylation
79
What are the three principal ways in which metabolic processes are regulated?
1. Controlling the amounts of enzymes (transcription/signaling)
2. Controlling catalytic activity (feedback inhibition)
3. Controlling the accessibility of substrates (pathway compartmentalization; mito, cytosol, etc.)
80
What enzyme digest short and medium-chain FAs?
**Lingual lipase**
81
What enzyme digests medium-chain FAs?
Lingual lipase
Gastric lipase
Phospholipase
Cholesterol esterase
Gastric lipase
82
What are the enzymes found in the small intestine? & their functions? (3)
Pancreatic lipase = TGs
Phospholipase = Phosphlipids
Cholesterol esterase = Cholesterol esters
83
Which vitamin?
Vitamin D; FA derived; Lipid Soluble
Ca2+ & Phosphorus metabolism
Milk, sunlight = Rickets (inadequate bone mineralization)
84
Vitamin?
Vitamin A
FA derived
Lipid Soluble
Carrots; Precurser beta-carotene
Night blindness
85
Vitamin?
Vitamin E
FA Derived
Lipid soluble
Veggie Oils; muscular dystrophy
86
Vitamin?
Vitamin K; FA derivative; lipid soluble
Leafy Veggies; blood clotting
87
What are the common electrolytes in the body?
Na+
K+
Cl-
88
Where are trace minerals obtained and what are the trace minerals?
Must be obtained from diet
ZISC = Zinc, Iodine, Selenium, Copper
MFCM
89
What are the common minerals in the body? Where can we obtain them from?
PMSIC
Phosphorus - dairy products
Magnesium - meat, fish, veggies
Sulfur
Iron
Calcium - milk
90
Coenzymes are:
A) Organic molecules
B) Inorganic molecules
Organic molecules = often vitamin derived
When bound tightly = prosthetic groups
91
Define Isomer and give the 2 subtypes
Same molecular formula but different structures
Constitutional and Stereoisomers
92
Constitutional Isomers
Same molecular formula that differ in the order of attachment of atoms
93
Enantiomer
Stereoisomers that are nonsuperimposable mirror images
(Diasteriomers = multiple chiral centers)
94
Anomers
Isomers that differ at a new asymmetric C atom formed upon ring closure
95
O-glycosidic bonds and which aa
Bonds created between the anomeric C of a carb and O of an OH
Typically Carb polymers and when polymers are attached to proteins
**SERINE = GalNac** (proteoglycan structure w/ xylose and 2 Galactose) = repeating disaccharides
96
N-glycosidic bonds and aa
Bonds created between the anomeric C of a carb and the N of an amine
Usually when bases are added to ribose to form nucleotides
**Asparagine = GlcNac**
97
Maltose disaccharide consists of what and what type of bond does it form
Glucose-Glucose
alpha-1,4-glycosidic bond
98
What are the common disaccharides and what type of bond do they form
Sucrose, Lactose, Maltose (SLM)
Formed by O-glycosidic bond
99
Sucrose is composed of what monosaccharides and what type of bond formation
Fructose and Glucose
alpha (1,2) beta
100
Lactose is composed of what monosaccharides and what type of bond formation
Glucose and Galactose
beta (1--\>4) alpha
101
Maltose is composed of what monosaccharides and what type of bond formation
Glucose-Glucose
alpha-1,4-glycosidic linkage
102
How to determine whether a sugar is D or L configuration
Whether -OH group furthest from the carbonyl C is left or right
103
What type of linkages does amylose form?
Glucose-Glucose units linked via alpha-1,4-glycosidic linkages
104
What type of linkages does amylopectin form?
Glucose-Glucose components linked via alpha-1,4 with **branching** linkages of **alpha-1,6-glycosidic bonds**
105
List the common polysaccharides w/ their linkages (3)
Starch **alpha-1,4 linkages w/ alpha-1,6 branches**
Cellulose **beta-1,4 linkages**
Glycogen **alpha-1,4 linkages w/ alpha-1,6 branches**
All glucose-glucose
106
Glycogenin
The **nonreducing** end of glycogen that is involved wiht making a primer that's involved in glycogen synthesis and it complexes with a **Manganese**
107
Which vitamin is an important cofactor for glycogenolysis?
B6, pyridoxial phosphate
108
What is the important enzyme utilized for blood clotting?
Gamma-carboxylase
Converts precursor clotting factor into a mature clotting factor
Warfarin inhibits coagulation by inhibiting Vit K reductase
109
Which molecule is least stable? ATP, ADP, AMP
ATP
Therefore, it gives off the most energy
110
Enantiomer example
D-glyceraldehyde and L-glyceraldehyde
111
What are the 5 common metabolically important monosaccharides?
**D**eoxyaldose - DNA
**A**cetylated amino sugars - glycoproteins, glycolipids (cell signaling, cell adhesion, etc.)
**A**cidic sugars - GAGs and proteoglycans
**S**ugar esters - gangliosides in oligodendrocyte
**S**ugar OHs - food additives
112
What are the 3 common disaccharides that are joined by O-glycosidic bond?
Sucrose (alpha1-beta2)
Lactose (beta1-4 bond)
Maltose (alpha1-4 bond)
113
GLUT 1
GLUT 2
GLUT 3
GLUT 4
**Glucose Uptake**
1 - RBCs and brain
2 - main transporter in liver, low affinity
3 - main transporter in neurons
4 - skeletal muscle, heart, adipose tissue
