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KCUMB Biochemistry - Erin > EXAM II Material > Flashcards

EXAM II Material Flashcards

1
Q

Ribonuclease/Deoxyribonuclease

A

Converts long RNA/DNA chain to short RNA/DNA oligomer

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2
Q

Phosphodiesterase

A

Converts RNA/DNA oligomers into nucleotide monophosphates (NMPs) or deoxynucleoside monophosphate (dNMPs)

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3
Q

Nucleotidase*

A

Converts NMPs and dNMPs to nucleosides and deoxynucleosides

Nucleotide –> Nucleoside

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4
Q

Nucleosidase

A

Removes the base from the ribose or deoxyribose

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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

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6
Q

Allopurinol

A

Inhibits the action of Xanthine Oxidase

Prevents the build up of uric acid which can lead to gout

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7
Q

Urate Oxidase

A

Catalyzes the oxidation of uric acid into Allantoin - a soluble compound

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8
Q

Gout symptoms

A

Painful, inflammed joints; mainly effects big toe (metatarsal pharangeal joint); can form cystals bc nonsoluble

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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

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10
Q

Types of organic solvents that lipids are soluble in

A

Ethanol (alcohols)

Oils

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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

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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)

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13
Q

Structure of Triacylglycerols (TAGs)

A

Glycerol backbone with 3 acetyl acid goups

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14
Q

Derivatives of TAGs can serve as:

A

Hormones, Signal Molecules, and Intracellular Messengers

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15
Q

How would you name this from both ends? assume n=4

A
  1. From omega end: omega-3
  2. From carboxy end: cis-delta7
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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

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17
Q

Which FA configuation is most common in the body?

A

Cis (always)

Ex: oleic acid - non ionized

Oletate = ionized

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18
Q

What are the major 3 functional classes of FA?

A

NEFAs

Omega-3s and Omega-6 Essential FA

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19
Q

What are the 2 NEFAs?

A

Palmitic acid (16:0) Hexadecanoic - ionized = palm oil

Stearic acid (18:0) Octadecanoic - ionized = several uses

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20
Q

What enzyme converts RNA to DNA?

A

Ribonucleotide reductase

oxy –> deoxy

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21
Q

List common:

Disaccharides

Oligosaccharides

Polysaccharides

A

Di = sucrose, maltose, lactose

Oligo = glycoprotein, glycolipid

Poly = Glycogen, starch, cellulose

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22
Q

Special features of the archaeon

A

Single-celled organism

  1. Avoids hydrolysis bc it has an ether bond b/w Phosphate head group and glyerol backbone (ROR)
  2. Branched and Saturated (linear) = more resistant to oxidation
  3. Inverted stereochemistry of central C in glycerol backbone
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23
Q

3 major membrane lipids

A

Phospholipids = PGs

Glycolipids = cerebroside

Cholesterol

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24
Q

Components of Phospholipid?

A
  1. Glycerol backbone
  2. 2 FAs (hydrophobic)
  3. Phosphate group = philic
  4. Alcohol = philic
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25
Q

Phosphoglycerol components:

A
  1. Glycerol backbone
  2. 2 Acyl groups (FA) (RCOO)

Unsaturated FA usually occupy C2, Sat = C1

  1. Phosphate + Alcohol
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26
Q

What is the intermediate in forming a number of phospholycerides?

A

Phosphatidate/Diacylglycerol 3-P

Glycerol backbone, 2 acyl/FA, P

Small amounts present in membrane

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27
Q

What are the 5 Phosphoglycerides that are derived from Phosphotidase? What type of bond is formed?

A

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
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28
Q

Components of Sphingolipids

A
  1. Sphingosine backbone
  2. Long, unsaturated hydrocarbon chain bound with double bond
  3. Amino OH (NH3+, 2 OH = all diff Cs on backbone)
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29
Q

Sphingomyelin components

A

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
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30
Q

Glycolipid components

A
  1. Sphingosine backbone
  2. Unsaturated hydrocarbon chain
  3. Amino group
  4. Sugar residue linked to OH (ECM = polar)
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31
Q

Cerebroside Components:

A

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
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32
Q

Why is cholesterol considered a sterol?

A

Contains branched aliphatic side chain of 8-10 C atoms

Contains an OH goup

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33
Q

What type of bonds are associated with the bilayer?

A

Noncovalent

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34
Q

What are the charge distributions along a bilayer membrane?

A

Phobic = negative (ICM)

Philic = positive (ECM)

Membrane is electrically polarized

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35
Q

What are the driving forces of lipid bilayer formation?

A
  1. Hydrophobic Interactions (predominate)
  2. VDW (b/w lipid tails)
  3. Electrostatic (b/w polar heads and water)
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36
Q

List the 3 things that occur due to the hydrophobic interactions of membranes

A
  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
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37
Q

Lipid bilayers have low permeability for:

A

Ions and polar molecules

i.e. Glucose (+)

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38
Q

What type of interactions are peripheral proteins involved with in the lipid bilayer and how can they be removed?

A

H-bonds and Electrostatic

Can be removed via salt or pH changes

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39
Q

List 2 examples of integral membrane proteins?

A
  1. Bacteriorhodopsin (BR)

light-driven proton pump; mainly alpha-helices (most common transmembrane structure bc flexible)

  1. COX 1/PGHS 1 integral protein but not membrane spanning
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40
Q

Function of lipids on lipid bilayer and how are they attached?

A

Consitute/mediate protein-protein interactions and covalently associated with proteins

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41
Q

What 3 modifications do lipid-linked proteins perform on the lipid bilayer?

A
  1. Palmitoylation
  2. Farnesylation
  3. GPI
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42
Q

Palmitoylation

A

One of the lipid-protein modifications

Covalent attachment via thioester bond of FA to a cys residue

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43
Q

Farnesylation

A

Covalent attachment of a farnesyl unit (C15) to C-terminal tetrapeptide (CAAX) with the further addition of a thioether linkage w/ Cys residue

Anchors protein to membrane & protein-protein interaction

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44
Q

GPI Anchor

A

Anchors proteins to outer leaflet of plasma membrane

Common with cell-surface hydrolytic enzyme and adhesions, tethered to cells via GPI

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45
Q

What are the 2 compartments of the mito membrane?

A
  1. Intermembrane space = Oxidative Phosphorylation
  2. Matrix = TCA and FA oxidation
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46
Q

Inner mito membrane is impermeable to:

A

Nearly all ions and polar molecules

47
Q

What is Tm defined as?

A

Rigidity = determined by saturation levels (length)

Tm is also effected by cis/trans bonds; cis = more fluidity (harder to pack together)

48
Q

What determines membrane fluidity?

A

FA composition

Cholesterol content

49
Q

The rate of recovery of fluorescence when using the FRAP technique depends on:

A

The lateral mobility of the labeled component

50
Q

T/F: Cholesterol is found only on the outer leaflet of the membrane lipid bilayer

A

False; present on both inner and outer leaflet

51
Q

Glycocalyx

A

Glycoprotein polysaccharide that lines the cellular membrane

Important for cell adhesion, lymphocyte homing

i.e. vascular cells adhere to blood vessels

52
Q

Glycosylation

A

The addition of carbohydrate to another group on a molecule; usually done on the ECM of the plasma membrane

53
Q

Receptor-mediated endocytosis is done by:

A

Invagination of the membrane which folds in and breaks off forming a vesicle “budding”

54
Q

Another form of receptor-mediated endocytosis is

A

“fusion”

55
Q

What is the postulated mechanism for mito proliferation?

A

Fission; via oligomers; more extensive than “pinching” done by bacteria due to the inner and outer membranes

56
Q

Name the salvage process that occurs in mitochondria

A

Fusion

57
Q

In order for fusion to occur, what type of environment must the mito be in?

A

High GTP levels (high energy)

A large electrochemical gradient across the inner membrane

58
Q

Protein import into mitochondria is done through what type of signal?

A

N-terminal signal sequence = “matrix targeting signal”

Proteins are usually unfolded before entering

59
Q

Under what conditions will ATP be required when a protein needs to be imported into a mito?

A

When being tranported into the matrix (crossing the inner membrane)

60
Q

Example of a polytopic membrane protein

A

GPCR = multiple domains/transmembrane

61
Q

Ionic composition of plasma membranes is determined by ____

A

Protein transporters

62
Q

Types of molecules that can undergo passive diffusion

A

Small

Nonpolar

Uncharged

63
Q

Cells have _______high or low energy when the ionic [gradient] is equal?

A

Low Energy

64
Q

What type of transport is occurring when you have a positive/negative free energy value?

A

Positive = active = not ideal so requires energy

Negative = facilitated = doesn’t require energy

65
Q

What are the Primary Type ATPases?

A
  1. Na+/K+ pump
  2. SERCA
  3. Plasma membrane Ca2+-ATPase (PMCA)
  4. H+/K+ ATPase

All form Aspartate Phosphorus Intermediates

66
Q

What are the differences b/w the P-type ATPases and ABC Transporters

A

In P-type, the phosphate that’s liberated forms a covalent bond on the enzyme and creates an enzyme-phosphorylated intermediate

67
Q

Enzyme of importance in P-type ATPases

A

Aspartate

During ATP hydrolysis, the rxn occurs on its residue

68
Q

What is the mechanism of action of plant steroids/cardiotonic steriods on Na+/K+ pump & what are these inhibitors called?

A

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
Q

Difference between PMCA and SERCA

A

PMCA contains a C-terminal domain (Zaidi’s study)

Both have 10 TM domains

70
Q

What’s the main driving force during the transport of K+ ions in the K+ channel?

A

Repulsion of like charges

71
Q

While most ion channels are tetramers, which channel is a pentamer?

A

Ligand gated channels; ACh receptor; the 5 subunits = pore

72
Q

What type of molecules can pass through gap junctions?

A

Small and hydrophilic (less than 1kDa; sugars, aa, nucleotides) NOT proteins, polysaccharides, nucleic acids

73
Q

What interactions stabilize the double helix of DNA?

A

H-bonds

VDW

Hydrophobic effect

74
Q

What type of bonds are associated with a nucleotide?

A

Beta-glycosidic bond (C1 of sugar and a base)

Ester bond (reduction of the OH on C3 of sugar linked to phosphate)

75
Q

Important feature of creatine phosphate

A

Stored in the brain and quickly releases energy; within seconds

76
Q

ATP features in metabolism

A

Immediate energy source via carbon fuels/breakdown via carbon oxidation

Body houses about 100g

77
Q

Which molecule has the most energy potential? (releases the most amount of energy by its oxidation)

A

Formaldehyde; more reduced, less oxidation, more negative deltaG

78
Q

Which metabolic cycle produces the most ATP?

A

Oxidative Phosphorylation

79
Q

What are the three principal ways in which metabolic processes are regulated?

A
  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
Q

What enzyme digest short and medium-chain FAs?

A

Lingual lipase

81
Q

What enzyme digests medium-chain FAs?

Lingual lipase

Gastric lipase

Phospholipase

Cholesterol esterase

A

Gastric lipase

82
Q

What are the enzymes found in the small intestine? & their functions? (3)

A

Pancreatic lipase = TGs

Phospholipase = Phosphlipids

Cholesterol esterase = Cholesterol esters

83
Q

Which vitamin?

A

Vitamin D; FA derived; Lipid Soluble

Ca2+ & Phosphorus metabolism

Milk, sunlight = Rickets (inadequate bone mineralization)

84
Q

Vitamin?

A

Vitamin A

FA derived

Lipid Soluble

Carrots; Precurser beta-carotene

Night blindness

85
Q

Vitamin?

A

Vitamin E

FA Derived

Lipid soluble

Veggie Oils; muscular dystrophy

86
Q

Vitamin?

A

Vitamin K; FA derivative; lipid soluble

Leafy Veggies; blood clotting

87
Q

What are the common electrolytes in the body?

A

Na+

K+

Cl-

88
Q

Where are trace minerals obtained and what are the trace minerals?

A

Must be obtained from diet

ZISC = Zinc, Iodine, Selenium, Copper

MFCM

89
Q

What are the common minerals in the body? Where can we obtain them from?

A

PMSIC

Phosphorus - dairy products

Magnesium - meat, fish, veggies

Sulfur

Iron

Calcium - milk

90
Q

Coenzymes are:

A) Organic molecules

B) Inorganic molecules

A

Organic molecules = often vitamin derived

When bound tightly = prosthetic groups

91
Q

Define Isomer and give the 2 subtypes

A

Same molecular formula but different structures

Constitutional and Stereoisomers

92
Q

Constitutional Isomers

A

Same molecular formula that differ in the order of attachment of atoms

93
Q

Enantiomer

A

Stereoisomers that are nonsuperimposable mirror images

(Diasteriomers = multiple chiral centers)

94
Q

Anomers

A

Isomers that differ at a new asymmetric C atom formed upon ring closure

95
Q

O-glycosidic bonds and which aa

A

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
Q

N-glycosidic bonds and aa

A

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
Q

Maltose disaccharide consists of what and what type of bond does it form

A

Glucose-Glucose

alpha-1,4-glycosidic bond

98
Q

What are the common disaccharides and what type of bond do they form

A

Sucrose, Lactose, Maltose (SLM)

Formed by O-glycosidic bond

99
Q

Sucrose is composed of what monosaccharides and what type of bond formation

A

Fructose and Glucose

alpha (1,2) beta

100
Q

Lactose is composed of what monosaccharides and what type of bond formation

A

Glucose and Galactose

beta (1–>4) alpha

101
Q

Maltose is composed of what monosaccharides and what type of bond formation

A

Glucose-Glucose

alpha-1,4-glycosidic linkage

102
Q

How to determine whether a sugar is D or L configuration

A

Whether -OH group furthest from the carbonyl C is left or right

103
Q

What type of linkages does amylose form?

A

Glucose-Glucose units linked via alpha-1,4-glycosidic linkages

104
Q

What type of linkages does amylopectin form?

A

Glucose-Glucose components linked via alpha-1,4 with branching linkages of alpha-1,6-glycosidic bonds

105
Q

List the common polysaccharides w/ their linkages (3)

A

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
Q

Glycogenin

A

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
Q

Which vitamin is an important cofactor for glycogenolysis?

A

B6, pyridoxial phosphate

108
Q

What is the important enzyme utilized for blood clotting?

A

Gamma-carboxylase

Converts precursor clotting factor into a mature clotting factor

Warfarin inhibits coagulation by inhibiting Vit K reductase

109
Q

Which molecule is least stable? ATP, ADP, AMP

A

ATP

Therefore, it gives off the most energy

110
Q

Enantiomer example

A

D-glyceraldehyde and L-glyceraldehyde

111
Q

What are the 5 common metabolically important monosaccharides?

A

Deoxyaldose - DNA

Acetylated amino sugars - glycoproteins, glycolipids (cell signaling, cell adhesion, etc.)

Acidic sugars - GAGs and proteoglycans

Sugar esters - gangliosides in oligodendrocyte

Sugar OHs - food additives

112
Q

What are the 3 common disaccharides that are joined by O-glycosidic bond?

A

Sucrose (alpha1-beta2)

Lactose (beta1-4 bond)

Maltose (alpha1-4 bond)

113
Q

GLUT 1

GLUT 2

GLUT 3

GLUT 4

A

Glucose Uptake

1 - RBCs and brain

2 - main transporter in liver, low affinity

3 - main transporter in neurons

4 - skeletal muscle, heart, adipose tissue

KCUMB Biochemistry - Erin (5 decks)

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