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Biochemistry > 1. Structure > Flashcards

1. Structure Flashcards

1
Q

Squalene (2)

A

Triterpene (30 Cs) that acts as precursor to cholesterol

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2
Q

Susquiterpenes Carbon Number

A

15

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3
Q

3 MCFAs

A

Caproic
Caprylic
Capric

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4
Q

4 LCFAs (+ C#)

A

Myristic - 14
Palmitic - 16
Stearic - 18
Arachidic - 20

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5
Q

4 Unsaturated Cis FAs (+ description #s)

A

Palmitoleic - 16:1 (9)
Oleic - 18:1 (9)
Linoleic - 18:2 (9,12)
Linolenic - 18:3 (9,12,15)

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6
Q

2.2 Essential FAs

A

Linoleic (omega-6) and linolenic (omega-3)

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7
Q

2 Fish Oils

A

EPA and DHA

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8
Q

Plasmalogens (2)

A

Glycerophospholipids with C1 ether linkage and an unsaturated tail, named phosphatidal instead of phosphatidyl

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9
Q

Platelet-Activating Factor

A

Glycerophospholipid with C1 ether linkage to saturated tail, C2 acetyl linkage, and ethanolamine head

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10
Q

Sphingomyelin Structure

A

Ceramide + Phosphocholine

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11
Q

Cerebroside (2)

A

Neutral glycosphingolipid consisting of Ceramide + Sugar

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12
Q

2 Acidic Glycosphingolipids

A

Sulfatides and gangliosides

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13
Q

Maltose

A

Glucose, glucose alpha-1,4’ linkage

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14
Q

Lactose

A

Galactose, glucose Beta-1,4’ linkage

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15
Q

Sucrose

A

Glucose, fructose Alpha-1,Beta-2’ linkage

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16
Q

2 Reducing Sugars

A

Maltose and lactose

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17
Q

1 Non-Reducing Sugar

A

Sucrose

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18
Q

Ribose Unique Ring Formation

A

Pyranose form most stable in solution but furanose form most preferred in nature

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19
Q

Glucan

A

Polysaccharide of D-glucose monomers

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20
Q

Starch

A

Mixture of amylose (20-30%) and amylopectin (70-80%) alpha-glucans

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21
Q

Amylose

A

Alpha-1,4’ glucan

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22
Q

Amylopectin (2)

A

Alpha-1,4’ glucose chain with Alpha-1,6’ glucose branching

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23
Q

Cellulose (2)

A

Dietary fiber, Beta-1,4’ glucan

24
Q

Ribonucleoside

A

Base + D-ribose

25
Q

Ribonucleotide

A

Base + D-ribose + Phosphate

26
Q

3 DNA Components

A
  1. 2’-deoxy-D-ribose-phosphate backbone
  2. 3’-5’ phosphodiester linkage
  3. 1’-Beta-glycolidic linkage to bases
27
Q

Chargaff’s Rule

A

Amount of A equals amount of T and amount of G equals amount of C in DNA samples

28
Q

5 Structural Properties of DNA

A
  1. Antiparallel double strands
  2. Right-handed helical twist
  3. Phosphate sugar backbone outside w/ (anti)-bases inside, resulting in major and minor grooves
  4. Complementary H-bonded AT and CG base pair planes perpindicular to helical axis
  5. Sequential base pairs stack along helical axis, 10bp per helical turn
29
Q

Topoisomers

A

DNA molecules w/ same number of base pairs that differ in coiling amount

30
Q

Prokaryotic vs. Eukaryotic DNA

A

Proks have circular plasmids whereas euks have linear chromatin

31
Q

DNA Central Dogma

A

DNA transcribes RNA translates protein

32
Q

3 Differences bw Prok and Euk mRNA

A
  1. Proks have polycistronic, euks have monocistronic
  2. Euks have 5’ 7-methylguanosine triphosphate cap
  3. Euks have 3’ poly-A tail
33
Q

2d and 3d Representations of tRNA

A

2d - cloverleaf

3d - L shape

34
Q

Prok Ribosome Sizes (3.3)

A

70S total
50S w/ 23S and 5S
30S w/ 16S

35
Q

Euk Ribosome Sizes (3.4)

A

80S total
60S w/ 28S, 5.8S, and 5S
40S w/ 18S

36
Q

2 Kinds of Polypeptide Rotation (+ point of each)

A

Phi: HN-Calpha rotation - heavily limited
Psi: Calpha-CO rotation - for alpha helices and beta sheets

37
Q

2 Stabilizing Factors of Alpha Helix

A
  1. Main chain H-bonding bw C=O and HN

2. Side chains projecting out

38
Q

3 Destabilizing Factors of Alpha Helix

A
  1. Branching Side Chains from CBeta (V,I,T)
  2. H-bonding side chains compete w/ main chain (S,D,N)
  3. Proline ring has no main chain NH so produces kink of not last in helix
39
Q

Alpha Helix Structure

A

60 deg Psi angle gives “coiled” main chain

40
Q

Beta Sheet Structure

A

150 deg Psi angle gives “extended” main chain

41
Q

Parallel vs. Antiparallel Beta Sheets

A

Parallel: Each AA H-bonds w/ 2 different AAs of adjacent strand
Antiparallel: Each AA H-bonds (twice) w/ 1 other AA of adjacent strand

42
Q

Loops (2)

A

Connect repetitive secondary structure elements, often on protein surface to mediate interactions w/ other molecules

43
Q

4 Alpha Domain Tertiary Structures

A

Helix bundles
Globin fold
Homeodomain
Alpha solenoid

44
Q

3 Beta Domain Tertiary Structures

A

Beta Barrels
Beta Propellers
Immunoglobin fold

45
Q

Helix Bundles

A

3-4 alpha helices tightly packed in coiled coil fashion

46
Q

Homeodomain

A

C-terminal helix roughly perpendicular to N-terminal helix-turn-helix pair

47
Q

Globin Fold

A

Alpha helices (8) tightly packed

48
Q

Alpha Solenoid

A

Alpha helices arranged in curved pattern that resembles jelly roll

49
Q

Beta barrel

A

Large antiparallel beta sheet that twists to a closed structure

50
Q

Beta propellers

A

Blade shaped beta sheets (4 antiparallel strands) arranged toroidally around a central axis

51
Q

Immunoglobin Fold

A

Two layer sandwich of antiparallel Beta strands in two sheets w/ Greek key topology

52
Q

2 Components of Salt Bridges

A

H-bonding and electrostatic attraction

53
Q

Alpha/Beta Barrels (3)

A

Closed parallel 8 Beta sheet structure with interconnecting alpha helices packed on outside of the barrel
One of the most common protein folds
Active site residues always located w/in C-terminal loops

54
Q

Alpha/Beta Twists

A

Open parallel 4-10 Beta sheet structure w/ interconnecting alpha helices packed on both sides of sheet

55
Q

Rossman Fold

A

Six parallel Beta strands linked to four alpha helices

Biochemistry (23 decks)

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