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Flashcards in 1. Structure Deck (55)
1

Squalene (2)

Triterpene (30 Cs) that acts as precursor to cholesterol

2

Susquiterpenes Carbon Number

15

3

3 MCFAs

Caproic
Caprylic
Capric

4

4 LCFAs (+ C#)

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

5

4 Unsaturated Cis FAs (+ description #s)

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

6

2.2 Essential FAs

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

7

2 Fish Oils

EPA and DHA

8

Plasmalogens (2)

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

9

Platelet-Activating Factor

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

10

Sphingomyelin Structure

Ceramide + Phosphocholine

11

Cerebroside (2)

Neutral glycosphingolipid consisting of Ceramide + Sugar

12

2 Acidic Glycosphingolipids

Sulfatides and gangliosides

13

Maltose

Glucose, glucose alpha-1,4' linkage

14

Lactose

Galactose, glucose Beta-1,4' linkage

15

Sucrose

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

16

2 Reducing Sugars

Maltose and lactose

17

1 Non-Reducing Sugar

Sucrose

18

Ribose Unique Ring Formation

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

19

Glucan

Polysaccharide of D-glucose monomers

20

Starch

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

21

Amylose

Alpha-1,4' glucan

22

Amylopectin (2)

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

23

Cellulose (2)

Dietary fiber, Beta-1,4' glucan

24

Ribonucleoside

Base + D-ribose

25

Ribonucleotide

Base + D-ribose + Phosphate

26

3 DNA Components

1. 2'-deoxy-D-ribose-phosphate backbone
2. 3'-5' phosphodiester linkage
3. 1'-Beta-glycolidic linkage to bases

27

Chargaff's Rule

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

28

5 Structural Properties of DNA

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

Topoisomers

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

30

Prokaryotic vs. Eukaryotic DNA

Proks have circular plasmids whereas euks have linear chromatin

31

DNA Central Dogma

DNA transcribes RNA translates protein

32

3 Differences bw Prok and Euk mRNA

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

33

2d and 3d Representations of tRNA

2d - cloverleaf
3d - L shape

34

Prok Ribosome Sizes (3.3)

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

35

Euk Ribosome Sizes (3.4)

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

36

2 Kinds of Polypeptide Rotation (+ point of each)

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

37

2 Stabilizing Factors of Alpha Helix

1. Main chain H-bonding bw C=O and HN
2. Side chains projecting out

38

3 Destabilizing Factors of Alpha Helix

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

Alpha Helix Structure

60 deg Psi angle gives "coiled" main chain

40

Beta Sheet Structure

150 deg Psi angle gives "extended" main chain

41

Parallel vs. Antiparallel Beta Sheets

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

Loops (2)

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

43

4 Alpha Domain Tertiary Structures

Helix bundles
Globin fold
Homeodomain
Alpha solenoid

44

3 Beta Domain Tertiary Structures

Beta Barrels
Beta Propellers
Immunoglobin fold

45

Helix Bundles

3-4 alpha helices tightly packed in coiled coil fashion

46

Homeodomain

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

47

Globin Fold

Alpha helices (8) tightly packed

48

Alpha Solenoid

Alpha helices arranged in curved pattern that resembles jelly roll

49

Beta barrel

Large antiparallel beta sheet that twists to a closed structure

50

Beta propellers

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

51

Immunoglobin Fold

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

52

2 Components of Salt Bridges

H-bonding and electrostatic attraction

53

Alpha/Beta Barrels (3)

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

Alpha/Beta Twists

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

55

Rossman Fold

Six parallel Beta strands linked to four alpha helices