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Biochemistry > Carbs and Lipids > Flashcards

Carbs and Lipids Flashcards

1
Q

What are 3 names for carbohydrates?

A

glycans, saccharides, sugars

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2
Q

Describe the structure of glucose.

A
  • 6 carbons
  • 5 have hydroxy groups, 1 has a carbonyl
    • aldose sugar
  • All but C1 and C6 are chiral, 4 stereocenters, 24 = 16 conformers for a 6 carbons sugar
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3
Q

What conformer of glucose exists in our body?

A

D - glucose

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4
Q

How do you identify D and L glucose?

A
  • look at carbon #5 (furthest from carbonyl)
  • observe if it looks like D-glyceraldehyde or L-glyceraldehyde
    • OH on right = D
    • OH on left = L
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5
Q

What are epimers?

A

sugars that differ by stereochemistry at 1 carbon

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6
Q

What is an aldose?

A

a sugar that has an aldehyde on the end

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7
Q

What is a ketose?

A
  • a sugar that has a ketone instead of an aldehyde
  • 1 less chiral center
  • 23 - 8 possible isomers
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8
Q

What two functional groups react in aldoses? (To cyclize)

A

alcohol + aldehyde react to form a hemiacetal

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9
Q

What two functional groups react in ketoses? (To cyclize)

A

alcohol + ketone react to form a hemiketal

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10
Q

How can you identify R or S configuration?

A
  • look at C2
  • R = OH on right, down on ring
  • S = OH on left, up on ring
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11
Q

How are the carbons numbered in a ring / linear glucose?

A
  • top to bottom 1 - 6 linear
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12
Q

How does glucose cyclize

A
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13
Q

How does fructose cyclize?

A
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14
Q

What is the anomeric carbon?

A
  • the carbonyl carbon
    • may be alpha or beta
    • alpha = below the ring
    • beta = aBove the ring
  • this is called the configuration of the anomeric center because interconversion requires bond breaking
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15
Q

Describe the alpha and beta anomers of glucose. What percent of each exists?

A
  • alpha and beta forms freely interconvert - the aldol reaction is a very reversible process (glucose is constantly changing between ring and linear forms)
  • D-glucose is 63% beta and 37% alpha
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16
Q

What is required for interconversion between chair conformers?

A
  • interconversion does not require bond breaking (conformations)
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17
Q

Why is beta more stable?

A
  • in the chair conformation the beta version (aBove) is more stable because the bulky groups are equatorial
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18
Q

How are sugars connected?

A

Glycosidic linkages - bonds connecting anomeric carbon to an alcohol oxygen

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19
Q

How does a glycosidic linkage change a sugar?

A
  • when a glycosidic linkage forms you can no longer convert alpha and beta
  • when you can interconvert this is called a reducing sugar
  • When you can’t interconvert this is a non-reducing sugar
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20
Q

How do you name a glycosidic linkage?

A
  • glucose (β/α) (1-4) glucose
  • 1 is the anomeric carbon, the second number is the number of the c it is bonded to
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21
Q

What is lactose?

A
  • galactose β(1 - 4) glucose
  • disaccharide
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22
Q

What is lactase?

A
  • β-galactosidase enzyme that cleaves β(1-4) linkage in lactose to break it down lactose
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23
Q

What is cellulose?

A
  • 15,000 glucose units polymer
  • glucose β(1 - 4) glucose
  • hydrogen bonding network, strong water insoluble
  • structural component of plants
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24
Q

What breaks down cellulose?

A

herbivores produce cellulases to break it down

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25
Q

What is chitin?

A
  • structural polysaccharide found in the exoskeletons of invertebrates
  • glcNac β(1 - 4) glcNac
  • GlcNAc = N-acetylglucosamine
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26
Q

What is GlcNAc?

A

N-acetylglucosamine

  • hydroxyl group on carbon 2 is replaced with an amide
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27
Q

What is starch?

A
  • polymer for glucose storage in plants
  • α-amylose + amylopectin
    • α-amylose - linear Glc - α(1-4) - Glc
    • amylopectin - branched Glc - α(1-4) and α(1-6) - Glc
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28
Q

What is glycogen?

A
  • polymer for glucose storage in plants
  • similar to amylopectin, but with increased branching
  • allows for faster degradation than a linear polymer
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29
Q

What are GAGs?

A
  • glycosaminoglycans
  • form a gel-like matrix in the extracellular space (eg around connective tissue)
    • they create a really negatively charged network because it is sulfated
  • Chondroitin - joint relief
  • Heparin - inhibits blood coagulation
    • made of Iduronic acid and GlcNAc
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30
Q

List some polysaccharides.

A
  • lactose, cellulose, chitin, glycogen, starch, glycosaminoglycans
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31
Q

What are the 3 types of glycogonjugates?

A
  • proteoglycans - mostly carbs
  • peptidoglycans - mostly carbs
  • glycoproteins - mostly proteins
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32
Q

What are proteoglycans?

A
  • mostly glycans
  • found in our extracellular matrix
  • highly charged (have sulfated sugars often GAGs)
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33
Q

What are peptidoglycans?

A
  • majority carbohydrates, found in bacterial cell wall
  • they are what is stained in gram positive bacteria
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34
Q

What are gram positive/gram negative bacteria?

A
  • Gram positive - bacterial cell wall has no outer membrane, peptidoglycans are stained in a gram stain
  • Gram negative - bacterial cell wall has an inner and an outer membrane, with a thin layer of peptidoglycans in the middle, this layer is not stained in a gram stain
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35
Q

Describe the structure of peptidoglycans.

A
  • GlcNAc β(1 - 4) MurNAc (N-acetyl Muraminic acid)
    • repeats this disaccharide unit
  • peptide is attached via amide linkage to the carboxyl off of 3’C of MurNAc
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36
Q

What process makes bacterial cell walls protective?

A
  • peptide crosslinks of peptidoglycans
  • peptide crosslinks prevent glycans from sliding across each other, this makes bacterial cell walls protective
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37
Q

What forms the glycopolymer in peptidoglycans?

A

transglycosylase

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38
Q

What forms peptide crosslinks in bacteria?

A

transpeptidase

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39
Q

What are glycoproteins and what are the types?

A
  • made of mostly protein with some sugars added
  • may be N-linked or O-linked
40
Q

What is common between N-linked and O-linked glycoproteins?

A
  • they are secretory proteins
  • there is diversity in what sugars are attached
41
Q

Describe N-linked glycoproteins.

A
  • sugar is β-linked to Asn (asparagin)
  • glycosylation occurs within a consensus sequence
    • N - X - S/T (must be one aa away from an S/T, X can be any aa except proline)
  • occurs in the lumen of the ER, co-translational, as it is threaded through the ribosome
42
Q

Describe O-linked glycoproteins

A
  • sugar is α linked to serine and threonine
  • there is no consensus sequence
  • occurs in the golgi
  • sugars are added one at a time using UDP- sugar donors
43
Q

Describe specifically how N-linked glycoproteins are added.

A
  • 14 unit oligosaccharide is synthesized on a lipid donor
  • transferred (en bloc = linked together) to Asn
  • 14- sugars are trimmed
  • other sugars are added
44
Q

What are the roles of sugars on proteins?

A
  1. dictate protein folding - structure
  2. shield protein from proteolysis - stability
  3. mediate recognition events - lectins are proteins that bind carbs - cell-cell communication
  4. antigenic determinants - blood type
45
Q

Describe the antibodies and antigens for each blood cell type.

A
46
Q

What class of antibiotics is penicilin? Describe how this class functions.

A

β - lactam

  • they are covalent inhibitors
  • transpeptidase cant form cross-links, and this significantly weakens the cell wall
47
Q

What is the general goal of antibiotics?

A

to target something in a bacterial cell that is not present in our cells - (cell wall!)

48
Q

How do β-lactam antibiotics function?

A
  • transpeptidase attacks the amide bond of a β-lactam instead of the amide bond in D-ala D-ala (glycoproteins)
  • this reaction has slow hydrolysis
  • Tpase is trapped by β-lactam and unable to performed peptide cross-links
  • weakens bacterial cell wall
  • cell death
49
Q

How is β-lactam resistance introduced?

A
  • bacterial cells produce β-lactamase which opens the ring on β-lactams
  • Transpeptidase does not bind to the ring opened product
50
Q

How do we overcome β-lactam resistance in bacteria?

A
  • treat people with a cocktail of antibiotics including β-lactamase inhibitors
  • people often treated with Augmentin
    • clavulanic acid - β-lactamase inhibitor
    • amoxycilin - β-lactam
51
Q

What is vancomycin?

A
  • antibiotic binds to substrate D-ala D-ala,
  • blocks the access of T-pase through capping D-ala, D-ala with 5 H-bonds
  • T-pase is unable to form crosslinks
  • weakened cell wall, cell death
52
Q

What is the peptide chain attached to in a peptidoglycan?

A
  • peptide sequence is attached via an amide linkage to the carboxyl off of the 3’C of MurNAc
53
Q

List the 5 genes involved in vancomycin resistance.

A
  • Van R - transcription factor - activates VanHAX
  • Van S - cell surface receptor for vancomycin
  • Van H - synthesizes D-lactate from pyruvate
  • Van A - couples D-lac + D-ala
  • Van X - cleaves and destroys D-ala - D-ala
54
Q

Describe lipids and biological membranes. What are some characteristics of these molecules?

A
  • not polymers
  • aggregate - non-covalently
  • large structural variability
  • hydrophobic
  • low water solubility
55
Q

How do lipids aggregate?

A

non-covalently

56
Q

What are some functions of lipids?

A

membrane, energy stores, signaling

57
Q

What are 7 types of lipids?

A
  1. Fatty acids
  2. Triaglycerols /triglycerides
  3. Glycerophospholipids
  4. Sphingolipids
  5. Steroids
  6. Isoprenoids
  7. Eicosanoids
58
Q

Describe fatty acids.

A
  • basic component of a lipid
  • carboxylic acid with long hydrophobic chain
  • may be saturated or unsaturated
  • 12:4
  • 12 carbons, 4 double bonds
59
Q

What is common to all natural fatty acids?

A
  • cis double bonds
  • trans-fats not natural
60
Q

Describe a saturated fatty acid.

A
  • C20:0 - no double bonds, “saturated” with H
  • melting point increases as length increases
  • Higher mp = better packed together
61
Q

Describe an unsaturated fatty acid.

A
  • kinks in the structure - less efficient packing
  • lower mp
  • C20:4 has a lower mp than C20:0
62
Q

Describe triacylglycerols/triglycerides.

A
  • energy stores
  • metabolizing lipids = slower, but more efficient
  • fatty acid triesters of glycerol
  • can have 3 fatty acids attached
63
Q

What are glycerophospholipids?

A
  • major component of membranes
    • glycerol + phosphate + fatty acids
64
Q

What breaks down glycerophospholipids?

A

phospholipases

PLA2, PLAC, PLAD

65
Q

What is the structure of glycerophospholipids?

A
66
Q

What are sphingolipids? What do they form?

A
  • contain a sphingosine (shown below)
  • combine with an N-acyl fatty acid (fatty acid bound to the NH3 of sphingosine) to form ceramides
67
Q

What are ceramides?

A
  • Made of a sphingosine and an N-acyl fatty acid
  • Ceramide + phosphocholine = sphingomyelin (main component of myelin sheath)
  • Ceramide + sugar = cerebroside
    • Ceramide + oligosaccharide = ganglioside (important for cell- cell communication)
68
Q

Describe the function of gangliosides.

A
  • the lipid portion is embedded in the membrane and the oligosaccharide remains on the outside of the cell (this is how they are involved in cell-cell communication)
69
Q

Describe the structure of steroids.

A
  • four fused non-planar rings
  • -one steroids have a carbonyl on A
  • -ol steroids have hydroxyl on A
70
Q

What is an important steroid?

A

cholesterol

71
Q

describe cholesterol.

A
  • makes up 40% of our plasma membrnes
  • amphiphilic - weakly
  • more rigid than other membrane lipids (causes a less fluid membrane)
  • makes up steroid hormones
72
Q

What are 4 things derived from cholesterol?

A
  • Steroid hormones:
    • cortisol/hydrocortisone - inflammation
    • aldosterone - water excretion by kidneys
    • androgens/estrogen - sexual development
    • vitamin D
73
Q

How is Vitamin D derived?

A
  • Ergosterol/Cholesterol converted non-enzymatically by UV irradiation to Vitamin D2/D3
  • Converted to active vitamin D by enzymatic hydroxylation
74
Q

What are isoprenoids?

A
  • made of 5 carbon unit (isoprene)
  • ubiquinone
  • Vitamin A/retinol - eyephotoreceptors
  • Vitamin K - blood clotting
  • Vitamin E - antioxidant
75
Q

What is an isoprene?

A
76
Q

What are eicosanoids?

A
  • derived from arachidonic acid
  • Eg: Prostacyclin, prostaglandin, thromboxanes
  • Role in inflammation
77
Q

What is important for eicosanoid synthesis and a drug target?

A

PGH2 synthase, a cycloxygenase enzyme (COX enzyme)

78
Q

What do NSAIDS target?

A

inhibit cox enzymes, reduce prostaglandin production (an eicosanoid) , reduce inflammation

79
Q

What are NSAIDS? What are examples?

A
  • Non-steroidal anti-inflammatory drugs
  • aspirin, ibuprofen, naproxen
80
Q

What are the cox enzymes?

A
  • COX 1 - constituitively expressed, found in stomach lining, protects from stomach acid
  • COX 2 - expressed at sites of inflammation, directly involved in pain + inflammation
81
Q

Describe an attempt to overcome NSAID side effects.

A
  • aspirin, ibuprofen, naproxen - cox 1 & 2 inhibitors cause stomach ulcers if taken for too long
  • Merck developed Vioxx - cox 2 inhibitor - increased heart attacks
82
Q

What do single tailed lipids form?

A

micelles

83
Q

What do double tailed lipids form?

A

phospholipid bilayers, liposomes

84
Q

What are liposomes?

A
  • solvent filled vesicle
  • bilayer
  • our cells are giant liposomes
85
Q

What are the two types of diffusion within a bilayer?

A
  • transverse - flip-flop across, rare, requires enzymes, energetically expensive
  • lateral - in plane, very common
86
Q

Describe fluidity of bilayer.

A
  • interior in constant motion
  • fluidity is temperature dependent
  • cholesterol decreases membrane fluidity
87
Q

What is an important temperature for membrane fluidity?

A
  • transition temperature - temp below which the bilayer turns into a gel-like solid
88
Q

What are 3 types of membrane proteins?

A
  • integral, lipid-linked, peripheral
89
Q

Describe integral membrane proteins.

A
  • associate tightly with membrane
  • have a transmembrane and a soluble region
    • tm may be alpha helix or beta sheet
    • beta sheets form beta barrels which form channels or pores
      • Porins - OmpF is a beta barrel trimer
90
Q

How can you predict the tm of an integral protein?

A
  • free energy of transfer of water of primary sequence aas
  • amount of energy required to transfer from hydrophobic to hydrophilic environment
    • more energy = more hydrophilic
    • >85 hydrophobi
    • Ile, Leu, Val, Gly
91
Q

What are lipid linked proteins? What are 3 types?

A
  • covalently linked to lipid which anchors to membrane
  • prenylation, fatty acylation, gpi-linkers
92
Q

What is prenylation?

A
  • an isoprene is attached to a cys in a CXXY motif at the C-term
  • this is an ester linkage
93
Q

What is fatty acylation?

A
  1. Myristoylation - amide linkage at an N-term glycine
  2. Palmitoylation - thioester formed at cysteine resideu
94
Q

What are GPI-linkers?

A

have hydrophobic groups attached that anchor these proteins

95
Q

What are peripheral membrane proteins/

A
  • H-bonding or electrostatic interactions
  • can be easily dissociated from the membrane

Biochemistry (12 decks)

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