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Second Quarter > Biochemistry Exam 1 Q2 > Flashcards

Biochemistry Exam 1 Q2 Flashcards

1
Q

Carbohydrates

A

Functions: Energy storage and use, structure and components of other compounds

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2
Q

Monosaccharide Structure

A
  • polyhydroxyl with a single aldehyde or ketone
  • All monosaccharides except DHA have at least one chiral carbon, thus many isomers occur
  • most common sugars in nature are D-glucose, D-fructose, D-ribose and D-galactose
  • this is due to photosynthetic and metabolic products
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3
Q

Aldoses

A

There are 8 significant aldohexose molecules we are concerned with.

  • when the -OH differs at a single carbon the isomers are called epimers.
  • glucose and galactose are epimers at C4, glucose and mannose are epimers at C2
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4
Q

Ketoses

A

ketoses use the -ulose suffix while aldose use the -ose suffix
-ketohexose named for natural extract…so fructose from fruit and sorbose from berries of the ash tree

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5
Q

Formation of cyclic sugar in aqueous solution

Monosaccharide

A

sugars are formed from chains of 4 or more.

  1. alcohol attacks a carbonyl
  2. covalent bond is formed between carbonyl and hydroxyl
  3. product is called a hemiacetal if the alcohol attacks an aldehyde, a hemiacetal if the alcohol attacks a ketone
  4. Anomeric carbopn can take on and alpha or beta configuration
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6
Q

Disaccharide Formation

A
  • condensation reaction involves alcohol reacting with the hemiacetal or hemiketal and water is removed
  • the product of the reaction is a ketal or acetal, another name for the bond is a glycosidic link, again it is an alpha link if the OH points down and a beta link if the OH is pointing up
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7
Q

Aldonic Acid

A

oxidation of a carbonyl on an aldose

-glucaronic acid is negatively charged and used to couple to positively charged drugs, such as quinone in drug delivery

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8
Q

Uronic Acid

A

oxidation of C6 which is the terminal carbonyl

  • common chemical modification in carbohydrates of the extracellular matrix
  • can be oxidized as linear or cyclical
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9
Q

Reducing Sugar

A

free anomeric carbon that can be oxidized in the linear form

  • sugars reach equilibrium between linear and cyclic in solution
  • sugar in a polysaccharide can become linear
  • the anomeric carbon produced by the hemiacetal is exposed and it can be reduced
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10
Q

Starch

A
  • Amylose is an a1->4 glycosidic linkage of glucose in a single chain, due to the rotation about the C-O bond and steric hinderance, amylose makes a helical structure at 6 residues per turn
  • Amylopectin has the same linkage of gluse but every 24-30 residues a a1->6 bond occur that cause branching\
  • glycogen is similar to amylopectin but this branching happens mroe frequently at 8-12 residues, this allows for enzymes to more easily attacks the glycogen sugars when needing immediate energy
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11
Q

Cellulose

A
  • is also a homopolysaccharide, but has a b1->4 linkage, this different bond gives a different folding pattern, each residue is 180 rotation from the plane so the polymer is linear
  • several polymers of cellulose will hydrogen bond with each other and create a wall with great tensile strength
  • vertebrates and termites dont have the enzyme to hydrolyze this link but they have a bacteria in the stomach that can break it down
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12
Q

Chitin

A

insect exoskeleton having a b1->4 link like cellulose, but the C2 of glucose has N-acetylamine

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13
Q

Peptidoglycan

A

bacteria cell wall component. repating units of b1->4 N-acetyl glucosamine and N-acetyl muramic acid

  • lysozyme of skin and tears hydrolyze the b1->4 bond
  • lysozyme is also found in bacteriophage to digest bacteria wall for infection
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14
Q

Agarose

A

red algae and seaweed

  • used for capsules of vitamins and drugs
  • biotechnology applications like electrophoresis and microbiology
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15
Q

Our taste senses

A

3 of our 5 taste senses relay flavor via G-protein coupled receptors

  • the transmembrane protein forms a heterodimer to bind substrate
  • Positive Allosteric Modulators can enhance the signaling and thus the sensation, of flavor
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16
Q

Glycosaminoglycans

A
  • unique to animal and bacteria
  • form extracellular matrix
  • negative charges due to chemical modifications of the sugar allows for water retention
  • negative charges serve as electrostatic ligands to proteins
  • rodlike helix that holds cahrges of COO- and SO4- on opposite sides of the helix
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17
Q

Hyaluronan

A

vitreous humor and cartilage

  • absorbing pressure and redistributing water as a way to distribute stress
  • Hyaluronidase is found in pathogenic bacteria such as streptoccocus, staphylococcus, and clostridium species. These bacterias use this enzyme to digest hyaluronic acid as a carbon source and results in pathology
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18
Q

Chrondroitin Sulfate

A

cartilage, tendons, ligaments, aorta

-similar to hyaluronate, but C4 has SO4-

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19
Q

Keratin Sulfate

A

cornea. cartilage, bone, horny structures
- has NO URONIC ACID!
- sulfates variable on the N-acetyl glucosamine
- it is less negatively charged so it will not absorb as much water

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20
Q

Heparan Sulfate

A

is produced by all animal cells

  • sulfate group is variable
  • variable sulfate group allows for variety of protein binding sites
  • glucoronate can be substituted by its epimer iduronate, in which C6 is pointing down
  • heparin is a version of heparan sulfate produced by mast cells
  • heparin binds antithrombin via electrostatic forces and inhibits thrombin, a protease involved in homeostasis
  • heparin has the highest negative charge density of any known macromolecule
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21
Q

Proteoglycan

A

a macromolecule with one or more glycosaminoglycans covalently bound to membrane proteins or secreted proteins

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22
Q

Glycoprotein

A

ogliosaccharide covalently bound to an intracellular or extracellular protein
-are ligands for lectins, proteins that bind to carbohydrates, this means that they are good for cell to cell communication

23
Q

Glycolyx

A

a sugar coating of the cell

24
Q

Functions of proteoglycans and glycoproteins

A
  • protein binding creating stability and used in signal sequencing and communication
  • recruit hormones or other ligans to a cell surface receptor
  • concentrate a ligand and/or receptor at the cell surface
  • hold association of protein such as collagen, fibrin, etc. for tensile strength
25
Q

Syndecan

A

transmembrane proteoglycan

26
Q

Glypican

A

lipid linked proteoglycan

27
Q

Mucins

A

these are O-linked glycoproteins that contribute to the slippery mucus of the glycolyx

28
Q

Linkages of carbohydrates to proteins

A
  1. O-linked - to serine or threonine hydroxyl bound to the anomeric carbon
  2. N-linked - to asparagine amine to the anomeric carbon

-this is how proteoglycans are linked to carbohydrates as well

29
Q

Ganglioside

A
  • sugar attached to the hydrophilic head of a lipid
  • recognized by lectins
  • important for myelin formation
  • important for neuronal signaling
30
Q

Important Reactions

A

Esterification - hexokinase
Glycosidic formation - O-linked and N-links and S-linked
Glucose Oxidase - important enzyme in immune cells for generating H2O2
Hydrolysis - important in digestion
Condensation- important in polymer formation

31
Q

Chemical Properties of Lipids

A

hydrocarbons, reduced state, insoluble in water

  • most fatty acids are even numbers due to synthesis: condensation of acetate (a 2 carbon chain sugar)
  • in blood, free fatty acids combine with amides to form an ester in acid/base reactions, makes it less soluble in water b/c the ionizable oxygen is in a covalent bond
32
Q

Saturated Fat

A
  • the bonds in a saturated fat have free rotation so they form an extended conformation to reduce the steric hinderance
  • multiple saturated fats can pack tightly forming Van Der Waal forces
  • higher melting point due to packing interactions
33
Q

Unsaturated Fat

A
  • double bonds are shorter and more planar, so to reduce the rotation of the C-C such that a kink is formed
  • carbons are pin cis conformation across the double bond
  • melting point is lower
34
Q

Storage Lipids

A

esters of glycerol and fatty acids
- more hydrophobic than glycerol or fatty acid alone because OH from each group react to form a polymer plus water
-C1 is saturated, C2 is unsaturated and C3 is variable
They can then be identified in 2 ways as simple - all fatty acids attached to the glycerol are the same, or, mixed - name the fatty acid attached to the carbon in glycerol

35
Q

Types of Lipid Reactions

A 
Acid catalyzed hydrolysis
Base Catalyzed (saponification)
Lipases - same reaction as in Biochem 1 using the catalytic triad 
Peroxidation
Hydrogenation
36
Q

Lipases

A

ggg

37
Q

Peroxidation

A
  • unsaturated fatty acis exposed to oxygen in the air become rancid
  • rancidity is the break of fatty acids at a double bond due to oxygen radical attack
  • the reaction begins at the methylene adjacent to the double bond
  • the products are small fatty acids that are volatile and lead to foul smell/taste
  • if per oxidation occurs on unsaturated fats of the plasma membrane, the chain reaction leads to lysis
38
Q

Use of antioxidants in Peroxidation

A
  • antioxidants donate an eectron to neutralize a radical
  • most antioxidants are water soluble, vitamin E (tocopherol) is lipid soluble antioxidant that donates the hydrogen of the hydroxyl to lipid radicals
  • tocopherol requires recycling, which is typically done with ascorbate, but can also occur with glutathione, ubiquinol or NAD( P) H
39
Q

Hydrogenation

A
  • converts unsaturated fat to saturated, so vegetable oils are solid at room temp
  • partial hydrogenation allows for soft fat, but also generates trans fats, trans fats are rare in nature and human don’t have enzymes to digest trans fats
40
Q

Phospholipids

A
  • are components of cell membranes because they are amphipathic molecules with fluidity
  • derived from diacylglycerol 3-phosphate, aka phosphatidate
  • C1 is typically saturated, while C2 is unsaturated
  • cells have differing compositions of phospholipids, in part due to lipids as a substrate for enzyme reaction or cell signalling cascade
41
Q

Glycerol

A
  • is a 3 carbone alcohol that a quires a phosphate at carbon 3 and fatty acids at carbons 1 and 2. this structure is phosphatidic acid, and all other glycerophospholipids are derived from it
  • examples of glycerol backbone phospholipids
  • phosphatidylethanolamino, phosphotidylcholine, phosphatidylserine, phosphatidylinositol bisphosphate, cardiolipin
42
Q

phosphatidylethanolamino

A

-phosphatidylethanolamino is important in cytokinesis and a large portion of neural membranes

43
Q

phosphotidylcholine

A

-phosphotidylcholine is dominant on the outer layer of the membrane, lecithin is purified phospholipids. P-choline is the dominant lipid in this preparation

44
Q

phosphatidylserine

A

-phosphatidylserine is on cytoplasmic side of the membrane, aids in learning and memory when a substrate for cello signalling is attached, marker for apoptosis when it flips to exterior of cell.

45
Q

phosphatidylinositol bisphosphate

A

minor membrane lipid, but is a substrate for phospholipase C
PLC makes IP3 to cause calcium flux
PLC makes DAG to activate protein kinase C

46
Q

cardiolipin

A

is dominant in the inner membrane of the mitochondria
structural support of electron transport enzyme
maintains protons in the inter membrane space to create the action potential needs in ATP production

47
Q

Sphingosine lipid backbone

A
  • the roles of sphingolipids is largely unknown, they are all derived from ceramide
  • sphingomyelin is dominant in the schwann cell plasma membrane for myelination of neurones, important as a substrate in neuronal signalling
  • gangliosides are implicated in cell;cell recognition and blood type
48
Q

Cholesterol

A
  • is a membrane component as well as a precursor for hormones
  • 4 fused rings, 3 proximal to hydroxyl are hexanes and 1 pentane ring
  • planar structure
  • synthesized from isoprene
  • Vitamin D3 is not a vitamin but a cholesterol derived hormone
  • specificity of the receptors for steroid hormones are extremely specific because of their similar geometric shapes
49
Q

Polyunsaturated Fatty Acids

A

-w-3 and w-6 are essential acids obtained from diet meaning the body cannot produce them
-they are both essential for health, and are prostaglandin precursors, which either stimulate or inhibit inflammation, depending on the environment or target cell
-the same enzymatic pathways bind to and convert both w-6 and w-3 fats into membrane lipids, which can then be converted to prostoglandins
-it can then bind to a neighbouring cell and stimulates mucus formation, smooth muscle contraction, vasodilation, or inflammation depending on target
-Series 2 prostaglandins are made rom w-6 and activate inflammation.
Series 1 is made for w-6 but is anti-inflammatory
Series 3 is made from w-3 and is anti-inflammatory
-accumulation of w-6 occupy enzymes generating membrane lipids and favours an accumulation of PIP’s

50
Q

Prostaglandin and Pain

A

Prostaglandin E2 is pro-inflammatory and enhances the release of substance P -> Substance P binds to G protein coupled receptors which activates phospholipase C -> Phospholipase C metabolizes inositol 4,5 biphosphate (PIPs) int diacylglycerol (DAG) and inositol 1,4,5 triphosphate (IP3) -> DAG activates protein kinase C, which induces NMDA receptor expression and propagates the pain signal

51
Q

Metabolism Basic Design

A

-multiple enzymes ordered in an assembly line
-economical
flexibility

52
Q

Metabolic Regulation

A
  • biological reactions are mediated by enzymes
  • in general, ATP increases, anabolic reactions are stimulated and catabolic reactions are inhibited
  • as ADP and/or AMP increase, anabolic reactions are inhibited and catabolic reactions are stimulated
  • enzyme regulation highlights the importance of energy coupling. ractionsa are highly regulated to meet real time demand for cellular work
  • enzyme effects = [S], [P], cofactors (vitamins), Km, Vmax and pH
  • regulatory enzymes = heterotropic regulation cutting pathway at beginning or highest energy needing step
  • genetic control in transcription and translation
  • hormonal by regulating blood, cytoplasm and nucleus
53
Q

ATP as energy

A

why is it so popular?

  • intermediate G allows for energy shuttling
  • regulation. one metabolite indicates the energy status of the cell
  • though ATP->ADP + P is energetically spontaneous, phosphoanhydride bonds are kinetically stable. This means ATP is a stable molecule in solution and requires energy to break the bonds.
  • cellular regulation maintains large concentrations of ATP so the equilibrium lies far to the left. holding concentrations above equilibrium allow for greater G values. As ATP levels decrease, the amount of energy decreases, but so does the drive or magnitude of G
  • cells also have variable levels of concentrations to favour greater G values
54
Q

ATP transfer groups

A

Transfer of the gamma phosphate increases the potential energy of the molecule it is transferred to so that it can trade for another one.
Transfer of the beta phosphate increase the potential of the molecule so that it has energy to trade for something else and it is great that gamma because there are 2 phosphates attached
Transfer of the alpha phosphate increases the free energy potential by giving the phosphate adenosine group to the molecule to use to trade

Second Quarter (4 decks)

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