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Medicinal Chem and Biochem > Chem > Flashcards

Chem Flashcards

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1
Q

proteins and polypeptides

A

are polymers of aa linked together by peptide bonds thanks to nucleophilic attack by amino group of one aa to carboxyl of other aa

reaction not spontaneous

  • to make it spontaneous;
    1. aa activated by tRNA
    2. forms aminoacyl-tRNA
    3. energy needed provided by hydrolysis of ATP
    4. peptide bond formed is spontaneous
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2
Q

peptides can be divided in

A

oligopeptides - few aa residues
polypeptides - many residues
proteins - more than 10,000

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3
Q

peptides - negative and positive

A

negative - c terminal carboxyl

positive - aa group

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4
Q

how to degrade protein quickly

A
  1. using enzymes
  2. spontaneous + thermodynamically favored BUT kinetically unfavored
  3. peptide bond - stable, broken by enzymes
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5
Q

mutation of proteins

A

carboxyl group is modified

  1. methylated
  2. amidated
  3. carboxyl groups converted to amide group
  4. negative charge lost
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6
Q

carbohydrates

A

biggest source of energy
building blocks for molecules
made of C, H and O and are also called saccharides

types:
monosaccharides - simplest
disaccharides - two mono.
polysaccharides - many mono.

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7
Q

hydrolysis

A

divided 2 mono. using a molecule of water

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8
Q

dehydration

A

the union/combination of two mono. with the loss of H2O

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9
Q

monosaccharide groups

A

many hydroxyl groups attached by chains of 3-8 C atoms
hydroxyl groups are attached to C except carbonyl C

aldehyde groups - aldoses
ketone groups - ketoses

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10
Q

fisher projections - aldehydes

A

top - most oxidized
center - OH and H
bottom - chiral atom

if OH is bonded on left - L isomer (L - left)
if OH is bonded on right - D isomer (D - destra)

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11
Q

most important 6Cs + 5C

A

D-glucose

  • aldohexose
  • building block for disaccharides

D-galactose

  • aldohexose
  • important in the cellular membranes of the brain

D-fructose

  • ketohexose
  • sweetest and only has 3 chiral centers
  • obtained from sucrose
  • important for the production of energy

D-ribose

  • aldopentose (5C)
  • sugar of RNA
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12
Q

hypoglycemia and hyperglycemia

A

hypoglycemia - the level of sugar in the blood is less than 40 because there is an overproduction of insulin

hyperglycemia - can be caused by diabetes [when the pancreas cannot produce enough insulin (diabetes 1) or when cells cannot respond to insulin (diabetes 2)]

normal blood sugar level - 70/90

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13
Q

haworth structure - ketones

A

either:
alpha - OH under anomeric carbon
beta - OH over anomeric carbon

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14
Q

oxidation of mono.

A

they have an aldehyde group and OH

OH can be oxidized to form carboxylic acid

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15
Q

reduction of mono.

A 
reduce carbonyl group 
convert aldehyde into alcohol 
producing alditol (sugar alcohol)
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16
Q

disaccharides

A

formed by 2 mono. bonded by glycosidic bond thanks to dehydration reaction

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17
Q

types of disaccharides

A

maltose

  • made from 2 D-glucose (either alpha or beta)
  • alpha contains hemiacetal group and therefore can interact with alcohols –> acetal group (bond on C4)

lactose

  • made from D-galactose and alpha/beta D-glucose
  • bond formed between C1-C4

sucrose

  • made from alpha-D-glucose and beta-D-fructose
  • bond formed between C1 and C2
  • cannot form an open chain or be ox.
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18
Q

polysaccharides (types)

A

starch
- formed from 2 poly. amylase and amylopectin

amylose

  • made of molecules of alpha-D-glucose bonded by alpha (1-4) glycosidic bond
  • form a coiled structure

amylopectin
- contains same bonds as amylose + alpha (1-6) bonds that allow the protein to be packed in a more condense way

glycogen

  • a polymer of glucose
  • in the liver and muscles and sometimes lungs
  • bonds are the same as amylopectin except bonds 1-6 happen every 10-15 units of glucose

cellulose

  • structural unit of wood and plants
  • formed by linear beta-(1-4) glycosidic bonds (opposite of amylose)
  • OH group cannot react with water thus molecule is insoluble and rigid
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19
Q

lipids

A

organic compounds from biological origins

soluble in organic solvents but insoluble in water thus most of them apolar

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20
Q

functions of lipids

A

energy storage
central components of membrane
produce energy for metabolism
signal molecules

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21
Q

fatty acids

A

long acyl chains with thermal carboxylic function
the longer the chain, the lower the solubility

can have two isomers - cis and trains

  • if H groups are on the same side (cis)
  • if H groups are on the opposite sides (trans)
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22
Q

prostaglandins - eicosanoids

A

derive from arachidonic acid
any of these acids can transform in a prostaglandin through activity of cyclooxyrgenase enzyme - responsible for inhibition and synthesis of prostaglandins

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23
Q

waxes

A

have vegetal or animal origin
esters that form through saturated Fas and long chain alcohols - hydrophobic
protective function

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24
Q

triglycerides

A

ester molecules with OH
glycerol if esterified –> 3Fas with formation of 3 ester bonds
- Fas can be sat. or unsat. or both
used as storage

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25
Q

triglyceride reactions

A
  1. addition of H2 to double bond –> hydrogenated fats
  2. addition of water –> alcohol
  3. hydrolysis of ester bond –> acid and alcohol
  4. oxidation –> aldehyde and acids
  5. saponification –> create soaps
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26
Q

glycerophospholipids

A

similar to triglycerides BUT have an ester linkage to phosphoric acid (thus forms phosphoester bond) in position 3 with an alcohol or aa alcohol

the aa alcohol can be:

  • choline
  • serine
  • ethanol amine
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27
Q

sphingolipids

A

composed of sphingosine (present in brain and nervous tissue)

ceramides - amide bond between amino group that is present in sphingosine and acyl chain

sphingomyelin - amino bond to fatty acid mol. and through ester bond to phosphoric ester of amino alcohol choline

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28
Q

glycosphingolipids

A

contains sugar and are divided in:

  1. cerebrosides - glycosidic linkage between alcohol function of terminal part of sphingosine and alpha anomeric C of either galactose or glucose (cellular recognition)
  2. gangliosides - 2 or more saccharodic units attached to sphingosine, characterized by silica acid presence (receptors)
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29
Q

steroids

A

common core structure composed by three 6-membered rings and one 5

cholesterol - basic core structure with double bond, OH group at position 3 and branched acyl chain at position 17
- maintains fluidity (HDL)

bile salt - derived from cholesterol and secreted in gall bladder
- helps us digest FAs (works as soap)

steroid hormones - synthesized by cholesterol and used to transport chemical messages in our body

cortisone - increases glycemia and synthesis in liver of aa

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30
Q

protein purification - chromatography

A

produce protein
isolation and purification
extraction
purification

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31
Q

protein purification - column chromatography

A

used to separate proteins

  1. stationary (solid porous matrix) and mobile (eluent) phase
  2. eluent poured in stationary phase
  3. protein present in sample is separated (depending on type of stationary phase and interaction)
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32
Q

protein purification - size or gel filtration chromatography

A

stationary phase - porous polymer bead
filtration based on size exclusion technique

  1. each bead that is hydrophilic has different size and molecule may enter or not
  2. also based on function of hydrodynamic radius, size and molecular weight
  3. small molecules take longer to be eluted
  4. after filtration we can attach spectrophotometer to measure absorbance
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33
Q

protein purification - ion exchange chromatography

A

stationary phase - chemically modified in order to have positive or negative charge
method based on interaction of protein with stationary phase

  1. beads are negatively charged when sample is loading proteins (+)
  2. proteins (+) bind with column while (-) will be eluted
  3. to detach + from column, change pH of eluent = change of charge of protein
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34
Q

protein purification - affinity chromatography

A

stationary phase - beads chemically modified with ligand of protein
based on interaction of protein with stationary phase by bio-selective non-covalent binding

  1. when proteins eluted, protein that can be bio-selective, eluent will bind to column
  2. impurities washed out
  3. to detach protein from column change pH or ionic strength or use denaturing agent
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35
Q

protein purification - hydrophobic interaction chromatography

A

stationary phase - beads chemically changed in order to have surface some hydrophobic group
technique based on interaction of hydrophobic regions of a protein with surface of beads

  1. protein with hydrophobic regions will bind to beads
  2. increasing length of hydrophobic group, increase hydrophobicity
  3. protein detached by decreasing salt conc.
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36
Q

dialysis

A

use for protein purification

methods used for separation of proteins from salts

37
Q

electrophoretic techniques

A

used for characterization of protein while chromatography for preparative functions

38
Q

electrophoretic techniques - polyacrylamide gel electrophoresis

A

based on migration of charged proteins in electric field

  1. proteins start to migrate in electric field and 2. migration depends on charge, size and molecular shape
39
Q

electrophoretic techniques - isoelectricfocusing

A

separate proteins as a function of isoelectric point

  1. put a gel into a tube
  2. after an electric current is applied, ampholytes migrate and create different pH along tube generating pH gradient
  3. put proteins at top of sample and protein migrates through gel
  4. migrate until they find their pH corresponding to isoelectric point
40
Q

purification and characterization of proteins - determination of aa sequence

A

edman degradation methods

  1. determine to allow aa composition
  2. need original protein intact
  3. need phenylisothiocynate (PITC)

we can label a protein of 50 aa so if protein is longer it needs to be cut and analyzed fragment by fragment

41
Q

protein denaturing and folding

A

denaturing = unfolding a protein = loss of function

denaturing agents:

  • heat
  • pH
  • solvent
  • urea
  • detergents

monitoring - with fluorescent tryptophan

42
Q

renaturing protein

A

anfinsen’s experiment - renaturing is a spontaneous process

levinthal’s paradox - describe folding of a protein with Molten globule model

  • protein start from disordered structure
  • becomes ordered

folding can be assisted by molecular chaperones
- both need to use ATP

43
Q

ligand

A

molecule that can bind a protein in a reversible way

it can bind to binding site of protein

44
Q

protein functions

A

protein that binds to O2

  • heme group is prostetic group (permanently bonded to protein)
  • O2 is bonded to heme group thanks to iron in it
45
Q

hemoglobin

A

multivalent allosteric homotropic

protein that undergo a conformational change when O2 binds to it

46
Q

multivalent

A

one mol. can bind more than one ligand

47
Q

allosteric

A

binding to O2 at one site can modify structures of others

48
Q

homotropic

A

one mol. of O2 can modify binding of another mol. of O2

49
Q

sequence and structure of aa

A

determine the structure and function of a protein

50
Q

general formula and structure of aa

A

an alpha C attached to:

  • amino group NH2
  • carboxylic group COOH
  • side chain R
  • hydrogen H
51
Q

non-polar –> hydrophobic

A

tends to stabilize proteins’ structure using hydrophobic interaction

  • glycine –> only non chiral –> R group and H
  • alanine –> R group –> methyl group
  • valine –> R group –> isopropyl group CH-(CH3)2
  • leucine –> more hydrophobic than valine –> R group –> isobutyl group (CH3)2-CH-CH2
  • methionine –> one of the 2 sulfur containing aa –> R group –> aliphatic side chain with 4C
52
Q

aromatic

A

relative non-polar (hydrophobic) = can participate in hydrophobic interaction

  • phenylalanine –> R group –> methyl + phenyl
  • tyrosine –> R group –> phenyl group + OH
  • tryptophan –> R group –> indoxyl group C8H7N (cyclic)
53
Q

polar uncharged

A

more soluble in water and contain functional group that can form H bond

  • serine –> R group –> OH and amido group
  • theorize –> R group –> OH
  • cysteine –> R group –> thiol group SH
  • aspartate –> R group –> carboxyl COOH
  • glutamate –> R group –> C3H5O2
  • proline –> R group –> amino group C-N
54
Q

positively charged (basic)

A
  • lysine –> second primary amino group on fourth C in aliphatic chain
  • arginine –> R group –> guanidine group CH5N3
  • histidine –> R group –> imidazole group C3H4N2
55
Q

negative charged - acidic

A

aspartate and glutamate

- both have second COOH but with OH not amino

56
Q

non standard aa

A

aa found in proteins

once protein have been produced in cell, can undergo any modification

57
Q

formation of S-S bond between cysteine residues

A

cysteine has thiol group that undergoes ox. to from S-S with another cysteine molecule in present of oxidant

58
Q

aa are amphoteric

A

can behave as either acid or a base

zwitterionic form - with charges

59
Q

enzyme inhibitor (reversibile inhibitors) - competitive inhibitor

A

molecule that competes against substrate to reach enzyme’s active site

increases Km
does not affect Vmax

60
Q

enzyme inhibitor (reversibile inhibitors) - uncompetitive inhibitor

A

only block processes beyond ES formation
binding site of inhibitor is different from substrate one and can bind to enzyme-substrate complex

both Vmax and Km are changed

61
Q

enzyme inhibitor (reversibile inhibitors) - mixed inhibitor

A

combination of competitive and uncompetitive inhibitor
the binding site of inhibitor is different from substrate one

can increase affinity of enzyme for substrate - uncompetitive inhibition
can decrease affinity for substrate - competitive inhibition

Vmax will decrease

62
Q

enzyme inhibitor (reversibile inhibitors) - non- competitive inhibitor

A

an inhibitor binds to enzyme at location other than active site

Km does not change
Vmax decreases

63
Q

enzyme inhibitor - irreversible inhibitors

A

substance that permanently blocks action of an enzyme

inhibitor and enzyme are bonded with covalent bond

64
Q

enzyme inhibitor - suicide inhibitors

A

inhibitors bind to enzyme’s active site creating irreversible covalent complex

leads to modification of inhibitor and formation of other molecules that react irreversibly with enzyme too

end of process the enzyme’s molecule is useless

65
Q

antibodies

A

are produced by B lymphocytes that differentiate into plasma cells that secrete antibodies into blood

66
Q

antibodies - immunogen

A

compound capable of inducing immune response

67
Q

antibodies - antigen

A

compound recognized by produce of immune response

68
Q

antibodies - hapten

A

compound that can induce an immune response only when couples by carrier protein

BUT after producing antibodies capable to recognize hapten + carrier complex
antibody will be able to bind also to hapten freed from carrier

69
Q

antibodies - antigenic determinant/epitope

A

antibody binding site of antigen

70
Q

antibodies - paratope

A

antigen binding site of antibody

71
Q

immune response

A

response that organism gives against pathogen or foreign compound

cellular response - mediated by cells
humoral response - mediated by secreted antibodies

72
Q

immunoglobuline (antibody)

A 
divalent molecules 
made of 4 chains 
structure not constant 
arms are flexible 
interacts with antibody --> change in conformation of paratope (inducing fitting)
73
Q

CDR

A

in arms of antibodies there are hyper variable regions that allow extensive range of antibodies

74
Q

fragment of antibodies

A

possible to generate fragments by using enzymes

papain claves the S-S so that Fc and one of the two Fab are detached from other Fab - monovalent antibody

pepsin claves C-C so that Fc is removed = 2 Fab - divalent antibody

75
Q

affinity

A

strength of interaction between epitope and paratope

76
Q

avidity

A

strength of overall binding

monovalent have higher affinity
divalent have higher avidity

77
Q

epitopes

A

small part of antigen that binds specific antibody

accessible region
hydrophilic region
flexible region
non=conservated region

78
Q

antibody classification

A 
IgM - represents first response 
IgG - replaced IgM + lower avidity but higher affinity and specificity 
IgA - defense of our mucosa 
IgE - allergic responses 
IgD
79
Q

production of monoclonal antibodies

A
  1. inject mouse with antigen
  2. collect spleen of mouse where B-cells are stimulated to proliferate
  3. fuse cell with myeloma cell
  4. hybridomas
  5. spleen cell dies and myeloma with them
  6. after few days hybridoma comes back
80
Q

select hybridomas we want

A
  1. separate cell
  2. all separate cells will duplicate
  3. immunoassay or acidic fluid
  4. precipitation with ammonium sulfate
    - affinity chroma.
    - ion exchange chroma.
    - gel filtration
81
Q

production of antibodies by phage libraries

A

phage libraries - virus that can infect bacteria

  1. column with immobilized antigen
  2. phages glow into column
  3. all other phages washed away
  4. gather bond phages and amplify it
82
Q

polyclonal and monoclonal application

A
  1. research
  2. in vitro diagnosis
  3. in vivo diagnosis
  4. therapy
83
Q

regulatory enzymes - allosteric mechanisms

A

a ligand binds to one side of mol. resulting in conformational change on other side of mol.

can be positive - increase activity - stabilize active form = curve shift to left

can be negative - decrease activity - stabilize inactive form = curve shift to right

84
Q

regulatory enzymes - covalently modified enzymes

A

enzymes can be activated or deactivated using phosphorylation and dephospho rylation reactions
- where phosphoric group attached or detaches to enzymatic protein

85
Q

phosphorylation

A

reversible
protein kinases are responsible for catalyzing transfer of terminal phosphoric group from ATP onto hydroxyl-containing residue

86
Q

methylation

A

irreversible

remove phosphoric group by using enzyme phosphatase

87
Q

regulatory enzymes - enzymes affected by regulatory proteins

A

protein binds to enzymatic protein

thanks to binding, enzyme activity can be regulated through allosteric mechanisms

88
Q

regulatory enzymes - enzymes activated by proteolytic cleavage

A

enzymes produced in an inactive form
can be activated through proteolytic cleavage operated by another enzyme
regulated by proteolytic cleavage of enzyme precursor

Medicinal Chem and Biochem (1 decks)

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