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Biochemistry > Biochemistry - Amino Acids, Proteins > Flashcards

Biochemistry - Amino Acids, Proteins Flashcards

1
Q

Primary (alpha) amino acids

A

all amino acids (except proline)

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2
Q

imino acid

A

proline, side chain connected to amino group

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3
Q

hydrophobic

A

non-polar, mostly c-h bonds, electrons equally distributed

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4
Q

hydrophilic

A

polar, o-h bonds, asymetric distibution of charge

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5
Q

hydrophobic effect

A

formation of the hydrophobic core in inside of proteins is a major force behind the folking of globular proteins

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6
Q

hydrogen bonds

A

sharing a h-atom between two electronegative groups, present in biomolecules, individually weak, but strong in aggregate

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7
Q

selenocystine

A

considered 21st protein, not encoded in genome

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8
Q

buffer

A

a weak acid/conjugate base pair, neutralizes addes acids or bases, maintains constant pH aroung the pKa

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9
Q

peptide bond

A

CO-NH and a pepide, formed when a carboxylix acid condenses with a Nitrogen bond and releases a water.

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10
Q

residue

A

an amino acid incorporated as part of a peptide or protein

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11
Q

peptide bond characteristics

A

partial double bond, rigid and planar, trans configuration, uncharged and polar, participate in hydrogen bonds.

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12
Q

secondary structure

A

a-helix, b-sheet, loops. Local folding of polypeptide backbone.

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13
Q

a-helix

A

hydrophobic residues packed in inside, two or three can combine to form a coiled-coil. Versile structure, may contain polar or nonpolar residues, depending on locatino of helix.

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14
Q

B-sheet

A

extended region where polypeptide chains lie next to one another. Each region called a strand. Stablized by inter-strand hydrogen bonds.

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15
Q

loop

A

non repeating, fixed structure within a protein. Serves as a connecting region, contains B-strangs composed of 4-5 amino acids.

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16
Q

motif

A

recognizable folding pattern involving two or more elements of a 2ndary structure and the connections between them. (super-secondary structure)

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17
Q

tertiary structure

A

folding and packing together of srtucture to give protein its function.

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18
Q

domains

A

stable structural elements within a protein that have a specific function by themselves. Eg vitamin h binding domain that will binf vitamin h.

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19
Q

protein families

A

proteins with similar domains that have related functions

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20
Q

quaternary structure

A

association of proteins into multi-subunit proteins.

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21
Q

UDP-GLUCOSE EPIMERASE

A

makes udp-calactose from udp-glucose

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22
Q

Enantiomers

A

mirror images of eachother (D and L). D is Natural, l in laboratory. Identical chemical characteristics.

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23
Q

mutarotation

A

change in the optical rotation because of the change in the equilibrium between two anomers, when the corresponding stereocenters interconvert.

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24
Q

a and b anomers

A

cyclical ring forms, alpha is below aldehyde group, beta on same side.

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25
Q

Glycation

A

non-enzymatic reaction of the aldehyde and ketone groups in sugars with amino groups in proteains to initially yield Schiff bases. Then undergo further chemical reactions such as oxidation to produce ‘advanced glycation end products’ or AGEs.

26
Q

schiff base

A

a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl oralkyl group. R1R2C=NR3, where R is an organic side chain, stable imine.

27
Q

glycated hemoglobin

A

a form of hemoglobin that is measured primarily to identify the average plasma glucose concentration over prolonged periods of time. non specific, caused by linear glucose. higher amounts of glycated hemoglobin, indicating poorer control of blood glucose levels, have been associated with cardiovascular disease, nephropathy, and retinopathy. Monitoring HbA1c in type 1 diabetic patients may improve outcomes.

28
Q

glycosylation

A

specific, enzymatic, occurs in ER and Golgi. Addition of a polysacchride and two proteins or two lipids. enzymatic process that attaches glycans to proteins, lipids, or other organic molecules. This enzymatic process produces one of the fundamental biopolymers found in cells (along with DNA, RNA, and proteins). A form of co-translational and post-translational modification.

29
Q

glycation

A

Non-enzymatic, single linear glucose, typically reduces physiological function. covalent bonding of a protein or lipid molecule with a sugar molecule, such as fructose or glucose, without the controlling action of an enzyme.

30
Q

Aldehyde

A

most reduced form of alcohol

31
Q

Oxidized sugars (sugfar acids)

A

sugars can be oxidized at the aldehyde carbon to form an acid. They are negatively charged in physiologically pH.

32
Q

glucoronic acid/glucoronate

A

commonly added/conjugated onto hydrophobic molecules in the liver in otder to make the molecule more hydriphillic/polar, thus more soluble and exccretable from the body.

33
Q

Reduced sugars (sugar alcohols)

A

sorbitol

34
Q

sorbitol

A

results of glucose reduction, also known as glucitol, is a sugar alcohol, which the human body metabolizes slowly. It can be obtained by reduction of glucose, changing the aldehyde group to a hydroxyl group.

35
Q

Glycosaminoglycans (GAGs)

A

long unbranched polysaccharides consisting of a repeating disaccharide unit. The repeating unit (except for keratan) consists of an amino sugar (N-acetylglucosamine or N-acetylgalactosamine) along with a uronic sugar (glucuronic acid or iduronic acid) orgalactose.[3] Glycosaminoglycans are highly polar and attract water. They are therefore useful to the body as a lubricant or as a shock absorber (joints).

36
Q

Glycosides

A

a molecule in which a sugar is bound to another functional group via an enzymatic reaction.

37
Q

glycosidic bonds

A

A type of covalent bond that joins a carbohydrate (sugar) molecule to another group. Human glycosidases are specific for ONLY for O and N bonds..

38
Q

fatty acid

A

a carboxylic acid with a long aliphatic tail (chain), which is either saturated or unsaturated. usually derived from triglycerides or phospholipids.

39
Q

trans fatty acids

A

firned during the partial hydrogenation of vegetables oils. Aidpose tissue, is about 5%.

40
Q

aldoses

A

An aldose is a monosaccharide (a simple sugar) that contains only one aldehyde (-CH=O) group per molecule. it has a carbonyl group at the end of the carbon chain instead of in the middle.

41
Q

Sucrose

A

glucose- fructose

42
Q

Lactose

A

galactose-glucose

43
Q

Maltose

A

glucosyl-a(1->4)glucose, from amylose as well as amylopectin digestion

44
Q

Isomaltose

A

glucose-a(1->6)- glucose,from amylopectin starch or glycogen digestion.

45
Q

polar/charged R-groups

A

arginine, aspartic acid (or aspartate), glutamic acid (or glutamate), histidine, lysine.

46
Q

non-polar R groups

A

alanine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, and valine

47
Q

polar/uncharged

A

glycine, serine, cysteine, threonine, tyrosine, asparagine, and glutamine.

48
Q

Hydrophobic Interactions

A

Non-polar side chain interactions

49
Q

a-helix

A

spiral of 3.6 amino acids, H-bonding occurs n+4 peptide bonds away, r-groups directed outward.

50
Q

coiled-coil

A

two a-helix combine with non-polar R-groups formingthe core.

51
Q

Alpha chain

A

3 a-helix combination ex: collagen

52
Q

B-sheets

A

pleated and riectional, parallel and anti paralell

53
Q

Loops

A

Non random, non repeating, no rotation, 4-5 AA residues per turn.

54
Q

Super Secondary Structure (motifs)

A

Combination of multiple elements of secondary structures.

55
Q

Conserved sequences

A

Non-identical sequences w/ similar functionality

56
Q

Tertiary Structure

A

Combination of secondary structures that are stabilized via covalent bonds and non-covalent bond. Globular or Fibrous.

57
Q

Quaternary Structure

A

Association of multiple Tertiary structures. Dimers, trimers, & tetramers. E.g., hemoglobin is a tetramer.

58
Q

Protein Folding

A

Unfolded proteins can partially fold into intermediates that will retain partly correct sequences. Partly correct sequences are at risks for creating insoluble aggregates due to exposed hydrophobic regions.

59
Q

X-ray crystallography

A

Used to examine proteins in crystal form

60
Q

Nuclear Magnetic Resonance

A

Examine small proteins (Less than 200 amino acid residues); doesn’t require crystal structure

61
Q

Cryo-electron microscopy

A

Examines very large proteins

62
Q

Sickle Cell Anemia

A

Point mutation causes the 6th amino acid of the Hemoglobin β-chain, Glutamic Acid, to be replace by Valine. Glutamic acid si polar, and side chain faces outwards, whereas valine is non-polar and its side chain faced inward. Effect: polymerization of Sickle Cell Hemoglobin (HbS) into fibrous form, causing low oxygen levels and blood vessel blockage.

Biochemistry (12 decks)

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