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Year 1 - Chemistry > Biological Molecules > Flashcards

Biological Molecules Flashcards

1
Q

What are the 4 important functions of proteins in the body?

A

Protection, structure, signals and reactions.

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2
Q

What does an alpha amino acid mean?

A

The amino group (NH2) is joined to the first carbon next to the carboxyl group. Almost all amino acids in living systems are alpha.

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3
Q

What are the 2 functional groups in amino acids?

A

Carboxyl and amine/amino.

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4
Q

What is a zwitterion?

A

A species that contains both positive and negative charges but has no overall charge. Many amino acids are zwitterions meaning they can act as both acids and bases (amphoteric).

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5
Q

What is the isoelectric point (pl)?

A

The pH at which the amino acid is balanced between anionic and cationic forms and is primary in the zwitterionic (neutral) form.

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6
Q

Are all natural amino acids L or D? Does this mean they are all S or R chirality?

A

L. They are all S chirality except glycine which is chiral and cysteine which is R.

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7
Q

What is the hydrophobic effect?

A

Causes the hydrophobic side chains to be clustered in the interior of the protein. Major driving force for protein folding.

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8
Q

Are glycine, alanine, serine and threonine small, medium or large? Hydrophobic or hydrophilic?

A

Small. Hydrophilic.

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9
Q

Are cysteine, valine, isoleucine, lecucine, proline, phenylalanine, tyrosine, methionine and tryptophan small, medium or large? Hydrophobic or hydrophilic?

A

Medium/large. Hydrophobic.

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10
Q

What are the 3 polar amino acids?

A

Asparagine, glutamine and histidine.

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11
Q

What are the 2 acidic amino acids?

A

Aspartic acid and glutamine acid (both hydrophilic).

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12
Q

What are the 2 basic amino acids?

A

Lysine and arginine (hydrophilic).

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13
Q

What is umami?

A

A common amino acid with a savoury taste also called monosodium glutamate. Important for cells osmotic balance.

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14
Q

How are proteins formed from amino acids?

A

In a dehydration/condensation reaction where the amino group of one amino acids forms a peptide bond to the carboxyl group of another amino acid. They are then referred to as amino acid residues.

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15
Q

What dipeptide does phenylalanine make?

A

Aspartame. People who cannot synthesis this reaction have phenylketonuria. A build up of The causes mental retardation if not discovered early.

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16
Q

How do we write the primary structure of a protein?

A

From the N terminus to C terminus, either as single letters or in 3 letters.

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17
Q

What role do hydrogen bonds play in protein structure?

A

They stabilise secondary structure by forming between the negatively charged O in C=O and the positively charged H in N-H.

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18
Q

What are salt bridges?

A

Strong interactions between charged amino acid side chains that can stabilise peptide and protein structures. Not common.

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19
Q

What are disulphide bridges?

A

Covalent bonds/bridges between the S-H groups of cysteine. Prialt (pain killer) has 3.

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20
Q

Why do proteins fold?

A

Because they are more stable in their folded/native state. They only remain folded in a narrow range of conditions of pH, salt concentration and temperature. Misfolding can lead to diseases such as Alzheimers.

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21
Q

What can the folding pattern of a protein be described by?

A

The angles of rotation around the bonds in the main chain.

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22
Q

What must protein structures achieve in the secondary structure?

A
  1. Low energy conformations of individual residues.
  2. Hydrogen bonding
  3. Formation of compact and well packed structures.
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23
Q

What is the alpha helix?

A

The pattern of hydrogen bonding is NH to C=O. Phi is -57 and psi is -47. Peptide bond is trans. 3.6 residues per turn(n). Displacement (d) between successive residues along the helix axis is 1.5 A. Distance along the helix axis per turn (pitch, p) is 5.5A. P=n x d.

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24
Q

What is the antiparallel B-sheet?

A

Has phi of -139 and psi +35. Peptide bond is trans. 2 residues per turn (n). Displacement (d) between successive residues along the helix axis is 3.4 A. Distance along the helix axis per turn (pitch, p)is 6.8 A.

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25
Q

What is the parallel B-sheet?

A

Phi -119 and psi +118. Peptide bond is trans. 2 residues per turn (n). Displacement between successive residues along the helix axis is 3.2 A. Distance along the helix axis per turn (the pitch, p) is 6.4 A. The strands which form the B-sheet may be far apart in the actual protein structure.

26
Q

What is a B-turn/reverse turn?

A

Often occurs between 2 antiparallel B-sheets. The chain doubles back on itself. Contains 3-4 amino acid residues. Stabilised by hydrogen bonds occurring between the carbonyl oxygen of one amino acid residue and the amend of the reside 3 places further along the chain.

27
Q

What does amino acid propensity mean?

A

The tendency for any amino acid to appear in a secondary structure type. Propensity values >1 mean a residue shows a preference for that secondary type and values <1 mean the residue does not favour that structural type. These values can be used to predict structural types of a protein.

28
Q

What is amyloid-B thought to be involved in?

A

Alzheimers.

29
Q

What does allostery mean?

A

A conformational change triggered by the binding of a molecule to a protein.

30
Q

What is the zinc finger motif?

A

Found in many DNA binding proteins. Conserved residues bind to zinc(II) and hold the protein in characteristic shape. Fits into the major glove of DNA which affects the expression of DNA encoded genes.

31
Q

What are monosaccharides?

A

The simplest CHO, cannot be broken down anymore. An example is glucose which can be open-chain or cyclic (most are cyclic).

32
Q

What do the terms aldose, and ketone mean?

A

Aldose - If the C=O is attached to terminal carbon in the chain (e.g. glucose).
Ketose - If the C=O is attached to the second carbon atom in the chain (e.. fructose).

33
Q

What does hemispheres-acetal mean?

A

When the central C is connected to OH or OR.

34
Q

What are anomers?

A

The 2 different stereo chemistries that the heme-acetal position can adopt. If the stereochemistry at C1/C5 is opposite, it is alpha, if it is the same than it is beta. Sugar stereochemistry is described as D or L, with most sugars being D.

35
Q

What are disaccharides?

A

Sugars formed by the linkage of 2 monosaccharides with the elimination of water to form a glycosidic bond. An example is maltose which consists of 2 glucose units joined together.

36
Q

What do the terms pyranose and furanose mean?

A

Pyranose - a 6 membered ring sugar (e.g. glucose).

Furanose - 5 membered ring sugar (e.g. fructose).

37
Q

What is sucrose made of and how?

A

Glucose (pyranose) and fructose (furanose) The glycoside bond is from position 1 on glucose to position 2 on fructose. Glucose is alpha anomer and fructose is beta anomer. Both are D.

38
Q

What is lactose made of and how?

A

Galactose (pyranose) and glucose (pyranose). Linked from position 1 on galactose to position 2 on glucose. Both are D. Galactose is beta anomer and glucose can be either.

39
Q

Describe how the polysaccharide starch is made?

A

Made of D-glucose units which are 1-4 alpha linked. It has 2 forms - amylose (linear) and amylopectin which has some 1-6 links in addition to the 1-4 links (branched). Can be metabolised by the body due to its a-links.

40
Q

Describe how the polysaccharide cellulose is made?

A

Made of D-glucose units which are 1-4 beta-linked. Cannot be metabolised by the body as we don’t have enzymes capable of dealing with B-linkages.

41
Q

What is glycogens structure?

A

It is branched like amylopectin with branches occurring every 10-15 units (25 in amylopectin).

42
Q

What are oils and fats?

A

Tri-esters of glycerol and long-chain carboxylic acids. Oils are liquids, fats are solids.

43
Q

What do the terms saturated, monounsaturated and polyunsaturated mean?

A

Saturated - No double bonds.
Monounsaturated - 1 double bond.
Polyunsaturated - more than 1 double bond.

44
Q

What is anandamide?

A

A fatty acid amide in the brain that interacts with the cannabinoid receptor to play a role in making and breaking short term neural connections. Cannabis may have a role in treatment of MS and glaucoma.

45
Q

What are glycerophosphilipids?

A

Elements of the cell membrane. Contains phosphodiester and amino alcohol.

46
Q

What is found in-between the lipid molecules of the lipid bilayer?

A

Cholesterol molecules.

47
Q

What is a steroid and what is its structure?

A

An organic molecule whose structure is based on the tetracyclic (4 ring) system. The rings are designated A, B, C and D, and the carbons are numbered starting in ring A. They have a variety of constituent groups attached and may have double bonds. The A and B rings can be joined in a ‘cis’ or ‘trans’ arrangement (trans is more common).

48
Q

What are 6 important steroids?

A
  1. Cortisone - anti-inflammatory drug used in treatment such as arthritis.
  2. Testosterone
  3. Estradiol - Female sex hormone.
  4. Norethindrone - Ovulation suppressant.
  5. Digitoxigenin - Foxglove constituent used as heart stimulant.
  6. Nandrolone - Anabolic (tissue-building steroid..
49
Q

What is the difference between nucleotides and nucleosides?

A

Nucleotides have a nitrogenous base, a sugar and a phosphate. Nucleosides do not have a phosphate.

50
Q

Which bases are pyrimidines (1 ring) ?

A

Cytosine, thymine and uracil.

51
Q

Which bases are purines (2 rings)?

A

Adenine and guanine.

52
Q

How are nucleotides joined together?

A

By phosphodiester bonds.

53
Q

how many H bonds between cytosine and guanine, and adenine and thymine?

A

Cytosine and guanine - 3.

Adenine and thymine/uracil - 2.

54
Q

Why can other base pair combinations not work?

A

Pyrimidines (T-C) cannot work because they are too small to enable complementary strands form the double helix.
Purines (A-G) cannot work because they are too bulky to enable complementary strands to form the double helix.
A-C cannot work because they can’t form enough hydrogen bonds. T-G cannot work because they can’t form enough H bonds.

55
Q

What are the 2 grooves on a strand of DNA called?

A

Major and minor.

56
Q

What does tRNA do?

A

Carries amino acids and allows ribosomes to synthesise peptide chains. The anticodon interacts with the codon on RNA.

57
Q

What are natural products/secondary metabolites?

A

A substance with no known role in the internal economy of the producing organism, may have defined ecological roles.

58
Q

What are terpenes?

A

Essential oils of many plants responsible for fragrances. May or may not contain oxygen joined to or in the hydrocarbon backbone.

59
Q

What are the 3 types opium?

A

Morphine, codeine and heroin.

60
Q

How is aspirin made?

A

By acetylating salicylic acid to give aspirin.

Year 1 - Chemistry (4 decks)

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