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Biological Sciences Foundation Year > Amino Acids, Proteins and DNA > Flashcards

Amino Acids, Proteins and DNA Flashcards

1
Q

Describe the general structure of an α amino acid.

A

An α amino acid has a central carbon atom (C) bonded to an amino group (NH2), a carboxylic acid group (COOH), a hydrogen atom (H), and a variable R group that determines the specific amino acid.

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2
Q

How does glycine differ from other amino acids in terms of chirality?

A

Glycine is the simplest amino acid and is not chiral because its R group is a hydrogen atom, meaning it does not have four different groups around the central carbon.

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3
Q

Define optical activity in amino acids.

A

Optical activity refers to the ability of amino acids, except glycine, to rotate plane polarized light due to their chiral nature.

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4
Q

What are zwitterions in the context of amino acids?

A

Zwitterions are the dipolar forms of amino acids that contain both a positive charge on the amino group and a negative charge on the carboxylate group, resulting in no net charge.

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5
Q

Explain the significance of zwitterions in amino acids.

A

Zwitterions contribute to the relatively high melting points of amino acids due to ionic interactions, which are stronger than the hydrogen bonding present in their no charge forms.

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6
Q

How do amino acids behave in terms of acidity and basicity?

A

Amino acids have both acidic (carboxylic acid group) and basic (amine group) properties, allowing them to act as weak buffers that resist changes in pH when small amounts of acid or alkali are added.

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7
Q

What happens to amino acids in alkaline solutions?

A

In alkaline solutions, amino acids can react and change form, often resulting in the deprotonation of the carboxylic acid group and the formation of a negatively charged carboxylate.

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8
Q

Describe the naming convention for amino acids using IUPAC.

A

Amino acids are named using IUPAC organic naming conventions, which include identifying the amino group and the carboxylic acid group, such as 2-aminobutanedioic acid for aspartic acid.

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9
Q

How do extra carboxylic acid or amine groups on the R group affect amino acids?

A

Extra carboxylic acid or amine groups on the R group can classify amino acids as acidic or basic and influence their behavior in different pH environments.

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10
Q

What is the role of amino acids as weak buffers?

A

Amino acids act as weak buffers by gradually changing pH in response to the addition of small amounts of acids or bases, helping to maintain a stable pH in biological systems.

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11
Q

Identify the structural feature that defines an α amino acid.

A

The defining feature of an α amino acid is that both the amino group (NH2) and the carboxylic acid group (COOH) are attached to the same carbon atom.

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12
Q

What is the relationship between the R group of an amino acid and its properties?

A

The R group of an amino acid determines its specific characteristics, including its polarity, charge, and overall behavior in biochemical processes.

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13
Q

How do amino acids exist in different pH environments?

A

In different pH environments, amino acids can exist in various forms: as zwitterions in neutral solutions, as positively charged species in acidic solutions, and as negatively charged species in alkaline solutions.

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14
Q

Explain the melting point of amino acids in relation to their structure.

A

The melting point of amino acids is relatively high due to the strong ionic interactions between zwitterions, compared to the weaker hydrogen bonds in their no charge forms.

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15
Q

What is the significance of the amino and carboxylic acid groups in amino acids?

A

The amino group provides basic properties, while the carboxylic acid group provides acidic properties, allowing amino acids to participate in various biochemical reactions.

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16
Q

Define dipeptides.

A

Dipeptides are simple combination molecules formed from two amino acids linked by one amide (peptide) bond.

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17
Q

Describe the combinations of amino acids in dipeptides.

A

For any two different amino acids, there are two possible combinations in the formation of a dipeptide.

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18
Q

How can amino acids undergo reactions?

A

The carboxylic acid group and amine group in amino acids can undergo typical reactions associated with these functional groups.

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19
Q

What is an example of a reaction involving amino acids?

A

An example is the esterification reaction, where an amino acid reacts with an alcohol in the presence of a strong acid catalyst.

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20
Q

Explain the hydrolysis of proteins.

A

Proteins can be hydrolyzed and split back into their constituent amino acids when heated with concentrated hydrochloric acid or strong alkalis.

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21
Q

What technique can be used to deduce the composition of a protein molecule?

A

Thin Layer Chromatography (TLC) can be used to deduce the composition of a protein molecule after hydrolysis.

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22
Q

How do R groups in amino acids affect their reactions?

A

If the R group contains an amine or carboxylic acid, it will participate in the same reactions as the α amine and carboxylic groups.

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23
Q

What happens to dipeptides when they are hydrolyzed?

A

When dipeptides are hydrolyzed, they break down into their individual amino acids.

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24
Q

Describe the role of strong acids in amino acid reactions.

A

Strong acids can act as catalysts in reactions involving amino acids, such as esterification.

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25
Q

What is the significance of peptide bonds in dipeptides?

A

Peptide bonds are the amide links that connect amino acids in dipeptides, forming the backbone of the molecule.

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26
Q

Describe the initial step in thin-layer chromatography of amino acids.

A

Wearing gloves, draw a pencil line 1 cm above the bottom of a TLC plate and mark spots for each sample, equally spaced along the line.

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27
Q

How should the amino acid solutions be applied to the TLC plate?

A

Use a capillary tube to add a tiny drop of each solution to a different spot and allow the plate to air dry.

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28
Q

What is the recommended depth of the solvent in the chamber for TLC?

A

Add solvent to a chamber or large beaker with a lid so that it is no more than 1 cm in depth.

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29
Q

Explain the importance of the pencil line in TLC.

A

The pencil line will not dissolve in the solvent, ensuring that the sample spots remain above the solvent level.

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30
Q

What should be done when the solvent level reaches about 1 cm from the top of the TLC plate?

A

Remove the plate and mark the solvent level with a pencil, then allow the plate to dry in the fume cupboard.

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31
Q

What is the purpose of spraying ninhydrin on the TLC plate?

A

Ninhydrin is sprayed to visualize amino acids, which are transparent and cannot be seen otherwise.

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32
Q

How is the Rf value calculated in TLC?

A

Rf value = distance moved by amino acid / distance moved by the solvent.

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33
Q

What precautions should be taken to prevent contamination during the TLC process?

A

Wear plastic gloves to prevent contamination from hands to the plate.

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34
Q

Why is it important to keep the lid on the chamber during TLC?

A

The lid is used to prevent evaporation of the toxic solvent.

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35
Q

What happens to amino acids when ninhydrin is sprayed and heated?

A

Red to blue spots appear, allowing visualization of the amino acids.

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36
Q

How can the position of spots be observed besides using ninhydrin?

A

Shine UV light to see the position of spots on the TLC plate.

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37
Q

What does it indicate if some spots in TLC contain more than one compound?

A

It indicates that similar compounds have similar Rf values and may not separate effectively.

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38
Q

What can be done to split a protein into amino acids?

A

A protein can be split into amino acids by reacting it with concentrated hydrochloric acid.

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39
Q

What is the significance of comparing Rf values in TLC?

A

Comparing Rf values to those for known substances helps identify the amino acids present in the sample.

40
Q

What should be done if the solvent is too deep in the TLC process?

A

If the solvent is too deep, it will dissolve the sample spots from the plate, leading to inaccurate results.

41
Q

What is the effect of allowing the solvent to rise near the top of the plate?

A

Allowing the solvent to rise near the top of the plate can yield more accurate results, but Rf values can still be calculated if it does not reach the top.

42
Q

What is the role of a fume cupboard in the TLC process?

A

The fume cupboard is used to dry the plate as the solvent is toxic.

43
Q

Define peptide links in proteins.

A

Peptide links are the amide functional groups that connect amino acids in proteins, formed through condensation reactions.

44
Q

Describe the 3D arrangement of amino acids in proteins.

A

The 3D arrangement of amino acids in proteins can form a corkscrew shape, held in place by hydrogen bonds between the hydrogen of the –N group and the oxygen of the C=O group of amino acids along the polypeptide chain.

45
Q

How is the primary structure of proteins characterized?

A

The primary structure of proteins is characterized by the sequence of the 20 different naturally occurring amino acids linked together by peptide bonds.

46
Q

Explain the secondary structure of proteins.

A

The secondary structure of proteins refers to the local folded structures that form within a polypeptide due to hydrogen bonding, commonly seen as α-helices and β-pleated sheets.

47
Q

What is an α-helix in protein structure?

A

An α-helix is a type of secondary structure in proteins where the R-groups of amino acids are oriented outward from the helical structure.

48
Q

Describe the β-pleated sheet structure in proteins.

A

The β-pleated sheet structure in proteins consists of parallel strands of the protein chain that are held together by hydrogen bonds, forming a pleated shape.

49
Q

How do hydrogen bonds contribute to protein structure?

A

Hydrogen bonds stabilize the secondary structure of proteins by forming between the hydrogen of the –N-H group and the oxygen of the C=O group in the polypeptide chain.

50
Q

What role do R-groups play in the secondary structure of proteins?

A

R-groups, or side chains, of amino acids influence the folding and stability of the secondary structure by determining how the polypeptide chain interacts with itself.

51
Q

Describe the tertiary structure of proteins.

A

The tertiary structure is the folding of the secondary structure into more complex shapes, held in place by interactions between the R-side groups of distant amino acids.

52
Q

How are tertiary structures stabilized in proteins?

A

Tertiary structures are stabilized by various interactions including hydrogen bonding, sulfur-sulfur bonds, and ionic interactions.

53
Q

Define hydrogen bonds in the context of protein structure.

A

Hydrogen bonds can form between two serine side chains in different parts of the folded protein chain, and other amino acid chains can also participate in hydrogen bonding.

54
Q

Explain the role of ionic interactions in protein tertiary structure.

A

Ionic interactions occur between acidic amino acids like aspartic acid and basic amino acids like lysine, involving the transfer of a hydrogen ion to form zwitterions.

55
Q

What is the significance of sulfur bridges in protein structure?

A

Sulfur bridges, or covalent bonds, can form between two cysteine side chains that are brought close together due to the folding of the protein chain.

56
Q

How do cysteine side chains contribute to protein stability?

A

Cysteine side chains can react to form sulfur bridges, which are covalent bonds that contribute to the stability of the protein’s tertiary structure.

57
Q

Identify the types of interactions that can stabilize tertiary protein structures.

A

The types of interactions that stabilize tertiary protein structures include hydrogen bonds, ionic interactions, and sulfur bridges.

58
Q

What happens to acidic and basic amino acids during ionic interactions?

A

During ionic interactions, a hydrogen ion is transferred from the -COOH group of an acidic amino acid to the -NH2 group of a basic amino acid, forming zwitterions.

59
Q

Summarize the importance of understanding tertiary structure in proteins.

A

Understanding the tertiary structure is crucial as it determines the protein’s overall shape and function, influenced by various interactions among amino acids.

60
Q

Describe the structure and function of enzymes.

A

Enzymes are proteins that act as catalysts in biochemical reactions. They have an active site, usually a hollow in their globular structure, where substrate molecules can bind.

61
Q

How do substrates interact with the active site of an enzyme?

A

Substrates interact with the active site through various interactions including hydrogen bonding, van der Waals forces, permanent dipole-dipole forces, and ionic interactions.

62
Q

Define the lock and key hypothesis in enzyme activity.

A

The lock and key hypothesis states that only substrate molecules with the right shape and correct positions of functional groups can fit and bind to the active site of an enzyme.

63
Q

What is an enzyme-substrate complex?

A

An enzyme-substrate complex is formed when a substrate molecule binds to the active site of an enzyme.

64
Q

Explain the significance of stereospecific active sites in enzymes.

A

Stereospecific active sites mean that if the substrate is chiral, only one enantiomer will fit properly in the active site, allowing only that specific isomer to be catalyzed.

65
Q

How do drugs function as enzyme inhibitors?

A

Many drugs act as enzyme inhibitors by blocking the active site, preventing substrates from attaching. Some inhibitors may bind elsewhere on the enzyme, altering the shape of the active site.

66
Q

What role do computers play in drug design related to enzyme inhibition?

A

Computers can be used to help design drugs that act as enzyme inhibitors by modeling interactions and predicting how inhibitors will bind to enzymes.

67
Q

Identify the types of interactions that hold the substrate in the active site.

A

The types of interactions include hydrogen bonding, van der Waals forces, permanent dipole-dipole forces, and ionic interactions.

68
Q

What is the importance of the strength of interactions between the substrate and the enzyme’s active site?

A

The interactions need to be strong enough to hold the substrate for the reaction to occur, but weak enough to allow the product to be released.

69
Q

Describe the components of a nucleotide.

A

A nucleotide is made up of a phosphate ion, a 2-deoxyribose sugar, and one of the four bases: adenine, cytosine, guanine, or thymine.

70
Q

Define the four bases found in DNA.

A

The four bases in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T).

71
Q

How is the structure of a nucleotide formed?

A

The structure of a nucleotide is formed by bonding a phosphate ion to a 2-deoxyribose sugar, which is then bonded to one of the four nitrogenous bases.

72
Q

Explain the role of 2-deoxyribose in DNA.

A

2-deoxyribose is a pentose sugar that forms part of the backbone of DNA, linking the phosphate groups and nitrogenous bases.

73
Q

Identify the type of sugar present in DNA.

A

The type of sugar present in DNA is 2-deoxyribose.

74
Q

What is the significance of the phosphate ion in a nucleotide?

A

The phosphate ion is crucial for forming the backbone of DNA, linking the sugar molecules together.

75
Q

Illustrate how the bases attach to the sugar in a nucleotide.

A

The bases attach to the sugar at specific atoms, which are defined in the structures provided in the Chemistry Data Booklet.

76
Q

Summarize the structure of DNA.

A

DNA is composed of a double helix structure formed by two strands of nucleotides, which include a phosphate group, a sugar, and nitrogenous bases.

77
Q

How do the nitrogenous bases pair in DNA?

A

In DNA, adenine pairs with thymine, and cytosine pairs with guanine.

78
Q

What is the chemical formula for 2-deoxyribose?

A

The chemical formula for 2-deoxyribose is C5H10O4.

79
Q

Describe the structure of a single strand of DNA.

A

A single strand of DNA is a polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide, forming a sugar-phosphate-sugar-phosphate chain with bases attached to the sugars.

80
Q

How do the two strands of DNA interact with each other?

A

The two strands of DNA interact through hydrogen bonding between complementary base pairs, leading to the formation of a double helix.

81
Q

Define complementary in the context of DNA strands.

A

Complementary refers to the matching base sequences of the two strands of DNA, where adenine pairs with thymine and cytosine pairs with guanine.

82
Q

Explain the significance of hydrogen bonds in DNA structure.

A

Hydrogen bonds are significant in DNA structure as they hold the two complementary strands together, with guanine pairing with cytosine by 3 hydrogen bonds and adenine pairing with thymine by 2 hydrogen bonds.

83
Q

What is the role of the sugar-phosphate backbone in DNA?

A

The sugar-phosphate backbone provides structural support to the DNA molecule, linking nucleotides together and forming the framework of the DNA strand.

84
Q

How many hydrogen bonds are formed between guanine and cytosine?

A

Guanine pairs with cytosine by 3 hydrogen bonds.

85
Q

How many hydrogen bonds are formed between adenine and thymine?

A

Adenine pairs with thymine by 2 hydrogen bonds.

86
Q

Describe the overall shape of DNA.

A

DNA exists as a double helix, which is formed by two complementary strands of the sugar-phosphate polymer chain.

87
Q

What is the significance of the base pairing rules in DNA?

A

The base pairing rules ensure that the two strands of DNA are complementary, allowing for accurate replication and transcription of genetic information.

88
Q

Identify the components that make up a nucleotide in DNA.

A

A nucleotide in DNA is made up of a phosphate group, a 2-deoxyribose sugar, and a nitrogenous base.

89
Q

Describe the role of cisplatin in cancer treatment.

A

Cisplatin is a Pt(II) complex used as an anticancer drug that prevents DNA replication in cancer cells by forming a dative covalent bond with a nitrogen atom on guanine.

90
Q

How does cisplatin affect healthy cells?

A

Cisplatin can also bond to healthy DNA, which may prevent the replication of healthy cells and lead to unwanted side effects such as hair loss.

91
Q

Define the mechanism by which cisplatin works against cancer cells.

A

Cisplatin works by displacing two chloride ions, allowing the molecule to bind to DNA and stop the replication of cancerous cells.

92
Q

What are the potential side effects of using cisplatin?

A

Potential side effects of cisplatin include hair loss and other adverse effects due to its action on healthy cells.

93
Q

How can the side effects of cisplatin be minimized?

A

The side effects of cisplatin can be minimized by administering the drug in small doses.

94
Q

Explain the importance of assessing drug benefits versus adverse effects in society.

A

Society needs to evaluate the balance between the therapeutic benefits of drugs like cisplatin and their potential adverse effects to make informed healthcare decisions.

95
Q

What type of reaction occurs when cisplatin binds to DNA?

A

A ligand replacement reaction occurs when cisplatin binds to DNA, forming a dative covalent bond.

96
Q

Identify the atoms in DNA that cannot bond with cisplatin.

A

The nitrogen and oxygen atoms involved in bonding within the DNA molecule cannot bond with cisplatin.

Biological Sciences Foundation Year (17 decks)

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