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macromolecular building blocks Flashcards

1
Q

Describe the composition of macromolecular building blocks

A

Macromolecular building blocks often contain phosphorus (P) and/or sulfur (S) in addition to carbon (C), nitrogen (N), oxygen (O), and hydrogen (H).

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2
Q

Define the role of amino acids in biochemistry.

A

Amino acids are the building blocks of proteins.

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3
Q

How do nucleotides contribute to genetic material?

A

Nucleotides make up DNA and RNA.

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4
Q

What is the major component of lipids?

A

The major component of lipids is hydrocarbons.

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5
Q

Explain the relationship between carbohydrates and polysaccharides.

A

Carbohydrates are the building blocks that make up polysaccharides, glycans, and more.

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6
Q

Describe the structure of an amino acid.

A

An amino acid consists of an amino group and an acidic group linked by a central carbon (α carbon), which is tetrahedral and has single bonds to four surrounding atoms, including a variable side chain (R)

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7
Q

How many variations of amino acids exist?

A

There are 20 variations of amino acids, leading to 20 different amino acids.

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8
Q

List the elements that are fundamental in the structure of biological macromolecules.

A

The fundamental elements are hydrogen (H), carbon (C), nitrogen (N), and oxygen (O).

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9
Q

What is the significance of the outer shell in atomic structure?

A

The outer shell of an atom determines its chemical properties and reactivity.

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10
Q

Describe the change in the carboxyl group at physiological pH.

A

At most physiological pH, the carboxyl group (COOH) loses a hydrogen ion (H+) and becomes COO-.

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11
Q

How does the amino group change at physiological pH?

A

At most physiological pH, the amino group (-CNH2) gains a hydrogen ion (H+) and becomes -CNH3+.

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12
Q

Define zwitterion in the context of amino acids.

A

A zwitterion is a form of an amino acid that has no net charge, occurring at virtually all physiological pH.

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13
Q

Explain the significance of the alpha carbon in amino acids.

A

The alpha carbon (Cα) is tetrahedral and connected to four different groups, making it chiral and allowing the amino acid to exist as two enantiomers.

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14
Q

What are the two forms of amino acids based on chirality?

A

The two forms of amino acids based on chirality are L (Laevo) and D (Dextrorotatory) forms.

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15
Q

How can L and D amino acid isomers be interconverted?

A

L and D amino acid isomers can only be interconverted by breaking a chemical bond.

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16
Q

Identify the common occurrence of amino acids in proteins.

A

Only L-amino acids are found in proteins, except on very rare occasions.

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17
Q

What happens to the electron pairs in the carboxyl group during ionization?

A

The pair of electrons that formed the OH bond and one of the bonds in C=O become delocalized and are shared between the COO- group.

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18
Q

Describe the role of side chains in amino acids.

A

The side chains, labeled as R groups, determine the character of each of the twenty amino acids, influencing their properties such as acidity, basicity, hydrophobicity, and hydrophilicity.

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19
Q

Define essential amino acids.

A

Essential amino acids are those that humans cannot synthesize and must obtain from their diet. There are eight essential amino acids.

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20
Q

How many variations of amino acids exist and what differentiates them?

A

There are twenty variations of amino acids, differentiated by the side chains (R groups) attached to the central carbon atom.

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21
Q

List the essential amino acids.

A

The essential amino acids are Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine.

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22
Q

What is the significance of the CORN law in amino acids?

A

The CORN law is a mnemonic used to determine the configuration of amino acids, indicating the arrangement of the amino group (C), the carboxyl group (O), the R group (R), and the hydrogen atom (N) around the central carbon.

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23
Q

Explain the difference between hydrophobic and hydrophilic amino acids.

A

Hydrophobic amino acids contain only carbon and hydrogen in their side chains, making them non-polar, while hydrophilic amino acids contain oxygen or nitrogen, making them polar and able to interact with water.

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24
Q

Identify the non-essential amino acids.

A

The non-essential amino acids are Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Histidine, Proline, Serine, and Tyrosine.

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25
Q

What are the three-letter and single-letter codes for Valine, Phenylalanine, and Tyrosine?

A

Valine is coded as Val (V), Phenylalanine as Phe (F), and Tyrosine as Tyr (Y).

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26
Q

How do the properties of amino acids affect protein structure?

A

The properties of amino acids, determined by their side chains, influence how they interact with each other, which in turn affects the folding and overall structure of proteins.

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27
Q

Describe the composition of side chains in amino acids.

A

The side chains of amino acids can consist of carbon, hydrogen, nitrogen, oxygen, and in some cases, sulfur, which contribute to the amino acid’s characteristics.

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28
Q

Describe the classification of R groups in amino acids.

A

There are 20 different R groups in amino acids, classified as follows: 6 are aliphatic and non-polar, 3 are aromatic and non-polar, 6 are uncharged and polar, and 5 are charged and polar.

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29
Q

How does histidine function in proteins?

A

Histidine is the only amino acid with an ionisable side chain that can switch between ionised and non-ionised states close to physiological pH (7.4), making it very reactive and common in protein active or binding sites.

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30
Q

Define the role of tyrosine in protein phosphorylation.

A

Tyrosine undergoes phosphorylation by protein kinase, a process that is part of a universal mechanism in signaling and regulation, similar to serine and threonine which also have terminal OH groups.

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31
Q

What is the significance of protein phosphorylation in cellular processes?

A

Protein phosphorylation is virtually universal in signaling and regulation, playing a crucial role in various cellular processes.

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32
Q

Explain the mechanism of protein phosphorylation involving metal ions.

A

The cleavage and transfer during protein phosphorylation are facilitated by metal ions, such as magnesium (Mg), and catalytic aspartic acid.

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33
Q

Identify the unique feature of histidine among amino acids.

A

Histidine is unique because it has an ionisable side chain that allows it to switch between ionised and non-ionised forms near physiological pH.

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34
Q

List the types of R groups found in amino acids and their characteristics.

A

The R groups in amino acids can be classified as aliphatic and non-polar, aromatic and non-polar, uncharged and polar, and charged and polar.

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35
Q

How many different types of R groups are there in amino acids?

A

20

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36
Q

Describe the linkage of N-linked carbohydrates to proteins.

A

N-linked carbohydrates are linked to proteins through N-acetylglucosamine (GlcNAc) and the amino acid asparagine, following the sequence Asn-X-Ser/Thr, where X cannot be proline.

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37
Q

Define O-linked carbohydrates and their common linkage.

A

O-linked carbohydrates typically involve a linkage between the monosaccharide N-acetylgalactosamine (GalNAc) and the amino acids serine or threonine, which have a terminal hydroxyl (OH) group.

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38
Q

How are glycoproteins formed?

A

Glycoproteins are formed when carbohydrate chains, known as glycans, are covalently attached to proteins.

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39
Q

What is the significance of the amino acid sequence Asn-X-Ser/Thr in N-linked glycosylation?

A

The sequence Asn-X-Ser/Thr is crucial for N-linked glycosylation, as it specifies the attachment site for the carbohydrate, with X being any amino acid except proline.

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40
Q

Explain the term ‘glycans’ in the context of proteins.

A

Glycans refer to carbohydrate chains that are covalently attached to proteins, contributing to the structure and function of glycoproteins.

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41
Q

Identify a specific example of a glycoprotein mentioned in the content.

A

An example of a glycoprotein mentioned is gp120, which has a molecular weight of 120 kD.

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42
Q

What are macromolecular building blocks in biochemistry?

A

In biochemistry, macromolecular building blocks refer to fundamental components such as amino acids that combine to form larger macromolecules like proteins.

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43
Q

Explain the structure of simple monosaccharides.

A

Simple monosaccharides have a carbon framework with a functional aldehyde or keto group, typically containing 3 to 8 carbon atoms and a hydroxyl group (OH) on each carbon.

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44
Q

Differentiate between aldoses and ketoses.

A

Aldoses have a functional group CHO (aldehyde), while ketoses have a functional group C=O (keto)

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45
Q

How are monosaccharides classified based on their carbon atoms?

A

Monosaccharides are classified by the number of carbon atoms they contain: triose (3), tetrose (4), pentose (5), hexose (6), heptose (7), etc.

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46
Q

What is the significance of the configuration of the enantiomeric carbon in monosaccharides?

A

Monosaccharides are classified as D or L based on the configuration of the enantiomeric carbon furthest from the functional group, with most vertebrate monosaccharides being D.

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47
Q

Describe the process of cyclic sugar formation in glucose.

A

in glucose, the functional aldehyde group reacts with the C5 hydroxyl to form a 6-membered pyranose ring.

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48
Q

What are the two configurations that C1 can have in the cyclic form of glucose?

A

C1 in the ring can have two configurations, which are alpha and beta.

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49
Q

Identify the common monosaccharides and their differences.

A

Common monosaccharides include glucose, mannose, and galactose, which differ in their structural arrangement.

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50
Q

Describe the difference between the α and β forms of glucose.

A

The α form has the OH group on the opposite side of the ring to C6, while the β form has both the OH group and C6 on the same side.

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51
Q

Define anomers in the context of carbohydrates.

A

Anomers are two configurations of a sugar that differ in the orientation of the hydroxyl group at the anomeric carbon (C1) in cyclic forms.

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52
Q

How is the cyclic form of glucose commonly referred to?

A

The cyclic form is commonly referred to simply as ‘glucose’ rather than ‘glucopyranose’.

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53
Q

Explain the orientation of the C5 hydroxyl group in D and L enantiomers of carbohydrates.

A

in D enantiomers, the C5 hydroxyl group is to the right, while in L enantiomers, it is to the left.

54
Q

What is the significance of the C6 group in the cyclic structure of D and L enantiomers?

A

In the cyclic structure, the C6 group is equatorial (in the plane of the ring) for D enantiomers and axial (perpendicular to the plane of the ring) for L enantiomers.

55
Q

How does the C6 group orientation differ in Haworth projections for D and L enantiomers?

A

In Haworth projections, the C6 group is up for D enantiomers and down for L enantiomers.

56
Q

Describe the formation of the furanose ring in fructose.

A

The furanose ring in fructose is formed when the functional group C2=O reacts with the C5 hydroxyl, resulting in a 5-membered ring.

57
Q

What are the anomeric configurations of fructose in its cyclic form?

A

Fructose has α (OH group on the opposite side of the ring to C6) and β (both on the same side) anomers.

58
Q

How is the cyclic form of fructose commonly referred to?

A

The cyclic form is commonly referred to simply as ‘fructose’ rather than ‘fructofuranose’.

59
Q

Explain how fructose can form a pyranose ring.

A

Fructose can form a 6-membered pyranose ring when the functional group C2=O reacts with the C6 hydroxyl.

60
Q

What is the total number of cyclic structures that can arise from D-fructose?

A

There are four cyclic structures that can arise from D-fructose.

61
Q

Describe the formation of cyclic sugars like ribose.

A

Cyclic sugars like ribose are formed when the HC1O functional group reacts with the C4 hydroxyl, resulting in a 5-membered cyclic furanose structure.

62
Q

Define the terms α and β anomers in cyclic sugars.

A

In cyclic sugars, α anomers have the OH group on the opposite side of the ring from C5, while β anomers have both the OH group and C5 on the same side.

63
Q

How are monosaccharides classified based on carbon atoms?

A

Monosaccharides are classified by the number of carbon atoms they contain, such as triose (3), tetrose (4), pentose (5), hexose (6), and heptose (7).

64
Q

Give examples of different types of carbohydrates.

A

Monosaccharide example: glucose; Disaccharide example: sucrose; Polysaccharide example: cellulose.

65
Q

What are N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc)?

A

GlcNAc and GalNAc are important sugars derived from glucose and galactose, respectively, with an N-acetyl substitution at C2.

66
Q

Explain the significance of GlcNAc in N-linked carbohydrates.

A

GlcNAc (N-acetylglucosamine) is crucial as it links N-linked carbohydrates to proteins through the amino acid asparagine.

67
Q

How many carbon atoms are in a hexose?

A

A hexose contains six carbon atoms.

68
Q

What is the structural difference between glucose and fructose?

A

Glucose is an aldose, while fructose is a ketose, which means they differ in the type of carbonyl group present.

69
Q

Identify the structural difference between glucose and ribose.

A

Glucose is a hexose (6 carbon atoms), while ribose is a pentose (5 carbon atoms).

70
Q

Describe the N-linked amino acid sequence.

A

The N-linked amino acid sequence is Asn-X-Ser/Thr, where amino acid X cannot be proline.

71
Q

Define glycoproteins.

A

Glycoproteins are proteins that have carbohydrate chains covalently attached to them, known as glycans.

72
Q

How are O-linked carbohydrates attached to proteins?

A

O-linked carbohydrates are typically linked to proteins through the monosaccharide GalNAc and the amino acids serine or threonine, which have a terminal OH group.

73
Q

What are glycans made from?

A

Glycans are built from nine carbohydrates: Glucose, Mannose, Galactose, GlcNAc, GalNAc, Xylose, Glucuronic acid, Sialic acid, and L-fucose.

74
Q

Explain the role of glycosaminoglycans (GAGs).

A

Glycosaminoglycans are polysaccharide chains made of repeating sugar units that, when linked to a protein core, form proteoglycans, which are important for cell surface interactions and signaling.

75
Q

How does glycosylation affect proteins?

A

Glycosylation plays a critical role in protein structure, function, and stability, and is important for pathogen recognition and immune evasion.

76
Q

What are peptidoglycans and their significance?

A

Peptidoglycans are polymers of sugar and amino acids that form bacterial cell walls, and their assembly is targeted by antibiotics like penicillin.

77
Q

Identify the core structure of N-linked glycans.

A

N-linked glycans have a conserved pentasaccharide core built from GlcNAc and Mannose.

78
Q

What is the significance of glycans in mammalian proteins?

A

Glycans decorate the surface of over half of all mammalian proteins and the vast majority of serum proteins.

79
Q

Discuss the importance of proteoglycans.

A

Proteoglycans, formed from GAGs linked to proteins, are crucial for cell surface interactions, ligand recognition, and cell signaling processes.

80
Q

Describe blood group antigens and their composition.

A

Blood group antigens are either sugars or proteins attached to various components in the red blood cell membrane, with the ABO blood group antigens being sugars.

81
Q

Define glycocalyx and its significance.

A

The glycocalyx is a surface coat of glycans that forms a protective layer on cells, playing a crucial role in cell recognition and interaction.

82
Q

How does viral glycosylation affect vaccine development?

A

Viral glycosylation can mask potential antibody sites on viral surface proteins, making it difficult to raise effective antibodies through vaccination.

83
Q

What are broadly neutralising antibodies (BnAbs)?

A

Broadly neutralising antibodies (BnAbs) are antibodies that target patches of glycosylation on viral surface proteins, offering a potential route towards effective vaccines.

84
Q

Explain the challenges faced in raising antibodies against viruses like HIV and the flu.

A

Challenges include the rapid mutation of viral surface proteins and the masking of antibody sites by glycosylation, complicating vaccine development.

85
Q

How do new methods in antibody targeting improve vaccine effectiveness?

A

New methods allow antibodies to target specific patches of glycosylation on viral surface proteins, enhancing the potential for effective vaccines.

86
Q

What role do glycan structures play in viruses?

A

Glycan structures on viruses can influence their ability to evade the immune system and affect how they interact with host cells.

87
Q

Describe the relationship between carbohydrates and macromolecular building blocks.

A

Carbohydrates are one of the key types of macromolecular building blocks, essential for various biological functions and structures.

88
Q

Describe the components of nucleotides.

A

Nucleotides consist of a base, a ribose sugar, and a phosphate group.

89
Q

Define macromolecular building blocks.

A

Macromolecular building blocks are the fundamental components that make up macromolecules, including amino acids, nucleotides, carbohydrates, and lipids.

90
Q

Identify the major component of lipids.

A

The major component of lipids is hydrocarbons.

91
Q

How are proteins formed from macromolecular building blocks?

A

Proteins are formed from amino acids, which are the building blocks of proteins.

92
Q

Explain the relationship between nucleotides and nucleic acids.

A

Nucleotides are the building blocks of nucleic acids, such as DNA and RNA, which are constructed from long chains of linked nucleotides.

93
Q

How many different bases are found in DNA and RNA nucleotides?

A

There are 4 different bases in DNA nucleotide building blocks and 4 in RNA, with 3 of the 4 being the same in both.

94
Q

Do nucleosides contain phosphate groups?

A

No, nucleosides do not have the phosphate group.

95
Q

Describe the formation of cyclic sugars in relation to ribose and glucose.

A

Cyclic sugars like ribose are formed when the HC1O functional group reacts with the C4 hydroxyl, resulting in a 5-membered cyclic furanose structure, similar to glucose.

96
Q

Define the term ‘anomeric’ in the context of cyclic sugars.

A

Anomeric refers to the C1 carbon in a cyclic sugar that can exist in two forms: α (where the OH group is on the opposite side of the ring from C5) and β (where both are on the same side).

97
Q

Explain the structure of a nucleoside.

A

A nucleoside consists of a base linked to a sugar via ribose C1 and the purine N9 or pyrimidine N1, forming an N-glycosidic bond.

98
Q

What is the significance of ribose in the context of nucleotides?

A

Ribose is a crucial component of both DNA and RNA nucleotides, serving as the sugar backbone that links to the nitrogenous bases.

99
Q

Identify the type of bond that links the sugar and base in a nucleoside.

A

The sugar and base in a nucleoside are linked by an N-glycosidic bond.

100
Q

How does the structure of ribose contribute to its classification as an aldose?

A

Ribose is classified as an aldose because it contains an aldehyde group, which is characteristic of aldoses.

101
Q

What distinguishes deoxyribose from ribose in terms of chemical structure?

A

Deoxyribose differs from ribose by lacking one oxygen atom at the 2’ position, which is why it is called ‘deoxy’.

102
Q

Illustrate the relationship between ribose and nucleotides in biochemistry.

A

Ribose serves as the sugar component in nucleotides, which are the building blocks of nucleic acids like DNA and RNA.

103
Q

Summarize the role of cyclic sugar formation in biochemistry.

A

Cyclic sugar formation is essential in biochemistry as it leads to the creation of stable sugar structures that are fundamental in the formation of nucleotides and nucleic acids.

104
Q

Define a nucleotide.

A

A nucleotide is a building block of DNA and RNA, consisting of a phosphate group linked to a sugar (ribose or deoxyribose) and a nitrogenous base.

105
Q

Describe the role of the polymerase enzyme in nucleotide synthesis.

A

The polymerase enzyme catalyzes the reaction where the last ribonucleotide in the chain acts as a nucleophile, attacking the 5’-triphosphate of the incoming nucleoside triphosphate, releasing pyrophosphate as a by-product.

106
Q

How is the glycosidic linkage in adenosine characterized?

A

The glycosidic linkage in adenosine is characterized as β (up), meaning the base is positioned above the sugar in the standard view.

107
Q

Explain the significance of the 3′ to 5′ directionality in DNA synthesis.

A

The 3′ to 5′ directionality is significant because the template strand is aligned in this direction within the polymerase, allowing the synthesised strand to be complementary and antiparallel to it.

108
Q

What is the relationship between the added nucleotide and the gene sequence?

A

The added nucleotide is not random; it is dictated by the gene sequence represented in the template strand.

109
Q

Identify the by-product released during nucleotide addition.

A

The by-product released during nucleotide addition is pyrophosphate.

110
Q

Describe the structure of a nucleotide in terms of its components.

A

A nucleotide consists of three components: a phosphate group, a sugar (ribose or deoxyribose), and a nitrogenous base.

111
Q

What type of bond links the phosphate to the sugar in a nucleotide?

A

The phosphate is linked to the sugar by a phosphodiester bond.

112
Q

How does the orientation of the growing strand relate to the template strand during DNA synthesis?

A

The growing strand is complementary and antiparallel to the template strand, meaning it runs in the opposite direction.

113
Q

What is the role of the anomeric carbon in nucleotide structure?

A

The anomeric carbon (C1) is involved in the glycosidic linkage between the sugar and the nitrogenous base in a nucleotide.

114
Q

Describe the process of DNA replication.

A

DNA replication involves splitting an existing DNA double helix into two strands, where each strand is replicated to form two new DNA molecules.

115
Q

How does transcription relate to DNA and RNA?

A

Transcription is the process where one of the DNA strands is used to make a complementary RNA strand, known as mRNA, which is essential for protein synthesis.

116
Q

Define reverse transcription and its significance.

A

Reverse transcription is the process where an RNA chain is used as a template to synthesize a complementary DNA strand, which is then replicated to form DNA, commonly used by retroviruses like HIV.

117
Q

Explain the role of tRNA in protein synthesis.

A

tRNA, or transfer RNA, plays a crucial role in translation by bringing the appropriate amino acids to the ribosome, where they are assembled into proteins based on the sequence of the mRNA.

118
Q

How do RNA-DNA hybrids form during replication?

A

RNA-DNA hybrids form when one chain is RNA and the other is DNA, occurring during processes like transcription and reverse transcription.

119
Q

Summarize the central dogma of molecular biology.

A

The central dogma of molecular biology is often summarized as ‘DNA makes RNA makes Protein’, illustrating the flow of genetic information.

120
Q

What is the role of polymerases in nucleic acid processes?

A

Polymerases are enzymes that facilitate the synthesis of nucleic acids, such as DNA and RNA, by adding nucleotides to a growing chain.

121
Q

Describe the general structure of a lipid.

A

A lipid generally has a hydrophilic head group and hydrophobic tail regions, which are characteristic of lipid membranes in cells.

122
Q

How do the head and tail regions of lipids vary?

A

The head and tail regions of lipids vary between different classes of lipids.

123
Q

What is the biological significance of lipids?

A

Lipids play a crucial role in forming cell membranes and other intracellular structures.

124
Q

Describe the structure of fatty acids.

A

Fatty acids consist of an extended hydrophobic hydrocarbon chain linked to a terminal acidic group (COOH).

125
Q

Define triacylglycerols.

A

Triacylglycerols, also known as triglycerides, are lipids formed by linking three fatty acid tails to a single glycerol molecule, primarily used for energy storage.

126
Q

How do glycerophospholipids differ from triacylglycerols?

A

Glycerophospholipids differ from triacylglycerols in that one of the fatty acid chains is replaced by a phosphodiester group, which usually has functional groups attached.

127
Q

What role do phospholipids play in cell membranes?

A

Phospholipids are the central component of lipid bilayer cell membranes, providing structural integrity and functionality.

128
Q

List the types of fatty acids mentioned and their classifications.

A

The types of fatty acids mentioned are: Arachidonic acid (polyunsaturated), Linoleic acid (polyunsaturated), Oleic acid (monounsaturated), and Palmitic acid (saturated).

129
Q

Explain the significance of lipid tails in cell walls.

A

In cell walls, lipid tails are linked together, and the terminal group is often extended, contributing to the structural properties of the membrane.

130
Q

What is the primary function of triacylglycerols in biological systems?

A

The primary function of triacylglycerols is energy storage.

131
Q

Define phospholipids and give examples.

A

Phospholipids are macromolecular building blocks that include phosphatidylcholine and phosphatidylethanolamine.

132
Q

How do sphingolipids differ from other lipids?

A

Sphingolipids, such as sphingomyelin, are a specific type of lipid that contains a sphingosine backbone.

biochem (7 decks)

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