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deck_5661105 Flashcards

1
Q

What is the definition of double helix?

A

Shape of DNA molecule, due to coiling of the two sugar-phosphate backbone strands into a right-handed spiral configuration

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2
Q

What is the definition of a monomer?

A

Molecule that when repeated makes up a polymer. Amino acids are the monomers of proteins. Nucleotides are the monomers of nucleic acids

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3
Q

What is the definition of a nucleotide?

A

Molecule consisting of a five-carbon sugar, a phosphate group and a nitrogenous base

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4
Q

What is the definition of a polynucleotide?

A

Large molecule containing many nucleotides

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5
Q

What are nucleotides?

A

Biological molecules that participate in nearly all biochemical processes

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6
Q

What are nucleotides made up of?

A

They are phosphate esters of pentose sugars, where a nitrogenous base is linked to the C1 of the sugar residue and a phosphate group is linked to either the C5 or C3 of the sugar residue by covalent bonds formed by condensation reactions

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7
Q

What do nucleotides form?

A

Monomers of nucleic acids, DNA and RNA

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8
Q

What is the nucleotide pentose sugar in RNA?

A

Ribose

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9
Q

What is the nucleotide pentose sugar in DNA?

A

Deoxyribose

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10
Q

How do nucleotides become phosphorylated nucleotides?

A

When they contain more than one phosphate group

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11
Q

What is an example of this?

A

ADP (adenosine diphosphate) and ATP (adenosine triphosphate). ATP is an energy-rich end product of most energy releasing biochemical pathways, and is used to drive most energy requiring metabolic processes in cells

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12
Q

What do nucleotides help regulate?

A

Many metabolic pathways eg by ATP, ADP and AMP (adenosine monophosphate)

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13
Q

What could nucleotides be components of?

A

Coenzymes. Adenine nucleotides are components of the coenzyme NADP-nicotinamide adenine dinucleotide phosphate, which is used in photosynthesis, and of NAD which is a coenzyme used in respiration, and of FAD (flavine……) and coenzyme A-both used in respiration

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14
Q

Where is DNA found?

A

In the nuclei of all eukaryotic cells, within the cytoplasm of prokaryotic cells and is also inside some types of viruses

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15
Q

What is DNAs role?

A

It is the hereditary material and carries coded instructions used in the development and functioning of all known living organisms

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16
Q

What is DNA one of….?

A

The important macromolecules that make up the structure of living organisms

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17
Q

What are the other important macromolecules?

A

Proteins, carbohydrates and lipids

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18
Q

What is a polymer of DNA made up of?

A

Many repeating monomeric units called nucleotides

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19
Q

What does a molecule of DNA consist of?

A

Two polynucleotide strands which run in opposite directions (antiparallel)

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20
Q

What does each DNA nucleotide consist of?

A

A phosphate group, a five-carbon sugar (deoxyribose) and one of four nitrogenous bases: adenine, guanine, thymine or cytosine

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21
Q

What is the covalent bond between the sugar and the phosphate group called?

A

A phosphodiester bond, which is broken when polynucleotides break down and are formed when polynucleotides are synthesised

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22
Q

Why are DNA molecules long?

A

So they can carry a lot of encoded genetic information

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23
Q

What differs in each nucleotide?

A

They contain the same phosphate an sugar groups but the organic (nitrogenous) base differs between purines or pyrimidines

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24
Q

What are purines?

A

Adenine or guanine (two rings)

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25
Q

What are pyrimidines?

A

Thymine or cytosine (one ring)

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26
Q

What does adenine always pair with?

A

Thymine, by means of two hydrogen bonds

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27
Q

What does guanine always pair with?

A

Cytosine, by means of three hydrogen bonds

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28
Q

What does a purine always pair with?

A

A pyrimidine, giving equal-sized ‘rungs’ on the DNA ladder, which can then twist, like twisting rope ladder around an imaginary axis, into the double helix coil-giving the molecule stability

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29
Q

What do hydrogen bonds allow?

A

The molecule to unzip for transcription and replication

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30
Q

What is the upright part of the DNA molecule formed by?

A

The sugar-phosphate backbones of the antiparallel polynucleotide strands

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31
Q

What do the ‘opposite directions’ of the two strands refer to?

A

The two strands refers to the direction that the third and fifth carbon molecules on the five-carbon sugar, deoxyribose, are facing

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32
Q

What is the 5’ end of the molecule?

A

Where the phosphate group is attached to the fifth carbon atom of the deoxyribose sugar

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33
Q

What is the 3’ end of the molecule?

A

Where the phosphate group is attached to the third carbon atom of the deoxyribose sugar

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34
Q

What do the rungs of the ladder consist of?

A

The complementary base pairs, formed by hydrogen bonds. The molecule is very stable and the integrity of the coded information within the base sequences is protected

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35
Q

How is DNA organised in eukaryotic cells?

A

Majority is in the nucleus, each molecule of DNA is wound tightly around histone proteins into chromosomes-each chromosome is one molecule of DNA, and there is a loop of DNA without histone proteins inside the mitochondria and chloroplasts

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36
Q

How is DNA organised in prokaryotic cells?

A

DNA is in a loop and is within the cytoplasm not enclosed in a nucleus, it is not wound around histone proteins and is described as naked (viruses also have a loop of naked DNA)

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37
Q

What is the definition of DNA polymerase?

A

Enzyme that catalyses formation of DNA from activated deoxyribose nucleotides, using single-stranded DNA as a template

38
Q

What is the definition of helicase?

A

Enzyme that catalyses the breaking of hydrogen bonds between the nitrogenous base pairs of bases in a DNA molecule

39
Q

What is the definition of semi-conservative replication?

A

How DNA replicates, resulting in two new molecules, each of which contains one old strand and one new strand. One old strand is conserved in each new molecule

40
Q

What does each DNA contain?

A

The coded instructions to make and maintain the organism?

41
Q

What happens every time a cell divides?

A

The DNA has to be copied so that each new daughter cell receives a full set of instructions, each molecule of DNA replicates

42
Q

When does this replication take place?

A

During interphase before the cell actually divides

43
Q

What does this result in, in eukaryotic cells?

A

Each chromosome (which is one molecule of DNA) having an identical copy of itself. At first they are joined together at the centromere, forming two sister chromatids

44
Q

When does the DNA within mitochondria and chloroplasts replicate?

A

Each time the organelles divide, which is just before the cell divides

45
Q

What does each DNA molecule have to do to make a new copy of itself?

A

Unwind and unzip

46
Q

What is unwinding?

A

The double helix is untwisted, a bit at a time, catalysed by a gyrase enzyme

47
Q

What is unzipping?

A

Hydrogen bonds between the nucleotide bases are broken. This is catalysed by DNA helicase, and results in two strands of DNA with exposed nucleotide bases

48
Q

What happens after this?

A

Free phosphorylated nucleotides, present in the nuceloplasm within the nucleus are bonded to the exposed bases, following complementary base-pairing rules

49
Q

What does DNA polymerase do?

A

Catalyses the addition of the new nucleotide bases in the 5’ to 3’ direction, to the single strands of DNA, using a single strand of unzipped DNA as a template

50
Q

What happens to the leading strand?

A

It is synthesised continuously, whereas the lagging strand is in fragments that are later joined, catalysed by ligase enzymes

51
Q

What happens after this?

A

Hydrolysis of the activated nucleotides, to release the extra phosphate groups, supplies the energy to make phosphodiester bonds between the sugar residue of one nucleotide and the phosphate group of the next nucleotide

52
Q

What is the product of this replication?

A

Two DNA molecules, identical to each other and the parent molecule

53
Q

What do each of these molecules contain?

A

One old strand and one new strand (semi-conservative replication)

54
Q

How do the loops of DNA in prokaryotes, mitochondria and chloroplasts replicate semi-conservatively?

A

A bubble sprouts from the loop and this unwinds, unzips and then complementary nucleotides join to the exposed nucleotides and eventually the whole loop is copied

55
Q

What can happen during DNA replication?

A

Errors may occur and the wrong nucleotide may be inserted, which could change the genetic code (example of a point mutation)

56
Q

How often is this estimated to happen?

A

In 1 in 10^8 base pairs

57
Q

How is this often avoided?

A

During the replication process there are enzymes that can proofread and edit out incorrect nucleotides

58
Q

What are genes called if they have changes to their nucleotide sequences?

A

Alleles or gene variants

59
Q

Are all variations harmful?

A

NO, some appear to give neither an advantage or disadvantage

60
Q

What is the definition of gene?

A

A length of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression

61
Q

What is the definition of polypeptide?

A

A polymer made of many amino acid units joined together by peptide bonds. Insulin is a polypeptide of 51 amino acids

62
Q

What is the definition of a protein?

A

A large polypeptide of 100 or more amino acids, however the terms are often used synonymously, and insulin may be described as a small protein

63
Q

What is the definition of transcription?

A

The process of making RNA from a DNA template

64
Q

What is the definition of translation?

A

Formation of a protein, at ribosomes, by assembling amino acids into a particular sequence according to the coded instructions carried from DNA to the ribosome by mRNA

65
Q

How is RNA structurally from DNA?

A

The sugar molecule in each nucleotide is ribose, the nitrogenous base uracil replaces the pyrimidine base thymine, the polynucleotide chin is usually single stranded, the polynucleotide chain is shorter, and there are three forms of RNA

66
Q

What are the three forms of RNA?

A

messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

67
Q

Where are genes?

A

On each chromosome there are specific lengths of DNA (genes), each gene contains a code that determines the sequence of amino acids in a particular polypeptide or protein

68
Q

How much of an organism’s dry mass is protein?

A

75%

69
Q

Some proteins are structural, like what?

A

The cytoskeleton threads inside the cell’s ‘tool-kit’ such as enzymes, and these may catalyse the formation of non-protein molecules such as lipids and carbohydrates

70
Q

What determines the amino acid sequence or primary structure of a polypeptide?

A

The sequence of DNA base triplets

71
Q

What happens, as long as the primary structure of a polypeptide is correct?

A

It will fold correctly and be held in its tertiary structure or shape, enabling it to carry out its function

72
Q

What are examples of this?

A

The shape of an active site must be complementary to the substrate molecule, part of an antibody molecule has to be complementary to the antigens on the invading pathogen, a receptor on a cell membrane has to be complementary to the shape of the cell signalling molecule it detects, and an ion channel proteins

73
Q

Genes are inside the cell nucleus, but where are proteins?

A

They are made in the cytoplasm, at ribosomes

74
Q

What has to happen due to the fact that instructions inside genes, on chromosomes can’t pass out of the nucleus?

A

A copy of each gene has to be transcribed into a length of mRNA-in this form the sequence of base triplets, now called codons, can pass out of the nucleus to the ribosome, ensuring that the coded instructions are translated and he protein is assembled correctly from amino acids

75
Q

Why is the genetic code near universal?

A

Because in almost all living organisms, the same triplet of DNA bases codes for the same amino acids

76
Q

Why is the genetic code described as degenerate?

A

Because for all amino acids, except methionine and tryptophan, there is more than one base triplet, which may reduce the effect of point mutations, as a change in one base of the triplet could produce another base triplet that still codes for the same amino acid

77
Q

Why is the genetic code described as non-overlapping?

A

It is read starting from a fixed point in groups of three bases. If a base is added or deleted then it causes a frame shift, as every base triplet after that is changed and eery amino acid coded for is changed

78
Q

Summarise the process of transcription of a gene into a length of mRNA.

A

A gene unwinds and unzips, hydrogen bonds between complementary nucleotide bases break, RNA polymerase catalyses the formation of temporary hydrogen bonds between RNA nucleotides and their complementary unpaired DNA bases (A with T, C with G, G with C and U with A) on one strand of the unwound DNA (template strand)

79
Q

What is produced?

A

A length of RNA that is complementary to the template strand of the gene. It is a copy of the other DNA stand-the coding strand

80
Q

What happens to the mRNA?

A

It passes out of the nucleus through the nuclear envelope and attaches to a ribosome

81
Q

Where are ribosomes made?

A

In the nucleolus in two smaller subunits. These pass separately out of the nucleus through pores in the nuclear envelope, and then come together to form the ribosome. Magnesium ions help to bind the two subunits together

82
Q

What are ribosomes made of?

A

Ribosomal RNA and protein in roughly equal parts

83
Q

Where are transfer RNA molecules made?

A

In the nucleolus and pass out of the nucleus into the cytoplasm. They are single stranded polynucleotides but can twist into a hairpin shape

84
Q

What is at one end of it?

A

A trio of nucleotide bases that recognises and attaches to a specific amino acid

85
Q

What is at the loop of the hairpin?

A

Another triplet of bases, an anticodon, that is complementary to a specific codon of bases on the mRNA

86
Q

How do ribosomes catalyse the synthesis of polypeptides?

A

Transfer RNA molecules bring the amino acids and find their place where the anticodon binds by temporary hydrogen bonds to the complementary codon on the mRNA molecule

87
Q

What happens as the ribosomes move along the length of mRNA?

A

It reads the code, and when two amino acids are adjacent to each other, a peptide bond forms between them

88
Q

What is needed for polypeptide synthesis?

A

Energy in the form of ATP

89
Q

What is the amino acid sequence for polypeptide therefore determined by?

A

The sequence of triplets of nucleotide bases on the length of DNA-a gene

90
Q

What happens after the polypeptide has been assembled?

A

The mRNA breaks down. Its component molecules can be recycled into new lengths of mRNA, with different codon sequences

91
Q

What then happens?

A

The newly synthesised polypeptide is helped, by chaperone proteins in the cell, to fold correctly into its 3D shape or tertiary structure, in order to carry out its function

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