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S112 all topics > Topic 16 - The DNA molecule > Flashcards

Topic 16 - The DNA molecule Flashcards

1
Q

Why do you think the relationship between structure and function is so important to biology?

A

Biology is essentially about figuring out how living things work. Determining what something looks like – its structure – has proven time and time again to be one of the best ways of working out its function (and vice versa – knowing how something works can give clues to its structure).

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2
Q

What is a genome?

A

An organisms genetic material in its entirety

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3
Q

what is a chromosome?

A

The individual DNA that make up the genome. Chromosomes consist of large DNA molecules that contain genetic information and mediate the process of inheritance.

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4
Q

What are genes?

A

The sections of chromosomes that form individual units of genetic inheritance, responsible for passing on traits but all organisms within a species have the same genes just different versions of these genes

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5
Q

What are nucleotides?

A

The chemical monomers from which all genetic material is composed

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6
Q

In Mendel’s pea plant experiments, which trait was recessive: tallness or shortness?

A

Shortness. To display a recessive trait, an organism must have inherited a recessive variant of a gene from both parents.

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7
Q

How does genes look physically?

A

genes are individual sections of the long strands of DNA that make up the chromosome. Compared with chromosomes, genes are tiny – there are usually hundreds of genes on a chromosome.

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8
Q

What information do genes contain in order to make a vital part of our body?

A

Genes contain the information our bodies need to make proteins. Proteins form the structure of our bodies, as well playing an important role in the processes that keep us alive.

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9
Q

What is the majority of a chromosome made of?

A

Intergenic DNA (DNA between genes) Intergenic DNA was once thought to have no purpose and was often referred to as ‘junk DNA’. We now know that intergenic DNA has key roles in regulating how genes function, an important and growing area of research.

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10
Q

What are the three building blocks that make up DNA?

A

phosphate
deoxyribose, a type of ribose sugar
base, a nitrogen-containing molecule; there are four bases in DNA, namely adenine, cytosine, guanine and thymine.

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11
Q

What are the 4 bases in DNA?

A

Adenine
Cytosine
Guanine
Thymine

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12
Q

What is a polymer?

A

You may be familiar with the term polymer, often used to describe certain plastics. A polymer is a long chain built up from smaller repeating units that are covalently linked together many times.

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13
Q

What is a monomer?

A

The small molecules that make up the polymer are known as monomers.

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14
Q

What is polymerisation?

A

The process of making polymers from monomers is called polymerisation

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15
Q

why is DNA described as a polymer?

A

DNA consists of multiple repeats of a unit composed of a phosphate, a deoxyribose sugar and a base.

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16
Q

What does a nucleotide consist of?

A

phosphate, a deoxyribose sugar and a base. Nucleotides are the monomers that polymerise to form DNA

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17
Q

What is a macromolecule?

A

A large molecule

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18
Q

What type of molecule is DNA described as?

A

A macro molecule

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19
Q

What is a phosphodiester bond?

A

The chemical bond that allows nucleotides to polymerise into DNA is one of the most important chemical bonds that you will study

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20
Q

What do phosphodiester bond link together in a nucleotide?

A

Phosphodiester bonds link the ribose sugar of one nucleotide to the phosphate of the second nucleotide.

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21
Q

What type of backbone does DNA be considered to have?

A

DNA is considered to have a ‘sugar–phosphate backbone’

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22
Q

What part of DNA is not involved in a phosphodiester bond?

A

nucleotide bases are not involved

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23
Q

What is the important number of carbon atoms for phsphodiester bonding?

A

By convention, ribose sugar carbon atoms are numbered. The important carbon atoms for phosphodiester bonding are the 3′ and 5′ carbons (pronounced ‘three prime’ and ‘five prime’). You will note that the phosphate group of each nucleotide is already linked to the 5′ carbon of its ribose sugar. Pay attention to these numbers, as they come up again and again!

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24
Q

How is a phosphodeister bond created?

A

A phosphodiester bond is created when the 3′ carbon of the first nucleotide forms a linkage to the phosphate of the second nucleotide. The reaction itself involves hydroxyl groups on each molecule (one on the 3′ carbon of the first nucleotide and another on the phosphate of the second nucleotide). ‘Group’ is the term used to describe a group of bound atoms that function together. A hydroxyl group is composed of an oxygen atom bound to a hydrogen atom (i.e. –OH)

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25
Q

What type of bonds are DNA strands held together by?

A

hydrogen bonding

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26
Q

Roughly how big is a typical human cell?

A

20 × 10−6 m

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27
Q

How can DNA be simplified to just 4 bases?

A

A, C, G and T These just repeat themselves and in any order

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28
Q

What has been observed when it comes to the ratios of bases of nucleotides?

A

The ratio of adenine to thymine (A:T) is always roughly 1, as is the ratio of cytosine to guanine (C:G). In other words, the amounts of adenine and thymine are always about the same, and the amounts of cytosine and guanine are always about the same.

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29
Q

Which bases are purines and which are pyrimidines?

A

The purines are adenine and guanine. The pyrimidines are cytosine and thymine.
Chargaff’s second observation was that the amounts of pyrimidines and purines are always about the same, with each comprising approximately 50% of the total. So: A ≈ T, C ≈ G, and pyrimidines (C + T) ≈ purines (A + G)

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30
Q

What is the iconic appearance of DNA?

A

double helix

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31
Q

What are the two grooves of a double helix called?

A

Major and minor grooves

32
Q

Why is the arrangement of DNA described as antiparrallel?

A

The strands run in opposite directions (the circles representing phosphate groups are top left in the left-hand strand, but bottom right on the right-hand strand).
the two strands are lined up next to each other, but whereas one strand runs from top-to-bottom, the other runs from bottom-to-top.

33
Q

The two strands of DNA are linked together by interactions between the bases. But how

A

Watson and Crick realised that the bases, when facing each other within the DNA double helix, would be capable of interacting via the formation of hydrogen bonds.

34
Q

What are hydrogen bonds?

A

As you learned in the Make me a molecule topic, hydrogen bonds are bonding interactions formed when a hydrogen atom that is covalently bound to an electronegative atom is in close proximity to another electronegative atom.

35
Q

How many hydrogen bonds are between adenine and thymine?

A

Adenine and thymine interact via two hydrogen bonds.

36
Q

How many hydrogen bonds are between cytosine and guanine?

A

Cytosine and guanine form three hydrogen bonds.

37
Q

In the Make me a molecule topic you learned the important hydrogen bonds in living things are the interactions between N–H bonds and N or O atoms, and interactions between O–H bonds and N or O atoms. What do you notice about the hydrogen bonds used in DNA base pairing?

A

The hydrogen bonds are either N–H bonds interacting with N atoms or N–H bonds interacting with O atoms. There are no O–H bonds involved in DNA base pairing!

38
Q

Why did the discovery that double-stranded DNA is formed by base pairs of adenine and thymine, and cytosine and guanine, indicate that Watson and Crick’s model must be correct?

A

Base pairing explains why Erwin Chargaff had found that the amounts of adenine and thymine are the same, and likewise the amounts of cytosine and guanine. And because each of these interactions involves a pyrimidine and a purine, base pairing also explains why Chargaff observed equal amounts of nucleotides containing pyrimidine and purine.`

39
Q

FLASH CARD

A

DNA is a polymer composed of monomers called nucleotides. Each nucleotide is itself composed of three parts: a phosphate group, a deoxyribose sugar, and one of four ‘bases’. Nucleotides are joined together into a polymer by phosphodiester bonds between the phosphate of one nucleotide and the deoxyribose sugar of the next.

40
Q

FLASH CARD

A

Chromosomes are like recipe books. Each chromosome contains many genes, each the recipe for a protein. The total of all the genetic information an organism possesses is its genome.

41
Q

FLASH CARD

A

The four nucleotide bases are adenine, cytosine, guanine and thymine, which can be abbreviated to A, C, G and T.

42
Q

FLASH CARD

A

Erwin Chargaff observed that in all living organisms, A and T are always present in equal amounts, and C and G are always present in equal amounts. Thus, the functions of A and T had to be linked, and likewise the functions of C and G were somehow dependent on each other.

43
Q

FLASH CARD

A

Watson and Crick made sense of Chargaff’s observations when they discovered the double helical structure of DNA. They realised that DNA is usually a double-stranded molecule, consisting of two antiparallel strands held together by hydrogen bonds between complementary pairs of nucleotides. Adenine base pairs with thymine via two hydrogen bonds, and cytosine base pairs with guanine via three hydrogen bonds.

44
Q

FLASH CARD

A

This structure allowed Watson and Crick to realise that the two strands of DNA in a chromosome are the inverse of each other, yet carry the same information, like a photo and its negative.

45
Q

What key features do all cells have in common?

A

they use DNA as their genetic material, and use this information to make proteins
they are composed of the same kinds of molecules – in particular the same four major types of macromolecules: nucleic acids, proteins, carbohydrates and lipids
they require a supply of energy.

46
Q

What are organelles?

A

The membranous structure that encloses a cell, in eukaryotic organisms

47
Q

What is the cytosol in a cell?

A

The liquid part of a cell

48
Q

What is the cytoplasm of a cell?

A

In cells with nuclei, the cytosol and the organelles outside the nucleus are collectively referred to as the cytoplasm.

49
Q

Probably the most obvious thing all cells have in common is that they are living. And like all living things, at least at some point in their lives, they must grow.

Think of two ways in which an organism composed of cells can grow?

A

Cells can grow by simply getting bigger, or by dividing and increasing in number.

50
Q

What does the division of one cell into two require?

A

The division of one cell into two requires all the components of the ‘mother’ cell to be divided equally between the two daughter cells.

51
Q

What is a cell cycle?

A

In eukaryotic organisms, cells grow and divide according to a programme of events called the cell cycle

52
Q

What are The two most important stages of the cell cycle for DNA replication?

A

The two most important stages of the cell cycle for DNA replication are the S-phase, which stands for synthesis, and the M-phase, which stands for mitosis.

53
Q

What does the S phase in a cell cycle stand for?

A

the S-phase, which stands for synthesis,

54
Q

What does the M phase in a cell cycle stand for?

A

the M-phase, which stands for mitosis.

55
Q

Why are S-phase and M-phase the two most important stages of the cell cycle for DNA replication?

A

S-phase is where the genome is copied, and M-phase is where the copies are separated into two nuclei.

56
Q

cells from a piece of garlic. Nuclei were visible in some cells, but in others the nuclei appeared to have been replaced by chromosomes. Given what you’ve just learned about the cell cycle, what can you say about the cells where chromosomes are visible?

A

Cells with chromosomes visible are in mitosis. The membrane surrounding the nucleus has broken down and the chromosomes have condensed and become visible. (Note that the chromosomes are always there, they just become more visible during mitosis.)

57
Q

The principle of cell division by mitosis is quite straightforward. The cell copies everything essential and then divides into two to produce diploid cells.

What does diploid mean?

A

Diploid refers to cells or organisms that have two identical sets of chromosomes

58
Q

What does haploid mean?

A

Haploid describes cells with just one copy of each chromosome

59
Q

What is the one exception where cell division does not involve DNA replication?

A

a type of cell division that is designed to produce haploid cells.

60
Q

How much DNA is this compared with the amount in a ‘normal’ diploid cell?

A

It is half the amount of DNA found in a diploid cell.

61
Q

How many chromosomes are found in a haploid human cell?

A

There are 23 chromosomes in a haploid cell (and 23 chromosome pairs in a diploid cell).

62
Q

What types of cell are typically haploid?

A

Gametes, the highly specialised cells used in sexual reproduction.

63
Q

Name a type of gamete?

A

Egg cells or sperm cells.

64
Q

What cells are made through meiosis?

A

Sperm and egg cells are made by a process distinct from mitosis called meiosis. You will learn more about meiosis in future study, but it can be thought of as cell division without prior DNA replication. Meiosis creates the two types of cell that come together to make a new cell (a fertilised egg) with a full, diploid genome. This new cell then begins a series of processes that trigger mitosis, and an embryo begins to develop.

65
Q

What is an enzyme?

A

a biological catalyst, that is, a molecule that increases the rate of a chemical reaction. In this case, enzymes increase the rates of reaction to make them very, very fast indeed!

66
Q

What are the 3 most important enzymes?

A

DNA helicase
DNA polymerase
DNA ligase.

67
Q

What property of double-stranded DNA do you think is most essential to DNA replication?

A

Complementarity.

68
Q

Imagine a piece of double-stranded DNA with two strands – A and B. Due to the power of complementarity, strand A can be used as a template to make a new copy of strand B, and strand B can be used as a template to make a new copy of strand A.
What do you think is the first step in the process?

A

The double-stranded DNA needs to be separated into two single strands.

69
Q

What is the key enzyme in this first step of DNA replication?

A

DNA helicase

70
Q

How does DNA helicase help with replication?

A

DNA helicase binds to double-stranded DNA and moves along it; as DNA helicase moves, it separates the DNA into two strands.

71
Q

What is a replication fork?

A

The point at which the double-stranded DNA is separated into single strands

72
Q

What are parent strands?

A

The key enzyme in this first step of DNA replication is DNA helicase. DNA helicase binds to double-stranded DNA and moves along it; as DNA helicase moves, it separates the DNA into two strands. The point at which the double-stranded DNA is separated into single strands is known as a replication fork. These strands become known as parent strands because they originate from the parent DNA.

73
Q

DNA polymerase associates with the exposed bases of the parental strands.

Thinking about the name of this enzyme and what you have learned already about the composition of DNA, what do you think DNA polymerase does?

A

DNA polymerase converts nucleotide monomers into DNA polymers. In other words, it is the enzyme responsible for synthesising new DNA.

74
Q

DNA polymerase moves along the parental strand, using the unpaired bases of the parent strand as a template to synthesise a new strand of DNA by base pairing. For example, where there is an unpaired thymine in the parent strand, DNA polymerase adds a complementary adenine to the new strand.

If DNA encounters an unpaired guanine on the parent strand, which base will be added to the new strand?

A

Cytosine, because cytosine is the complementary base to guanine.

75
Q

What term is used to describe the opposite strands?

A

anti parallel

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