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The Lego Bricks Of Life > Molecular basics > Flashcards

Molecular basics Flashcards

1
Q

What is the whole name for DNA?

A

Desoxyribonucleic acid

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2
Q

What are the building blocks of DNA?

A

Sugar, Nitrogenous bases/ Nucleobases, Phosphate

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3
Q

What type of sugar does DNA contain?

A

Desoxyribose (Desoxy- because at C5 an oxygen is missing)

It is a beta-pentose

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4
Q

How can you classify the nitrogenous bases of DNA?

A

Purine (Two-Ring bases) A, G

Pyrimidine (Single-Ring bases) T, C

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5
Q

What are the Names of the purine bases?

A

Adenine and Guanine

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6
Q

What are the names of the pyrimidine bases?

A

Thymine and Cytosine

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7
Q

What is the correct complementary base pairing in DNA?

A

Adenine + Thymine

Guanine + Cytosine

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8
Q

What are the bonds between the nitrogenous bases?

A

Hydrogen bonds

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9
Q

How many hydrogen bonds are between Adenine and Thymine?

A

2

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10
Q

How many hydrogen bonds are between Guanine and Cytosine?

A

3 (more energy is needed to separate the bases)

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11
Q

What is the role of phosphate in the DNA?

A

It connects sugars over phosphodiester bonds

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12
Q

What is a Nucleoside?

A

Sugar and base

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13
Q

What is a Nucleotide?

A

Sugar, base and phosphate

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14
Q

What is the backbone of the DNA composed of and how is it connected?

A

It is composed of sugar (desoxyribose) and phosphate.

C3 of the sugar is linked to the C5 of the next sugar by phosphodiester bonds.

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15
Q

What is the Nucleoside of Adenine?

A

Adenosine

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16
Q

What is the Nucleoside of Guanine?

A

Guanosine

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17
Q

What is the Nucleoside of Thymine?

A

Thymidine

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18
Q

What is the Nucleoside of Cytosine?

A

Cytidine

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19
Q

What is the Nucleoside of Uracil?

A

Uridine

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20
Q

How and where is the DNA of prokaryotes stored?

A
  • In the cytoplasm (they don’t have a nucleus)
  • Only coding DNA
  • 1 circular molecule
  • Supercoiling to reduce length
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21
Q

What is negative and what is positive Supercoiling?

Wich enzyme is responsible for this process?

A

Negative Supercoiling:
- DNA has one turn less

Positive Supercoiling:
- DNA has one turn more

Introducing or removing turns lead to DNA molecule turning around itself. That reduces the length of the DNA.

Topoisomerase is responsible for supercoiling.

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22
Q

What is the general structure of the DNA?

A
  • The DNA is a double Helix
  • The DNA hat antiparallel strands
  • The DNA consists of sugar, bases and phosphate
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23
Q

How and where is DNA in Eukaryotes stored?

A
  • DNA is stored in the nucleus
  • DNA coils around Histones -> Nucleosome
  • Fiber packed of nucleosomes: Chromatin
  • Nonhistone proteins form chromatin loops
    (While Mitosis: Condensed chromatin loops form a chromosome)
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24
Q

What is the structure and what are the compounds of a Histone?

A
  • A histone is a octamer (consists of 8 proteins)
    Octamer of core histones: H2A, H2B, H3, H4 (Each one 2x)

Histone H1 stabilizes

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25
Q

How often does the eukaryotic DNA wrap around a histone?

A

Twice

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26
Q

What are the two types of chromatin?

A

Heterochromatin and Euchromatin

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27
Q

What is the difference between heterochromatin and euchromatin?

A

Heterochromatin: Light part in the nucleus: low density (reduced level of H1)
Euchromatin: Dark part of the nucleus: high density (high level of H1; not transcripted)

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28
Q

What kind of proteins form the chromatin loops of eukaryotic DNA

A

Nonhistone Proteins

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29
Q

How many chromosomes make up the human genome?

A

23 Chromosome pairs, so in total 46 chromosomes

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30
Q

What is the genome?

A

A cells set of DNA

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31
Q

How can you classify chromosomes? (Two types)

A

Autonomes (Chromosomes of pairs 1-22)

Allosomes (Chromosomes of pair 23): Sex chromosomes

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32
Q

How do you call the graphic representation of a human genome?

A

Karyogram

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33
Q

A gene always carries….?

A

Exons and Introns

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34
Q

How do you call the protein complex, that is responsible for the DNA replication?

A

Replisome

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35
Q

How is DNA replicated?

A

DNA is replicated semiconservative, Bidirectional, semidiscontinuous and each strand is a template for a new strand.

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36
Q

Wich enzyme unzips the DNA while replication?

A

Helicase

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37
Q

How does the enzyme Helicase unzip the DNA?

A

It unzips and separates the DNA strands by breaking of the hydrogen bonds between the bases at a origin of replication.

38
Q

What is a origin of replication?

A

It is a special sequence (e.g. TATA-Box in prokaryotes). Helicase recognizes this sequence and separates the two DNA strands.

39
Q

How do you call the crotch of the two DNA strands while replication?

A

Replication fork

40
Q

Wich proteins keep the DNA strands apart each other while DNA replication?

A

Single-strand binding Proteins

41
Q

What are the steps of DNA replication?

A
  • Topoisomerase removes supercoils in double helix
  • Helicase unwinds and separates DNA at origin of replication
  • Single-strand binding proteins keep strands apart
  • Primase/RNA-polymerase synthesizes primers of RNA (3‘ -> 5‘)
    (Leading strand: 1; Lagging strand: Many)
  • DNA polymerase 3 synthesizes new strand with complementary nucleotides (3’ -> 5’)
    (Leading strand: Continuously towards replication fork; Lagging: Discontinuously against replication fork (Okazaki fragments))
  • DNA Polymerase 1 replaces primers with DNA
  • Lagging strand: Ligase connects Okazaki fragments trough phosphodiester bonds
42
Q

Wich proteins are part of the Replisome?

A

Topoisomerase, Helicase, Single-strand binding proteins, Primase/RNA-Polymerase, DNA polymerase III, DNA polymerase I, Ligase

43
Q

What is the primosome?

A

While the DNA replication the Primase/RNA polymerase attaches to the Helicase and forms the primosome.

44
Q

What is the responsibility of RNA polymerase/Primase while DNA replication?

A

It synthesizes primers of about 20 nucleotides length consisting of RNA in 5‘ to 3‘ direction.

45
Q

What are the properties of DNA Polymerase III ?

A
  • It polymerizes complementary nucleotides from the cytoplasm starting from the primers
  • Synthesizes nucleotides in 5‘ to 3‘ direction
  • It splits off diphosphate of the triphosphate to release energy (5‘)
  • It has a 3‘5‘Exonuclease ability (It proofreads the DNA in 3‘ to 5‘ direction for possible errors and fixes them)
46
Q

What is a Telomere?

A

Telomeres prevent the loss of genes as chromosome ends wear down, the tips of eukaryotic chromosomes have specialized DNA-Caps.
Hundreds to thousands repeats of the same short DNA sequence
(In humans often 5‘-TTAGGG-3‘)

47
Q

What are different types of carbohydrates?

A

Mono-, di-, tri-, oligo-(3-9), polysaccharides (more than 9)

48
Q

What is the general formula for a monosaccharide?

A

CxHxOx

49
Q

Names for different monosaccharides based on the number of carbons:

A

C3: Triose
C4: Tetrose
C5: Pentose
C6: Hexose

50
Q

When is a sugar a Ketose and when an Aldose?

A

Ketose: ketone group (C=O in the middle)
Aldose: aldehyde group (C=O at the end)

51
Q

What is the difference between L and D sugars?

A

E.g.: D-Glucose is the enatiomer of L-Glucose
For a sugar drawn in the fisher projection with the most oxidized carbon at the top:
- D: If the OH on the bottom chiral centre is on the right
- L: If the OH on the bottom chiral centre is on the left

52
Q

What is a chiral centre?

A

An atom that has four different groups bonded to it in such a manner that is has a non-superimposable mirror image.

53
Q

What is an enatiomer?

A

One of two molecules, that are mirror images of each other and are non-superposable.
They have identical chemical and physical properties except for their ability to rotate plane-polarized light (+/-) by equal amounts but in opposite directions.

54
Q

What is the name for a 5-memered sugar ring?

A

Furanose

55
Q

What is the name for a 6-memered sugar ring?

A

Pyranose

56
Q

What is the name for the reaction when a disaccharide is formed?

A

Dehydration between the OH groups of C1 and C4

57
Q

What are two types of glycosidic bonds?

A

Alpha (Both H above) and Beta (One H above and one H under)

58
Q

Trough wich bond are monosaccharides connected?

A

Glycosidic bond

59
Q

What are common disaccharides?

A

Lactose (Galactose+Glucose), Maltose (Glucose+Glucose), sucrose (Glucose+Fructose)

60
Q

What are common Polysaccharides?

A

Glycogen (Beta(1-4)-glucopyranose), Starch (Alpha(1-4)-Glucopyranose)

61
Q

What are the functions of sugar in the human body?

A
  • Energy source (Sugars are processed into glucose wich acts as a source of energy)
  • Energy storage (Limited amount is stored in the liver and muscles as Glycogen; excess is turned into fat)
  • Building macromolecules ( Glucose is also converted to ribose and desoxyribose -> compounds of DNA and RNA and ATP)
  • Signaling
  • Structural compound
62
Q

How does the body metabolize sugars?

A

Mouth+Small intestine:
Amylase breaks down polysaccharide chains to disaccharides; Sucrase, maltase and lactase break them further down to monosaccharides

Liver: Carbohydrates enter the liver trough transport proteins, where they are broken down and stored as glycogen or released back in the brood.

63
Q

What is the structure of a fatty acids?

A

Have both, hydrophobic and hydrophilic compounds. The hydrophobic hydrocarbon chain is attached to a hydrophilic carboxylic acid group (COO-)

64
Q

What is the difference between saturated and unsaturated fatty acids?

A

Saturated: No double bonds
Unsaturated: Double bonds

65
Q

What are different types of unsaturated fatty acids?

A

Monounsaturated: Only one double bond
Polyunsaturated: Multiple double bonds
Cis: Both H on one side
Trans: H‘s on different sides

66
Q

How can you classify mutations in general?

A
  • Hereditary (germline) mutations

- Acquired (somatic) mutations

67
Q

What is a Hereditary (germline) mutation?

A
  • Inherent from a parent

- Present in every cell of the body

68
Q

What is an Acquired (somatic) mutation?

A
  • Occur at some point of a persons life
  • present in certain cells
  • Caused by environmental factors
  • Only affect one individual
69
Q

What is a point mutation?

A

A change of one or a few base pairs, that only affect one codon.

70
Q

What are the two general categories of point mutations?

A
  • Base pair Substitutions

- Base pair deletions or insertions

71
Q

What are the two types of base-pair substitution mutations?

A
  • Transition mutation: From one purine-pyrimidine base pair to the other. (Such as A-T to G-C)
  • Transversion mutation: Purine-pyrimidine to pyrimidine-purine (such as G-C to C-G)
72
Q

What is a missense mutation?

A

Mutation leads to change from one amino acid to another

73
Q

What is a Nonsense Mutation?

A

Change from an amino acid to a stop codon

74
Q

What is a neutral mutation?

A

Change from an amino acid to another amino acid with similar chemical properties.

75
Q

What is a silent mutation?

A

Change in codon such that the same amino acid is specified.

76
Q

What is a frameshift mutation?

A

Insertion or deletion of base pairs wich involve a non-multiple of three DNA base pairs.
Leads to a change in the reading frame

77
Q

What are the two types of insertion or deletion mutations?

A
  • Frameshift

- In-Frame

78
Q

What is a promoter mutation?

A

May block or activate transcription

79
Q

What is a splice site mutation?

A

May block splicing or create new splice signals

80
Q

What are the three phases of transcription?

A

Initiation
Elongation
Termination

81
Q

Where does transcription take place?

A

EU: Nucleus
PRO: Cytoplasm

82
Q

What happens while Initiation of transcription?

A

RNA-Polymerase holoenzyme (enzyme+cofactor) separates DNA strands and binds to promoter (includes TATA box) of the antisense strand (template strand).
It is detected by the sigma factor.
Synthesis of a short RNA primer

83
Q

What is a different name for template strand?

A

Antisense strand

84
Q

What happens while the elongation of transcription?

A

RNA polymerase polymerizes complementary RNA nucleotides.
(Matching the coding strand and complementary to the template strand)
It also catalyzes the formation of phosphodiester bonds in 5‘ to 3‘ direction.

DNA-RNA hybrid

85
Q

What happens while the termination of transcription in prokaryotes?

A

After reaching the terminator sequence (GC rich region) at the end of a gene, the RNA polymerase releases the newly synthesized RNA strand.
Rho-dependent: a Rho-Factor recognizes sequence and leads to the detachment of polymerase
Rho-independent: Formation of hairpin structure because of certain sequence of nucleotides (complementary) leads to destabilizing.

86
Q

What happens while termination of transcription in Eukaryotes?

A

After reaching the terminator sequence (GC rich region) at the end of a gene, the RNA polymerase releases the newly synthesized RNA strand.

  • Enzyme recognizes a certain RNA sequence and binds
  • Enzyme makes a cut (10-30 nucleotides downstream) and creates a new 3‘ end
  • PAP (polyA polymerase) synthesizes many A nucleotides to the end (50-250)
  • PAB (polyA binding protein) binds to poly A tail and increases stability
87
Q

What is meant by post transcriptional processing of mRNA?

A 
Happens in the nucleus eukaryotes:
5‘-capping
3‘-Polyadenylation
=> Loop formation of mRNA
Splicing
88
Q

Wich enzymes cut out the introns of mRNA?

A

Snurps

89
Q

What is meant by alternative splicing?

A

Introns are always removed, exons can be removed.

Its possible to make different proteins out of one mRNA

90
Q

What are the three terminator sequences of translation?

A

UAA, UAG, UGA

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