Molecular basics Flashcards
1
Q
What is the whole name for DNA?
A
Desoxyribonucleic acid
2
Q
What are the building blocks of DNA?
A
Sugar, Nitrogenous bases/ Nucleobases, Phosphate
3
Q
What type of sugar does DNA contain?
A
Desoxyribose (Desoxy- because at C5 an oxygen is missing)
It is a beta-pentose
4
Q
How can you classify the nitrogenous bases of DNA?
A
Purine (Two-Ring bases) A, G
Pyrimidine (Single-Ring bases) T, C
5
Q
What are the Names of the purine bases?
A
Adenine and Guanine
6
Q
What are the names of the pyrimidine bases?
A
Thymine and Cytosine
7
Q
What is the correct complementary base pairing in DNA?
A
Adenine + Thymine
Guanine + Cytosine
8
Q
What are the bonds between the nitrogenous bases?
A
Hydrogen bonds
9
Q
How many hydrogen bonds are between Adenine and Thymine?
A
2
10
Q
How many hydrogen bonds are between Guanine and Cytosine?
A
3 (more energy is needed to separate the bases)
11
Q
What is the role of phosphate in the DNA?
A
It connects sugars over phosphodiester bonds
12
Q
What is a Nucleoside?
A
Sugar and base
13
Q
What is a Nucleotide?
A
Sugar, base and phosphate
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.
15
Q
What is the Nucleoside of Adenine?
A
Adenosine
16
Q
What is the Nucleoside of Guanine?
A
Guanosine
17
Q
What is the Nucleoside of Thymine?
A
Thymidine
18
Q
What is the Nucleoside of Cytosine?
A
Cytidine
19
Q
What is the Nucleoside of Uracil?
A
Uridine
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
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.
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
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)
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
25
How often does the eukaryotic DNA wrap around a histone?
Twice
26
What are the two types of chromatin?
Heterochromatin and Euchromatin
27
What is the difference between heterochromatin and euchromatin?
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)
28
What kind of proteins form the chromatin loops of eukaryotic DNA
Nonhistone Proteins
29
How many chromosomes make up the human genome?
23 Chromosome pairs, so in total 46 chromosomes
30
What is the genome?
A cells set of DNA
31
How can you classify chromosomes? (Two types)
Autonomes (Chromosomes of pairs 1-22)
| Allosomes (Chromosomes of pair 23): Sex chromosomes
32
How do you call the graphic representation of a human genome?
Karyogram
33
A gene always carries....?
Exons and Introns
34
How do you call the protein complex, that is responsible for the DNA replication?
Replisome
35
How is DNA replicated?
DNA is replicated semiconservative, Bidirectional, semidiscontinuous and each strand is a template for a new strand.
36
Wich enzyme unzips the DNA while replication?
Helicase
37
How does the enzyme Helicase unzip the DNA?
It unzips and separates the DNA strands by breaking of the hydrogen bonds between the bases at a origin of replication.
38
What is a origin of replication?
It is a special sequence (e.g. TATA-Box in prokaryotes). Helicase recognizes this sequence and separates the two DNA strands.
39
How do you call the crotch of the two DNA strands while replication?
Replication fork
40
Wich proteins keep the DNA strands apart each other while DNA replication?
Single-strand binding Proteins
41
What are the steps of DNA replication?
- 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
Wich proteins are part of the Replisome?
Topoisomerase, Helicase, Single-strand binding proteins, Primase/RNA-Polymerase, DNA polymerase III, DNA polymerase I, Ligase
43
What is the primosome?
While the DNA replication the Primase/RNA polymerase attaches to the Helicase and forms the primosome.
44
What is the responsibility of RNA polymerase/Primase while DNA replication?
It synthesizes primers of about 20 nucleotides length consisting of RNA in 5‘ to 3‘ direction.
45
What are the properties of DNA Polymerase III ?
- 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
What is a Telomere?
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
What are different types of carbohydrates?
Mono-, di-, tri-, oligo-(3-9), polysaccharides (more than 9)
48
What is the general formula for a monosaccharide?
CxHxOx
49
Names for different monosaccharides based on the number of carbons:
C3: Triose
C4: Tetrose
C5: Pentose
C6: Hexose
50
When is a sugar a Ketose and when an Aldose?
Ketose: ketone group (C=O in the middle)
Aldose: aldehyde group (C=O at the end)
51
What is the difference between L and D sugars?
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
What is a chiral centre?
An atom that has four different groups bonded to it in such a manner that is has a non-superimposable mirror image.
53
What is an enatiomer?
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
What is the name for a 5-memered sugar ring?
Furanose
55
What is the name for a 6-memered sugar ring?
Pyranose
56
What is the name for the reaction when a disaccharide is formed?
Dehydration between the OH groups of C1 and C4
57
What are two types of glycosidic bonds?
Alpha (Both H above) and Beta (One H above and one H under)
58
Trough wich bond are monosaccharides connected?
Glycosidic bond
59
What are common disaccharides?
Lactose (Galactose+Glucose), Maltose (Glucose+Glucose), sucrose (Glucose+Fructose)
60
What are common Polysaccharides?
Glycogen (Beta(1-4)-glucopyranose), Starch (Alpha(1-4)-Glucopyranose)
61
What are the functions of sugar in the human body?
- 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
How does the body metabolize sugars?
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
What is the structure of a fatty acids?
Have both, hydrophobic and hydrophilic compounds. The hydrophobic hydrocarbon chain is attached to a hydrophilic carboxylic acid group (COO-)
64
What is the difference between saturated and unsaturated fatty acids?
Saturated: No double bonds
Unsaturated: Double bonds
65
What are different types of unsaturated fatty acids?
Monounsaturated: Only one double bond
Polyunsaturated: Multiple double bonds
Cis: Both H on one side
Trans: H‘s on different sides
66
How can you classify mutations in general?
- Hereditary (germline) mutations
| - Acquired (somatic) mutations
67
What is a Hereditary (germline) mutation?
- Inherent from a parent
| - Present in every cell of the body
68
What is an Acquired (somatic) mutation?
- Occur at some point of a persons life
- present in certain cells
- Caused by environmental factors
- Only affect one individual
69
What is a point mutation?
A change of one or a few base pairs, that only affect one codon.
70
What are the two general categories of point mutations?
- Base pair Substitutions
| - Base pair deletions or insertions
71
What are the two types of base-pair substitution mutations?
- 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
What is a missense mutation?
Mutation leads to change from one amino acid to another
73
What is a Nonsense Mutation?
Change from an amino acid to a stop codon
74
What is a neutral mutation?
Change from an amino acid to another amino acid with similar chemical properties.
75
What is a silent mutation?
Change in codon such that the same amino acid is specified.
76
What is a frameshift mutation?
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
What are the two types of insertion or deletion mutations?
- Frameshift
| - In-Frame
78
What is a promoter mutation?
May block or activate transcription
79
What is a splice site mutation?
May block splicing or create new splice signals
80
What are the three phases of transcription?
Initiation
Elongation
Termination
81
Where does transcription take place?
EU: Nucleus
PRO: Cytoplasm
82
What happens while Initiation of transcription?
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
What is a different name for template strand?
Antisense strand
84
What happens while the elongation of transcription?
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
What happens while the termination of transcription in prokaryotes?
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
What happens while termination of transcription in Eukaryotes?
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
What is meant by post transcriptional processing of mRNA?
```
Happens in the nucleus eukaryotes:
5‘-capping
3‘-Polyadenylation
=> Loop formation of mRNA
Splicing
```
88
Wich enzymes cut out the introns of mRNA?
Snurps
89
What is meant by alternative splicing?
Introns are always removed, exons can be removed.
| Its possible to make different proteins out of one mRNA
90
What are the three terminator sequences of translation?
UAA, UAG, UGA
