Cell Bio- Dna: Genes, Replication, Repair

Front 1

What is genetic information?

Back 1

Internal information of cell which is passed on from parental cell to daughter cell. It represents information concerning the structure and function of the cell, including the function of the cell in the framework of an organism.

Front 2

Requirement of genetic information?

Back 2

- Must be lasting and stable enough
- Must be capable of changing during evolution
- Must be able to reproduce and be easily available for realization (expression)

Front 3

Genophore?

Back 3

- Carrier of genetic information
- In cells the genophore is DNA
- In some viruses it may be RNA

Front 4

Structure of DNA:

Back 4

A polymer of nucleotides. Usually contain two polynucleotide chains forming a double helix.

Front 5

Nucleotide:

Back 5

Nitrogen containing base+ sugar pentose+ phosphate

Front 6

Nucleoside:

Back 6

Nitrogen- containing base+ pentose sugar

Front 7

Bases in DNA:

Back 7

A adenine, G guanine (purines)
C cytosine, T thymine (purimidines)

Front 8

Binding of polynucleotides:

Back 8

Phosphodiester bond between the OH group on the 3` carbon of one deoxyribose and the 5` carbons phosphate on another deoxyribose

Front 9

What does complementary and antiparalell mean?

Back 9

- Complementary means that a base from one chain always binds specifically with a base from the other chain
- Antiparalell means that one strand goes in 5` end to 3`prime end and the other one 3`end to 5`end

Front 10

How is DNA present within the cell?

Back 10

As chromosomes (big amount of comprised genetic information) or in the form of plasmids (small amount of comprised genetic information)

Front 11

Prokaryotic chromosome:

Back 11

- 1 chromosome
- Circular
- 10 to 6- 10 to 7 base pairs
- attached to the plasma membrane of the cell at one specific point
- contains proteins (some similar to histones of eukaryotes)

Front 12

Eukaryotic chromosomes:

Back 12

- Many chromosomes
- linear
- 10 to the 8 base pairs
- human genome: 5,25 * 10 to the 7th base pairs
- located in the nucleus of the cell
- contain histone proteins (basic proteins that contain many basic aminoacids, lysine and arginine)
- acidic proteins (non- histone proteins)

Front 13

Histones:

Back 13

H1, H2A, H2B, H3 and H4
All these 5 types of histones are present on each chromosome and are all involved in the basic structure of eukaryotic chromosomes

Front 14

Acidic proteins:

Back 14

Heterogenous group of proteins all probably involved in the three dimensional structure of chromosomes

Front 15

What is the basic structural unit of eukaryotic chromosomes

Back 15

Nucleosome

Front 16

Structure of a nucleosome:

Back 16

- The core is made up of octamer of histones: (H2A, H2B, H3 and H4) *2.
- DNA is wound around the core
- 146 base pairs long DNA is wound around the core, and there is 60 free base pairs between two nucleosomes
- Thus there are about 200 base pairs/ nucleosome
- Individual histones are joined by histone H1

Front 17

Structural levels of eukaryotic chromosomes: (6)

Back 17

1. Double helix of DNA (the diameter of fiber is 2nm)
2. Nucleosomes with bound DNA (11nm)
3. Chromatin fiber (30nm)
4. Chromatin loops (300nm)
5. Condensed part of chromosome (chromatid) (700nm)
6. Entire metaphase chromosome (1400nm)

Front 18

Why is metaphase chromosome 10 000 times shorter then chromosomes in extended form?

Back 18

Because of condensation

Front 19

Basic structure of metaphase chromosome:

Back 19

2 chromatids, centromere and telomeres

Front 20

What are plasmids?
Where are they usually found?

Back 20

Plasmids are cytoplasmic genophores which do not carry genetic information indispensable for the function of the cell (vital genetic information is in chromosomes)
Usually found in prokaryotes.

Front 21

Structure of prokaryotic plasmids:

Back 21

Circular double stranded DNA, 1,5- 200* 10 to the third base pairs

Front 22

Types of prokaryotic plasmids:

Back 22

- F (fertile) plasmids: necessary for the conjugation of bacteria (the exchange of genetic information)
- R (resistance) plasmids: they produce resistance against antibiotics and chemotherapeutic
- Col plasmids: they provide the capability of producing proteins colicins which can kill other bacteria

Front 23

What is genetic information?

Back 23

A sequence of individual bases that encodes the sequence of amino- acids (the primary structure of cell proteins) It means that the sequence of bases in DNA determines the sequence of amino- acids in the relevant protein.

Front 24

What is a genetic code?

Back 24

A rule by which certain sequences of bases determines relevant amino- acids.

Front 25

How many amino- acids are encoded in an organism?

Back 25

20

Front 26

What is a triplet?

Back 26

A triplet is a sequence of 3 bases that determine one amino- acid.
The genetic code is based on triplets

Front 27

How many combinations of triplets (codons) are there?
And how many of these triplets encode amino- acids?

Back 27

There are 4 bases (4 to the third)= 64 combinations of triplets.
61 triplets encode amino-acids

Front 28

What is the function of the remaining 3 triplets (codons) that do not encode amino- acids?

Back 28

They function as stop codons

Front 29

What is the initiation codon?

Back 29

Methionine

Front 30

How many triplets can one amino- acid be encoded from?

Back 30

1-6 triplets (codons), because 61 triplets encode only 20 amino- acids

Front 31

How many codons encode:
1. Methionine
2. Tryptophan
3. Leucine
4. Serine
5. Arginine

Back 31

1. Methionine: 1 codon
2. Tryptophan: 1 codon
3: Leucine: 6 codons
4: Serine: 6 codons
5: Arginine: 6 codons

Front 32

What does it mean that "Genetic code is redundant"?

Back 32

That one amino- acid can be coded by several triplets

Front 33

What does it mean that the genetic code is "universal"?

Back 33

It means that all organisms use the same triplet (codon) for the same amino- acid

Front 34

What is the "reading frame"?

Back 34

One of three possibilities a how a sequence of triplets can be read

Front 35

Gene?

Back 35

A gene is a segment of DNA (or RNA) which encodes a single polypetide chain (protein) or a single RNA chain (rRNA, tRNA)

Front 36

What is a gene locus?

Back 36

A stable site within the sequence of the relevant chromosome. A specific site where the gene is located on the chromosome

Front 37

Structural genes:

Back 37

Encode proteins

Front 38

Genes for RNA:

Back 38

They encode RNA which is not a template for translation (rRNA & tRNA)

Front 39

DNA regulatory region:

Back 39

They do not encode proteins as well as RNA, but they carry information for binding specific molecules regulating gene expression

Front 40

Prokaryotic gene contains:

Back 40

it contains uninterrupted DNA sequence that encodes corresponding polypeptide chain

Front 41

Eukaryotic gene:

Back 41

it contains coding DNA sequences (exons), which are interrupted by non- coding sequences (introns)
Human gene comprises about 3* 10 to the 4th base pairs

Front 42

Non- gene DNA, how large part of DNA are genes that are expressed?

Back 42

In mammalian cells, genes which are expressed represents only 7-10% of the entire DNA

Front 43

Regulatory regions:

Back 43

are involved in regulation of expression

Front 44

Repetitive sequences function?

Back 44

they are involved in the regulation of expression

Front 45

Mobile elements (transposons):

Back 45

they do not show a stable position within DNA sequence

Front 46

Pseudogenes:

Back 46

Genes which lost their function due to accumulation of mutations

Front 47

Genome:

Back 47

Genome is the complete set of DNA (set of all genophores) of the cell (organism)

Front 48

Genome of prokaryotic cell consists of:

Back 48

chromosome + possible plasmids

Front 49

Genome of eukaryotic cell consists of?

Back 49

- Nuclear chromosome
- Mitochondrial chromosome
- Chloroplast chromosome (in plants)
- Possibly plasmids (only in some cases)

Front 50

How many genes do the human genome contain? (haploid set)

Back 50

30 000 genes

Front 51

What is DNA replication?

Back 51

DNA replication is doubling of DNA. Two identical double helixes of DNA are derived from one original double helix of DNA. It means that entire genetic information is saved in two double helixes of DNA

Front 52

What does it mean that DNA replication has a semiconservative character?

Back 52

It means that a new strand is synthesized on the basis of complementary pairing according to each of both original strands of the double helix. The original strand functions as a template.

Front 53

Replicon:

Back 53

a specific sequence of DNA (rich in A-T base pairs) where replication starts after unwinding the double helix. It happens after binding of initiator proteins.

Front 54

Replication fork:

Back 54

From replication origin replication continues in both directions. It results in TWO replication forks (the shape of letter Y) which are moving apart.

Front 55

Speed of prokaryotic chromosome replication fork:

Back 55

1000 bp/s (base pairs/ second)

Front 56

Speed of eukaryotic chromosome replication fork:

Back 56

100 bp/s

Front 57

What is the function of DNA polymerase?

Back 57

Catalyze the formation of phosphodiester bonds between two nucleotides (between the 3`end of the deoxyribose on one nucleotide and the 5`end of the deoxyribose of another nucleotide via relevant phosphate)

Front 58

Process of adding of base pairs:

Back 58

1. Nucleotide is added to the new growing DNA strand and binds complementary by its base to the relevant nucleotide of the template
2. Then the nucleotide forms phosphodiester bonds with the previous nucleotide of the growing strand

Front 59

In what form do the nucleotides enter the polymerization reaction?

Back 59

As nucleoside triphosphate s. (ATP, CTP, GTP, TTP)

Front 60

Where do we get the energy for this reaction?

Back 60

From the freeing of pyrophosphate (PPi)

Front 61

Limitation of DNA polymerase?

Back 61

1. It can synthesize new DNA strand in only 5`- 3`direction. That means according to the template in 3`- 5`.
2. It is unable to start synthesis of new DNA strand. It can only extend existing of nucleic acid.

Front 62

Types of DNA polymerase in eukaryotic cells:

Back 62

- DNA polymerase α
- DNA polymerase δ
and other types (DNA polymerase β, DNA polymerase γ).

Front 63

The mechanism of DNA replication: (5)

Back 63

1. After binding to the replication origin, enzyme helicase unwinds the double helix of DNA (with energy from ATP)
2. Single- strand binding protein molecules stabilize single strand of DNA.
3. The replication is started by enzyme primase, which produces a short strand of RNA referred to as primer.
4. Protein known as sliding clamp keeps DNA polymerase attached to the template strand and it allows DNA polymerase to slide along the template strand.
5. The synthesis of new strand in 5`- 3`direction on 3`- 5`template runs continuously (DNA polymerase δ): the leading strand.

Front 64

The mechanism of DNA replication: (continued)

Back 64

6. The synthesis of new strand in 3´- 5`direction on the 5`- 3`template runs discontinously(DNA polymerase α): the lagging strand. DNA polymerase "skips" here forward along the template and then it synthesizes backward in the proper 5`- 3`direction.

Front 65

What is an Okazaki fragment?
+ the mechanism of DNA replication continued.

Back 65

- The synthesis of new strand (lagging strand) is done piece after piece. These pieces are called "Okazaki fragments".
- Each fragment starts with its own primer.
7. Afterwards, RNA primers are removed and missing DNA is synthesized by relevant DNA polymerase.
8. Finally, individual fragments are joined by enzyme DNA ligase.

Front 66

Ho many base pairs in eukaryotic and prokaryotic primers:

Back 66

Eukaryotic cell primer: 10 bp
Prokaryotic cell primer: 5 bp

Front 67

What is the function of a primer?

Back 67

Primer provides DNA polymerase with 3`end. DNA polymerase continues the synthesis of new DNA strand according to the template.

Front 68

Number of nucleotides in eukaryotic and prokaryotic Okazaki fragments:

Back 68

Okazaki fragment of eukaryotic cell: about 200 nucleotides
Okazaki fragment of prokaryotic cell: about 1000 nucleotides

Front 69

Telomerase:

Back 69

It solves the problem of synthesizing the lagging strand at the end of chromosome (telomere)
It adds noncoding repeats to the 3`end in the telomere region to avoid loss of genetic information during degradation of telomers.

Front 70

Proofreading:

Back 70

DNA polymerase synthesize a new DNA strand in the 5`- 3`direction, but simultaneously it has proofreading activity in 3`- 5` direction on the new DNA strand.

Front 71

Action of proofreading:

Back 71

Before binding a new nucleotide, DNA polymerase verifies wether the previously bound nucleotide has the base complementary to the template. If yes, DNA polymerase continues to bind a new nucleotide. If no, DNA polymerase removes the wrong nucleotide and bind the correct nucleotide instead.

Front 72

Why is it not possible for DNA polymerase to synthesize in 3`- 5`?

Back 72

Because of the proof reading activity. Proofreading in 5`- 3`is not possible from a chemical point of view.

Front 73

Mismatch repair:

Back 73

Mechanism that corrects wrongly paired bases of newly synthesized DNA strand. Thus it corrects mistakes of the replication machinery.

Front 74

How do the mismatch repair proteins recognize mismatch pairing by:

Back 74

Due to deformation of DNA double helix.

Front 75

How many errors do the replication machinery make?
How many of these errors do the mismatch repair machinery repair?

Back 75

1 error/ 10 to the 7th nucleotides.
Mismatch repair mechanism repairs 99% of these mistakes.

Front 76

What is the overall accuracy DNA reproduction within the cell and thus accuracy of genetic information transfer from one DNA molecule to another DNA molecule:

Back 76

1 error in 10 to the 9th nucleotides

Front 77

Mechanism of repair of accidentally damaged DNA: (3)

Back 77

1. Recognition of damage on DNA strand and excision of the damaged DNA by specific nucleases.
2. Synthesis of removed DNA according to complementary strand by repair DNA polymerases
3. Rejoining newly synthesized DNA segment with repaired DNA strand by DNA ligase (ligation)

Front 78

The stability of DNA, and thus the genetic information depends on:

Back 78

Mechanisms of DNA repair.

Front 79

5 classes of mammalian DNA polymerases:

Back 79

alpha- synthesis of lagging strand
delta- synthesis of leading strand
beta- DNA repair
gamma- synthesis of mitochondrial DNA

Front 80

Most frequent chemical reactions known to make DNA damage:

Back 80

- Deamination
- Depurination
- UV radiation in sunlight promotes covalent linkage between two adjacent pyrimidine bases forming a pyrimidine dimer.

Front 81

Consequence of depurination:

Back 81

Deletion of nucleotide pair.

Front 82

Consequence of deamination from cytosine to uracil:

Back 82

Results in substitution of one base for another, because uracil preferentially base- pairs with adenine.

Front 83

Consequence of pyrimidine dimer:

Back 83

Stall of the DNA replication machinery.

Front 84

Mutation:

Back 84

When the cells replication and repair process fails and allow permanent damage in the DNA