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Chemistry > Nucleaic Acids > Flashcards

Nucleaic Acids Flashcards

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1
Q

What controls activity in the cell?

A

GENES

+

ENVIRONMENTAL FACTORS

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2
Q

What represents the genes ?

A

Nucleic acids

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3
Q

What are the internal information in the cells ?

A
  • Genotype (genes)
  • Cell lineage
  • Developmental stage
  • Cell cycle stage
  • Metabolic stage
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4
Q

What are the external info of the cells ?

A
  • Soluble signalling molecules
  • Interaction with other cells
  • Interaction with substrates
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5
Q

What are the cell responses to internal and external stimuli?

A

A. Cell growth and division
B. Quiescence
C. Differentiation
D. Apoptosis

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6
Q

What are the nucleic acids ?

A

STORAGE and EXPRESSION of genetic info

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7
Q

What are the types of nucleic acids?

A 
DNA = GENOTYPE = DEOXYRIBONUCLEIC ACID 
RNA = PHENOTYPE = RIBONUCLEIC ACID
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8
Q

What do you know about DNA?

A
  1. Have to maintained the same throughout the life time

2. Req faithful replication during cell division

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9
Q

What do you know about RNA?

A
  1. Content is diff in diff cells and tissues depending on the func of cell bcz it is made of the DNA so not always the same
  2. Selective expression of the genotype

So, same genotype but diff phenotype

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10
Q

What are the eukaryotes?

A

DNA
A. arranged in chromosomes in NUCLEUS

B. found in the mitochondria and in chloroplasts of plans

So majority in the nucleus

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11
Q

What are the prokaryotes?

A
  1. Lack NUCLEI
  2. Single chromosome
  3. Non-chromosomal DNA: circular DNA but only in some bacteria
  4. Their cell wall is made of cellulose
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12
Q

What are the 3 types of organisms ?

A
  1. Eukaryotes
  2. Prokaryotes
    C. Viruses
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13
Q

What is the flow of genetic info in the cell?

A

DNA —> mRNA —> protein —> correctly folded and localized protein —> post-translational modification (خطوة جانبية)—> cellular response

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14
Q

What are DNA and RNA composed of ?

A

Nucleotide subunits joined together

Nucleotides are

  1. Nitrogenous base
  2. Ribose sugar
  3. Phosphate group

Nucleoside is 1 and 2 only

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15
Q

What are the Purines?

A

Nitrogenous bases with 2 rings

  1. Adenine
  2. Guanine
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16
Q

What are the pyrimidines?

A

Nitrogenous bases with 1 ring الهرم عنده بوز واحد من فوق 😄

  1. Thymine —> DNA
  2. Cytosine
  3. Uracil —> RNA
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17
Q

What are the names of the nucleoside of each base?

A 
A —> adenosine 
G —> guanosine
T —> thymidine
C —> cytidine 
U —> uridine
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18
Q

What is the diff btwn ATP in DNA and in RNA ?

A

In DNA —> dATP —> deoxy

In RNA —> ATP

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19
Q

What is the diff between the terminals of the AA and the nucleic acids ?

A

In AA —> N terminal and C terminal

In NA —> 5’ end ( with free phosphate group ) and 3’ end ( with free hydroxyl group )

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20
Q

How are the nucleotides joined together ?

A

By phosphodiester bond ( very strong covalent bond )

The phosphate in one nucleotide with the hydroxyl group of the other one

He said it is a 3’, 5’ phosphodiester bond

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21
Q

How to write the seq of NA ?

A

From the 5’ —> 3’

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22
Q

What is the charge of the DNA and is it polar?

A
  1. Negative bcz of the phosphate charges

2. it has polarity bcz one end it’s diff from the other ( one has free PO4 and the other has free OH )

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23
Q

What are the no. of strands in DNA, RNA, and protein?

A

DNA —> 2 —> double helix —> twisted ladder
RNA —> 1
Protein —> 1

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24
Q

How are the strands held together ?

A

The nucleotide bases of one strand are paired with bases on the other strand by Non-covalent H bonds

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25
Q

Where are the hydrophilic and hydrophobic parts of the DNA strands?

A

Hydrophilic deoxyribose x phosphate backbone facing outside

Hydrophobic bases are stacked inside PERIPENDICULAR to the axis of the helix

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26
Q

How many H bonds btwn the bases?

A

2 H bonds btwn A and T

3 H bonds btwn C and G

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27
Q

How is the size of the DNA expressed?

A

By the length of the nucleotides

  1. Base pairs (bp)
  2. Nucleotides على طول
28
Q

What is the diff btwn + and - supercoiling?

A

+

  1. overwinding DNA and occur during DNA replication
  2. Right handed helix
  3. B-DNA that have minor and major grooves

-

  1. underwinding DNA and occur in the nucleosome ( at rest when no replication )
  2. Left handed helix
  3. Have zigzagged phosphates —> Z-DNA
  4. occur when there is alternating Purines and pyrimidines in one strand
  5. Easier to separate the strands - > promote RNA syn

Conversion from B-DNA to Z-DNA is facilitated by 5-methylcytosine

29
Q

What are the forces affecting the stability of DNA double helix?

A
  1. Hydrophobic interactions inside btwn N bases
  2. Hydrophilic interactions outside btwn the DNA and other molecules
  3. stacking interaction: relatively weak but additive van der Waals forces
  4. H bonding: relatively weak but additive and facilitates stacking
  5. Electrostatic interaction:
    A. primarily by -ve P
    B.affects intra strand and inter strand interactions
    C. Repulsion neutralized by +ve charges ex: Na+ or proteins
30
Q

What is DNA denaturation/melting ?

A
  1. Loss of helical structure when DNA is heated
  2. It is very imp for replication and transcription
  3. What happens is that the double strands become 4 single strands if cooled they return to their strands state ( spontaneously renature ) —> hydrogen bonds break
  4. Blue one can’t renature with a red one bcz of the arrangement of the base pairs
  5. Happen in vivo ( during DNA replication bcz 2 strands have to separate in order for them to be copied into new strands )
  6. Happen in vitro ( using agent that makes denaturation —> heat )
  7. REVERSIBLE PROCESS
  8. Happen also during the synthesis of RNA —> bcz one of the strands of DNA is copied into RNA
31
Q

Does renaturation need energy and what do they depend on?

A

No Energy is required

Depends on base pairing

32
Q

How to know if the DNA is denatured?/ how to differentiate btwn single and double stranded DNA?

A

See it’s absorbance

Single stranded absorbs more than double stranded —> hyperchromacity

Diff btwn single and double

33
Q

What is Tm?

A

The temp where half the DNA become single stranded

It depends on the G-C content —> ⬆️ G-C —> ⬆️temp needed

34
Q

What does the melting temperature of DNA determine?

A

Average base composition ( G-C content )

35
Q

Is the Human genome the largest ?

A

Not the largest

Some amphibians, algae, and plants have more

36
Q

Why do we need genome seq?

A
  • Lead to identification of many genes

* Provided information on gene organisation and function

37
Q

What up is the haploid human genome

A

3*10’9 bp

So no of nucleotides is double that

38
Q

Talk about genes

A

19000 genes

Most of genes are single-copy in the haploid genome

genes are composed of 1 to >75 exons

genes vary in length from <100bp to >2,300,000 bp —> dextrofin —> largest protein —> found in muscles

> 50% are repeated sequences (microsatellites; eg CACACACACA)

Alu repeat sequences are present throughout the genome

28% is transcribed into RNA

1.1-1.4% encodes protein —> function of DNA but only 1%

39
Q

Do we all have the same DNA ?

A

Almost 99.5 % identical

We differ in about 3 million bp - out of the 3000 million

But we don’t look the same bcz we express our genes differently —> same genotype but duping phenotype

40
Q

What is mitochondria DNA ?

A
  • circular genome of ~17,000 bp

* contains <40 genes —> Mostly involved in mitochondrial function —> don’t completely rely on them #

41
Q

Why does mitochondria have their own DNA ?

A

Bcz mitochondria before existed alone and then lived symbiotically with our cells —> so that’s why it has DNA in it

42
Q

What has the largest genome ?

A

Rice 🙂

43
Q

Does the no of genes determines complexity?

A

the complexity of humans is not proportional to the number of genes

44
Q

What are plasmids ?

A
  1. in Prokaryotic organisms -
  2. small, circular, extra-chromosomal DNA molecules
  3. In VIVO —> present in a superhelix form —> it is supercoiled from an open circle to the super helix form —> contracts as you twist it —> occupies less space
  4. What keeps it twisted is —> DNA gyrase
  5. Very little super helix bcz it needs gyrase to hold it
  6. Sometimes the open circle is broken by physical means and you end up with a linear form of DNA
  7. All of them are the same length
45
Q

How can antibiotic resistance happen ?

A
  1. Plasmids often carry antibiotic resistance genes
  2. Plasmids can pass from one bacterium to another and therefore transfer resistance
  3. Transfer through sex pious until all become antiB resistant
46
Q

What is plasmids useful in?

A
  1. Carry antibiotic resistance genes —> transfer resistance to other bacteria
  2. Cloning vectors —> carry foreign DNA —> cut the DNA with sequence specific restriction enzymes —> join them with DNA ligase
47
Q

What are the characteristics of viral DNA?

A
  1. Viruses are very simple —> can only replicate inside cells
  2. their genome is composed of either RNA (—> retroviruses ) or DNA surrounded by a protein coat
  3. Their DNA is circular —> can be used as vehicles for insertion of foreign genes – same as plasmids

Viral genomes are used as carriers for DNA

48
Q

How is eukaryotic DNA organized?

A
  1. Highly condensed
  2. Have 46 chromosomes
  3. Bound with +ve his tone proteins —> lys+arg —> order DNA into nucleosomes —> resembles beads on a string
  4. Form IONIC bonds with -ve charged DNA
  5. Protamines are small proteins + numerous enzymes + regulatory proteins that also bind to DNA
  6. DNA-protein complex —> chromatin
49
Q

How is DNA organized in eukaryotic cells?

A

Organized by histones into nucleosomes which is made of : 8 small +ve charged proteins called core histones

50
Q

What is the remarkable feature of DNA ? What can reveal the size of one chromosome?

A

Q1: It is squeezed and codense in the cell and still able to function

Q2: partial lysis with lysozyme

51
Q

When can DNA replicate itself

A

When cells divide

52
Q

What happen in DNA replication?

A
  1. Change from parenteral to daughter DNA that must be exactly the same
  2. At some point, During the cell cycle the amount of DNA doubles inside the cell —> end up with 2 double stranded DNA
  3. Semi-conservative replication —> one old strand + one new strand —> half of our DNA is new and Half belongs to the mother and father
53
Q

What are genes ?

A
  1. The DNA that codes for a single polypeptide
  2. A single unit of transcription
  3. Was called proteins but proteins are made of several polypeptides that are coded by Diff genes —> so now they are not called proteins
  4. Diff sizes of DNA —> diff sizes of proteins
54
Q

What are exons?

A

Protein coding regions

55
Q

What are introns?

A

Between the exons

The gene contains both exons and introns but only exons code for proteins —> only in eukaryotes

EXONS form only a very small part of the gene – most of it is made up non-coding INTRON sequences

56
Q

Compare the length of the final RNA with the gene ?

A

Much shorter than the gene

57
Q

What is special about the genes of prokaryotes and viruses?

A

They don’t have introns

SO

translated RNA is the SAME LENGTH as gene

58
Q

How does the RNA differ from DNA?

A
  • The sugar is Ribose not Deoxyribose
  • Thymine is replaced by Uracil —> have ACGU NOT ACGT
  • DNA is double stranded, RNA is single stranded —> one exception
  • DNA is much longer than RNA —> bcz DNA is the whole chromosome but RNA is the transcribed part only
  • There are several different types of RNA
  • RNA can also contain some modified bases not found in DNA —> have some side chains
  • RNA is located in both nucleus and cytoplasm —> where as DNA is confined in the nucleus and a little bit in the mitochondria but not in the cytoplasm
  • mRNA is different in each cell whereas DNA is the same —> other types of RNA are the same in all the cells but mRNA is diff as it represents the phenotype
  • have intrachain bonding —> fold back on itself but not ##
59
Q

What is mRNA?

A

information transfer from DNA

And it is a template for protein synthesis

Only type translated to RNA

  • Each mRNA is an exact copy of a single gene
  • Each different protein or polypeptide chain has its own mRNA which contains a variable number of nucleotides
  • Usually have relatively short half life in the cytoplasm and it is determined by its protein product and the function of the protein that it codes —> if the protein is structural and long time needed and large amount —> stay stable if not it gets degraded
60
Q

TRNA

A

adaptor molecules to carry amino acids for protein synthesis

  • not the smallest bcz of the microRNA -60-90 nucleotides
  • contains modified bases
  • intra-chain double strand regions
  • Each tRNA covalently linked to a specific amino acid
  • at least 20 different tRNA’s —> in human cell there are more than the required

Loop structure bcz of the bonds it forms ##

Amino acid binds to the 3’ end —> which AA depends on the anticodon ( 3 nucleotides ) which match the codon that is on the mRNA

Link between the 4 letter code of nucleic acids (A,T,C,G) and the 20 letter code of proteins (the 20 amino acids)

61
Q

rRNA

A

Func: protein synthesis

Most abundant

Found in ribosomes

Found in the ER also

Have to units :
Major sub unit
Minor subunit

ribosomes are large complex structures approximately 50% rRNA and 50% protein

62
Q

Small untranslated RNA (miRNA)

A

##

63
Q

What are microRNA ?

A

Can control many diff mRNA ##

64
Q

How can we analyze the NA?

A

Isolate them from sources:

  • fresh tissue, body fluids, cell/bacterial/viral cultures
  • frozen tissue
  • fixed tissue (formalin) - embedded in paraffin blocks (pathology)
  • fossil material - > bones to study genes of things that no longer exist

When DNA is isolated —> it gets fragmented into small icees —> not whole chromosomes

RNA -> remain intact bcz it is smaller

65
Q

How do we separate diff sizes of DNA

A

By several types of gels made up of several polymers

If we have low% —> larger pore size so more suitable for long DNA and there are three types:

  1. Agarose : from seaweed for DNA between 100bp - 50kbp.
    used at 0.5-3% conc (1g in 100 ml buffer = 1% gel)- > wide range and #
  2. Polyacrylamide : for DNA < 100bp, for high resolution
    can separate fragments with 1bp difference, can separate single strand DNA . Used at 8-20% —> for very small DNA and also for RNA
  3. Spreadex : most useful for high resolution separation; easier
    to use than polyacrylamide : useful range 50 - 800bp

Chemistry (3 decks)

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