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Biochemistry > Chapter 17 Nucleic Acids > Flashcards

Chapter 17 Nucleic Acids Flashcards

1
Q

What is a chromosome?

A

They are the carriers of the genetic information, made of DNA

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2
Q

What is a DNA?

A
  • Stands for deoxyribosenucleic acid, composed of two polydeoxynucleotide strands forming a double helix
  • They are also a genetic information carrier & direct the function of living cells being also transmitted into their offsprings
  • Found by James Watson & Francis Crick
  • Establish the science of molecular biology
  • The information on the DNA is encoded in the form of sequence of purine and pyrimidine base
  • 3.3nm per turn, approximately 10 nucleotides (base pair per turn)
  • DNA nucleotide (linked together by 3’,5’-phosphodiester bonds “joined by the 3’-hydroxyl of one nucleotide to the 5’-phosphate of another”) monomer is composed of a nitrogenous base (purine 2 rings “adenine & guanine” or a pyrimidine 1 ring “thiamine, cytosine & uracil”) they are connected to the sugar via b-glycosidic linkage, deoxyribose sugar, & a phosphate
  • Its second carbon is a deoxyribose sugar and carbon number five is attached to a phosphate
  • Phosphodiester bond can be synthesized by the phosphate on carbon number 5 an the carbon 3 of another sugar making it a polymer
  • If we want to add nucleotides it happens on the 3’ side of the chain and not the 5’
  • Its strands have a anti parallel nature allowing hydrogen bonds to form between the nitrogen bases
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3
Q

What is a gene?

A

All DNA strands have the same backbone (sugars and phosphate) but the sequence of their DNA nucleotide is different, it is the DNA sequence (base sequence) that codes for a product (protein or RNA)

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4
Q

What is meant by genome?

A

It is the complete DNA base sequence of an organism

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5
Q

How is a DNA synthesized?

A

It is a semi conservative replication process, involving the pairing between the parental and a newly synthesized strand

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6
Q

Why do we need to translate the DNA?

A

Because the DNA is not functional, and we need to convert it to its protein (RNA) in order for it to be functional

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7
Q

Why do we need to transcript DNA?

A

To protect it from mutations

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8
Q

How is RNA synthesized (transcription)?

A

1) decoding the genetic information, pairing the complementary bases nucleotides into DNA bases producing a transcript (Newly synthesized RNA)

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9
Q

What is meant by a transcriptome?

A

It is the total RNA transcripts of an organism

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10
Q

What are the different types of RNA?

A

1) Messenger RNA (mRNA): specifies the primary protein sequence (the product of transcription)

2) Transfer RNA (tRNA): delivers specific amino acids into the ribose (for translation)

3) Ribosomal RNA (rRNA): Composes the ribosomes which translates the code from the DNA into functional proteins

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11
Q

What is a proteome?

A

The entire set of proteins synthesized

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12
Q

What is meant by gene expression?

A

The process by which the cells controls the timing of gene product synthesis in response to environmental or developmental effects

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13
Q

What are the factors which contributes to the gene expression?

A

1) Proteins: Transcriptional factors, non-coding RNA molecules (ncRNAs), which regulate the gene expression process by binding to specific DNA sequences

2) Metabolites:: the total low molecular weight metabolites produced by the cells as a result of the gene expression pattern

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14
Q

What is meant by the central dogma?

A

How the genetic information flows in all organisms except for viruses

Keeping a copy of the DNA (Replication)

DNA - RNA (Transcription)

RNA- Protein (Translation)

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15
Q

What is the chargaffs rules?

A

They have noticed the the whole DNA has the same width “2.4nm” which means that a purine must be attached to pyrimidine and not itself and vice versa forming a three carbon linkage by hydrogen bonds, GC are connected by three hydrogen bonds while AT are connected by two, chargaff then stated that the ration of adenine to thymine is 1:1 and cytosine to guanine is 1:1

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16
Q

What are the factors that stabilizes the DNA?

A

1) Hydrophobic interactions: the bases minimizes their interactions with water molecules

2) Hydrogen bonds: the commutative effect of the hydrogen bonds keeps the strands in a correct complementary orientation

3) Base stacking: the bases are planar and stacked, allowing for weak van der waals forces between the rings

4) Hydration: each phosphate can bind to 6 water molecules, which are on group ribose 3’ & 5’-oxygen, which interacts with the structure of the DNA to stabilize it

5) electrostatic interactions: DNA external surface contains sugar-phosphate backbone, which posses a negatively charged phosphate group, which water minimizes their repulsion effects

17
Q

What is meant by DNA mutation?

A

It is the change in the DNA’s nucleotide/nitrogen sequence which occurs during DNA replication as our cells divide (Mitosis), which is usually due to the disruptive forces, mutations are rare because:

1) The DNA replication process is off high accuracy
2) Damaged “Mutated” DNA can be repaired

Mutations can be:
1) deleterious (negative) mutations which can cause abnormalities
2) Neutral (silent killers) which has no effects
Rarely positive

18
Q

What are the types of mutations?

A

1) single-base changes (point mutation): replacement of a nucleotide with another it has two types:

  • Transition: the replacement of a nucleotide with another of the same group (purine/pyrimidine) by deamination
  • Transversion: the replacement of a nucleotide with another nucleotide from a different group, caused by alkylating agents or ionizing radiation

This type of mutation can result into:

1) silent mutations
2) missense mutation
3) nonsense mutation

2) insertions or deletions (indel mutation) can result into:

  • Frameshift mutation
  • Repeat expansion mutation

3) Duplication
4) genome rearrangement

19
Q

What is meant by redundancy?

A

Some amino acids are coded by more than one codon, which protects the DNA from some mutations named silent mutations

20
Q

What is meant by a missense mutation?

A

Changing one of the nucleotide/nitrogen bases to another which will make the codon encode for a different protein have an observable effect

21
Q

What is meant by nonsense mutation?

A

Mutating the codon to a stop codon in the protein producing a incomplete/nonfunctional polypeptide distrusting the entire length of the protein

22
Q

What is meant by frameshift mutation?

A

The addition or removal of one or more nucleotide when the base added or removed isn’t a multiple of three, shifting the whole reading which has a drastic effect on the protein producing a altered/truncated protein

23
Q

What is meant by repeat expansion mutation?

A

A insertion mutation caused by DNA replication mistakes, increasing the number of small nucleotide sequence like a trinucleotide sequence, if the expansion is large it can cause rare diseases like huntingtons

24
Q

What is meant by genome rearrangement?

A

Rearranges the whole chromosome, distrusting the gene structure, as the DNA strand breaks due to errors in cell division, exposure to mutagens or radiation it can lead to:

1) Duplication: repeating some of the genes instead of ABC it becomes ABBC

2) Inversion: when the deleted DNA is inserted into its original position but in a opposite orientation like ABC/DEF becomes AED/CBF

3) Translocation: when the DNA fragment of one chromosome is inserted into a different position in the same or a different chromosome

25
Q

What causes DNA damage (mutation)?

A

We have two forces:

1) Endogenous sources (within the cell):

  • Tautomeric shifts
  • Depurination
  • Deamination
  • ROS-induced oxidative damage (reactive oxidative species)

2) Exogenous factors:

  • Radiation
  • Xenbiotic exposure
  • Mutagenic materials
26
Q

What are the conformations of DNA?

A

1) B-DNA: Sodium salt of DNA under highly humid conditions (right handed) “MOST COMMON”

2) A-DNA: dehydrated form of B-DNA (right handed)

3) Z-DNA (Zig-zag DNA): due to torsion during transcription (Left handed)

27
Q

What is meant by DNA supercoiling (DNA packing)?

A
  • Packing the DNA into a compact form that can fit within the cell
  • Linear & circular DNA can be relaxed or supercoiled
  • In the prokaryotic organisms DNA is a circular molecule that is extensively looped and coiled, while in eukaryotic cells it is linear DNA molecule that is complexed with histones and other proteins forming nucleosomes (formed by the binding of the DNA & histone proteins) which is supercoiled into chromatin, which is compacted into chromosomes
28
Q

What are the major classes of histone proteins?

A

1) one copy of H1

Two copies of:

2) H2a
3) H2b
4) H3
5) H4

29
Q

What is a RNA?

A
  • Ribose Nucleic acid
  • involved in protein synthesis & has structural and enzymatic roles
30
Q

What is the differences between RNA & DNA?

A

1) RNA has a ribose sugar instead of deoxyribose which makes it more reactive
2) It has Uracil nucleotide instead of thymine
3) RNA exists as a single strand which can coil on itself
4) RNA doesn’t follow chargaffs rule 1:1 ration
5) Some of them have catalytic properties (ribozymes, cleaves RNA)

31
Q

What is a tRNA?

A

Transfer RNA:

  • Transports amino acids to ribosomes for their assembly into polypeptides
  • It consists 15% of the cellular RNA
  • Its length varies from 75 to 90 nucleotides, with their bases being paired
  • Each amino acid has his own tRNA
  • It has extensive inter chain base pairing
  • Attaches amino acids via aminoacyl-tRNA synthetase enzyme to the CCAC codon
  • Its Anti-codon allows it recognize the correct mRNA codon aligning its amino acid for the protein synthesis
  • Its loops facilitates it interactions with the correct aminoacyl-tRNA synthetase
  • It has a high specificity and accuracy
32
Q

What is a rRNA?

A

Ribosomal RNA:

  • Most abundant RNA in living cells with a complex secondary structure
  • A component of ribosomes (composed of two subunits “80s” between 60s and 40s in eukaryotic, while “70s” between 50s and 30s in prokaryotic)
  • Where translation takes place
33
Q

What is mRNA?

A

Messenger RNA

  • The carrier of genetic information from the DNA to protein synthesis
  • Contains three base sequence “codons” which dictates amino acids that are synthesized in the proteins
  • The polypeptide coding sequence in a mRNA is called a open reading frame (ORF), which begins with a initiation codon and end with a terminating codon “stop codon”, connected to untranslated sequence regions (UTR) before 5’ and after 3’, which guide mRNA to move from the nucleus to the cytoplasm, attach the mRNA to the ribosomes, protect mRNA
  • prokaryotic mRNA are polycistronic (contains coding info for several polypeptides) while the one of eukaryotic are monocistronic (codes for a single polypeptide)
34
Q

What is ncRNA?

A

No coding RNA:

  • Don’t directly code for polypeptides
  • There roles includes DNA replication, gene expression, transcription, translation, stress management, genome structure and defense

Classified according to their length and function:

Length:

  • Small ncRNA (less than 200 nucleotide)
  • Large ncRNA (more than 200 nucleotide)

Function:

  • Housekeeping: (splicing RNA snRNA), chemical modification of nucleotide bases (snoRNA)
  • Regulatory RNAs: (Activates and inhibited gene expression)

Biochemistry (12 decks)

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