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Biology > - Module 2 - Nucleic acids > Flashcards

- Module 2 - Nucleic acids Flashcards

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1
Q

What are nucleotides?

A

Monomers that form the basis of the nucleic acids DNA and RNA.

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2
Q

What elements do all nucleotides contain?

A

C, H, N, O and P

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3
Q

What is the difference between the structure of the pentose sugar in DNA and RNA.

A

DNA - deoxyribose pentose sugar.
RNA - Ribose

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4
Q

What are the bases found in RNA and DNA

A

DNA - ATCG
RNA - AUCG

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5
Q

What bases are purines? What does this mean?

A

Adenine and Guanine are purines, they have the larger bases and have double carbon ring structures.

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6
Q

What bases are pyrimidines? What does this mean?

A

Thymine and Cytosine (and uracil).
Pyrimidines are the smaller bases and have single ring carbon structures.

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7
Q

How is a nuleotide formed?

A

The phosphoric acid and the nuecleoside combine and a molecule of water is formed (condensation) in a phosphodiester bond between and OH group on the acid and a OH group on carbon 5 of the sugar.

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8
Q

How are polynucleotides formed?

A

Nucleotides join together. They join up between the phosphate group of one nucleotide and the sugar of another nucleotide via a condensation reaction forming a phosphodiester bond.

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9
Q

What are the 5’ and 3’ ends of polynucleotides?

A

Every polynucleotide has a 5’ (5 prime) and a 3’ (3 prime) end.
At the 5’ end C5 of the pentose sugar is nearest the end, at the 3’ end C3 is nearest the end.

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10
Q

How can polynucleotides be broken down?

A

They can be broken down into nucleotides by hydrolysis reactions.

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11
Q

What is the basic structure of DNA?

A

Two polynucleotide strands joined together to form a double helix shape. The two strands are held together by hydrogen bonds between the bases.

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12
Q

What does it mean by ‘the strands of DNA run anti-parallel to one another’?

A

They run in opposite directions.

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13
Q

How many hydrogen bonds are A and T linked by? What about C and G?

A

A and T are linked by 2.
C and G are linked by 3.

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14
Q

What is the name of the protein that allows DNA to be packed up tightly?

A

Histones.

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15
Q

Why must DNA be tightly coiled and packaged?

A

To fit into the nucleus.

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16
Q

What is ATP made up of?

A

A sugar (ribose), a base (adenine) and three phosphate groups.

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17
Q

How is ATP broken down?

A

The bonds between the phosphate groups are unstable which means they are easily broken (in a hydrolysis reaction).

ATP —> ADP + Pi

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18
Q

What is the addition of an inorganic phosphate group to a molecule like ADP called?

A

Phosphorylation. This requires free energy.

ADP + Pi —> ATP

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19
Q

How is ATP suited for energy transfer?

A

Small and soluble - moves in and out of cells easily.
Releases small amounts of energy - prevents wasted energy
Has an unstable phosphate bond (which is easily broken)
Easily reformed

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20
Q

How do RNA nucleotides differ from DNA nucleotides?

A

Presence of a ribose sugar rather than deoxyribose.
T replaced with U.
RNA polymers are small enough to leave nucleus to go to ribosomes.
After protein synthesis, the RNA molecules are degraded in the cytoplasm. Phosphodiester bonds are hydrolysed and the RNA molecules are recycled.
RNA is single stranded.

21
Q

When does DNA replication take place?

A

Just before the cell divideds

22
Q

What happens to chromosomes right before the cell divides?

A

They become shorter, thicker and more visible (condense).
Each chromosome duplicates and becomes two strands, each called a chromatid. The two chromatids are joined at the centromere

23
Q

What happens to hydrogen bonds between complementary bases during DNA replication?

A

They are broken to separate two strands.
Each strand then acts as a template for the creation of a new double stranded DNA molecule.
Complementary base pairing will ensure that the two new strands of DNA are identical to the original strand.

24
Q

What are the 9 stages of DNA replication?

A

1- Helicase separates the two strands.
2- The strands are kept apart by single-stranded binding (SSB) protiens.
3- DNA polymerase reads the sequence and adds free floating DNA nucleotides that have complementary bases to form new strands (phosphodiester bonds).
4- DNA polymerase reads the parent strand in the 3’ 5’ direction and builds the leading strand in the 5’ 3’ direction, towards the replication fork (continuous process).
5- The lagging strand is built away from the replication fork but still in a 5’ 3’ direction. (discontinuous) built in Okazaki fragments.
6- Okazaki fragments joined with DNA ligase.
7- DNA helix continues to grow continuously towards the replication fork. The lagging strand continues to grow away from the replication fork.
8- There are multiple replication forks across the DNA molecule.
9- Eventually, all the individual segments of the new strands meet up and are joined together, creating new DNA molecules, each one identical to the parent molecule.

25
Q

What are replication errors? What can be their effects?

A

Errors that occur randomly and spontaneously and are referred to as gene mutations or point mutations. The genetic code could be changed, some have no effect, some are fatal and some can be advantageous.
During replication enzymes proofread and edit out incorrect nucleotides which reduce the rate that mutations are produced.
Occur every 10^8 base pairs.

26
Q

What are the 3 possible mechanisms of DNA replication?

A

Conservative,
Semi-conservative,
Dispersive

27
Q

What is the genetic code of an organism?

A

The sequence of bases along it’s DNA. It contains thousands of sections called genes.

28
Q

What does each gene code for?

A

A specific polypeptide.

29
Q

What are polypeptides made up of? Therefore what do the bases in genes code for?

A

Amino acids, so the sequence of bases in a gene must code for amino acids.

30
Q

What does it mean by the genetic code is universal?

A

It’s in almost all living organisms, the same triplet of bases codes for the same amino acids.

31
Q

What does it mean by ‘the triplet code is degenerate’?

A

More than one triplet code can code for each amino acid.
There are more possible triplet codes than amino acids.

32
Q

Do ALL triplets code for amino acids?

A

No. Some are used to tell the ribosome when to stop production of a protein, they are called stop signals and are found at the ends of mRNA.
There are also start signals.

33
Q

What are the 4 stages of protein synthesis?

A

Transcription - of the genes in the nucleus, mRNA formed.
Processing - of mRNA
Translation of the mRNA in a ribosome, polypeptide chain formed.
Modification of the protein.

34
Q

What are the 4 stages of transcription?

A

1 -DNA helicase separates the strands by breaking the H bonds between the bases in a specific region of DNA.
2- RNA polymerase binds to the promoter region of the DNA (at the 5’ end of the antisense or template strand).
3- RNA polymerase moves along the DNA in a 5’ 3’ direction forming a complementary mRNA strand from free RNA nucleotides in the nucleus.
4- The mRNA strand separates once formed and the double stranded DNA recoils behind it.
5- The mRNA detatches when the terminator region is reached, and it can now exit the nucleus via a nuclear pore.

35
Q

What triplet is almost always the start codon? What does it code for?

A

AUG, methionine.

36
Q

What are the similarities between DNA replication and transcription?

A

DNA unzips and unwinds.
Helicase enzymes
Template DNA
Complementary base pairing
Hydrogen bonds
Free, activated nucleotides
Polymerase enzymes

37
Q

What are the differences between DNA replication and transcription?

A

Only a small section of DNA unzips in transcription.
Both strands act as templates in replication, only one does in transcription.
RNA vs DNA free nucleotides.
RNA polymerase vs DNA polymerase.
Different helicase enzymes
Product in replication is two new daughter strands of DNA and in transcription it’s one mRNA strand.
mRNA leaves nucleus whereas DNA doesn’t

38
Q

What are tRNA molecules?

A

Transfer RNA molecules are single-stranded RNA polynucelotides that fold into a three-looped hairpin structure. They attach to a specific amino acid.

39
Q

Where are tRNA molecules made?

A

Nucleolus and they leave it via nuclear pores to enter the cytoplasm.

40
Q

What is the structure of tRNA?

A

Three looped hairpin structure.
The bottom loop is an anticodon that is complementary to a specific codon of bases on the mRNA.

41
Q

What are the 5 stages of translation?

A

1- mRNA attaches to the ribosome at the start codon
2- tRNA molecules contain a sequence of three bases called an anticodon that bind with a complementary codon on the mRNA strand.
3- A peptide bond forms between the two amino acids.
4- Another tRNA molecule enters the ribosome carrying an amino acid. The first tRNA molecule is discharged from the ribosome.
5- The polypeptide is released from the ribosome and must undergo folding and further processing before use.

42
Q

What is a mutuation?

A

A change in amount or structure of DNA.

43
Q

What is a point/gene mutation?

A

A change in the base sequence of a gene which can cause a change in the polypeptide chain.

44
Q

What is a point mutation caused by?

A

Errors that occur during DNA replication.

45
Q

Why is the mutation rate in humans low?

A

There are enzymes that check the bases and correct errors.

46
Q

What are the 8 steps of DNA purification?

A

1- Add washing up liquid, to degrade cell membranes, including the nuclear membrane.
2- Add sodium chloride, To shield the (-) charged phosphate groups from DNA causing them to coalesce.
3- Place in 60oC water bath for 15 mins to partially denature DNAse enzymes.
4- Place in an ice bath for 15 mins, to slow down the breakdown of DNA
5- Blend for 5 mins, to degrade cell walls and membranes further, permitting the release of DNA.
6- Filter, to obtain filtrate containing proteins and DNA.
7- Add protease, to hydrolyse the proteins associated with the DNA.
8- Add ice cold ethanol, to precipitate the DNA as it is insoluble in ethanol.

47
Q

How is DNA packed?

A

Nucleosome fibre - The DNA is wrapped around histone proteins, forming chromatin. Histones associate in octameters to form ‘bead on a string’ structures called nucleosomes. These are the basic structural units of a chromosome.

Solenoid fibre - More histones help the nucelosome fibre form a tightly-coiled structure called a solenoid fibre.

Foiled/coiled solenoid fibre - The solenoid fibre is thought to wrap and coil around scaffolding proteins, but the exact mechanism of this is not known.

Supercoiling - To reduce the stress on the molecule, the solenoid fibre twists and writhes, like a phone cable.

Chromosome - The DNA molecule is packaged so much that a chromosome is only 6um long.

48
Q

What was the Meselson Stahl experiment?

A

Two american biochemists showed that DNA replicates semi-conservatively. (one original strand and one new strand in the new DNA double-strand)

Biology (16 decks)

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