Nucleic Acids Flashcards
1
Q
What are nucleotides?
A
They are monomers of nucleic acids
2
Q
Describe the structure of a nucleotide
A
- A pentose monosaccharide sugar with 5 carbon atoms.
- A phosphate group, PO4-2
- A nitrogenous base
- one ring structure or a two ring structure (pyrimidines or purines)
3
Q
Differences between DNA and RNA nucleotides
A
- DNA has deoxyribose sugar whereas RNA has ribose sugar. * RNA has uracil rather than thymine.
- RNA is usually single stranded rather than double.
- RNA is shorter than DNA.
- RNA has 3 forms- mRNA, tRNA and rRNA
4
Q
How many carbon rings are there in purines and name them
A
2 - Adenine and Guanine
5
Q
How many carbon rings are there in pyrimidines and name them.
A
1 - Cytosine and Thymine
6
Q
Type of pentose sugar in DNA
A
Deoxyribose
7
Q
Type of pentose sugar in RNA
A
Ribose
8
Q
Type of bond in polynucleotides
A
Phosphodiester bonds
9
Q
How do phosphodiester bonds form in polynucleotides?
A
- Condensation reactions * between phosphate group on 5th carbon of pentose of nucleotide and hydroxyl group on the 3rd carbon of pentose of other nucleotide.
10
Q
How do you break phosphodiester bonds?
A
Hydrolysis reactions
11
Q
What do phosphodiester bonds form?
A
Sugar-phosphate backbone
12
Q
Describe the structure of DNA (6 marks+)
A
- DNA nucleotides join to another with phosphodiester bonds forming btwn phosphate group of one nucleotide and the sugar of next. * Forms strand (sugar phosphate backbone)
- DNA is double stranded held together by hydrogen bonding btwn bases of two strands.
- purine pairs with pyrimidine, ensuring equal-length ‘rungs’ in the molecule.
- A to T base pairs . C to G base pairs. = complementary base pairing.
- two strands are antiparallel: run in opposite directions
- DNA molecule twists so structure is a double helix.
13
Q
How to extract DNA from plant material:
A
- Grind sample - break cell walls 2. Mix with detergent - break down cell membrane + release cells content
- Add salt - break hydrogen bonds btwn DNA + water
4.Add protease enzymes - break down proteins associated with DNA
5.Add layer of ethanol on top of sample to precipitate DNA out of solution - Spool out white strand of DNA using glass rod
14
Q
What does ATP and ADP stand for?
A
Adenosine Triphosphate and Adenosine Diphosphate
15
Q
Structure of ADP/ATP
A
Phosphorylated nucleotides (add one or more phosphate group)
16
Q
What do ADP and ATP contain?
A
ribose sugar, adenine base, phosphate groups (ATP = 3, ADP = 2)
17
Q
How is each strand organised?
A
Phosphate group at one end, hydroxyl group at the other end, 5’3’
18
Q
How are the strands organised with respect to each other?
A
Antiparallel
19
Q
Number of hydrogen bonds between A and T
A
2
20
Q
Number of hydrogen bonds between C and G
A
3
21
Q
Purine bases
A
A, G
22
Q
Pyrimidine bases
A
C, T (or U)
23
Q
Why is base pairing important?
A
Allows DNA to be copied and transcribed, important for heredity
24
Q
Why is DNA a double helix?
A
- bases are hydrophobic so sugar-phosphate backbone chains stop bases from coming into contact with water * chains skew themselves to block holes btwn bases but causes atoms to collide with each other
- more twisting required, twisting of DNA produces double-helix
25
Process of semi-conservative replication
* DNA molecule unwinds from its helical shape, a section at a time catalysed by the enzyme DNA gyrase. * DNA helicase is the enzyme responsible for breaking of the hydrogen bonds between the bases on either strands, causing it to unzip.
* This exposes the bases on both strands so that DNA replication can occur.
* Where the two strands separate a Y-shape is formed this is known as a replication fork.
* The enzyme DNA polymerase is responsible for catalysing the addition of free nucleotides to the two exposed template strands using complementary base pairing in a 3' to 5' direction.
* One stand is known as the leading strand, it is oriented in the 3' to 5' direction , towards the replication fork .
* On the leading strand the nucleotides are added continuously. Whereas with the lagging strand the process has to be done discontinuously using Okazaki fragments.
* The fragments are then later joined together by DNA ligase.
26
Semi-conservative replication
Two new molecules of DNA are produced, each with a strand of old DNA and another strand of new DNA
27
Enzymes involved in semi-conservative replication
DNA helicase, DNA gyrase, DNA polymerase, DNA ligase
28
Role of DNA helicase
To travel along the DNA backbone and break hydrogen bonds between between complementary base pairs, leading to the strand unzipping
29
Role of DNA polymerase
To catalyse the formation of phosphodiester bonds between nucleotides
30
What can occur in semi-conservative replication?
Mutations
31
How can mutations occur in semi-conservative replication?
Sequences of bases not matching exactly, an incorrect sequence may occur in the newly copied strand
32
Nature of the genetic code
Triplet, non-overlapping, degenerate, universal
33
Triplet nature of the genetic code
A sequence of three bases called a codon codes for an amino acid
34
Gene
Section of DNA that codes for one polypeptide (protein).
35
Universal nature of the genetic code
All organisms have the same triplets/codons that code for the same amino acids
36
Degenerate nature of the genetic code
Many amino acids have more than one triplet/codon that codes for them.
37
Non-overlapping nature of the genetic code
* Base triplets do not share their bases. * A single codon signals the start of a sequence which makes sure that the codons are read in frame, meaning they start from base 1.
38
What does transcription produce and where does it occur?
* Produces mRNA * Occurs in nucleus
39
Process of transcription
* Transcription occurs in the nucleus of a cell. A section of DNA called a gene unwinds and unzips. Each gene codes for one polypeptide. * The free RNA nucleotides complementary base pair with the exposed DNA bases on the template strand.
* A length of RNA is created which is a copy of the other DNA strand, called the coding strand.
* The strand of messenger RNA once created, leaves the nucleus through a nuclear pore
40
What does translation produce and where does it occur
* Produces proteins (polypeptides) * Occurs on ribosomes attached to the RER
41
Process of translation
* After leaving the nucleus through a nuclear pore mRNA attaches to a ribosome on the rough endoplasmic reticulum. * Two codons on the mRNA strand are exposed by the ribosome at a time.
* Transfer RNA brings amino acids to the ribosome .
* The tRNA molecule has a binding site made up of three bases which are specific to particular amino acid .
* The tRNA molecule also has three exposed bases called anticodons , this is complementary to the codon on the mRNA strand .
* Temporary hydrogen bonds form between the codon and the anticodon.
* As two amino acids brought close to one another by adjacent molecules an enzyme catalyses the formation of peptide bond between them.
* Energy in the form of ATP is required for this process.
* Eventually a stop codon is reached on the mRNA strand which signals the end of the polypeptide, which is then released.
* The polypeptide can then fold into its 3D shape with the help of chaperone proteins.
* The polypeptide breaks loose from the ribosome and mRNA is broken down and recycled.
42
How can multiple identical polypeptides be formed at once?
Many ribosomes can follow on the mRNA behind the first
43
Role of mRNA
To carry the sequence of bases making up the gene in the DNA to the ribosomes where it can be translated
44
Role of tRNA
To carry the correct amino acids to the ribosomes in translation
45
Role of rRNA
To maintain the structural stability of the protein synthesis sequence and to catalyse the reaction
46
Role of DNA gyrase
Unwinds the double helix structure of the DNA
47
Role of DNA ligase
Catalyses the joining of Okazaki fragments on the lagging strand.
48
What are the three main types of activities a cell requires energy?
* Synthesis - large molecules such as proteins * Transport - pumping molecules or ions across cell membranes by active transport * Movement - protein fibres in muscle cells that cause muscle contraction
49
What does phosphorylate mean?
To add one or more phosphate groups
50
Describe the Cycle of ATP
* ATP provides energy for chemical reactions in the cell. * ATP is synthesised from ADP and inorganic phosphate (Pi ) using the energy from an energy - releasing reaction , e.g. the breakdown of glucose in respiration. (condensation reaction)
* The ADP is phosphorylated to form ATP and a phosphate bond is formed. Energy is stored in the phosphate bond.
* When this energy is needed by a cell, ATP is broken back down into ADP and Pi (hydrolysis reaction-add water).
* Energy is released from the phosphate bond and used by the cell.
