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Biology > 6 Nucleic acid and protein synthesis > Flashcards

6 Nucleic acid and protein synthesis Flashcards

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1
Q

Nucleotides

A

the basic units which make up a group of the most important chemicals in all organisms, the nucleic acids

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2
Q

The nucleic acids are:

A
  • Ribonucleic acid (RNA)
  • Deoxyribonucleic acid (DNA)
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3
Q

The structure of a nucleotide is as follows: (made of THREE components)

A

*A pentose / 5C sugar represented by a pentagon. (Ribose or deoxyribose).
*A phosphate group represented by circle.
*A nitrogenous organic base. (A, C, G, T, or U).

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4
Q

There are two groups of bases:

A
  • Pyrimidines (C, T, U); 6 sided ring (single ring structure)
  • Purines (A, G); 6 sided ring joined to 5 sided ring (double ring structure)

So, PENTOSE SUGAR + PHOSPHATE GROUP + NITOGENOUS BASE (joined by CONDENSATION RXN) = nucleotide

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5
Q

Dinucleotide and polynucleotide

A
  • Two nucleotides
  • Many nucleotides
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6
Q

How nucleotides are joined together

A
  • via a condensation reaction between the 5C sugar of one nucleotide and the phosphate group of another.
  • The resultant strong covalent bond is a PHOSPHODIESTER BOND
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7
Q

Phosphodiester bond

A
  • ONE phosphoester bond between phosphate group and 5’ carbon of pentose sugar and ONE phosphoester bond from same phosphate attached to 3’ carbon of pentose sugar of next nucleotide. Both these bonds from complete phosphodiester bond.
  • All these phosphodiester bonds joining nucleotides forms phosphate backbone of polynucleotide.
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8
Q

The structure of RNA is as follows:

A

RNA - a polymer made of repeating nucleotide subunits.
*5C always ribose
*A, C, G, U (uracil replaces thymine)

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9
Q

Three types of RNA:

A
  • rRNA
  • tRNA
  • mRNA
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10
Q

rRNA

A
  • ribosomal RNA manufactured in nucleolus.
  • very large molecule that is complexed with proteins and forms subunits of ribosomes.
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11
Q

tRNA

A
  • transfer RNA very small molecule made up of about 80 nucleotides.
  • makes up 10-15% total RNA in cell.
  • different types of tRNA each complementary to an amino acid.
  • three leaf clover shape made of folded single strand
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12
Q

mRNA (describe this structure)

A
  • messenger RNA made in transcription in nucleus (because DNA too big to leave nucleus).
  • single linear strand; made of thousands of nucleotides
  • base sequences and length of mRNA depends on length and sequence of transcribed DNA genes, as well as post-translational modification.
  • mRNA leaves nucleus via nuclear pores in nuclear envelope and enters cytoplasm then ribosomes for transcription.
  • broken down quickly; exists temporarily just to fulfil its function
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13
Q

ATP

A
  • a phosphorylated nucleotide.
  • It is the universal energy currency of ALL cells
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14
Q

Phosphorylation

A

the chemical process of adding a phosphate group to an organic compound, e.g., a protein or a sugar

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15
Q

Structure of ATP:

A
  • adenine molecule (purine; double 6-sided and 5-sided ring)
  • ribose molecule (5C sugar)
  • three phosphate molecules
    Adenine + ribose = adenosine
    Adenine + ribose + 1 phosphate = AMP
    Adenine + ribose + 2 phosphate = ADP
    Adenine + ribose + 3 phosphate + ATP
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16
Q

Structure of DNA:

A
  • two nucleotide polymer strands (very long) winding around each other to form double helix.

For each complete turn of double helix there are 10 base pairs.
* deoxyribose sugar
* nitrogenous bases: A, T, C, G
* sugar-phosphate backbone has “direction” it runs in (5’ to 3’ or 3’ to 5’; refers to carbon atoms on deoxyribose sugars)
*two strands are an equal distance apart (gives stability and strength to molecule) because of complementary base paring between purines and pyrimidines but are ANTIPARALLEL.
*Bases are held together because of hydrogen bonding. C-G have a TRIPLE hydrogen bond but A-T have a DOUBLE hydrogen bond, which is weaker.

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17
Q

DNA able to be passed unchangingly from generation to generation because of extremely stable structure ensured by:

A

*Double helix (enclosed and protected from outside chemical or physical forces))
*Sum of all hydrogen bonds
*Equidistant base pairing

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18
Q

Ratios

A

Ratio of A:T is equal; ratio of C:G is equal, but these quantities may not equal each other, and will differ from species to species.

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19
Q

Differences between DNA and RNA:

A

in notes

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20
Q

Semi-conservative replication

A
  • Occurs during synthesis phase of mitotic cell cycle, which is 2nd phase of interphase.
  • Known as semi-conservative because each new DNA molecule contains one parent strand and one daughter strand.
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21
Q

Anabolism and catabolism

A

Anabolism = energy required
Catabolism = energy released

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22
Q

How does semi-conservative replication work: 4 steps

A
  • Opening and unwinding DNA double helix
  • Assembling leading strand
  • Assembling lagging strand
  • Removing wrongly coded DNA
    .
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23
Q

What are the nucleotides activated with? (in first step of semi-conservative replication)

A

These nucleotides were activated by the addition of two phosphate molecules (now have 3, much like ATP – because anabolism requires energy

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24
Q

Difference between eukaryotic and prokaryotic cells when it comes to semi-conservative replication

A
  • In eukaryotic cells there are many replication origins with many sections of DNA being unwound and replicated at the same time. These “open” sections are called replication bubbles.
  • In prokaryotic cells there is only one replication origin because less DNA.
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25
Q

Opening and unwinding DNA double helix

A
  • DNA helicase (enzyme) breaks hydrogen bonds between base pairings to unwind helix.
  • Unwinding occurs at a number of points (each called a replication origin) and forms replication forks (like a zipper).
  • Each exposed strand acts as a template to which free DNA nucleotides can bind.
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26
Q

Assembling leading strand

A
  • Activated nucleotides joined one at a time to form new polynucleotide strand of DNA.
  • DNA polymerase (enzyme) facilitates building of new DNA strand.
  • This is a continuous process.
  • Occurs in 5’-3’ direction (only direction that DNA polymerase works in).
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27
Q

Assembling lagging strand

A
  • Lagging strand is antiparallel and runs in 3’-5’ direction.
  • DNA polymerase builds up short sections of lagging strand in 5’-3’ section simultaneously.
  • Short sections known as Okazaki fragments.
  • Okazaki fragments are then linked by DNA ligase (enzyme) to from phosphodiester bonds.
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28
Q

Why does ligase only function on lagging strand

A

it is the only strand containing Okazaki fragments.

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29
Q

Removing wrongly coded DNA

A
  • Sometimes errors occur during DNA replication, e.g., incorrect nucleotide being added.
  • DNA polymerase performs DNA proofreading to check for errors and repair them.
  • Proofreading is highly accurate but is rarely uncorrected, this leads to mutations.
  • Mutations are basis for genetic variation.
30
Q

DNA polymerase only ADDS nucleotides to EXTEND a chain; it cannot start one.

A
31
Q

Other proteins involved in DNA replication:

A
  • Topoisomerase (enzyme)
  • RNA primase (enzyme)
  • Single-stranded DNA-binding proteins
32
Q

Topoisomerase (enzyme)

A

temporarily causes a break in one strand to release tension and rejoins strand after unwinding has occurred.

33
Q

RNA primase(enzyme)

A
  • catalyses synthesis of short strands of RNA (known as RNA primers) on DNA strand in order to allow DNA polymerase to begin polypeptide synthesis.
  • Lengths of RNA replaced by DNA nucleotides before replication completes.
34
Q

Single-stranded DNA-binding proteins

A

bind to DNA after unwinding to help keep strands apart and protect them until replication process is complete

35
Q

Three possible theories of DNA replication:

A
  • Conservative model: separate parental DNA and daughter DNA
  • Semi-conservative: one strand original, one strand new per each DNA molecule
  • Dispersive model: parental DNA broken down and nucleotides replicated then randomly dispersed throughout new molecules. Not necessarily equal amounts old and new material in each molecule.
36
Q

Experiments of Meselson and Stahl

A

To figure out correct theory of DNA replication need a way to “mark” original DNA then track its distribution.

37
Q

Process

A

Cells grown on N14 medium. 1st control.

Some of cells transferred to heavier isotope N15. N15 in form of ammonium chloride.

Bacteria grown using nitrogen from N15 isotope. 2nd control.

After many generations DNA was exclusively heavy type.

Samples of heavy DNA then transferred to medium of N14.

Bacteria grown long enough for cells to divide once.

Sample removed, DNA extracted, placed in solution of caesium chloride and centrifuged.

Caesium establishes density gradient. DNA molecules sink in density gradient and float at certain level. N15 heavier than N14 and sinks to lower level.

Bacteria sinks to density mid way between light N14 and heavy N15, meaning it contains one strand N14 and one strand N15. Acts as evidence fro semi-conservative replication.

38
Q

A gene

A

a section of DNA molecules containing a sequence of nucleotides that code for a polypeptide

39
Q

Nucleotide triplet

A

codes for amino acids; amino acids codes for polypeptide (polypeptide chains lead to proteins

40
Q

Genetic code

A
  • refers to the 64 (4^3) codes available to be formed by nucleotide triplet.
  • It is often given in the from of mRNA codons
  • only applicable to exons
41
Q

mRNA codon

A

sequence of three adjacent nucleotides in mRNA that codes for an amino acid with exception of STOP codons

42
Q

Exons and introns

A

Exons- coding sequences in DNA.
Introns- non-coding sequences in DNA that interfere with synthesis of a functional polypeptide

43
Q

Features of the genetic code:

A

2 of the amino acids are coded for by a single triplet.

Remaining amino acids coded for by between 2-6 codons each.

Codon is always read in 5’-3’ direction.

Known as degenerate code. ‘The genetic code is degenerate because there are many instances in which different codons specify the same amino acid.’

Start of the genetic sequence is always the codon AUG. AUG codes for amino acid methionine.

If methionine does not from part of genetic sequence it is later removed.

STOP codons are: UAA, UAG, UGA

Genetic code is non overlapping.

The code is universal – each triplet codes for same amino acid in all organisms.

44
Q

The central dogma:

Theory centred around DNA as a key molecule.

A
  • DNA is able to undergo replication to make more DNA.
  • DNA is able to be transcribed to make RNA.
  • RNA is able to be translated with protein.
45
Q

Transcription and its 3 steps:

A
  • process of copying sequence of DNA bases from DNA template to form copy transcript known as primary transcript
  • 3 steps: Initiation , Elongation, Termination
46
Q

Translation

A
  • process by which sequence of nucleotide bases in mRNA produces a sequence of amino acids, which join together to form a polypeptide chain at ribosome.
  • DNA template strand also known as transcribed strand. Strand that is not copied and doesn’t play a part in transcription known as non-transcribed strand.
  • 4 parts: Amino acid activation, Starting polypeptide construction, Making the polypeptide, Post-translational modification (assembling the protein)
47
Q

Post-transcriptional modification

A
  • Primary transcript modified in nucleus to form mRNA.
  • mRNA then carries information out of nucleus to ribosomes in cytoplasm
48
Q

Initiation

A

RNA polymerase attaches to promoter.

Promoter – close to section of DNA that will be transcribed.
- DNA molecule unwinds.
- Hydrogen bonds broken.

49
Q

Elongation

A

RNA polymerase moves along strands of DNA.

Strands continue to separate. This exposes nucleotides on template strand.

Exposed nucleotide bases on DNA template strand pair with complementary activated free RNA nucleotides from nucleotide pool in nucleus.

Nucleotides joined to neighbouring nucleotides by phosphodiester bond.

RNA polymerase moves along and adds nucleotides one at a time to build a strand of primary transcript RNA. As it does this, DNA strands rejoin behind it.

Rejoining allows newly synthesised sections of RNA molecule to be released from DNA template strand. As a result, only 12 base pairs on DNA exposed at any given time.

50
Q

Termination

A
  • RNA polymerase reaches termination sequence on DNA.
  • RNA polymerase detaches. Production of primary RNA transcript is complete.
  • Single-stranded transcript represents copy of gene on DNA. Therefore, length of RNA primary transcript = length of DNA gene.
51
Q

Process of post-transcriptional modification: (Wherein primary transcript RNA forms mRNA; occurs before mRNA can leave nucleus)

A
  • GUANINE nucleotide added to 5’ end of primary transcript RNA. This guanine cap is used to trigger TRANSLATION when the mRNA reaches a ribosome.
  • Tail of about 100 ADENINE nucleotides added to other end of RNA. Possible reason is that this tail protects RNA from being broken down in the cytoplasm by nucleases.
  • In eukaryotic cells, splicing now occurs.
52
Q

Splicing of introns

A
  • Splicing is the process by which the base sequences corresponding to the intervening introns are removed, and the functional exons are joined together.
  • Once introns have been spliced, exons can rejoin in a variety of different combinations. Therefore, a single DNA gene can code for up to a number of proteins – depends on order exons are recombined in.
  • mRNA is shorter than original transcribed DNA length
  • mRNA molecules too large to diffuse out of nucleus so leave via nuclear pore
53
Q

Structure of tRNA:

A
  • Basic structure always the same.
  • Triplet on anticodon loop varies according to amino acid to which tRNA molecule is complementary.
  • Each tRNA anticodon complementary to particular sequence on mRNA codon.
  • Other end of tRNA molecule always A-C-C. Amino acid attaches to this end.
54
Q

Amino acid activation

A
  • Forms an intermediate with ATP (phosphate).
  • Intermediate combined with tRNA to form amino-acyl tRNA complex. This reaction is controlled by enzyme amino-acyl tRNA synthetase.
  • Once joined to tRNA ATP -> AMP.
55
Q

Starting polypeptide construction

A
  • Ribosomes consist of one SMALL subunit and one LARGE subunit. They are usually separated but come together like a CLAMP during translation.
  • Starting point for translation on mRNA is START codon (AUG).

Ribosome attachment points for mRNA:
- A-site (aminoacyl site)
- P-site (peptidyl site)
- E-site (exit side)

  • Amino-acyl tRNA molecule with anticodon sequence of UAC (also known as tRNA methionine) moves to ribosome and attaches to P-site.
  • Here it pairs up with AUG START codon on mRNA due to complementary base pairing.
  • As a result of this, all polypeptides begin with amino acid methionine, however, if not actually part of polypeptide, removed after synthesis.
56
Q

Making the polypeptide
(mRNA does not move; ribosomes move along strand of mRNA)

A
  • Second activated tRNA molecule binds to ribosome adjacent to tRNA methionine at A-site.
  • This brings two animo acids close together. (Holds them in place so can join through polypeptide bond).
  • Ribosome moves to third codon and allows second and third amino acids to join.
  • First tRNA released from its amino acid, briefly occupies E-site then released into cytoplasm to collect another methionine molecule from amino acid pool.
  • Process continues this way until complete polypeptide chain built up. Up to 15 amino acids linked per second.
  • Up to 50 ribosomes can pass behind first so that many identical polypeptides can be made at same time. This is made possible because mRNA is being read by many ribosomes, but tRNA molecules are going off to find new amino acids before returning. So constant influx of tRNA and continuous reading of mRNA enables polysome.
  • Process continues until ribosome reaches STOP codon. STOP codons: UGA, UAG, UAA. They do not attract tRNA molecule.
  • Polypeptide is complete. Ribosomal subunits separate. Will become cytoplasmic or bind to RER.
57
Q

Post-translational modification (assembling the protein)

A
  • Single polypeptide chain folds/coils into tertiary structure and becomes functional protein.
  • Quaternary structure may also occur.
  • Other examples include removal of methionine (1st AA), glycolysation, addition of lipids.
58
Q

Difference between chromosome and gene mutation

A

Chromosome mutations- changes in structure/number of chromosomes.

Gene mutations or point mutations- changes to DNA that affect a single locus and produce a different allele of a gene.

59
Q

Mutation

A
  • change in sequence of nucleotide bases of DNA.
  • Mutations in somatic cells do not get passed on. Mutations to gametes can be inherited.
60
Q

Change in nucleotides may cause change in ?

A

codon
- Change in codon may cause change in amino acid. Change in amino acid may change primary structure/polypeptide, which will alter tertiary and quaternary structures, thus whole functionality of protein.

61
Q

If this protein is an enzyme

A

may result in enzyme being non-functional due to non-complementary active site.

62
Q

If alteration to codon produces STOP codon

A

polypeptide may be shortened and produce non-functional protein.

63
Q

Types of gene mutations:

A
  • Insertions
  • Deletions
  • Substitutions
64
Q

Insertion

A
  • One or more extra nucleotides added.
  • These extra nucleotides are transcripted and reflect in mRNA.
  • Insertion can completely alter sequence of amino acids from point of mutation onwards. Alters primary, alters secondary, tertiary etc…
65
Q

Frame shift (type of insertion mutation)

A
  • one inserted nucleotide causes whole reading frame to be changed/shifted up by one.
  • Frame shift could cause creation of STOP codon and result in premature chain termination.
  • Insertion of three nucleotides will only cause change at site of insertion (one extra amino acid).
65
Q

Deletions

A
  • One or more nucleotides lost from sequence.
  • Frame shift could be caused.
  • Deletions of 3 or multiples of 3 result in missing amino acids.
  • Enzymes often not produced or function incorrectly.
    E.g., cystic fibrosis is caused by deletion of three nucleotides.
66
Q

Substitutions

A
  • Nucleotide is replaced by a nucleotide with a different nitrogenous base.
  • Three possible consequences: nonsense mutation, mis-sense mutation and silent mutation
67
Q

Nonsense mutation

A

Base change results in STOP codon. Results in premature chain termination

68
Q

Mis-sense mutation

A
  • Base change results in different amino acid. Polypeptide will be different.
  • Amino acid substituted likely to have LESS effect on tertiary structure if the nature of the R-groups is the same (hydrophobic vs hydrophilic).

E.g., sickle cell anaemia. Change to red blood cell shape caused by hydrophobic R-group amino being substituted by hydrophilic amino. Loses globular structure.

69
Q

Silent mutation

A
  • Substitution results in different base that still codes for amino acid (because of degenerate code).
  • Polypeptide produced has no change.
70
Q

Mutagens

A
  • agents that increase natural mutation rate.
    Include:
  • Chemicals
  • High-energy radiation

Biology (8 decks)

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