Topic 7 - Nucleic Acids Flashcards
1
Q
nucleic acids
A
- chains of nucleotides
- contains CHONP
- very large molecules
- constructed by linking together nucleotides to form a polymer
2
Q
types of nucleic acids
A
- DNA
- RNA
3
Q
chromosome
A
DNA molecule
4
Q
types of metabolism
A
- anabolism
- catabolism
5
Q
anabolism
A
- synthesis of complex molecules from simpler molecules
- requires energy (usually in ATP form)
6
Q
examples of anabolic reactions
A
- formation of macromolecules from monomers by condensation reactions
- protein synthesis using ribosomes
- DNA synthesis during replication
- photosynthesis
- synthesis of complex carbohydrates (e.g. starch, cellulose, glycogen)
7
Q
catabolism
A
- breakdown of complex molecules into simpler molecules
- releases energy and in some cases this energy is captured in the form of ATP
8
Q
examples of catabolic reactions
A
- digestion of food in the mouth/stomach/small intestine
- cell respiration in which glucose/lipids are oxidized to CO2 and water
- digestion of complex carbon compounds in dead organic matter by decomposers
9
Q
composition of nucleic acids
A
- pentose sugar (has 5 C atoms)
- phosphate group
- base containing nitrogen and has 1-2 rings of atoms
10
Q
formation of nucleic acids
A
- covalent bonds form between the phosphate of one nucleotide and the pentose sugar of another
- creates a strong backbone for the molecule of alternating sugar and phosphate groups (with a base linked to each sugar)
- there are 4 different bases in both DNA and RNA so there are 4 nucleotides
- they can be linked together in any sequence
11
Q
strand
A
nucleotide polymer in nucleic acids
12
Q
differences between DNA and RNA
A
- the sugar in DNA is deoxyribose while the sugar in RNA is ribose (deoxyribose has 1 less O atom)
- DNA is double-stranded while RNA is single-stranded
- 1 of the 4 bases in DNA and RNA differ
13
Q
types of DNA bases
A
- adenine
- cytosine
- guanine
- thymine
14
Q
types of RNA bases
A
- adenine
- cytosine
- guanine
- uracil
15
Q
structure of DNA
A
- each strand contains 1 chain of nucleotides linked by covalent bonds
- the 2 strands are antiparallel (run in opposite directions: 3’ to 5’ or 5’ to 3’)
- they’re wound together in double helix formation
- the strands are held together by hydrogen bonds between the nitrogenous bases in a specific alignment (complementary base pairing)
- hydrogen bonds are weak, but in a DNA molecule there are a lot of them so they can successfully hold strands together at body temp
16
Q
complementary base pairing
A
rule that one specific base will always pair with another to form a hydrogen bond
Adenine with Thymine
Cytosine with Guanine
17
Q
semi-conservative replication of DNA
A
- when a cell divides, the 2 double helix strands separate
- each of those original strands serve as a template for the creation of a new strand
- new strands are formed by adding nucleotides and linking them together one by one
- the result is 2 DNA molecules: one is the original and one is newly synthesized
- the base sequence of the template strand determines the base sequence of the new strand
18
Q
helicase
A
- group of enzymes that unwind the double helix and separates the two strands by breaking their bonds
- they use energy from ATP to break hydrogen bonds between complementary bases
- coz double-stranded DNA can’t be split into 2 strands while still helical
19
Q
DNA polymerase
A
- links nucleotides together to form a new strand using the pre-existing strand as a template
- it assembles the new strand as a complementary base sequence to the template
20
Q
DNA replication process
A
- free nucleotides are available in the area where DNA is being replicated
- but only the complementary base pair of the template’s nucleotide in that position can be added
- DNA polymerase will bring nucleotides into the position where hydrogen bonds can form, but if it’s incompatible the nucleotide will break away again
- once a nucleotide with the correct base is brought in, a hydrogen bond will form between the 2 bases
- a covalent bond forms between the phosphate group of the free nucleotide and the sugar of the template’s nucleotide
- the sugar is the 3’ terminal while the phosphate is the 5’ terminal
- DNA polymerase will gradually move along the template strand, adding a complementary base sequence to form a new strand
21
Q
alternating sugar-phosphate backbone of DNA chains
A
- molecules held together by phosphodiester covalent bonds
- forms between a hydroxyl group of 3’ C and a phosphate group of 5’ C
- formation of this bond is due to a condensation reaction
- there’ll be a 5’ C free on one end and a 3’ C free on the other
- the 5’ C will always have a phosphate group attached
- the 3’ C will always have a hydroxyl group attached
22
Q
how are the sugar-phosphate backbones attached to each other?
A
- by their nitrogenous bases
- they run antiparallel (opposite directions)
- so one has the 5’ C carbon on top and the other has it on the bottom
23
Q
how is DNA packaged?
A
- eukaryotic DNA is paired with histone
- tends to have more than 1 histone per strand
24
Q
why does DNA wrap around histones?
A
- DNA is negatively charged
- histones are positively charged
- mutual attraction
25
how does histone induce supercoiling?
- there's a 5th type of histone attached to the linking
string of DNA near each nucleosome
- leads to further wrapping (packaging) of the DNA molecule
- eventually to highly condensed (supercoiled) chromosomes
26
nucleosome
- section of DNA coiled around 8 histone molecules
| - coiling is held in place by a 9th histone molecule
27
linker DNA
short sections of DNA that connect nucleosomes together
28
satellite DNA
repetitive DNA clustered in discrete areas
29
process of semi-conservative replication of DNA
1. - replication begins at origin
- appears as a bubble because of the separation of the two strands
- helicase 'unzips' the DNA strands by breaking hydrogen bonds between nucleotides
2. - at each end of a bubble is a replication fork
- this is where the double-stranded DNA opens to provide the 2 parental DNA strands
- parent strands act as templates to produce the daughter DNA molecules by semiconservative replication
3. - bubbles enlarge in both directions, showing that the replication process is bidirectional
- bubbles eventually fuse with one another to produce 2 identical daughter DNA molecules
30
process of elongation of a new DNA strand
1. - primer produced with primase at replication fork (refer to semi-conservative DNA replication)
- the primer is a short sequence of RNA, usually only 5–10 nucleotides long
- primase allows the joining of RNA nucleotides that match the exposed DNA bases at the point of replication
2. DNA polymerase III allows the addition of nucleotides in a 5ʹ to 3ʹ direction to produce the growing DNA strand
3. DNA polymerase I removes the primer from the 5ʹ end and replaces it with DNA nucleotides
31
why is there a difference in process between the assemblies of the 2 daughter DNA strands in the semi-conservative replication of DNA?
- a DNA molecule has 2 antiparallel strands
- due to DNA polymerase III, nucleotides can only be added in 5' to 3' direction
- so the production of the 3' to 5' strand is a much faster process than the other
32
phosphodiester bond
the covalent bond between nucleotides that are added to the 3' end during elongation
33
leading strand
- the 3' to 5' strand
| - produced much faster than the 5' to 3' strand
34
lagging strand
- the 5' to 3' strand
- produced much slower than the 3' to 5' strand
- undergoes discontinuous replication
35
Okazaki fragments
fragments of the lagging strand
36
process of elongation of the 5' to 3' strand (lagging strand)
1. - the leading strand is assembled continuously towards the progressing replication fork in the 5ʹ to 3ʹ direction
- but the lagging strand is assembled by Okazaki fragments being produced
- lagging strand is also assembled in 5' to 3' direction but gradually moves away from replication fork
4. Primer, primase, and DNA polymerase III are required to:
- begin the formation of each Okazaki fragment
- begin the formation of the continuously produced leading strand.
- but for the leading strand the primer and primase are only needed once because the production of the leading strand is continuous
6. Once the Okazaki fragments are assembled, an enzyme called DNA ligase attaches the sugar–phosphate backbones of the lagging strand fragments to form a single DNA strand
37
role of DNA polymerase III in DNA replication
- adds nucleotides in 5' to 3' direction
| - on the leading strand it moves in the same direction as the replication fork
38
role of DNA gyrase in DNA replication
- moves in advance of helicase
- relieves strains in the DNA molecule created when the double helix is uncoiled
- without it, the separated strands would supercoil
39
role of DNA polymerase I in DNA replication
- removes RNA primer
- replaces it with DNA
- nick is left in sugar-phosphate backbone where 2 nucleotides are still unconnected
40
role of DNA ligase in DNA replication
- seals up the nick made by DNA polymerase I
- by making another sugar phosphate bond
- also facilitates joining of DNA segments and Okazaki fragments by creating phosphodiester bonds
41
role of DNA primase in DNA replication
- synthesizes RNA primer
| - necessary to begin synthesis of a strand (leading) or Okazaki fragment (lagging)
42
DNA's only function is to code for proteins: T/F?
- false
| - nucleotide sequences with other functions include telomeres, satellite DNA, short tandem repeats
43
telomere
- nucleotide sequences occurring at the ends of chromosomes
- serves to protect the chromosomes
- they shorten with each chromosomal replication
- plays a role in number of reproductive cycles of a cell
44
how does DNA profiling work?
- short tandem repeats are unique to each individual
| - can be analyzed with restriction enzymes or gel electrophoresis
45
gel electrophoresis
- technique used to separate proteins or fragments of DNA according to their size
- involves separating charged molecules in an electric field according to their size and charge
- charged molecules in the sample will move through the gel
- the gel used consists of a mesh of filaments that resist the movement of molecules in a sample
- eukaryotic DNA molecules are broken up into smaller fragments bc they're too long to move through the gel
- as all DNA molecules carry negative charges, they will move in the same direction
- but small fragments will move faster than large ones
46
DNA sequencing process
1. - single-stranded fragments placed in 4 diff tubes
- all test tubes contain primers + DNA polymerases necessary for DNA replication + DNA nucleotides
2. - each tube contains a special nucleotide (dideoxynucleotide)
- this nucleotide prevents any further nucleotide additions to a chain
- there are 4 diff types of this nucleotide (symbols are same as ACTG but with *)
3. - synthesis of each new DNA strand then begins at the 3ʹ end of the primer
- synthesis ends when a dideoxynucleotide is added
- dideoxynucleotides are only available in limited amounts but allow chains of various lengths to be assembled
4. - DNA from each tube is placed in a separate lane of an electrophoresis gel
- gel electrophoresis is carried out
- bands produced in each lane is used to determine the exact sequence of that particular fragment of DNA
47
Sanger technique for genome sequencing
- a DNA sample is chopped up and single stranded copies are made with DNA polymerase
- before the whole sequence is replicated, small quantities of a non-standard nucleotide are added to the reaction mixture
- this is done separately with each of the 4 possible DNA bases
- then each sample is separated with gel electrophoresis
48
how has technology enhanced gel electrophoresis?
- colored fluorescent markers are used to mark the DNA copies
- each of the 4 samples is distinguished by a particular color
- the samples are mixed together and all the DNA copies are separated in 1 lane of a gel according to the no of nucleotides
- a laser scans along the lane to cause fluorescence
- an optical detector detects the colors of fluorescence
- a computer deduces the base sequence from the sequence of colors detected
49
transcription
- synthesis of mRNA that is copied from the DNA base sequences by RNA polymerase
- as RNA is single-stranded, transcription only occurs along 1 of the 2 DNA strands
50
enzymes involved in DNA replication
- DNA polymerase III
- DNA polymerase I
- helicase
- DNA ligase
- DNA gyrase
- primase
51
DNA transcription
- synthesis of mRNA that is copied from the DNA base sequences by RNA polymerase
- as RNA is single-stranded, transcription only occurs along 1 of the 2 DNA strands
52
enzymes involved in transcription
- RNA polymerase
53
product of transcription
- a RNA molecule
- has a base sequence complementary to the DNA template strand used
- should be identical with the other strand (with the exception of thymine)
54
role of helicase in transcription
- trick question! helicase is not used in DNA transcription
| - instead, RNA polymerase unwinds the double helix
55
role of RNA polymerase in transcription
- combines with a DNA strand (a promoter)
- this causes the DNA double helix to unwind
- works similarly to DNA polymerase, only allows movement in 5' to 3' direction
56
DNA sections involved in transcription
promoter → transcription unit → terminator
57
effect of terminator sequence on transcription
- causes the RNA polymerase to detach from the DNA upon its transcription
- though in eukaryotes, transcription continues a while beyond the terminator before being released
58
NTP
- nucleoside triphosphates
- they are the RNA nucleotides used in transcription
- contains three phosphates and ribose
59
transcription process
1. RNA polymerase binds to a site on the DNA at the start of a gene sequence
2. RNA polymerase moves along the gene to separate DNA into single strands and pair up RNA nucleotides with complementary base pairing (as there's no thymine for RNA, uracil pairs with adenine)
3. Elongation occurs with the help of energy obtained from release of 2 phosphates from NTP
4. RNA polymerase forms covalent bonds between RNA nucleotides
5. transcription stops after termination seqence
6. the new RNA strand is released and the double helix reforms between the DNA parent strands
60
introns
- stretches of non-coding DNA
| - only present in eukaryote DNA
61
pre-mRNA
- primary/first mRNA transcript
- due to the presence of introns, it can't be used unless it undergoes splicing
- introns must be removed
62
exons
- coding DNA
- exons are what's left after introns are spliced out
- can be rearranged to result in various different proteins
63
spliceosome
- composed of small nuclear RNA molecules (snRNA)
| - pronounced snurps
64
cap (mRNA splicing)
- added at 3' end of mature mRNA (after end codon)
| - made of modified guanine nucleotide with three phosphates
65
poly-A-tail (mRNA splicing)
- added to 5' end of mature mRNA (before start codon)
| - composed of 50–250 adenine nucleotides
66
process of mRNA splicing
- the original pre-mRNA is capped with a promoter and terminator
- but during splicing, a cap is added at 3' end and poly-A-tail is added at 5' end
- spliceosomes replace the introns on the pre-mRNA and rearrange exons
- as exons can be rearranged to result in different types of proteins, this increases the number of possible proteins produced by a single gene
67
functions of cap and poly-A-tail
- protects mature mRNA from degradation
| - enhances translation process (which occurs later in the ribosome)
68
transcription activators
- proteins that cause looping of DNA
| - results in shorter distance between activator and promoter region
69
silencers
- specific segments of DNA that repressor proteins may bind to
- the binding prevents transcription and gene expression of that segment
70
roles of protein in gene expression
- some proteins assist RNA polymerase's binding to the promoter region of a gene
- transcription activators
- silencers
71
ribosome bindings sites
- E
- P
- A
72
ribosomal binding site E
Site from which tRNA that has lost its amino acid is discharged (exit binding site)
73
ribosomal binding site P
Holds the tRNA carrying the growing polypeptide chain
74
ribosomal binding site A
Holds the tRNA carrying the next amino acid to be added to the polypeptide chain
75
initiation phase of translation: process
1. - translation occurs in 5ʹ to 3ʹ direction
- start codon located at 5' end
- each codon (other than the three stop codons) attaches to a specific tRNA
- 3ʹ end of tRNA is free and is where the amino acid attaches
2. - hydrogen bonds form at 4 areas of tRNA, causing it to fold and take a 3D structure (like a clover leaf if flattened)
- one of the clover leaf loops contains an exposed anticodon specific to each tRNA type
3. - tRNA's exposed anticodon pairs with a specific mRNA codon
- a specific enzyme catalyses the binding of amino acids to their appropriate tRNA (there's one specific enzyme for each of the 20 amino acids)
- attachment to enzyme's active site requires ATP
- at this point, the structure (of tRNA attached to amino acid) is referred to as an activated amino acid
- the tRNA delivers the amino acid to a ribosome
4. - the small ribosomal subunit moves down mRNA until it contacts the start codon
- contact starts translation and hydrogen bonds form between initiator tRNA and start codon
- the large ribosomal subunit combines with these
parts to form the translation initiation complex
- initiation factor proteins use GTP (similar to ATP) to join the translation initiation process
76
elongation phase of translation: process
1. tRNAs brings amino acids to the mRNA–ribosomal complex in order specified by codons of mRNA
2. elongation factor proteins assist in binding tRNAs to exposed mRNA codons at the A site
3. - initiator tRNA moves to the P site
- ribosomes catalyse the formation of peptide bonds between adjacent amino acids brought to the polypeptide assembling area
77
translocation phase of translation
- is actually a part of elongation phase
| - involves the movement of tRNAs from one site of the mRNA to another
78
translocation phase of translation: process
1. a tRNA binds with the A site
- its amino acid is then added to the growing polypeptide
chain by a peptide bond
- causes the polypeptide chain to be attached to the
tRNA at the A site
2. - tRNA moves to P site
- it transfers its polypeptide chain to the new tRNA, which moves into the now exposed A site
- the now empty tRNA is transferred to the E site and released
79
termination phase of translation: process
1. - begins when one of the three stop codons appears at the open A site
- release factor protein then fills A site
- release factor catalyses hydrolysis of the bond linking the tRNA in the P site with the polypeptide chain
- this releases the polypeptide from the ribosome
2. - ribosome separates from mRNA and splits into its two subunits
- mRNA detaches from the ribosome
- all tRNAs detach from the mRNA–ribosomal complex
- the protein is released from the ribosome
3. - if produced by free ribosomes, they're primarily used within the cell
- if produced by ribosomes bound to rER, they're primarily secreted from the cell or used in lysosomes
80
initiation phase of translation tl;dr
- activated amino acid combines with mRNA strand and small ribosomal subunit to form translation initiation complex
- small ribosomal unit begins translation with the help of initiation factor proteins
81
re-annealing
- upon being cooled in PCR, the DNA strands that have been separated can pair up again
- this is called re-annealing
82
primer
short sections of single-stranded DNA
83
Taq DNA Polymerase
- a variant of DNA polymerase
- taken from a bacterium found in hot springs
- so they're very heat-stable and can resist temperatures up to 95°C
- optimum temp is 72°C
84
polymerase chain reaction process
STAGE 1
- the DNA sample is loaded into a PCR machine
- the double-stranded DNA is separated into 2 single strands by exposure to 95°C for 15 seconds (thereby breaking the hydrogen bonds)
- they are then quickly cooled back to 54°C (which could allow re-annealing)
- however, there are a lot of primers present
- if primers bind rapidly to target sequences, they could prevent re-annealing
STAGE 2
- Taq DNA polymerase is used
- bc it can resist the brief 95°C heating
- it's used to attach the primers
- after being cooled to 54°C, the mixture is heated up to 72°C (optimum temp for this enzyme)
- at optimum temp, Taq DNA polymerase can add 1000 nucleotides per minute
- at this point 1 cycle is complete
- 1 cycle normally takes < 2 minutes
- up to 30 cycles are typical for this process and take < 1 hour
85
sense strand
the DNA strand with the same sequence as the new RNA strand in transcription
86
antisense strand
- the DNA strand used as the template
| - it has a complementary base sequence to the RNA and the sense strand
87
translation
- the synthesis of a polypeptide
| - takes place on ribosomes
88
mRNA
- messenger RNA
- carries the codons specifying the amino acid sequence of the polypeptide to be synthesized
- it's the new RNA strand that was created in the transcription process
- its length is dependent on the number of amino acids in the polypeptide
- but the average length for mammals is 2000 nucleotide units
89
types of RNA
- mRNA: messenger RNA
- tRNA: transfer RNA
- rRNA: ribosomal RNA
90
tRNA
- transfer RNA
- involved in decoding the base sequence of mRNA into an amino acid sequence
- used during translation process
- each tRNA has a 3-base anticodon complementary to the mRNA codon for that particular amino acid
- they also carry the amino acid corresponding to that codon
91
rRNA
- ribosomal RNA
| - part of the ribosome structure
92
codon
- a sequence of 3 bases on the mRNA
- each codon codes for a specific amino acid
- there are also start/stop codons used to denote the start/end of translation
93
degenerate codons
codons that code for the same amino acid
94
role of ribosomes in translation
- acts as the binding site for mRNAs and tRNAS
- catalyses the assembly of the polypeptide
- has 2 subunits (1 big, 1 small)
- the small subunit is the binding site
- the large subunit is the site that makes peptide bonds between amino acids
95
translation process
1. an mRNA binds to the small ribosome subunit
2. a molecule of tRNA binds to the ribosome (it must have a complementary anticodon to the first codon on the mRNA)
3. another tRNA binds to the next codon (again, it must be the complementary anticodon to the 2nd codon) -- a maximum of 2 tRNAs can be bound to the mRNA at the same time
4. the ribosome transfers the amino acid carried by the 1st tRNA to the 2nd tRNA by forming a peptide bond between the 2 amino acids, so the 2nd tRNA is carrying a dipeptide
5. the ribosome moves along the mRNA so that the 1st tRNA is released, moving the 2nd tRNA to the 1st position
6. another tRNA binds (again, a complementary anticodon to the 3rd codon)
7. the ribosome transfers the dipeptide on the 2nd tRNA to the 3rd RNA
8. stages 6-7 are repeated over and over until a stop codon is reached
9. at that point, the polypeptide is complete and is released
