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Biology IB (reset stats for Jan mocks) > DNA > Flashcards

DNA Flashcards

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1
Q

What is the structure of DNA?

A

DNA is formed of two antiparallel nucleotide strands, forming a double helix . Nucleotides are made up of deoxyribose sugar, one phosphate and one base. The nucleotide is a subunit. There are four bases, Adenine Thymine, Guanine and Cytosine and Guanine, there is complementary base pairing between A-T C-G. Hydrogen bonds form between these pairs, two hydrogen bonds between A and T and three hydrogen bonds between C and G. There are covalent bonds between sugar and phosphate groups/ between sugar and bases. There is an alternating sugar-phosphate backbone

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2
Q

What are the differences between DNA and RNA?

A
  • RNA has one polymer of nucleotides (single-stranded (mostly)), whereas DNA has two polymers of nucleotides (double-stranded)
  • RNA has a ribose sugar whereas DNA has a deoxyribose sugar
  • RNA has AUCG whereas DNA has ATCG
  • RNA is single-stranded, DNA is a double helix
  • RNA is synthesised and translated in the 5’→ 3’ direction whereas DNA is antiparallel (one runs in the 5’→3’ direction the other is 3’→5’)
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3
Q

what direction is the coding for transcription in?

A

5’→3’

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4
Q

What Did Chagraff do?

A

He used paper chromatography to separate the components of DNA and to measure the concentrations of the bases A,T,C and G.

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5
Q

what did Chagraff find?

A
  • The number of Purine bases (A and G) always equalled the number of Pyrimidine bases (T and C)
  • the number of A is always equal to the number of T (and the same for G and C)
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6
Q

What was the Wattson and Crick model?

A
  • they fit perfectly as they are the correct length (A-T, C-G)
  • purines are double ring bases, pyramidines are single ring bases
  • therefore purines (A and G) will always pair with pyramidines (C and T)
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7
Q

What are the Purine Bases?

A

Adenine
Guanine
They are a double ring structure

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8
Q

What are the pyramidine structures?

A

Cytosine
Thymine
They are a single ring structure

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9
Q

What did Hershey and Chase do?

A

Hershey and Chase used bacteriophages (viruses) to perform experiments to determine whether DNA or proteins were the genetic material.

They labeled the viral DNA with radioactive phosphorus-32, because phosphorus is found in DNA but not in proteins.
They labeled the viral proteins with radioactive sulfur-35, because sulfur is found in proteins but not in DNA.
They allowed the labeled viruses to infect bacterial cells.
After infection, they blended the mixture to break up and separate the viruses from the bacteria.
They then centrifuged the mixture to separate the heavier bacteria from the lighter virus particles, allowing them to study the bacteria.
They found that the radioactive phosphorus-32 from the viral DNA entered the bacterial cells during infection, while the radioactive sulfur-35 from the viral proteins did not. This demonstrated that the genetic material responsible for directing the production of new viruses was DNA, not proteins.Hershey and Chase’s used bacteriophages (viruses) to perform experiments to see if DNA or proteins were the genetic material.
- they blended the experiment after infection to break up and separate the virus from the bacteria
- they centrifuged it to separate the bacteria from the virus, so they could study the bacteria

They found that the radioactive viral DNA entered the bacterial cell during infection (protein did not), therefore genetic material was DNA, not proteins.

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10
Q

What are nucleosomes

A
  • They consist of DNA wrapped around histones;
    • Histones are in an octamer (group of eight)
  • These are held together by another histone in the linker region
  • These help to supercoil chromosomes
  • Needed to regulate gene expression
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11
Q

What is semi conservative replication of DNA?

A

each strand of DNA splits, both strands are copied as a template. The daughter DNA then has one new strand and the original parent strand

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12
Q

What is the process of semi-conservative DNA replication?

A
  1. Gyrase relieves strain and prepares for uncoiling
  2. DNA helicase unwinds the double helix and separates the two strands by breaking the hydrogen bonds at the replication fork
  3. Each exposed strand acts as a template for a new strand (semi-conservative replication)
  4. DNA primase adds RNA primer (short length of RNA nucleotides)
  5. This then enables the DNA polymerase III to bind and copy the DNA by adding nucleotides in a 5’→3’ direction using complementary base pairing (A+T, C+G)
  6. Replication has to happen in the 5’→3’ direction. Therefore, DNA polymerase moves towards the replication fork on one strand and away on the other
  7. DNA polymerase I replaces the primers with DNA
  8. Continuous on leading strand and fragments formed (discontinuous) on the lagging strand. On the lagging strand these short lengths of DNA that are formed with each primer called the Okizaki fragments
  9. DNA ligase joins the fragments together by forming sugar-phosphate bonds
  10. deoxynucleoside triphosphate provide energy to add nucleotides
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13
Q

What is PCR?

A

PCR- polymerase chain reaction, it is a process which amplifies the amount of DNA exponentially in a very short space of time

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14
Q

What is required for PCR?

A
  • sample of DNA
  • DNA polymerase
  • Primers
  • DNA nucleotides
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15
Q

Why are primers important for PCR?

A

A short single stranded length of DNA, about 20-30 nucleotides long. These complementary base pair with DNA allowing DNA polymerase to bind and DNA synthesis to occur as they show the enzyme where to start copying the DNA as the enzyme needs a starting strand to attach nucleotides to. They are also important as they keep DNA strands separate.

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16
Q

What are the steps for PCR?

A
  1. Add DNA sample, primers, nucleotides and DNA polymerase
  2. DNA heated to 90-95°C to break the hydrogen bonds and separate the double-stranded helix
  3. DNA is then cooled to 52°C, to allow for the bonding of primers
  4. It is then heated to 70-75°C to provide optimum temperature for DNA polymerase. N.B. this DNA polymerase is taken from bacteria that thrive in high temperature environments (it is Taq DNA polymerase)
    • DNA polymerase forms new double stranded DNA by adding complementary base pairs- joining together forming phospho-diester bonds during condensation reactions
  5. The cycle is then repeated many times
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17
Q

What is DNA amplification? (in relation to PCR)

A

many genetically identical copies of a DNA molecule are made using PCR

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18
Q

What is gel electrophoresis?

A

method used to separate the DNA fragments according to their size by using electricity

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19
Q

Why do DNA fragments move to the anode in gel electrophoresis?

A

DNA fragments move from the cathode (-ve) to the anode (+ve). They diffuse towards the positive electrode due to the negative charge on the phosphate group in the DNA

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20
Q

How does gel electrophoresis work?

A

DNA fragments are placed in wells. Large enough samples are generated using PCR to amplify DNA first, before cutting it into fragments using a restriction endonuclease enzyme (which breaks covalent phosphodiester bonds)

A current is passed through the gel. Negatively charged DNA moves towards the positive electrode.

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21
Q

Why do different patterns appear on the gel electrophoresis?

A

Smaller fragments move more rapidly as they encounter less resistance from the gel. Fragments are separated due to size as small fragments move further.

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22
Q

what is genetic fingerprinting?

A

This is a unique DNA profile formed of non-coding DNA regions called minisatellites

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23
Q

What are minisatellites and tandem repeats? (for genetic fingerprinting)

A

Minisatellites are non-coding regions on DNA. These are formed from short repeating base sequences called tandem repeats. The number of times these tandem repeats are repeated determines the length of the minisatellite region
(this determines the distance travelled in gel electrophoresis)

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24
Q

what is a non overlapping triplet code?

A

Three consecutive bases in DNA is a triplet, each triplet codes for one specific amino acid, neither the second nor the third base of a triplet forms part of the next triplet

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25
Q

what does universal mean with regards to protein synthesis?

A

The same codon codes for the same amino acid in all species

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26
Q

what does degenerate mean with regards to protein synthesis?

A

One amino acid is coded for by more than one triplet (4 possible bases in 3 positions 4^3=64)

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27
Q

what does triplet mean with regards to protein synthesis?

A

Each amino acid is coded for by a mRNA codon, which is coded for by a sequence of three bases

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28
Q

what does non-overlapping mean with regards to protein synthesis?

A

Each base is read only once during transcription. This means each base is a part of one triplet only

29
Q

what do non-coding stop codons mean with regard to protein synthesis?

A

These do not code for amino acids but mark the end of the code for a polypeptide chain

30
Q

what is mRNA

A
  • straight single stranded molecule
  • contains a ribose sugar
  • has uracil instead of thymine
  • has codons instead of triplets or anticodons
31
Q

what is tRNA

A
  • found in the ribosome
  • arranged in a ‘clover’ shape
  • hydrogen bonds are partly present
  • contains a ribose sugar
  • has uracil instead of thymine
  • it is more stable than mRNA but less stable than DNA
32
Q

What are the stages of transcription

A
  1. initiation
  2. elongation
  3. termination
  4. RNA-splicing (only occurs in eukaryotes)
33
Q

what happens in the initation phase of transcription (protein synthesis)

A
  • Transcription factors move from the cytoplasm to the DNA nucleus. They bind to a specific sequence of bases called the promoter region
  • This allows the enzyme RNA polymerase (and DNA helicase) to bind and separate the two strands of DNA
34
Q

what happens in the elongation phase of transcription (protein synthesis)

A
    • RNA polymerase uncoils the DNA by breaking hydrogen bonds (using ATP). This causes the strands to separate exposing the DNA template strand
    • Free RNA nucleotides complementary base pair with the DNA template strand, Cytosine with Guanine and Adenine with Uracil. Each base triplet codes for one mRNA codon. Hydrogen bonds form between RNA nucleotides and base
    • RNA polymerase joins nucleotides together by forming new phosphodiester bonds. This is a condensation reaction. RNA nucleoside triphosphates used. Hydrolysis of two phosphates is used to gain the energy required.
    • A strand of pre-mRNA is formedNB- RNA polymerase binds to the antisense strand of DNA as it moves along in a 5’→3’ direction
35
Q

what happens in the termination phase of transcription (protein synthesis)

A

When RNA polymerase reaches the termination sequence RNA polymerase detaches and releases the pre mRNA molecule (which includes both introns and exons). RNA polymerase detaches and then the DNA rewinds

36
Q

what happens during RNA splicing in transcription (protein synthesis) (eukaryotes only)

A
  • Pre-mRNA contains some regions that do not code for proteins called introns (they intrude on the code)
  • To produce functional proteins these introns need to be spliced out of the pre-mRNA, leaving only the regions that code for proteins called exons. This is carried out by a protein complex called the spliceosome which is made of snRNP’s
  • The exons are then joined together to form mature mRNA and a 5’ cap and 3’ poly-A tail are added to the mRNA
37
Q

what is the process of transcription? (whole thing)

A
  1. Transcription- Initiation
    • Transcription factors move from the cytoplasm to the DNA nucleus. They bind to a specific sequence of bases called the promoter region
    • This allows the enzyme RNA polymerase (and DNA helicase) to bind and separate the two strands of DNA
  2. Transcription- Elongation
    • RNA polymerase uncoils the DNA by breaking hydrogen bonds (using ATP). This causes the strands to separate exposing the DNA template strand
    • Free RNA nucleotides complementary base pair with the DNA template strand, Cytosine with Guanine and Adenine with Uracil. Each base triplet codes for one mRNA codon. Hydrogen bonds form between RNA nucleotides and base
    • RNA polymerase joins nucleotides together by forming new phosphodiester bonds. This is a condensation reaction. RNA nucleoside triphosphates used. Hydrolysis of two phosphates is used to gain the energy required.
    • A strand of pre-mRNA is formedNB- RNA polymerase binds to the antisense strand of DNA as it moves along in a 5’→3’ direction
  3. Transcription- Termination
    • When RNA polymerase reaches the termination sequence RNA polymerase detaches and releases the pre mRNA molecule (which includes both introns and exons). RNA polymerase detaches and then the DNA rewinds
  4. RNA splicing-(ONLY OCCURS IN EUKARYOTIC CELLS)
    • Pre-mRNA contains some regions that do not code for proteins called introns (they intrude on the code)
    • To produce functional proteins these introns need to be spliced out of the pre-mRNA, leaving only the regions that code for proteins called exons. This is carried out by a protein complex called the spliceosome which is made of snRNP’s
    • The exons are then joined together to form mature mRNA and a 5’ cap and 3’ poly-A tail are added to mRNA
38
Q

Where does translation take place?

A

the mRNA leaves the nucleus through the nuclear pores and into the cytoplasm, where ribosomes are required for translation

39
Q

what happens during the process of translation (protein synthesis)

A
  1. Mature mRNA leaves through nuclear pore and binds to the small sub unit of the ribosome. The ribosome then slides along the mRNA to the start codon (AUG). This is called initiation
  2. Anticodons on tRNA complementary base pair to specific codon sequence on mRNA. The second tRNA then pairs with the next codon. Each tRNA brings a specific amino acid
  3. Peptide bonds form between amino acids in a condensation reaction. This is called elongation
  4. tRNA that has lost its amino acid detaches due to bond between tRNA and amino acid being hydrolysed. tRNA goes to collect another specific amino acid- it requires a specific activating enzyme to do this
  5. Ribosome moves along the mRNA by one codon in the 5’ to 3’ direction. Another tRNA pairs with the next codon (moves into A site). This is called translocation
  6. Ribosome reaches a stop codon and detaches. Polypeptide chain released. This is called termination.
40
Q

what are polysomes?

A

Polysomes are formed from many ribosomes joined to one RNA strand.

Free Ribosomes: Produce proteins for intracellular use

Bound Ribosomes: Produce proteins for extracellular use (put into vesicle)

41
Q

What is the structure of ribosomes?

A

Ribosomes are 80s in eukaryotic cells and are made up of:

  • small subunit- mRNA binding site
  • large subunit- three tRNA binding sites (A,P,E)
  • made of protein and rRNA (ribosomal RNA) in both subunits
    • rRNA catalyses the formation of peptide bonds
42
Q

what happens at the A binding site of a ribosome?

A

The A binding site holds tRNA with the next amino acid to be added, and then a peptide bond is formed between amino acids of the A site and polypeptide at the P site

43
Q

What happens at the P site of the ribosome?

A

The large subunit binds with the tRNA in the P site

44
Q

what happens at the E site of a ribosome?

A

E binding site (exit) is where the tRNA from P site (without amino acid) leaves the ribosome

45
Q

What are the roles of the different binding sites for tRNA on the ribosomes during translation?

A
  • A, P and E binding sites are on the large subunit of the ribosome
  • Initiation of translation starts with binding of met-tRNA to the start codon (AUG)
  • Large subunit binds with the start tRNA in the P site
  • A binding site holds the tRNA with the next amino acid to be added
  • Peptide bond is formed between the amino acids of the A site and the polypeptide at the P site
  • Polypeptide is transferred to the tRNA in the A site
  • The tRNA with polypeptide in the A site then moves to the P site
46
Q

what is a mutation?

A

A mutation is a permanent change in the sequence of bases that make up a gene.

47
Q

how do mutations arise?

A
  • mutations may take place at random due to errors during DNA replication (even though DNA polymerase has a proofreading mechanism)
  • Rates of mutation can be increased by UV radiation, ionising particles, x-rays and carcinogens
48
Q

Are mutations good or bad?

A

Mutations are vital in the mechanism of natural selection as they are ultimately the source of genetic variation within a population that selective pressure can act upon.

A mutation can be…

  • neutral- no effect on fitness
  • positive (advantageous)- increases an individual’s fitness
  • negative (deleterious)- decreases an individual’s fitness
49
Q

what are the types of mutations?

A
  1. substitution
  2. deletion
  3. addition
50
Q

what is a substitution (point) mutation?

A

One base is replaced by another.

There are three outcomes of a substitution mutation:

  • Silent mutations- do not affect the sequence of amino acids during translation
  • Nonsense mutations- result in a stop codon where an amino acid should be, causing translation to stop prematurely
  • Missense mutations- change the amino acid specified by a codon.
51
Q

What is a deletion mutation?

A

Where a base is deleted causing a frameshift

Because the genetic code is read in codons, deleting bases may change the “reading frame” of the sequence. These types of mutations are called frameshift mutations

52
Q

What happens during addition mutations?

A

when a base is added, causing a frame shift.

Deletion and addition mutations case frameshifts. There is now a change in DNA triplets after the point of mutation, meaning changes in mRNA codons and therefore sequence of amino acids

53
Q

What is gene knockout and why might we want to do it?

A
  1. Gene knockout is a technique in which a specific gene is intentionally removed or changed in some way so that its expression of it is permanently prevented.
  2. To research and understand the role of specific genes (or the proteins they code for) on an organisms development, physiology or disease susceptibility
54
Q

What is the CRISPR-Cas9 system?

A
  • the enzyme Cas9, which is used to cut DNA at specific target sites on a chromosome
  • CRISPR (clustered regularly short palindromic repeats) which are specific regions of DNA that are found in bacteria and contain short, repeated sequences and unique spacer sequences that are incorporated, usually from viral DNA encountered by bacteria
55
Q

why might bacteria need CRISPR-Cas9?

A

Natural defence mechanism for bacteria to defend against viruses that previously infected them

56
Q

How can scientists use CRISPR-Cas9 for gene editing?

A
  • CRISPR creates single guide RNA’s
  • These target specific genes by binding to specific base sequences
  • Cas9 enzyme is then guided to the location and is allowed to make the cut in the DNA
  • This results in the breaking of the double strand
  • Scientists then add, delete, or modify the DNA sequences at that point
57
Q

what might be possible ethical concerns about the use of CRISPR-Cas9?

A

ethical and safety concerns about the editing of human embryos or the genetic modification of entire species e.g. cancer

58
Q

what are transcription factors?

A
  • regulates transcription
  • binds to promoter region near the start of the target gene
  • allows RNA polymerase to bind
59
Q

what are the two types of transcription factor?

A

Activators:
1. bind to promoter region and help RNA
2. stimulates RNA polymerase to bind
3. leads to transcription

Repressors:
1. bind to promoter region
2. prevent RNA polymerase from binding
stops

60
Q

why can oestrogen act as a transcription factor?

A

Oestrogen is a lipid soluble steroid hormone. This means that it can diffuse across both the plasma membrane and the nuclear membrane to act as a transcription factor.

61
Q

The oestrogen receptor complex (transcription factors)

A
  1. The steroid hormone oestrogen binds to a receptor (Erα) on the plasma membrane. Oestrogen then enters the cell via diffusion
  2. The oestrogen receptor complex is composed of transcription factor and an inhibitor. The inhibitor blocks the DNA binding site on the transcription factor
  3. Oestrogen has a complementary shape to a binding site on the oestrogen receptor complex. When it binds, this complex changes shape, causing the inhibitor to be released. The oestrogen-oestrogen receptor complex can now enter the nucleus
  4. The transcription region of the Oestrogen-oestrogen receptor complex binds to the gene. Under most circumstances it acts as an activator, allowing RNA polymerase to bind
62
Q

what is siRNA and what does it do? (summation)

A

siRNA (small interfering RNA) is a short, double strand of RNA that prevents the expression of a particular gene. This is done through causing the breakdown of mRNA and consequently prevents translation from occurring. This process is known as RNA interference.

63
Q

what is siRNA and what does it do?

A
  1. siRNA is a short double stranded RNA molecule about 20 base pairs long.
  2. In the cytoplasm siRNA binds to an enzyme called the RNA-induced silencing complex (RISC)
  3. RISC breaks down the double stranded siRNA into its separate single strand. One strand remains attached to the RISC enzyme, while the other strand is discarded
  4. The RISC-RNA complex now binds to mRNA molecules in the cytoplasm by complementary base pairing. Any mRNA molecules with a base sequence complementary to the 20-base siRNA sequence will bind
  5. This binding causes RISC to cut the mRNA molecule into pieces (using ATP)
  6. These mRNA fragments can no longer be used in translation, and are broken down by nuclease enzymes (this process is often used to break down viral RNA)
64
Q

what are epigenetics and how might they change gene function without changing the base sequence of DNA?

A
  1. When environmental factors (e.g. diet, stress, hormones, nutrition, toxins) can cause heritable changes in the gene function without changing the base sequence of DNA.
  2. By switching the genes on and off (altering gene expression); the packaging of the gene is altered (more tightly packed= less gene expression)
    - DNA is normally wrapped around histones
    - Histones and DNA covered in chemicals called tags
    - These tags form a second layer called an epigenome
    - The epigenome determines the shape of the DNA-histone complexes
    - If tightly packed (condensed) → genes cannot be transcribed → gene silencing
    - If loosely packed → genes can be transcribed as transcription factors can access DNA → gene switched on
65
Q

how might environmental changes have an influence on gene expression?

A

Chemical tags respond to the environmental changes → adjust wrapping of the histones → switch genes on and off.

66
Q

what is acetylation and how can it determine how tightly packed the DNA-histone complex is (epigenetics)

A

Acetylation of histones (addition of an additional acetyl group from acetylcoenzyme A to a molecule)

Less acetylation
→ more positive charges on phosphate groups of DNA
→ increased association between DNA and histones

67
Q

what is methylation and how can it determine how tightly packed the DNA-histone complex is (epigenetics)

A

Methylation of DNA (addition of a methyl group (CH₃) to the cytosine bases of DNA

More methylation
→ prevents binding of transcription factors
→ attracts proteins that induce deacetylation of histones

68
Q

What is the start codon?

A

AUG, which codes for the amino acid “methionine” or Met

69
Q

What are the different protein structures?

A

Primary structure: the specific sequence and number of the amino acids in the polypeptide chain

Secondary structure: formed when the long chain of polypeptides fold into a 3D shape (e.g. alpha-helix or beta pleated sheet).

tertiary structure: the alpha-helices fold to give specific 3D tertiary structures

quaternary structure: when more than one tertiary polypeptide chains link

Biology IB (reset stats for Jan mocks) (10 decks)

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