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Biology - Grade 12 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Background to the Hershey-Chase Experiment

A

-1800-1940s: scientists knew chromosomes were involved in genetics
The main opinion was that the hereditary part was the protein, not the NA
- Hershey and Chase wanted to solve this problem

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2
Q

How does a virus infect cells (Hershey-Chase)?

A
  • Inject genetic material into a cell
  • Non-genetic part (protein capsid) remains outside
  • Infected cells produce large amounts of the virus
  • Cells burst released copied virus
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3
Q

How did the Hershey-Chase experiment happen?

A
  • They studied the T2 bacteriophage which infects the E. Coli bacterium
  • Radioactive isotopes label the virus (sulfur on capsid, phosphorous on DNA)
  • Centrifuge is used to separate T2 and E. Coli (smaller virus remained in the supernatant, infected bacteria formed a pellet)
  • Deduced DNA was the genetic material
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4
Q

Rosalind Franklin and Maurice Wilkins’s investigation of DNA by X-ray Diffraction

A
  • X-rays directed at a material can be scattered by the material
  • Works best with crystalized materials, due to repeating patterns
  • DNA was arranged in such a way that it worked
  • Deduced a helix structure from the images
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5
Q

Watson and Crick’s model

A
  • One of their first models had phosphorous on the inside
  • Franklin determined bases were hydrophobic meaning they were on the inside not phosphorous.
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6
Q

What is the role of nucleosomes in DNA packing?

A
  • Protects DNA and allows it to be packaged
  • Formed by wrapping DNA around histone proteins (octamer) allowing it to be supercoiled.
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7
Q

What is the structure of a nucleosome like?

A
  • Octamer has 2 copies of 4 histones (8 total)
  • H1 holds DNA in place around the octamer
  • ‘linker DNA’ connects nucleosomes together
  • H1 binds to the 3nm fibre (Solenoid) that facilitates further packing
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8
Q

What is supercoiling?

A
  • DNA strands are wound around itself many times
  • Aprrox. length is 2m, diameter of nucleus is 10nm
  • Organizes DNA for cell division
  • Controls DNA expression and its ability to transcribe or not
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9
Q

What is heterochromatin?

A

Allows cell to permanently supercoil, no transcription

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10
Q

What is euchromatin?

A

Promotes transcription of active chromatin

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11
Q

DNA replication

A
  • Helix unwinds
  • H-bonds break separating 2 polynucleotide strands
  • ATP moves helicase along molecules
  • Separated strands become parent strands
  • DNA polymerase created complimentary strands
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12
Q

Helicase

A

Unwinds DNA at the replication fork

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13
Q

Topoisomerase

A

Releases strand ahead of helicase

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14
Q

RNA Primase

A

Primes for DNA polymerase, only one on a leading strand, many on a lagging

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15
Q

DNA polymerase III

A

Links phosphate on nucleotide to 3 prime of growing strand

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16
Q

DNA polymerase I

A

Replaces RNA primers with nucleotides

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17
Q

DNA ligase

A

Connects gaps between Okazaki fragments

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18
Q

Single Strand Binding Proteins

A

Keeps the separated strands apart so that nucleotides can bind

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19
Q

Direction of Replication

A
  • Initiated at many pints in Eurkaryotes
  • Points are called origins of replication
  • Phosphate of new DNA is added to 3’ C of deoxyribise at end of chain
20
Q

Detailed Summary of Replication

A
  • Occurs during interphase, helicase unwinds DNA by breaking H bonds b/w strands
  • Single stranded binding proteins keep strands apart
  • DNA topoisomerase is ahead of helicase to prevent supercoiling again
  • Synthesis starts on strands, continuous on leading strands, pausing on lagging (okazaki fragments)
  • RNA primate first synthesizes strands
  • DNA polymerase III attaches to primer, adds nucleotides
  • Added through deoxynucleoside triphosphate, 2 phosphate groups released and energy released joins nucleotides in a chain
  • DNA polymerase I removes RNA primers and replaces them with DNA
  • DNA lipase joins okazaki fragments on the lagging
21
Q

Non-Coding Regions of DNA

A
  • Areas of DNA not expressed as polypeptides but still important
  • Genes are the regions of DNA that code for polypeptide, contain both intron and exon
  • Introns are edited out of mRNA, translated by ribosome into polypeptide
  • Therefore, only exons code for polypeptide
22
Q

What are promoters, enhancers and silencers

A

Promoters: attachment points for RNA polymerase adjacent to the gene
Enhancers: binding sites of activators, sequences that increases rate of transcription
Silencers: inhibit transcription bind to repressors

23
Q

What are Introns and Exons

A

Exons: coding regions
Introns: non-coding regions that are removed and used for other cell purposes

24
Q

What is the function of the promoter?

A

A form of non coding DNA sequence near a gene, adjacent gene is transcribed. Serves as a binding site of RNA polymerase

25
Q

How is Gene Expression Regulated by Proteins?

A
  • Some poteins are necessary to survival and are always expressed
  • Others only need to be produced at certain times and they are regulated.
  • In prokaryotes expression is regulated due to the environment
    Ex. Metabolism of lactose in E. Coli
26
Q

Impact of the environment on gene expression

A
  • Environment of a cell affects gene expression
  • Only a small number of genes determine body patterns during embryonic development
  • These are regulated by morphagens that diffuse across cell surface from a concentrated source
  • Regulate the rate of transcription factors resulting in activation and inhibition of genes
27
Q

Nucleotides Regulate Transcription

A
  • Methylation is the addition of a methyl group to DNA:
    Inhibits translation by binding DNA more tightly on histones (heterochromatin)
  • Acetylation is the addition of acetyl groups to histones:
    Promotes transcription loosens DNA around histones (euchromatin)
28
Q

What is the study of epigenetics

A
  • Study of heritable changes not due to DNA
  • Methylation and acetykation mark DNA with epigentic tags to affect transcription.
  • Each cell has a different epigentic pattern
  • Tags are erased through reprogramming when reproductive cells meet to form an embryo
29
Q

What are the 3 stages of DNA transcription

A
  1. Initiation:
    RNA polymerase binds to promoter sequence and opens helix. Key element of promoter in eukaryotes is the TATA box (in 24% of genes)
  2. Elongation:
    RNA polymerase build mRNA, no primer used. Unused DNA is called the coding/sense strand. DNA that is transcribed reminds into double helix
  3. Termination:
    RNA polymerase stops at Termination sequence at the end of a gene. mRna dissociated from template. RNA polymerase is free to transcribe another gene
30
Q

Post Transcription Modifications

A
  • Only happens in eukaryotes
  • Most gene expression regulation in prokaryotes occurs during transcription
  • In prokaryotes transcription and translation are coupled as they have no nuclear membrane
  • On eukaryites introns must be removed through splicing
31
Q

mRNA Splicing

A
  • Happens on the same gene in different ways
  • Exons may be included or excluded
  • Allows multiple proteins to be produced by a single gene varying in function
  • no quality control, results in errors but is insignificant as many transcriptions occur
  • errors result in a protein susceptible to degradation.
32
Q

What is capping and tailing in splicing

A

Capping: adds 5’ cap be transcription completes, involved in initiation
Tailing: poly-A tail added after transcriptionnis completed, prevents degradation of mRNA

33
Q

Ribosomes

A
  • composed of protein (stability) and RNA (catalysis)
  • composed of a small (mRNA binding) and large (tRNA binding) subunits
  • If protein is for intracellular use, ribosome is free in cytoplasm
  • If protein is for secretion ribosome binds to ER
34
Q

Determination of ribosome location

A
  • bound or free is determined by the presence of an initial signal sequence
  • signal sequence attaches to a signal recognition protein (SRP) which stops translation until binding to ER
  • After binding translation restarts
  • New protein is transported to the golgi or lysosome
  • Signal sequence removed an SRP released
35
Q

tRNA

A
  • transfers AA from cytoplasm to a polypeptide
  • gathers AA’s when activated by a specific enzyme, requires ATP
  • 20 enzymes specific for 20 AAs and tRNAs
    1. Enzyme binds ATP to AA to form AA-AMP (diphosphate released, link via high E bond)
    2. AA coupled to tRNA and AA released
  • AA is covalently bonded to tRNA
36
Q

3 stages of translation

A
  1. Initiation - Ribosome units and tRNA assemble at mRNA
  2. Elongation - elongation of polypeptide chain
  3. Termination - completed polypeptide released ribosome complex disassembles
37
Q

Initiation in translation

A
  1. mRNA binds to the small subunit of a ribosome
  2. Small subunit moves along the mRNA in a 5’ to 3’ direction until it reaches the start codon (AUG)
  3. tRNA carrying methionine binds to AUG
  4. A large subunit of ribosome binds to the tRNA (p site) and the small subunit to form the complex.
38
Q

Elongation in translation

A
  1. A second tRNA pairs with the next codon in the A site
  2. AA carried by the tRNA in the P site is covalently attached by a peptide bond to the AA in site A
  3. tRNA in P site is now deacylated (no AA) while the tRNA in site A carries the peptide chain
  4. Translocation: ribosome moves one codon along the mRNA
  5. Another tRNA binds to A site
  6. ELongation repeats until a stop codon is reached
39
Q

Termination in translation

A
  1. when a stop codon is reached translation stops:
    - polypeptide chain released
    - ribosome complex disassembles
40
Q

Coupling of transcription and translation in prokaryotes

A

Prokaryotes: Ribosomes can be adjacent to the chromosomes as there is no nucleus, translation happens immediately after transcription
Eukaryotes: mRNA needs to be spliced then relocated from nucleus to cytoplasm, thus it can’t be coupled

41
Q

Polysomes

A

Structure that consists of multiple ribosomes attached to a single mRNA enabling the cell to quickly create many copies of the required polypeptide.

42
Q

Primary structure

A

order of AA in the polypeptide chain, determines all levels because it determines how R groups of AAs will interact

43
Q

Secondary structure

A

Chain of AAs has polar covalent bonds within its backbone. Folds so that H-bonds are between carboxyl groups and amine of another chain. Can be a-helix or b-pleated sheet or just a random coil.

44
Q

Tertiary structure

A

Overall 3D structure from different interactions of R groups:
Ionic bond: +ve R with -ve R
Hydrophobic: AA drawn into the center
Hydrogen bond: polar R with polar R
Disulphite bridge: R group of cysteine can form covalent bond with another

45
Q

Quarternary structure

A

More than one polypeptide chain fitted together. Many or prosthetic groups
- Prosthetic group: inorganic compound in a structure
- Conjugated protein: protein containing a prosthetic

Biology - Grade 12 (6 decks)

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