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Grade 12 biology > Molecular Genetics > Flashcards

Molecular Genetics Flashcards

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1
Q

Plasmids

A
  • Not part of the nucleoid
  • Can be copied and transmitted between cells
  • Can be incorperated into the cell’s chromosomal DNA and reproduced during cell division
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2
Q

Telomeres

A
  • Chromosomes contain highly repetitive sequences called telomeres
  • Created by telomerase
  • Structures made up from DNA sequences and proteins found at the ends of chromosomes
  • Cap and protect the end of a chromosome
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3
Q

Determine the % of a nucleotide in a DNA change

A
  • The amount of A = T and C = G
  • A + T cannot equal C + G
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4
Q

Frederick Griffith

A
  • 1928 Experiment revealed the transforming principal
  • Led to the discovery that DNA is the carrier of genetic info
  • Experiment included injecting mice with non pathogenic r-strain bacteria, pathogenic s-strain bacteria, heat killed s-strain bacteria, and a mix of r-strain and heat killed s-train
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5
Q

Hershey and Chase

A
  • Ruled out protein as hereditary material in favour of DNA
  • Experiment included radioactively tracing proteins and DNA then centrifuging the infected bacteria to separate DNA and the protein in two separate experiments. When centrifuged, infected bacterial cells formed a pellet at the bottom of the centrifuge tube, and the liquid medium, which contained the remnant bacteriophage “ghosts”. When the proteins were traced they separated with the dead viruses, meaning they had not infected the bacteria and replicated within the bacteria, but the opposite was true when the DNA was traced it showed up within the bacteria after centrifuged
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6
Q

Determining chemical composition

A
  • 1869: Feiedrich Miescher isolated the nuclei from white blood cells and from this extracted a weakly acidic substance containing nitrogen and phosphorus. Later, researchers named it nucleic acid
  • 1900s: Phoebus Levene isolated 2 types of nucleic acids. (ribonucleic acid and deoxyribonucleic acid)
  • He also proposed that RNA and DNA are made up of individual nucleotides containing bases, a sugar molecule and a phosphate group
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7
Q

Chemical composition of nucleotides

A
  • Each nucleotide in DNA is composed of a five-carbon deoxyribose sugar, a phosphate group and a nitrogen-containing base, all linked together by covalent bonds
  • There are 4 types of nitrogenous bases in DNA that can be categorised in 2 different forms: purines and pyrimidine
  • Thymine (DNA only), Uracil (RNA only)
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8
Q

Chargaffs Rule

A
  • 1940’s: Erwin Chargaff showed that there is variation in the composition of nucleotides among different species
  • He demonstrated that all DNA, regardless of its source, maintains certain properties, even though the composition varies.
  • Example: He found that the amount of adenine in any sample of DNA is always approximately equal to the amount of thymine
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9
Q

George Beadle and Edward Tatum

A
  • Evidence of the relationship between genes and enzymes
  • Conclusion: “one gene/one-enzyme hypothesis”
  • Now called the “one-gene/one-polypeptide hypothesis” as not all proteins are enzymes, and that many enzymes are composed of more than one polypeptide chain
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10
Q

Crick and Brenner

A
  • To support this hypothesis of 3 nucleotide sequences, they added nucleotide sequences to a specific protein in bacteriophages
  • Result: when they added one or two nucleotides, the viral protein was not produced. When they added three nucleotides, the protein was produced but slightly different
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11
Q

Important features of DNA

A
  • There are two polynucleotides strands that twist around each other to form a double helix.
  • Each polynucleotide strand has a backbone of alternating phosphate groups and sugars.
  • Each base is attached to a sugar and protrude inward
  • Two strands are complementary to each other. A purine is always bonded with a pyrimidine (Adenine bonds to thymine, and guanine bonds to cytosine) This is called complementary base pairing.
  • Hydrogen bonds link each complementary base pair. A and T have 2 hydrogen bonds, and G and C have 3 hydrogen bonds
  • The two strands of a DNA molecule are antiparallel. Each strand has directionality (specific orientation). At the 5’ end of one strand lies across from the 3’ end of the complementary strand. The 5’ and 3’ come from the numbering of the carbons on the deoxyribose sugar. The phosphate group is on the 5’ carbon and the OH group is on the 3’ carbon.
  • The sequence of a DNA molecule is always written in the 5’ to 3’ direction.
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12
Q

DNA structure in prokaryotes

A
  • Genetic material is in the form of circular, double stranded DNA molecules
  • Each chromosome is packed into a specific region of the cell called a nucleoid
  • Specialised proteins bind to the DNA to help fold sections of the chromosome into loop-like structures that make DNA 10 times more compact.
  • A DNA segment under “twist strain”, it takes on a different shape, reminiscent of a figure eight (8)
  • Plasmids exist outside the nucleoid and contain non-essential/rubbish genes
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13
Q

Structure of DNA in eukaryotes

A
  • Genetic material is kept in the nucleus
  • Some DNA is kept in the mitochondria and chloroplasts
  • DNA compaction is achieved through: Histone structuring, coiling nucleosome by H1 histone proteins into 30 nm fibres - these fibres are then anchored to a supporting scaffold of nucleus protein.
  • For most of a cell’s life, genetic material is in the form of chromatin - which appears as a mass of long, intertwined strands.
  • During cellular division, chromatins reorganise and become chromosomes
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14
Q

How histones structure DNA

A
  • Histones bind to DNA to help give chromosomes their shape and control gene activity
  • Each nucleosome is composed of a double stranded DNA that is wrapped around a group of eight histone proteins
  • They are able to structure DNA by allowing the DNA to wrap around histone complexes, giving DNA a more compact shape
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15
Q

Proteins involved in DNA replication

A
  • DNA polymerase 3 - Enzyme that catalyses the addition of new nucleotides, it attaches to the 3 end of the preexisting chain of nucleotides and travels from 5 to 3` direction, “The builder” - Appears only in DNA replication
  • Enzyme helicase - Cleaves hydrogen bonds that link bases together, “Unzips the DNA”
  • Single strand binding protein - Help stabilise the unwound single strands so that they dont reform into a double helix
  • Enzyme Topoisomerase 1 - Helps relieve stress and regulate/stop supercoiling
  • Enzyme Topoisomerase 2 - Helps to relieve the strain on the double helix ahead of the replication fork
  • Primase - Polymerase can’t figure out where to start without a primer. Primase makes it so that DNA polymerase can figure out where to start to work, “The initializer”, the primer is actually made of RNA
  • Ligase - Helps glue the DNA fragments together, “The gluer”
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16
Q

Proteins involved in Transcription

A
  • RNA polymerase - Enzyme that catalyses the addition of new nucleotides, it attaches to the TATAbox end of the preexisting chain of nucleotides and travels downstream, “The builder” - Appears only in transcription
  • TATA box - Transcription is initiated at the TATA box in TATA-containing genes. The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic genes
  • Transactivator - Activates gene transcription
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17
Q

Proteins involved in Translation

A
  • Ribosome - Composed of rRNA and proteins; involved in the process of protein synthesis
  • Peptidyl transferase - Forms peptide bonds
  • Release factors - Recognize stop codons in the P site, Release factors make the enzyme that normally forms peptide bonds add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and the newly made protein is released
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18
Q

Characteristsics of genetic code

A
  • There are only four nucleotides in RNA but 20 different amino acids
  • It takes 3 nucleotides to create an amino acid
  • Genetic code is always interpreted in term of mRNA codon rather than
  • It is redundant: There are more than one codon that can code for the same amino acid
  • It is continuous: It reads as a series of 3 letter codons. A shift in one or two nucleotides in either direction can alter the codon groupings and make an incorrect amino acid
  • Its nearly Universal: Almost all organisms build proteins with this same genetic code
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19
Q

Difference between DNA and RNA

A
  • DNA is double stranded with bases Adenine, Thymine, Guanine, Cytosine (A, T, G, C)
  • RNA is single stranded with bases Adenine, Uracil, Guanine, Cytosine (A, U, G, C)
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20
Q

Steps of Transcription

A

Initiation
- The correct position for transcription to start is selected and the transcription machinery is assembled
- Once the polymerase complex has bound to the anti-sense strand on the DNA molecule, it unwinds and opens a section of the double helix
- Transcription begins when RNA polymerase binds tightly to the promoter region on the DNA which contains a special sequence of DNA
- There are two sets of promoter sequences that make up the promoter region of which are close together so that it allows the RNA polymerase (Different to DNA polymerase, RNA polymerase only appears in transcription while DNA polymerase only appears in DNA replication) complex to bind to the correct strand in the correct orientation. So that it is copied in the correct direction
- One of these sequences is called the TATA box as it contains a high percentage of thymine and adenine bases

Elongation
- RNA polymerase works its way downstream (5 - 3) along the section of DNA molecule transcribing one complementary strand
- As one RNA polymerase moves along, another one can bind to the promoter region and transcribe another RNA molecule at the same time
- RNA transcription happens much faster because RNA polymerase doesn’t have a proofreading feature

Termination
- Specific nucleotide sequences signal RNA polymerase to stop transcription
- When it reaches this signal, it (the mRNA) detaches and is released to be translated

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21
Q

Steps of Translation

A

tRNAs bind to mRNAs inside of a protein-and-RNA structure called the ribosome (In the cytoplasm). As tRNAs enter slots in the ribosome and bind to codons, their amino acids are linked to the growing polypeptide chain in a chemical reaction. The end result is a polypeptide whose amino acid sequence mirrors the sequence of codons in the mRNA.
Initiation:
- Proteins called initiation factors assemble the small ribosomal sub unit, mRNA, initiatior tRNA (P site), snd the large ribosomal sub unit
- The small ribosomal sub unit attaches to the mRNA near the start codon, then the first tRNA with a UAC anticodon, then the large sub unit join to form the active ribosome
- The start codon sets the reading frame (how each codon will be read)

Elongation:
- Amino acids are brought to the ribosome by tRNAs and linked together to form a chain
- Our first, methionine (start codon)-carrying tRNA starts out in the middle slot of the ribosome, called the P site. Next to it, a fresh codon is exposed in another slot, called the A site. The A site will be the “landing site” for the next tRNA, one whose anticodon is a perfect (complementary) match for the exposed codon
- Once the matching tRNA has landed in the A site, it’s time for the action: that is, the formation of the peptide bond that connects one amino acid to another. This step transfers the methionine from the first tRNA in the P site onto the amino acid of the second tRNA in the A site
- Repeats

Termination:
- The finished polypeptide is released to go and do its job in the cell
- Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site.
- A protein called a release factor is added, this reaction separates the chain from the tRNA and the protein is released

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22
Q

Modifications of pre-mRNA

A
  • Addition of a 5 cap - This involves the covalent linkage of a modified Guanine nucleotide to the 5 end of the pre-mRNA - This cap is recognized by the protein synthesis machinery
  • Addition of a 3 poly-A tail - This involves the covalent linkage of a series of Adenine nucleotides to the 3 end of the pre-mRNA (AAAAAAAAA…) - This tail makes the mRNA more stable and allows it to exist longer in the cytoplasm
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23
Q

Difference between leading and lagging strand

A
  • Leading strand can be done in one continuous move with no extra primase activity
  • Lagging strand must be done in small segments called Okazaki fragments and primase is forced to work its ass off
  • Lagging strand has an additional enzyme called ligase to connect the Okazaki fragments
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24
Q

Purine and Pyrimidines

A

Purines and Pyrimidines are always bonded to each other, a purine is always bonded to a pyrimidine and a pyrimidine is always bonded to a purine
Purines (A and G)
- Purine is a compound that consists of two rings fused together. It is water-soluble

Pyrimidines (C, T, and U)
- Pyrimidine is an organic compound similar to pyridine. It has nitrogen atoms at positions 1 and 3 in the ring (1 ring)

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25
Q

What is the process to change DNA to mRNA to tRNA to amino acids

A

Its called protein synthesis and consists of trancription then translation

Transcription processes DNA to mRNA

Translation processes mRNA to tRNA to amino acids

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26
Q

Types of single gene mutations (Changes in the nucleotide sequence of a gene)

A

Point mutations:
Mutations involving a single base pair
Can result in a frameshift mutation, silent mutation, missense mutation, or nonsense mutation

Frameshift mutations:
Deletes of inserts an extra nucleotide
Causes the entire reading frame to be altered ( ATA CCG CAG to GAT ACC GCA G or TAC CGC AG)

Silent mutations:
Has no effect on the amino acid sequence
May occur when one nucleotide is substituted for another but the error will still code for the same amino acid

Missense mutations:
Change in amino acid sequence
Occurs when one base is substituted for another that does result in a new amino acid

Nonsense mutations:
Occurs when a gene’s coding sequence is changed in such a way that it results in a premature stop
A shorted protein or no protein at all will be made

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27
Q

Types of chromosome mutations (changes in the chromosome and involve many genes)

A

Deletion:
Loss of one or more nucleotides from a segment of DNA
A deletion can involve the loss of any number of nucleotides, from a single nucleotide to an entire piece of a chromosome
Duplication:
One or more copies of a DNA segment (which can be as small as a few bases or as large as a major chromosomal region) is produced

Inversion:
A chromosome breaks and when put back together one half is placed backwards

Translocation:
Occurs when a piece of one chromosome breaks off and attaches to another chromosome
This type of rearrangement is described as balanced if no genetic material is gained or lost in the cell - If there is a gain or loss of genetic material, the translocation is described as unbalanced

28
Q

Lac operon

A
  • This encodes proteins that are able to break down lactose to use as energy
  • Inducible operon - Usually inactive until lactose is present, then an activator will turn it on
  • Consists of a coding region and a regulatory region
  • In the absence of lactose, the lac repressor proteins binds to the operator and prevents RNA polymerase from binding to the promoter, and transcription cannot occur
  • In the presence of lactose, a derivative called allolactose is produced, which binds to the repressor and the repressor can no longer bind to the operator. This results in the transcription of the genes to produce the required enzymes
29
Q

TRP operon

A
  • A group of genes that encode biosynthetic enzymes for the amino acid tryptophan
  • Under normal conditions, tryptophan must be synthesised, so the repressor does not bind to the operator, and transcription takes place
  • When tryptophan reaches a certain level in the cell, some of it will bind to the repressor protein in order to shut it off
30
Q

Physical mutagens

A

When the genome is physically destroyed or changed. Example: X-rays or high energy radiation

31
Q

Chemical mutagens

A

A molecule that can enter the nucleus of a cell and induce mutations by reacting chemically with the DNA. Example: nitrites, gasoline fumes, and many chemicals in cigarette smoke

32
Q

Plasmid mapping

A
  • Shows the relative locations of all the known restriction enzyme recognition sites on a particular plasmid and the distances, in base pairs (bp), between the sites
  • Allows molecular biologists to determine which plasmids might be most suitable for a particular recombinant DNA procedure
  • A plasma will tell you the location that certain restriction enzymes will cut at a certain number of base pairs.
  • The total number of bp in a plasmid will also be given.
  • There will be a mark somewhere on the plasmid indicated bp 0.
  • Location of genes on the plasmid may also be indicated (ex. Amp, tet, ori)
33
Q

Dideoxy sequencing

A
  • DNA polymerase is used to synthesise a series of DNA fragments of differing lengths
  • All fragments produced all start at the same position, but terminate at different specific bases.
  • The different-sized fragments occur because replication is terminated due to incorporation of one of four possible dideoxynucleotides (ddA, ddG, ddC or ddT)
34
Q

Types of RNA

A

Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Small nuclear RNA (snRNA)
Micro RNA (miRNA)
Small interfering RNA (siRNA)
RNA in RNaseP RNaseP
7S RNA
Viral RNA

35
Q

Function of mRNA

A

The template for translation

36
Q

Function of tRNA

A

Involved in the translation of mRNA

37
Q

Function of rRNA

A

Involved in the translation of mRNA

38
Q

Function of snRNA

A

Involved in modification of mRNA molecules

39
Q

function of miRNA

A

involved in regulation gene expression

40
Q

Function of RNA in RNaseP

A

RNaseP is an enzyme; the RNA is the part of the enzyme

41
Q

function of 7S RNA

A

involved in targeting proteins to particular regions in
eukaryotic cells

42
Q

function of viral RNA

A

found in some viral genomes

43
Q

mRNA in Eukaryotes vs Prokaryotes

A

In prokaryotes, mRNA can be used immediately for protein synthesis.

In eukaryotes, mRNA must first undergo modifications before being used for protein synthesis.

44
Q

mRNA modifications

A
  • Addition of a 5` cap.
  • This involves the covalent linkage of a modified G nucleotide to the 5` end of the pre-mRNA. The cap is recognized by the protein synthesis machinery.
  • Addition of a 3` poly-A tail.
  • This involves the covalent linkage of a series of A nucleotides to the 3` end of the pre-mRNA. The tail makes the mRNA more stable and allows it to
    exist longer in the cytoplasm.
  • Removal of introns (non-coding regions interspersed between coding regions (exons)). This is called splicing
45
Q

Splicing

A
  • The removal of introns in mRNA
  • Particles composed of snRNA and
    proteins, called snRNPs recognize regions where exons and introns meet
  • They bind to those areas. The snRNPs interact with other proteins, forming a larger spliceosome complex that removes the introns.
  • For most genes, all of the exons are spliced together. In some cases, however, only certain exons are
    used to form a mature RNA transcript.
  • This allows for one gene to code for more than one protein. As a result, certain cell types are able to produce forms of a protein that are specific for that cell.
46
Q

Splicing steps

A
  1. snRNA forms base-pairs with 5` end of intron, and at branch site.
  2. snRNPs associate with other factors to form spliceosome.
  3. 5 end of intron is removed and forms bond at branch site, forming a lariat. The 3 end of the intron is then cut.
  4. Exons are joined; spliceosome disassembles.
47
Q

What are ribosomes

A
  • composed of rRNA and proteins
  • involved in the process of protein synthesis
  • Cytoplasmic structure
  • Composed of two sub-units
  • Each sub-unit is composed of different proteins and rRNA molecules
  • Have one binding site for mRNA and 3 binding sites for tRNA
  • Several ribosomes can attach to and translate one mRNA
48
Q

What are translation factors

A
  • proteins that act as accessory factors
  • needed at each stage of translation
49
Q

what is tRNA?

A
  • contains an anticodon that base-pairs with a codon on the mRNA
  • has the corresponding amino acid attached to it, according to the genetic code
50
Q

What is aminoacyl-tRNA synthetase?

A

An enzymes that is responsible for attaching the appropriate amino acid to a tRNA according to its anticodon

51
Q

What direction are anticodons written?

A

3-5

52
Q

What is a photorepair mechanism?

A
  • A way of fixing mutations
  • two thymines can be covalently linked by uv radiation, called a dimer
  • photolyase binds to the damaged DNA and cleaves the covalent bond.
53
Q

What is excision repair?

A

A protein complex binds to incorrect bases, removes them, and lets DNA polymerase come back to fix it

54
Q

What is a transposon?

A
  • a class of genetic elements that can “jump” to different locations within a genome
  • they move from one genomic location to another by a cut-and-paste mechanism
55
Q

What is a constitutive gene?

A
  • Aka housekeeping gene
  • Is always active at a constant level
  • Usually needed for the survival of the cell
56
Q

What is an operator in gene expression?

A

a DNA sequence to which a protein binds to in order to inhibit transcription initiation

57
Q

What is an activator or repressor in gene expression?

A

The protein which binds to the operator that either turns it on or off

58
Q

What is an inducible operon?

A

Transcription from it is induced/it is activated when a specific molecule or thing is present

59
Q

What is a repressible operon?

A

In the presence of enough or too much of a thing that the gene produces, a repressor will bind to the operator in order to shut it off

60
Q

Types of gene expression in prokaryotes

A
  • during transcription, during translation, and after the protein is synthesized
  • Transcription is most common
61
Q

Types of gene expression in eukaryotes

A
  • pre-transcriptional, transcriptional, post-transcriptional, translational, and post-translational
62
Q

Pre-transcriptional and Transcriptional Control

A

Activator proteins or specific sequences of DNA called enhancers may bind to transcription factors in order to enhance transcription initiation

63
Q

Post-transcriptional and Translational Control

A
  • Alternative splicing can produce different RNA molecules
  • miRNA uses RNA interference, which can associate with protein complexes and turn off gene expression by promoting mRNA cleavage or inhibiting transcription. They interact by forming base pairs
  • A chain of ubiquitin molecules can bind to a protein to signal for the protein to be degraded
64
Q

How is insulin activated

A
  • Insulin starts as a folded structure
  • When needed several amino acids will be removed, leaving two polypeptide chains
  • then a sulfur will covalently bond onto each chain
  • Finally a phosphate group will covalently link to one or more amino acid
65
Q

What is a restriction enzyme?

A

An enzyme that cleaves or cuts viral DNA in order to deactivate it

66
Q

What is endonuclease?

A
  • Endonuclease is an example of a restriction enzyme, they cleave DNA from the interior of the strands rather than at the ends
  • They do so by recognizing a short sequence of nucleotides called the “target sequence”
  • Next the enzymes cut the strand at a particular point within the sequence, this is called the restriction site
  • The cuts made by this enzyme are specific and predictable
  • They will also mostly make a staggered cut that leaves a few unpaired nucleotides
67
Q

What are the steps of recombinant DNA tech?

A
  1. . A restriction endonuclease is selected that can cut both DNA fragments to be combined. Ideally, these are enzymes that produce sticky ends, although different enzymes can be used.
  2. Each piece of DNA is reacted with the restriction endonuclease enzyme to produce cut DNA fragments.
  3. The two cut DNA fragments are incubated with another enzyme, DNA ligase. This enzyme seals the breaks in the DNA, forming covalent bonds between the two different fragments. The result is a stable, recombinant DNA molecule. Recall that DNA ligase also joins Okazaki fragments when the lagging strand is synthesized during DNA replication

Grade 12 biology (6 decks)

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