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Biology 243 > Theme 2: Overview of Central Dogma of Molecular Biology > Flashcards

Theme 2: Overview of Central Dogma of Molecular Biology Flashcards

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1
Q

What is the central dogma of molecular biology?

A
  • The universal information flow from DNA to protein in order to convert genotype to phenotype
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2
Q

What’s the difference between eukaryotes and prokaryotes in how they convert their genotype to phenotype?

A
  • Prokaryotes - transcription and translation both occur in the cytoplasm, so they happen simultaneously
  • Eukaryotes - transcription and processing of the precursor mRNA molecules occur in the nucleus and translation occurs in the cytoplasm (they happen one after the other)
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3
Q

From eukaryotes, how did scientists conclude that DNA could not encode directly for proteins?

A
  • The DNA in eukaryotes cannot leave the nucleus, so they figured that translation must occur in some intermediate in the cytoplasm (RNA)
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4
Q

What’s the one gene-one enzyme (protein) hypothesis

A
  • In 1940s, Beadle and Tatum hypothesized that genes encode enzymes that function at each step of a biochemical pathway needed to make an essential nutrient (in this case an enzyme)
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5
Q

What would occur if in the one gene-one enzyme, a mutation to occur in one of the genes?

A
  • This would cause a block in the metabolic pathway and the organism can no longer synthesize the needed nutrient.
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6
Q

What did the experiment regarding the isolation of arginine auxotrophic mutants help explain?

A
  • Proved that in order for the mold to grow, arginine was required (considered the essential ingredient
  • The experiment involves islating different mutants in the species, and seeing whether or not if they would grow.
  • Each mutant has a defective gene for enzyme needed to synthesize an intermediate product to produce arginine.
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7
Q

What two types of RNA do genes encode for?

A

1) Coding RNA (codes for a protein/polypeptide
2) Noncoding RNA (tRNA, rRNA, snRNA, microRNA), does not code for a protein

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8
Q

What is the genetic code?

A
  • Nucleotide information to amino acid sequence (builds a protein)
  • Each three nucleotides on DNA code for a three letter code on RNA called a codon
  • Genetic code os also universal (same code in prokaryotes, eukaryotes and viruses)
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9
Q

What is a unique characteristic of genetic code being unviersal for all organisms?

A
  • It can allow foreign genes to be transferred and expressed in different host organisms.
  • Helps with vaccine development
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10
Q

What’s the relationship between the DNA template strand and the newly synthesized RNA strand?

A
  • For ever gene, only 1 RNA molecule is produced from one gene on the template strand
  • The template strand is always read in the 3’-5’ direction by the RNA polymerase.
  • The RNA strand is synthesized in the 5’-3’ direction (antiparallel to the region on the template strand)
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11
Q

What’s the relationship between the DNA coding strand and the newly synthesized RNA strand?

A
  • The coding strand is also known as the non-template strand or sense strand
  • It has the same 5’-3’ orientation and sequence as the RNA molecules, except uracil is substituted with thymine
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12
Q

What’s the difference between the sense strand and the antisense strand?

A
  • The sense strand is the same as the coding strand. Shares the same orientation and sequence as the RNA molecule
  • The antisense strand is the same as the template strand ince it is the complete oposite as the RNA molecule.
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13
Q

How do chromosomal maps work?

A
  • The highlighted regions show the genes, which are always found on the coding strand
  • Genes alternate between the two different strand, they aren’t all on the same one
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14
Q

What is reverse transcription and where does it occur?

A
  • It’s when RNA is converted into DNA.
  • It is found in viruses in RNA genomes (known as a retrovirus), where once it enters a host cell it is able to convert its viral RNA into viral DNA.
  • The host’s transcription and translation machinery is hijacked to prodice viral proteins from the viral DNA
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15
Q

What are the 3 enzymes involved in reverse transcription?

A
  • Reverse transcriptase - Converts the viral RNA into viral DNA
  • Integrase - Integrates DNA into host chromosome by making a nick
  • Protease - breaks up polyprotein chains, which helps the virus mature
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16
Q

What makes viruses like HIV highly mutagenic?

A
  • When reverse transcription is occuring in the host cell, reverse transcriptase makes many mistakes when converting RNA into DNA
  • That’s why HIV is so hard to cure, since each individual will hiave their own specific HIV genotype.
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17
Q

What is the life cycle of the SARS-CoV-2 virus?

A
  • The viruses genome is composed of a a single stranded sense RNA strand, composed of only 28 viral proteins
  • Once it has entered the host cell (the +sense strand), it undergoes translation via a ribosome, whcih produces an RNA-dependent-RNA polymerase synthesizes a -sense ssRNA for viral transcription and replication
  • Proliferation of the virus occurs in the endoplasmic reticulum
  • Once released through exocytosis, the virus targets tissues such as the alveolar lung cells, heart cells and intestinal cells, all which contain ACE2 receptors
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18
Q

What is believed to have come first, RNA or DNA?

A
  • Most likely RNA because besides able to store genetic information (code for amino acids like DNA), can catalyze reactions, similar to an enzyme
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19
Q

What are ribozymes?

A
  • Also known as ribonucleic acid enzymes, they can catalyze their own synthesis and cleave RNA molecules
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20
Q

What are the advantages of DNA over RNA?

A
  • DNA is moleculary more stable than RNA, and it’s also double-stranded, allowing for the complimentary strand to be used as a template when damaged or requiring repairs.
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21
Q

What’s a promotor?

A
  • A component found within a gene sequence that includes a TATA box that indicates where transcription begins on the chromosome
  • It is located on the 5’ end of the trascriptional start point of the template strand of DNA.
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22
Q

How do RNA polymerases work?

A
  • Synthesizes the RNA transcript in a 5’-3’ direction (adds ribonucletorides to the 3’-OH end) while it reads DNA in the 3’-5’ direction
  • Synthesis is antiparallel, so it starts at the 3’ end of the DNA template strand
  • Does not need a primer for initiation, and it also unwinds and rewinds the DNA helix itself (no helicase required)
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23
Q

What are the three types of RNA polymerases?

A
  • RNA Pol 1: rRNA (ribosome RNA)
  • RNA Pol 2: mRNA (coding for proteins)
  • RNA Pol 3: tRNA (transfer/taxi RNA)
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24
Q

What are DNA-binding proteins involved in?

A
  • They directly mediate transcriptional initiation as they bind to specific regulatory sequences of the gene
  • They are the rate-determining step of transcriptional initiation
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25
Q

What are the two transcriptional initiation processes?

A
  • General transcription factors: proteins bind to promotor and recruit RNA polymerase 2 resulting in low basal level transcription (slow)
  • Transcriptional activator: proteins bind to enhancer regions distant from the promotor to cause DNA looping, bringing mediator and RNA pol. to the promotor resulting in higher rate of transcription
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26
Q

What is a TATA box?

A
  • The gene sequence (promotor) that is found on the template strand of DNA that indicates where transcription should begin. Usually found 25-35 base pairs from where the actually transcription should begin.
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27
Q

What processes occur when RNA Pol. 2 is transcribing the DNA template strand?

A
  • A transcription bubble forms, where DNA is being unwinded in front of the RNA Pol. and rewinded behind the enzyme.
  • Ribonucelotides are added to the 3’ end of the RNA transript
  • The growing RNA transcript is displaced from the DNA template strand to allow reannealng back into double-stranded DNA
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28
Q

What are the three types of transcriptional termination?

A
  • Rho-independent termination (prokaryotes): terminator sequence in mRNA base pairs with itself to form G-C hairpin and causes RNA pol. to stall and dissociate.
  • Rho-dependent termination (prokaryotes): terminator sequence in mRNA is recognized and bound by the Rho helicase which unwinds the RNA from the template DNA and RNA polymerase
  • Cleavage and polyaderylation specific factor (CPSF) (eukaryotes): poly-A sequence in mRNA signals the CPSF to cleave the completed mRNA transcript thereby separating it from the RNA polymerase (breaks the pentose-phosphate backbone of the RNA transcript
    *Rho factor is a protein
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29
Q

What are some major differences between DNA replication and RNA transcription?

A
  • Only RNA molecules are single-stranded
  • Transcription only occurs at specific locations along the genome
  • Can synthesize multiple copies of one gene many different times
  • RNA pol. does not need a primer
  • RNA transcript does not remain base-paired to template DNA strand
  • For both processes, synthesis occurs in the 5’-3’ direction
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30
Q

What happens to mRNA strands as they approach the 5’ end of te DNA template strand?

A
  • The mRNA strands get longer since transcription initially starts at the 3’ end of the DNA strand, so as it approaches the 5’ end, many ribonucleotides have been added to the transcript already.
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31
Q

What are the purposes of the untranslatable regions (UTRs) found at either end of the RNA transcript?

A
  • Help contribute to mRNA stability and translational efficiency
  • Able to remain in cytoplasm for longer periods of time
  • The 5’ end contains a ribosome binding site/Shine Dalgarno sequence in prokaryotes, or Kozak box for eukaryotes
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32
Q

What is the open reading frame?

A
  • The region of the mRNA that is translated and includes the start and stop codons at the borders
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33
Q

Where in the cell does posttranscriptional modification occur?

A
  • In the nucleus.
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34
Q

What sort of modifications does pre-mRNA undergo prior to being released into the cytoplasm?

A
  • 5’ cap - a modified guanosine triphosphate is added to the 5’ end and acts as a ribosome binding site and protects from degradation
  • Poly(A) tail - a long string of adenine nucleotides added via poly-A-polymerase to protect from degradation and to increase translational efficiency (fold/create circular shape to help bind promotor to 5’ cap)
  • Introns are removed/spliced
35
Q

Why is intron removial important?

A
  • The splicing of introns allows for the creation of the open reading frame that is composed of strictly exons and UTRs that is used during translation.
  • Coding mRNA with introns and exons will produce a dysfunctional protein since introns do not code for proper codons, meaning ther eare no corresponding amino acids.
36
Q

What are the components found within the mature mRNA transcript once it makes it into the cytoplasm?

A
  • Strictly the UTRs found at either ends of the transript and the exons that make up the open reading frame.
37
Q

How does splicing occur on the pre-mRNA?

A
  • Carried out by a large ribonucleoprotein (i.e., made up of 5 noncoding RNAs called snRNAs, which are small ribonucleoprotein, better known as “slurps”)
  • The spliceosome binds to the intron-exon junction and loops the intron section out of the pre-mRNA, creating a lariat structure, which ends up bringing the exons closer together
  • The spliceosome clips the intron at each exonboundary, releasing the lariat structure, and joining the adjacent exons together.
  • The released introns degrade in the cytoplasm
38
Q

Why is alternative splicing so important?

A
  • Able to generate different combinations of mature mRNA from the same gene, therefore, several related protein products known as isoforms can be generated, without expanding the genome
  • Different isoforms are made in different tissues, producing different phenotypes
  • Dramatically increases the the number and variety of proteins that can be encoded by the genome.
39
Q

What are the two major groups of small regulatory RNAs involved in RNA interference?

A
  • MicroRNAs (miRNA) - found within a protein complex called miRNA induced silencing complex (miRISC) binds to sequences in the 3’-UTRs of target mRNAs. If the miRNA and mRA pair imperfectly, the double-stranded segment formed blocks ribosomes from translating the mRNA. Dicer helps cleave the miRNA and RISC unwinds the RNA
  • Small interfering RNA (siRNA) - produced from double-stranded RNA that is not encoded by nuclear genes (synthetically made), it is cut by Dicer into short, double-stranded RNA molecules, and then a protein complex binds to the molecules and degrades one of the RNA strands to produce single-stranded siRNA. Similar to the protein complex found on miRNA, siRISC, single-stranded RNAs complimentary to the siRNA are targeted and the target RNA is cleaved and the pieces ae then degraded.
40
Q

Where does RNA interference occur? And why?

A
  • In the cytoplasm of all eukaryotes
  • Likely evolved as an antiviral mechanism to destroy viral mRNA
41
Q

What does transcriptional rate depend upon?

A
  • The speed of transcriptional initiation (i.e., promotor strength)
42
Q

What determines the stability of mRNA?

A
  • The presence of the 5’-cap and the length of the poly(A) tail. These help prevent degradation (moreso the poly(A) tail) and increase translational efficiency (5’-cap)
43
Q

What factors determine the expression level of a specific gene?

A
  • The abundance of mRNA (which depends on the rate of synthesis during transcription) and the rate of degradation of mRNA (posttranscription)
    *Can have a a gene with a high rate of transcription but even higher rates of degradation, making it difficult for gene expression to occur and for the gene to be actually expressed.
44
Q

What are the major components of an amino acid?

A
  • An amino group and a carboxyl group bonded to either end of the central carbon, which also contains a bonded hydrogen
  • An R-group is also attached to the central carbon. This gives the unique character of the amino acid.
45
Q

How are amino acids joined together?

A
  • By a covalent peptide bond (long chains of these are what form polypeptides)
  • During translation, the peptide bond forms between the carboxyl group of the first amino acid and the amino group of the following amino acid.
46
Q

What are the major groups of amino acids?

A
  • Non-polar amino acids: R groups usually contain -CH2 or -CH3
  • Uncharged polar amino acids: R groups usually contain oxygen/-OH
  • Charged amino acids - R groups that contain acids or bases that can ionize
  • Aromatic amino acids - R groups contain a carbon ring with alternating single and double bonds
  • Special functional amino acids: Methionine (start codon), proline (causes kinks in polypeptides), Cysteine (disulfide bridge contributes to structure of polypeptides)
47
Q

What are the different levels of protein structure?

A

1) Primary - the basic amino acid sequence of a polypeptide
2) Secondary - Depends on hydrogen bonding in the polypeptide backbone (alpha helices and beta sheets)
3) Tertiary - the 3D structure of a single polypeptide and is composed of interactions between amino acid side chains
4) Quaternary - Interactions between more than one polypeptide to form a multisubunit protein.

48
Q

What are different factors that may disrupt proper protien folding?

A
  • Denaturation caused by heat and chemicals or mutations that may change the amino acid sequence.
  • Diseases such as Alzheimer’s and Parkinson’s
49
Q

What’s the purpose of chaperones?

A
  • Protect amino acid sequences during slow-folding of a polypeptide or denatured proteins by preventing their aggregation (sticking together)
  • Allows protein to successfully reach final shape.
50
Q

What are the major areas of a tRNA molecule?

A
  • The acceptor stem is where the amino acid is attached
  • The anticodon is found at the bottom of the loop, and runs antiparallel to the codon found on the mRNA
51
Q

What does chargiing a tRNA molecule involve?

A
  • The protein aminoacyl-tRNA synthase adds the appropriate amino acid to the acceptor stem of the correct tRNA
  • There are 20 different aminoacyl tRNA synthases for the 20 different amino acids (stop codons are identified by different proteins.
  • Reaction: amino acid + tRNA + ATP = aminoacyl-tRNA + AMP + PPi
52
Q

How does the genetic code consist of 61 sense codons, but only 21 different amino acids?

A
  • There is an element of degeneracy in the genetic code that allows for many sense codons to code for 1 amino acid. This allows for space of mutations to occur.
53
Q

Does tRNA bind to stop codons?

A
  • NO THEY DO NOT. They are instead recognized by proteins called release factors that bind to the A-site.
54
Q

How can a tRNA molecule read and recognize more than 1 codon?

A
  • due to the wobble effect.
  • The 5’ end of the anticodon can form hydrogen bonds with more than one type of base located at the 3’ end of the codon.
  • The pairing of the other two nuceltides is precise.
55
Q

What are the major components of a ribosome?

A
  • Two major subunits, one large one small, that is made up of proteins and ribosomal RNA
  • The large subunit contains the peptidyl-transferase center for formation of peptide bonds
  • The small subunit contains the decoding center where charged tRNAs read and decode the codon of the mature mRNA
  • Each subunit exists separately in the cytoplasm, and then come together when translation needs to occur on the mRNA molecule
56
Q

What are the different tRNA binding sites of the ribosome?

A

1) P-site (peptidyl) - binds to the tRNA attached to the growing peptide chain (where initiator tRNA binds to first)
2) A-site (aminoacyl) - binds to the tRNA carrying the next amino acid to be added (i.e., waiting in line)
3) E-site (exit) - binds the tRNA that carried the previous amino acid (now empty) added.

57
Q

What makes up the translation initiation complex?

A
  • Both ribosomal subunits, mRNA transcript, and the initiator tRNA bound to methionine.
58
Q

What are the basic steps of translational initiation?

A

1) the initiator tRNA (meth) is brought to the P site of the small ribosomal subunit (reaction requires GTP)
2) This initial tRNA and the small ribosomal subunit bind to the 5’ cap of the mRNA and scan along the codons until it encounters the start codon.
3) Complimentary base pairing occurs between the codons and the anticodons found between the mRNA and tRNA once the large ribosomal subunit is attahced to the intiation complex and the A site i ready to accept tRNA
4) Once GTP is hydrolyzed, translation can offocially begin

59
Q

What are the major steps of translational termination?

A

1) When the ribosome reaches the stop codon, the release factor binds to the A site and stimulates peptidyl transferase to cleave the polypeptide from the P site
2) The ribosome units separate and detach from mRNA and the empty tRNA and release factors also separate

60
Q

What does phosphorylation do?

A
  • It’s a form of posttranslational regulation where there’s an addition of a phosphate group to a protein by kinases (enzymes that trasnfer a phosphate group from ATP to a protein) that can activate or inhibit their activity
61
Q

What’s ubiquitination?

A
  • A form of posttranslational regulation where an addition of ubiquitin molecules to proteins targets them for destruction by the proteasome, which breaks down the targeted proteins into individual amino acids
62
Q

What is proteolysis?

A
  • A form of posttranslational regulation where there’s specific cleavage of a protein that can help induce activity within the cell.
  • Protein are broken down into polypeptides
63
Q

What is histone acetyltransferase?

A
  • A molecule that adds acetyl groups to histone tails to increase gene transcription by loosening DNA binding
  • Acetyl groups have a negative charge, so when attached to the also negative DNA repulsion occurs and the DNA strand opens up
  • A form of epigenetics
64
Q

What does methylation of histone tails do?

A
  • Can help activate or repress transcription of genes
  • DNA can be methylated at CpG islands close to promotor repressing transcription
    *CpG islands - found near promotors, so when methylated, gene gets turned off
65
Q

What’s the difference between acetylation and methylation of histone tails?

A
  • Acetlyation helps increase gene transcription while methylation can either activate or suppress gene transcription.
66
Q

How does chromatin remodelling activate gene expression?

A
  • It displaces the nucelosomes from promotor regions, helping activate transcription because now the histomes aren’t in the way of DNA Pol.
  • This process is ATP dependent.
67
Q

How can people with the exact same genomes express different phenotypes?

A
  • Through various processes called epigenetics, which is a form of posttranslational modifications on the histone tails of DNA that, in turn, affect transcription.
68
Q

What factors affect the expression levels of a specific gene?

A
  • The abundance of the protein avaialble, as well as its activity
  • Ex. You can still get low protein expression from a protein with a very high rate of synthesis but also a very hugh rate of degradation.
69
Q

What’s the difference between germline mutations or somatic mutations?

A
  • Germline mutations are inherited, while somatic mutations are not
  • Somatic mutations can occur in all cell types except gametes
70
Q

What’s the difference between transitions and tranversions as small-scale mutations?

A
  • Transitions - Purine to purine or pyrimidine to pyrimidine changes
  • Transversions - purine to pyrimidine or pyrimidine to purine changes
    *These are types of base substitutions
71
Q

What are the different types of mutations?

A
  • Missense mutation (nonsynonymous) - Codon change causes change in an amino acid
  • Nonsense mutation - Sense codon changes into a stop codon, creating a truncated polypeptide
  • Silent mutation (synonymous) - Codon change does not change the the amino acid due to the degeneracy of the genetic code
  • Frameshift mutation - Insertion or deletion of a small number of base pairs that alter the reading frame
72
Q

What are the different large scale chromosomal mutations?

A
  • Deletion - loss of genes
  • Duplication/amplification - increasing dosage of genes
  • Translocation - interchange of genetic parts from nonhomologous chromosomes (i.e., different genes)
  • Inversion - Reversing orientation of a segment of the chromosome (change order of segments)
73
Q

What’s the difference between spontaneous and induced mutations?

A
  • Spontaneous mutations are naturally occurring and are mainly caused by mutation errors and spontaneous lesions (very rare)
  • Induced mutations are caused by environmental factors, artificial agents, or mutagens that cause mutations at a rate much higher than spontaneous mutagens
74
Q

What is the G0 phase in cells?

A
  • Known as the resting phase, it’s the point in the cell cycle where they reside until they recieve signals o perform again
  • When cells are done dividing for there lifetime, this is where they remain (cause their telomeres are too short)
75
Q

What’s the function of CDK?

A
  • Cyclin-dependent kinase
  • It helps regulate the progression of the cell cycle as it needs to be activated so that each phase properly occurs
76
Q

What are the different checkpoints of the cell cycle?

A

1) DNA damage (G1/S) checkpoint: Is DNA ok for replication?
2) DNA replication (G2/M) checkpoint: Is DNA fully replicated before mitosis?
3) Mitotic spindle (M) checkpoint: Are chromosomes aligned properly in metaphase (before anapahse)

77
Q

What is cancer?

A
  • Malignant growth caused by uncontrolled cell division and is caused by altered expression of multiple genes as a result of mutations.
78
Q

What are the different genes that are involved in the promotion or inhibition of cancer?

A
  • Oncogenes - Positive regulators of the cell cycle, help promote cell division and cancer growth when highly active. Include cyclin D/E (gene amplification) and CDK4 alleles (insensitive to inhibition, can’t be stopped)
  • Tumor suppressor genes - negative regulators of the cell cycle including checkpoint genes p53 and Rb (prevent cell from undergoing rapid cell division)
79
Q

What does the haploid number represent?

A
  • The number of unique chromosomes in a genome
80
Q

What are homologous chromosomes?

A

The maternal and paternal pair of chromosomes, where the number and order of genes are the same, but the alleles may be different.

81
Q

What’s the difference between kinetochores and centromeres?

A
  • Kinetochores are the exact proteins that the microtubules attach their spindles to, while centromeres are the DNA sequences that indiciate where the center of the chromosome is.
82
Q

What’s the synaptonemal complex?

A
  • The protein structure that attaches the two non-sister chromosomes from homologous chromosomes during recombination
83
Q

How does recombination occur?

A
  • Homologous chromosomes align with each other during prophase 1 and exchange sections of the chromosome between non-sister chromatids by crossing over
  • There is precise and equal breakage of the strands on the same genes.
  • Helps create genetic variation within a species

Biology 243 (8 decks)

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