Lecture Reviewer Flashcards
It explains the flow of genetic materials in organisms.
Central Dogma
It uses DNA as a template to produce another DNA.
Replication
It uses DNA as the template for the synthesis of an RNA.
Transcription
It uses RNA as the template for the synthesis of a protein.
Translation
It is an
RNA-driven DNA synthesis.
Reverse Transcription
3 major steps in DNA replication, transcription, and translation.
Initiation
Elongation
Termination
An enzyme that unwinds the double helix of the DNA and splits it open.
DNA Helicase
This enzyme relieves the tightening of the supercoil to prevent DNA damage.
Topoisomerase
It stabilizes the unwound DNA, preventing them from re-annealing.
Single-strand Binding Protein (SSB)
This enzyme adds a short piece of RNA at the 3’ end of the DNA to serve as a primer.
RNA primase
A strand of DNA where the addition of nucleotides is continuous.
Leading Strand
A strand of DNA where several RNA primers are required to gradually guide the DNA polymerase.
Lagging Strand
It is involved in the initial addition of DNA nucleotides.
DNA polymerase ɑ (alpha)
It adds DNA nucleotides to the leading strand.
DNA Polymerase ɛ
(epsilon)
It adds DNA nucleotides to the lagging strand, and is also responsible for proofreading and nipping the RNA primer, initiating removal.
DNA polymerase δ (delta)
It adds DNA nucleotides to both strands and is only found in prokaryotes.
DNA Polymerase III
It detaches the short RNA primer.
Flap Endonuclease 1 (FEN1)
It coats the long flap of RNA primer; prevents FEN1, and helps DNA2.
Replication Protein A
It cleaves the long RNA primer, making it shorter for final cleaving by FEN1.
Dna2 Endonuclease
Short DNA segments that are formed between the RNA primers.
Okazaki Fragments
It binds the Okazaki fragments together to form a single continuous DNA strand.
DNA ligase
The DNA strand that contains the code is referred to as _______.
Sense strand
Its
complementary DNA strand is called _______ and it serves as the template for transcription.
Antisense strand
TFIIs that comprise the pre-initiation complex.
TFIID, TFIIA, TFIIB, TFIIF
It is the first transcription factor that
binds to the TATA box.
TFIID
Once attached, it bends the promoter
by 80o, which helps in the binding of
TFIIA and TFIIB.
TATA Box-binding protein (TBP)
It stabilizes TFIID.
TFIIA
It interacts with TBP molecule and
recruits the RNA Polymerase II.
TFIIB
It assists in the binding of the RNA
Polymerase II on the promoter
TFIIF
TFIIs that comprise the open complex.
TFIIE, TFIIH
It binds to the pre-initiation complex
and helps the binding of TFIIH.
TFIIE
It splits open the promoter.
TFIIH
It adds RNA nucleotides to antisense strand.
RNA Polymerase
This is the process of modifying
the terminal nucleotide of the
pre-mRNA.
5’ capping
It removes terminal phosphate at 5’ end.
RNA Triphosphatase
It attaches guanyl phosphate to 5’ end.
Guanylyl Transferase
It attaches methyl group to guanine nucleotide.
Methyl Transferase
It is the final structure formed at the 5’ end, which protects the pre-mRNA from degradation and is also important for translation.
5’ cap or Methylguanosine cap:
It cleaves the pre-mRNA and separates it from the RNA Polymerase II.
Cleavage Stimulation Factor (CstF)
Similar to the 5’ end, the 3’ end is also protected.
3’ Poly (A) Tail
It recruits Poly A polymerase.
Cleavage & Polyadenylation Specificity Factor
It adds about 200 adenine(A) residues at the 3’ end of the pre-mRNA giving rise to the Poly (A) Tail.
Poly A Polymerase
It binds to the poly A tail to prevent the
degradation of the 3’ end of the pre-mRNA
Poly A-binding protein
It is the coding sequence of the Pre-mRNA.
Exons
It is the non-coding sequence of the Pre-mRNA.
Introns
It is where a newly-made pre-mRNA transcript is transformed into a mature mRNA.
Splicing
It cuts off the introns and joins the remaining exons to form the final or mature mRNA.
Spliceosome
Three types of RNAs that participate in the process of translation.
mRNA (messenger
RNA)
rRNA (ribosomal RNA)
tRNA (transfer RNA)
eIFs that bind to small subunits of the ribosome.
elF-1, elF-1A, elF-3
eIFs that bind to 5’ cap and poly A tail, respectively.
elf-4E & elF-4G
eIFs that carry mRNA to small subunit of the ribosome.
elF-4A & elf-B
eIF that carries initiator met-tRNA to the P site.
elf-2
eIF that detaches elF-2 and signals the large ribosomal subunit.
elF-5
The site for attachment of tRNA carrying an amino acid.
A- site (Aminoacyl Site)
The site where tRNA with an amino acid forms a peptide bond to form an amino acid chain.
P-site (peptidyl site)
The site where tRNA with no amino acid exits the ribosome.
E-site (exit site)
It binds amino acid to tRNA.
Aminoacyl Synthetase
Initial complex is the ______.
met-tRNA
It is the transfer of one or more amino acids between peptides.
Transpeptidation
It catalyzes the binding of the second amino acid to the first
(methionine) amino acid by forming a peptide bond.
Peptidyl Transferase
A process where the ribosome moves to the next codon.
Translocation
This is a complete set of relationships among amino acids and codons, which is summarized in a table.
Genetic Code
What happens when the ribosome reaches the stop codon?
Translation is terminated / stopped.
What are the stop codons?
UAG, UAA, UGA
It binds to the stop codon.
Cytoplasmic Termination Factor (CTF) / Cytoplasmic Release Factor (CRF)
It binds the amino acid chain to the water molecule, which detaches the a.a. chain from the mRNA.
Peptidyl Transferase
In reverse transcription, this is used as a template to synthesize DNA strands.
Viral RNA
In reverse transcription, this is used as a template to synthesize DNA strands.
Viral RNA
What are steps in reverse transcription?
Refer to pp. 15-16 of Module 3.1 / slide 34-38 in PPT of central dogma.
This is a system of genes that regulates gene expression.
Operon System
These are adjacent structural genes that code for required proteins.
Cistrons
A component of the Operon system that controls transcription.
Operator
It promotes RNA Polymerase binding.
Promoter
It is a type of inducer operon system.
Lactose (Lac) Operon System
How many cistrons does a Lac Operon System have? What are these cistrons?
Three (3)
Lac Z (transcribes for galactosidase)
Lac Y (transcribes for lactose permease)
Lac A (transcribes for transacetylase)
It is a type of regulatory protein of the lac operon system which binds to the operator gene to turn it off.
Lac Repressor
It is a molecule that binds to the repressor protein to inactivate it.
Lac Inducer
It is a type of repressor operon system.
Tryptophan (Trp) Operon System
How many cistrons does a Trp Operon System have? What are these cistrons?
Five (5)
Trp E and Trp D (transcribes for anthranilate synthase)
Trp C (transcribes for indoglycerol phosphate synthase)
Trp B and Trp A (transcribes for tryptophan synthase)
It is a regulatory protein that cannot bind to the operator on its own.
Aporepressor Protein
It is a non-protein compound that may either come from outside of the cell or a product
of metabolism within the cells.
Corepressor
What are the 2 types of gene regulation?
Prokaryotic gene regulation
Eukaryotic gene regulation
These genes may be turned on or off depending on the need of the cell.
Facultative Genes
These genes are never turned off because they are important for
the maintenance of the cell.
Constitutive Genes
How does eukaryotic gene regulation occur?
Regulation of Transcription Factors
Regulation of Transcription
Regulation AFTER Transcription
Regulation of Translation
Regulation AFTER Translation
This regulation ensures that only required transcription factors enter the nucleus and
bind to their respective promoter.
Regulation of Nuclear Localization
Even if TFs are already inside the nucleus, DNA binding is still regulated in two ways: alteration of DNA-binding domain & multimerization.
Regulation of DNA-binding
Assuming that the transcription factors were able to bind with the promoter,
transcription will still be regulated by either activators or repressors.
Regulation of Transcription
It facilitates the binding of transcription factors to the promoter.
Enhancer DNA
Transcription inhibition may done
in either of these three ways.
Repressors may either bind to a:
Promoter - prevents binding of transcription factors
Enhancer - prevents binding of activators
Silencer - loops the repressor towards the promoter
Transcription may have occurred
but another mechanism can
regulate gene expression after
transcription.
Regulation AFTER Transcription
Regulatory proteins bind to the mRNA and tell the spliceosomes where to cut the mRNA.
Regulation of mRNA Processing
Micro RNAs (miRNAs) are responsible for the life span of mRNAs.
Regulation by miRNAs
eIFs that participate in the translation are phosphorylated and rendered inactive, thus translation cannot occur.
Regulation of Translation
Regulation AFTER translation can occur in two ways. What are these?
Phosphorylation
Ubiquitination
It activates or inactivates translated proteins.
Phosphorylation
It uses ubiquitin, which binds to proteins and delivers them to the proteasome for degradation.
Ubiquitination
The expression of the genes involved is pretty straightforward.
Qualitative Traits
These traits are
controlled by genes with a cumulative effect such that the phenotypes show small, gradual
differences.
Quantitative Traits
It refers to the proportion of a population that will exhibit a particular trait if the allele is found in their genotype.
Penetrance / Quantitative Concept
100% of all individuals with the same allele in their genotype expresses the trait.
Complete Penetrance
Not all individuals with the same allele in their genotype expresses the trait.
Incomplete / Reduced Penetrance
It refers to the degree of expression of a penetrant gene.
Expressivity / Qualitative Concept
It is due to an environmental factor but mimics a phenotype.
Phenocopy
It means that the trait has a genetic basis.
Concordance
It means that the trait has no genetic basis and is due to an environmental factor.
Discordance
These are alleles with quantifiable traits and have additive effects to the expression of the trait.
Polygenes
The distribution of quantitative traits in a population can be analyzed by statistical
methods that compute for the mean, variance, and standard deviation.
Analysis of Quantitative Characteristics
It is determined by the genes of an individual and the environment.
Phenotypic variance
Formula for phenotypic variance
VP = VG + VE
It is determined by incomplete dominance, complete dominance, and gene
interactions and epistasis.
Genotypic variance
Formula for genotypic variance
VG = VA + VD + VI
It refers to the percentage of phenotypic variation that is due to genotypic variations.
Heritability
It is the proportion of the phenotypic variation due to ALL the genetic factors.
Broad Sense Heritability (H2)
Formula for broad sense heritability
H2 = (VG/VP) X 100
It is the proportion of the phenotypic variation based on the additive genetic variance.
Narrow Sense Heritability (h2)
This is the alteration of the phenotype without altering the genotype.
Epigenetic Inheritance
These are molecules that alter gene expression.
Epigenomes
What are the characteristics of an epigenome?
Irreversible
Permanent
Reprogrammed
It adds a methyl group to turn off transcription.
DNA Methylation
It is a mechanism where histone tails either promote or prevent transcription.
Histone modification
It is when non-coding RNAs (ncRNAs) regulate gene expression.
Gene silencing
This is the transfer of epigenetic genes from parent to offspring.
Transgenerational Epigenetic Inheritance
This is when one allele prevents the expression of another allele.
Paramutation
This occurs when one allele is marked for silencing while the other gene is expressed (depending of the sex of the parent where the allele came from) .
Genomic Imprinting
It balances the expression of the X-linked genes in males and females.
Dosage Compensation
To balance the expression of X-linked genes in males and females, one of the X chromosomes of the female undergoes ________ and forms a _______.
X-inactivation
Barr body
This happens when more X-chromosomes from one parent are inactivated than the other.
Skewed Inactivation
It refers to the inheritance of traits outside of the nucleus.
Extranulear Inheritance
This is the inheritance of cytoplasmic materials that contain DNA (e.g. mitochondria, chloroplasts).
Maternal Inheritance
Traits governed by the DNA in the
organelle are all ________
in origin.
MATERNAL
Phenotype of the offspring depends on the ____________.
Phenotype of the mother
This is the inheritance of cytoplasmic materials that were synthesized during oogenesis (mRNA, proteins).
Maternal Effect Inheritance
Phenotype of the offspring depends on the ___________.
Genotype of the mother
This is the inheritance of the cytoplasm containing infectious particles that previously entered the maternal cell.
Infectious Inheritance
Give an example of infectious inheritance.
Kappa particles turn cell to killer strain.
These are abnormalities of the genetic material that give rise to various lethal and non-
lethal disorders.
Mutations
Mutations are either due to _________ or _________.
Intrinsic factors (errors during DNA replication)
Extrinsic
factors (environmental)
It is passed on only to the
products of its mitotic cell division giving rise to a localized mutation.
Somatic Mutation
It can be passed from parent to child and all cells of the child carry the mutation.
Germline Mutation
It is a condition wherein the cell (or organism) has one complete set of chromosome.
Monoploidy (n)
It is a condition wherein cell (or organism) has two or more complete sets of chromosomes.
Euploidy
A type of euploidy with 2 sets of chromosomes, which is normal in most organisms.
Diploidy (2n)
A type of euploidy with more than two sets of chromosomes, which are normal in plants but abnormal in most organisms.
Polyploidy
Types of Polyploidy
Triploidy (3n)
Tetraploidy (4n)
Hexaploidy (6n)
Octaploidy (8n)
It is a condition wherein a cell (or organism) has gained or lost an entire chromosome.
Aneuploidy
It involves the loss of one chromosome.
Monosomy (2n-1)
An example for monosomy
Turner’s Syndrome (45, XO)
It is the loss of a pair of homologous chromosome, which causes the death of the embryo.
Nullisomy (2n-2)
It is the loss of one chromosome each from two pairs of homologous chromosomes.
Double Monosomy (2n-1-1)
It occurs when you gain one chromosome.
Trisomy (2n+1)
Givd an example of a trisomy.
Down’s Syndrome (47,+21)
Edward’s Syndrome (47,+18)
Patau’s Syndrome (47,+13)
Klinefelter’s Syndrome (47,XXY) (48,XXXY)(48,XXYY)(49,XXXXY)(50,XXXXXXY)
It occurs when you gain one pair of homologous chromosome.
Tetrasomy (2n+2)
It occyrz when you gain two pairs of homologous chromosomes.
Double Tetrasomy (2n+2+2)
A mutation due to a missing DNA segment from a chromosome.
Deletion
It is a deletion in the X chromosome of males where the gene originally
had 1000 kb (kilobases) but the transcribed mRNA only contained 14kb.
Muscular Dystrophy
A mutation due to a duplicated part of a chromosome.
Duplication
It is a mutation that occurs when a chromosomal segment breaks at both ends, is inverted
(turned around), and reunites with the rest of the chromosome.
Inversion
A type of inversion wherein the inverted area includes the centromere.
Pericentric Inversion
A type of inversion wherein the inverted area does not include the centromere.
Paracentric Inversion
It is a mutation caused by a change in position of a chromosomal segment.
Translocation
A type of mutation caused by a change in one base on a DNA strand.
Point Mutation / Base Pair Substitution
purine replaced with another purine or pyrimidine replaced with another
pyrimidine
Transition
purine to pyrimidine or pyrimidine to purine
Transversion
A type of point mutation which does not result in a new amino acid in the protein sequence.
Silent Mutation
A type of point mutation which results to a new amino acid in the sequence.
Missense Mutation
A type of point mutation that produces a protein shorter than the required protein.
Nonsense Mutation
This is a mutation due to the insertion or deletion of one or more bases.
Frameshift Mutation
Anything with the ability to produce a mutation is called a _________.
Mutagenic Agent
This involves exposure to radiation.
Physical Mutagens
It disrupts chemical bonds in the DNA that could lead to single-strand or double-strand breaks.
Ionizing Radiation
It affects the pyrimidines cytosine and thymine and could either form photoproducts or dimers.
Nonionizing Radiation
They break the amino group (-NH2) (deamination) of a base transforming the nucleotide into another type of nucleotide.
DNA-reactive Agents / Reactants
These are chemicals that structurally resemble purines and pyrimidines and may be incorporated into DNA in place of the normal bases during DNA replication.
They cause transition mutations.
Base Analogs
A pyrimidine analog that resembles thymine.
Bromouracil (BU)
A purine analog that resembles adenine, which can pair with T.
Aminopurine
Substances that insert into the DNA strand and can cause frameshift mutation.
Intercalating agents
Methyl, ethyl, occasionally propyl groups are added to the bases or backbone of DNA that can lead to spontaneous breakdown (deamination) or mispairing of bases
Alkylating agents
They are also known as jumping genes because these DNA segments can move from their position to another region of the same DNA or region of another DNA.
DNA Transposons
They insert their genetic material into the host DNA, disrupting base sequences and genetic functions.
Virus
Helicobacter pylori triggers the formation of reactive oxygen species (ROS) that damage nitrogenous bases of the DNA.
Bacteria
How does Direct DNA Repair occur?
It involves the reversal of damage caused by radiation, a process called photoreactivation, using the enzyme photolyase to catalyze the process in the presence of light.
How does Based Excision Repair (BER)
occur?
- a specific glycosylase recognizes and removes a damaged nitrogenous base
- DNA polymerase adds a new nitrogenous base
- DNA ligase binds the new base to adjacent bases
How does Nucleotide Excision Repair (NER) occur?
- removal of a damaged polynucleotide segment from the affected DNA strand
- DNA polymerase replaces the removed nucleotides with new DNA nucleotides, using
the complementary segment as the template - DNA ligase binds adjacent nucleotides.
How does Mismatch Repair (MMR) occur?
- if complementary base pairs are replaced by a non-complementary pair or by an
inserted base analog, a mismatch occurs - this mismatch must be immediately repaired before the cell enters the division
- “proofreading” by DNA polymerase during DNA replication detects mismatched
bases, removes the wrong base, and inserts the correct base.
Polynucleotide kinase/phosphatase catalyzes the production of 3’-OH and 5’ phosphate ends to allow both ends to undergo ligation.
Repair of DNA Breaks
