(P) Lesson 1: Molecular Basis of Genetics Flashcards
workbook-based
then study of how traits are inherited from one generation to another, how genes are organized and expressed, and how genes behave in populations and evolve over time
genetics
T or F. Genetics plays a central role in all modern EARTH SCIENCES and is essential for an understanding of the living world.
F (biology)
scientific discipline focused on investigating the fundamental principles of inheritance and diversity.
Genetics
T or F. RNA is a macromolecule that contains the genes which encode the amino acid sequences of proteins.
F (DNA)
units of heredity
Genes
T or F. DNA does direct protein synthesis
F (not - they only code for the sequence of amino acids in proteins)
genetic information in the DNA is decoded in the form of
MRNA
which is translated to amino acid sequence of a protein?
MRNA
Try to explain the central dogma of molecular biology
Main point: DNA to mRNA to protein or DNA replication, transcription and Translation
T or F. the flow of information may start from RNA to DNA, the RNA can also be replicated.
T
This stage shows the genetic information in the DNA is copied into mRNA. The sequence of the mRNA bases is the same as that of the DNA.
Transcription
What do you call when the genetic code in the mRNA directs the sequence of amino acids in the protein?
It’s a phase
Translation
Composition of DNA
1.) 5-Carbon sugar (2’-deoxyribose or ribose)
2.) Nitrogenous base (Purines and Pyrimidines)
3.) Phosphate group
T or F. 2’-deoxyribose is a a 5-carbon sugar that forms a ring.
T
What bond does the phosphate group form with C5?
phosphoester bond
What bond does the nitrogenous base form with C1?
N-glycosidic bond
T or F. This N-glycosidic linkage with the sugar involves either the N-1 of the purine or the N-9 of the pyrimidine.
F (opposite)
contain nitrogen within the rings
heterocyclic bases or nitrogenous bases
two types of nitrogenous bases
purines and pyrimidines
this nitrogenous base consist two fused rings
Purine
this nitrogenous base consist 6-sided single ring.
Pyrimidines
enumerate pyrimidine bases
T, U and C
enumerate purine bases
A and G
T or F. nucleoside is composed of three components: a phosphate, a sugar and a base.
F (nucleotides)
T or F. It is possible for nucleotides to combine with additional phosphate units to make diphosphates and triphosphates.
T
relatively short single-stranded nucleic acid chain
oligonucleotide
single-stranded polymer of several nucleotide units.
polynucleotide
catalyze the unwinding of the two strands
helicases
bind to the DNA stabilize the single-
stranded form. A single-stranded DNA is very susceptible to destruction by
nucleases.
SSBP
relaxes the supercoil that forms ahead of the replication fork and aids
with the unwinding process.
DNA gyrase
catalyzes the synthesis of RNA primers, which are required for initiation of DNA synthesis. These provide the required free 3’ hydroxyl group where a nucleotide is added.
Primase
the principal polymerase in the DNA replication in bacteria. It catalyzes the incorporation of new nucleotides to the elongating DNA.
DNA polymerase III
removes the RNA primer. It fills the gaps formed in the growing molecule that result from the removal of the RNA primer. It also proof-reads and corrects any error in base pairing.
DNA Pol 1
forms a phosphodiester bond between 3’-OH and 5’-PO4 groups between the DNA fragments. This forms a continuous DNA molecule.
DNA ligase
The 5’–3’ strand that proceeds to the direction of the replication fork is called?
leading strand
More RNA primers are added by the primase as the DNA helix is unwound, and is elongated by Pol III. The short DNA fragments added to the primase are called the?
Okazaki fragments
made up of unbranched chain of nucleotides as in DNA
RNA
T or F. RNA differs from DNA in that the sugar unit is B-D-ribose, uracil pairs with adenine instead of thymine and is in general, double-stranded.
F (single stranded)
process of copying of a DNA template in the form of RNA
Transcription
T or F. All RNAs are synthesized using a DNA template.
T
This enzyme acts like DNA polymerase, requiring a template, nucleotide triphosphates (ATP, CTP, GTP, and UTP), and magnesium ion.
RNA Polymerase (transcription)
T or F. The RNA polymerase is able to initiate RNA synthesis without a primer, unlike DNA polymerase.
T
a core enzyme and a sigma (σ) subunit are referred to as?
holoenzyme
What subunit is involved in initiating transcription at the beginning of a gene?
σ subunit
p’wede rin naman -10 and -35 kasi σ subunit lang rin nakakarecognize nto
Where specific DNA do subunits bind? Transcription
promoter
defines the beginning of a gene for transcription
promoter site
The transcription start site (+1) has two groups before the first base of the DNA that will be transcribed into the first base of RNA.
Transcription
-35 and -10
T or F. The bases to the left (negative numbers) of the transcription start site are said to be DOWNSTREAM, and the bases to the right (positive numbers) are said to be UPSTREAM
F (opposite)
template used for RNA synthesis is the
anti-sense strand
strand that codes for the sequence of the gene is called the
sense or coding strand
What phase is this?
The start of RNA synthesis occurs at the +1 position, utilizing nucleotide triphosphates (NTPs). The sigma subunit is no longer required at once the helix is opened and is released from the core polymerase shortly after this phase of synthesis.
under Transcription
Initiation
How do the RNA polymerase elongates the RNA?
Transcription
by adding NTPs to the 3’OH end guided by the DNA template
What is formed when the termination sequence is reached that stalls the RNA polymerase, which causes the release of the mRNA and RNA polymerase and the reformation of the DNA double helix?
Transcription
hairpin loop
Type of RNA: It is a copy of a portion of the gene except that uracil replaces thymine. It is linear and does not form secondary structure.
mRNA
composed of rRNAs and proteins
ribosomes
ribosomes subunits of eukaryotes
80S, consisting of 40S and 60S subunits
ribosomes subunit of prokaryotes
30S and 50S subunits that associate to form a 70S ribosome
The big subunit has an enzyme component, peptidyl transferase, which is not a protein but RNA called a?
ribozyme
T or F. Peptidyl transferase catalyzes the formation of peptide bonds between amino acids to form polypeptide chains.
T
A big ribosome subunit contains two or three binding sites for the tRNAs
called the A-site, P- site, and E-site
rRNA
A & P in eukaryotes, E is only present in pro
site where the incoming amino- acyl-tRNA binds
Acceptor site
site where the elongating peptidyl-tRNA binds
P-site
the site where the uncharged tRNA binds, and is found in prokaryotes only.
E-site
carries amino acids to the ribosomes during translation
tRNA
T or F. The rRNA folds up into precisely defined 3-dimensional structures, a cloverleaf appearance.
F (tRNA)
T or F. The tRNA carries a specific amino acid and its anticodon (a triplet of nucleotides) binds with the complementary ANTICODON in an mRNA molecule that specified the amino acid to be added to the polypeptide
F (codon)
set of rules that transmits the message from a gene by specifying the amino acids in proteins
genetic code
possible combinations that form the genetic code
64
each triplet is called a
codon
4 bases in the mRNA
A, U, C, G
each codon specifies for an amino acid, an amino acid can be coded by more than one codon
degenerate or redundant
non-sense or termination codons
UAG, UGA, UAA
first codon
AUG
it is universal, meaning it is the same for all types organisms except for some differences in code found mainly in the DNA of the mitochondrial DNA
genetic code
T or F. The reading of the codons is punctuationless, and the codons are overlapping
F (non-overlapping)
Translation AKA
protein synthesis
T or F. Transcription is the process by which the nucleotide base sequence in an mRNA molecule directs what amino acids will be incorporated in the protein
F (Translation)
Translation of the code from the mRNA involves matching what?
tRNA anticodons and the mRNA codons
In the initiation phase of Translation, protein synthesis is initiated by the assembly of an?
initiator tRNA
what comprises the initiation complex?
Translation
initiator tRNA attached to an N-formylated-methionine, initiation factors (IF) 1, 2, and 3, and the 30S (small) ribosomal subunit
After forming the initiation complex, this is followed by the binding of the?
Translation
50S (large) ribosomal subunit to the small subunit
The initiator tRNA binds to?
P-site
Translation
Familiarize yourself with the 3 repeated steps in Elongation
Translation
(a) binding of new aminoacyl-tRNA to the A site, the P-site is already occupied by the initiator tRNA;
(b) peptide bond formation between the previous amino acid and the new amino acid, the tRNA in the P site is uncharged; and
(c) the release of uncharged tRNA.
The peptidyl t- RNA is translocated to the
P site.
The next aminoacyl-tRNA occupies the
Translation
empty A-site
Elongation
Termination occurs when an mRNA termination codon is in what site?
Translation
A site
In the termination, the entire complex dissociates into
free polypeptide, release factors (RFs), tRNA, mRNA, and small and big subunits of the ribosomes
What do you call when newly synthesized polypeptides undergo modification before they attain their final form which exhibit biologic activity
Post-Translational Modification
The N-formyl- methionine in prokaryotes or initiation methionine in eukaryotes are removed.
Proteolytic cleavage
In the proteolytic cleavage, leader sequences are cleaved by specific proteases, and the finished protein is brought by the?
Golgi apparatus
What bonds may form due to proteolytic cleavage?
Disulfide bonds
Many polypeptides acquire modifications at their N-terminal ends such as the addition of an?
acetyl group
Which among does not belong
Sugar residues
Phosphate groups
Proteolytic cleavage
co-factors
Preproinsulin
Preproinsulin
T or F. DNA polymerases sometimes adds one or wrong nucleotides but some of them have proof reading abilities that correct the mistakes.
T
any change in the base sequence of DNA that make up the genes
mutation
occurs during normal genetic and metabolic functions in the cell resulting from internal factors such as error in replication; mistakes in recombination; misrepair of damaged DNA; base modifications, such as depurination or deamination, caused by spontaneous hydrolytic reactions.
spontaneous mutation
This results when organisms are exposed, accidentally or purposely, to any chemical or physical agents called mutagens. Mutagens increase the frequency of mutation.
Induced mutation
T or F. Mutations are transmitted from a offspring to its parent cell.
F
T or F. Higher organisms tend to have two copies of each gene and if one copy is mutated, the other can’t function.
F (can)
any agent that can alter the structure or sequence of the DNA
Mutagen
first reported mutagenic agen
radiation
two types of radiations that cause mutations
ionizing and non-ionizing radiation
- non-ionizing radiation.
- causes formation of pyrimidine dimers (thymine-thymine) in the DNA by forming a covalent cyclobutane ring between two adjacent pyrimidines.
- results in error in replication
UVL
- x-rays and gamma rays
- alter the DNA by producing hydroxyl free radicals, which are very reactive to hydrogens present on the DNA
Ionizing radiation
This is transferred to the DNA, making it highly reactive, and ultimately, the DNA strand breaks
Radical
These are compounds that are able to enter the cell, and react with the DNA. These increase the frequency of mutations.
chemical agents
some chemicals look like normal bases
base analogues
chemical agents: 5- bromouracyl (5-BU)
base analogues
chemical agents: Nitrous acid
Chemicals which modify the structure and pairing properties of bases.
flat, multiple ring molecules which insert between stacked bases that causes helix distortion
Intercalating agents.
chemical agents: acridine dyes
Intercalating agents
The DNA polymerase may insert an additional nucleotide opposite an intercalated molecule. These insertions cause?
frameshift
two types of base pair substitutions
transition and transversion
substitution of purine to purine or pyrimidine to pyrimidine
transition
substitution of purine to pyrimidine or pyrimidine to purine
transversion
causes replacement of 1 amino acid residue
Missense mutation
produced if base substitution creates a stop codon, thereby terminating protein synthesis prematurely
nonsense mutation
when a base substitution produces a different triplet but which codes for the same amino acid as the original triplet (redundancy of the genetic code). The change usually occurs at the 3rd base.
silent mutation
the acquisition of one or more nucleotides
insertion
loss of one or more nucleotides
deletion
All the amino acids are changed after the insertion or deletion point
frameshift mutation
T or F. All the amino acids are changed after the insertion or deletion point. This mutation can still cause the resulting protein to function.
F (non-functional)
This is a simple repair system. It uses the enzyme photolyase, which is active only in the presence of visible light. It removes the covalent bond between the pyrimidine dimer restoring the normal DNA structure. This repair mechanism is found in many bacteria and lower eukaryotes.
Photoreactivation or light repair
this involves enzymes that remove the altered DNA, usually including the nucleotides on either side of the mutation. DNA polymerase can then fill the gap, repairing the DNA. It does not require light, but it may also occur in the presence of light.
Excision or Dark Repair
Use the table
Identify which here is an example of Missense mutation
Original:
AGU-CGU-GGA-AAU-UGU-CCU-CGA
A.) AGU-CGU-UGA-AAU-UGU-CCU-CGA
B.) AGU-CGU-GGU-AAU-UGU-CCU-CGA
C.) AGU-CGU-GCA-AAU-UGU-CCU-CGA
D. AGU-CGU-GAG-AAA-UUG-UCC-UCG-A-
C
Use the table
Identify which here is an example of Nonsense mutation
Original:
AGU-CGU-GGA-AAU-UGU-CCU-CGA
A.) AGU-CGU-UGA-AAU-UGU-CCU-CGA
B.) AGU-CGU-GGU-AAU-UGU-CCU-CGA
C.) AGU-CGU-GCA-AAU-UGU-CCU-CGA
D. AGU-CGU-GAG-AAA-UUG-UCC-UCG-A-
A
Use the table
Identify which here is an example of Silent mutation
Original:
AGU-CGU-GGA-AAU-UGU-CCU-CGA
A.) AGU-CGU-UGA-AAU-UGU-CCU-CGA
B.) AGU-CGU-GGU-AAU-UGU-CCU-CGA
C.) AGU-CGU-GCA-AAU-UGU-CCU-CGA
D. AGU-CGU-GAG-AAA-UUG-UCC-UCG-A-
B
Use the table
Identify which here is an example of Insertion
Original:
AGU-CGU-GGA-AAU-UGU-CCU-CGA
A.) AGU-CGU-UGA-AAU-UGU-CCU-CGA
B.) AGU-CGU-GGU-AAU-UGU-CCU-CGA
C.) AGU-CGU-GCA-AAU-UGU-CCU-CGA
D. AGU-CGU-GAG-AAA-UUG-UCC-UCG-A-
D
