Exam 2: Ch 8 Flashcards
what genes are
how they carry information
how information is expressed
how genes are replicated
Genetics
a segment of DNA that encodes for a functional product, usually a protein.
gene
refers to all of the genetic material in a cell
Genome
is the molecular study of genomes
Genomics
refers to the genes of an organism
Genotype
refers to the expression of the genes, observable traits.
Phenotype
Know and describe 3 routes in which genetic materials flow in bacteria: within the cell, horizontal transfer, vertical transfer
Central Dogma(within a cell): genetic information flows in a one-directional path from DNA to RNA to protein, meaning DNA is transcribed into RNA, which is then translated into a protein
Transcription: DNA is copied into messenger RNA(mRNA) molecule.
Translation: The mRNA is read by ribosomes to assemble amino acids into a protein.
Horizontal Transfer: the process of acquiring genetic material from another cell that is not a direct ancestor. Combination of DNA from two cells.
Vertical Transmission: transfer of genetic information through cell division. Parent cell replicates DNA to form two daughter cells with
genetic information flows in a one-directional path from DNA to RNA to protein, meaning DNA is transcribed into RNA, which is then translated into a protein
Transcription: DNA is copied into messenger RNA(mRNA) molecule.
Translation: The mRNA is read by ribosomes to assemble amino acids into a protein.
Central Dogma (within a cell):
DNA is copied into messenger RNA(mRNA) molecule.
Transcription
The mRNA is read by ribosomes to assemble amino acids into a protein.
Translation
the process of acquiring genetic material from another cell that is not a direct ancestor. Combination of DNA from two cells.
Horizontal Transfer:
transfer of genetic information through cell division. Parent cell replicates DNA to form two daughter cells with identical DNA.
Vertical Transmission
a singular circular, double stranded DNA molecule, which is the main chromosome. In addition, some prokaryotes possess smaller circular DNA molecules called plasmids that carry additional genetic information
Prokaryotes Genome Structure
DNA is linear, meaning it forms a long straight strands instead of circles. Double helix formed from two complementary strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs, sugar-phosphate backbone.
Eukaryotic Genome Structure
How are chromosomes packaged in eukaryotes
Eukaryotic: Complex process where long strands of DNA are tightly wound around proteins called histones, forming structures called nucleosomes, which then further coil and compact into chromatin.
small circular molecule of DNA (usually found in prokaryotes)
Plasmid
meaning they replicate independently within a cell. Carry information required for their own replication and often for one or more cellular traits.
Plasmids
Fertility factors, resistance factors, bacteriocin factors, virulence plasmids, cryptic plasmids.
Types of plasmids
How many origins of replication does a plasmid have?
A plasmid typically has one origin of replication, since plasmids are small circular DNA molecules.
Double helix formed from two complementary strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs, sugar-phosphate backbone.
Antiparallel
in replication means one parent molecule into the separation of parental strands into templates to form two new strands complementary to template strands.
DNA replication is Semiconservative
in replication mean it occurs in two directions simultaneously, with two replication forks moving away from the origin of replication
DNA replication is bidirectional
How are new nucleotides added into the growing strand of nucleotides? (which enzyme, which direction, which bond, which specific components)
DNA Polymerase: binds to each strand and adds nucleotides to hydroxyl group at 3’ end of the strand- Replicates DNA in 5’-3’ direction
Describe ALL steps in DNA replication: enzymes, what occurs, products, energy, what may go wrong at each step? For example, what would likely happen if single-strand binding proteins failed to bind to the unzipped DNA? etc.
DNA Replication:
Step 1- Initiation:
Topoisomerase relieves overwinding strain ahead of replication forks
Helicase attaches to the DNA double helix and break the hydrogen bonds between the bases, separating the two strands
Primase assembles a short stretch of nucleotides called primer in each strand of the DNA (the tips)
Step 2- Elongation:
Refers to the stage where new nucleotides are added to the DNA strand
Polymerase this enzyme is responsible for adding nucleotides to the growing DNA strand, selecting the correct base pair according to the template (the insertion of incorrect nucleotides or mismatched bases by polymerase that causes damaged mutated DNA)
Due to the antiparallel nature of DNA, one strand (leading strand) is synthesized continuously, while the other (lagging strand) is made in fragments called Okazaki fragments.
Ligase forms bonds between DNA fragments.
the synthesis of this strand in DNA replication occurs continuously in the direction of the replication fork, requiring only one RNA primer to initiate replication
Leading Strand
the synthesis of this strand in DNA replication occurs discontinuously, meaning it is built in short fragments called Ozaki fragments, initiated by RNA primers and later joined by Ligase. This is because Polymerase can only synthesize DNA in the 5’-3’ direction while the lagging strand template runs in the opposite direction at the replication fork.
Lagging Strand
Proof-reading activity of DNA polymerase, RNA polymerase
DNA Polymerase: has proofreading potential, mismatched bases are pulled out and replaced 1/1,000,000,000 may be incorrect, spontaneous mutations
Polymerase adds an incorrect nucleotide to the new DNA strand. Polymerase detects that bases are mispaired. Polymerase uses 3’-5’ exonuclease to remove the incorrect nucleotide.
Mismatch Repair
mutation repair mechanism
is a DNA repair mechanism that removes damaged DNA that’s caused by i.e radiation and chemicals. Nuclease removes the damaged piece of DNA, DNA Polymerase comes in and replaces it, DNA Ligase seals it together
Nucleotide Repair
Mutation repair mechanism
function is to carry genetic information from a cells DNA in the nucleons into the cytoplasm where it serves as a template for protein synthesis.
mRNA
What are the steps of gene expression?
Keep in mind: transcription vs replication: replication creates an identical copy of an entire DNA molecule, while transcription produces a single RNA strand from a specific DNA sequence(gene)
key components of ribosomes
rRNA
is the entire DNA region that is transcribed into RNA
Transcription Unit
Describe ALL steps of transcription and translations: starting materials, enzymes at each step, energy requirement, location/organelles, additional modification
Transcription
The process which converts DNA into RNA
Initiation: RNA Polymerase binds to the promoter, a region of the gene that signals the DNA to unwind.
Elongation: RNA Polymerase reads the unwound DNA strand and builds the mRNA molecule using complementary base pairs usually 10-20 bases at a time
Termination: RNA Polymerase crosses a stop sequence in the gene, the mRNA strand is complete and it detaches from the DNA. Keep note no primer is needed.
Transcription takes place in the cytoplasm of the prokaryotes and in the nucleus, mitochondria, and chloroplasts in eukaryotes.
Translation Steps:
Is the step in gene expression that decodes messenger RNA (mRNA) to produce proteins.
Process: a ribosome within the cells cytoplasm reads reads the mRNA and adds amino acids to create a protein.
Genetic Code: the genetic code matches each sequence of three nucleotides in the mRNA called a codon to a specific amino acid.
serves as an adaptor molecule in protein synthesis, carrying specific amino acids to the ribosome based in the codon sequence in the mRNA
tRNA
signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point
Promoter
is the exact nucleotide within the promoter where transcription begins marking the first base pair that is transcribed into RNA.
Start Point
Roles of RNA polymerase. How is RNA polymerase different from DNA polymerase?
Does not require helicase
Slower than DNA polymerase
Uracil incorporated instead of thymine
Lacks proofreading function (more errors)
Know how to convert a DNA sequence into an RNA sequence, and into an amino acid sequence. And in the reverse direction?
DNA Template: 5’ ATT CGG ACG TAA CCG 3’
RNA Template: 3’ UAA GCC UGC AUU. GGC 5’
What are present in a transcription initiation complex? Where is the TATA box located? Rate of transcription? How many mRNA molecules can be made from one gene/gene cluster?
A transcription initiation complex typically includes: RNA polymerase II, the TATA-binding protein, and a set of general transcription factors (TFs) like TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH; all of which assemble on the promoter region of a gene on DNA to initiate the process of transcription by positioning the RNA polymerase to start RNA synthesis
The TATA box is located about 25 to 35 base pairs upstream of the transcription start site on a gene, it is positioned before the point where transcription begins in a eukaryotic cell; acting as a marker for where the RNA polymerase should start reading the DNA to produce RNA
The rate of transcription is around 40-80 nucleotides per second. Bacteria are faster than eukaryotes.
Some genes only produce a few mRNA copies while others may produce hundreds or thousands. How often the gene is transcribed by RNA polymerase directly impacts the number of mRNA molecules produced. The lifespan of an mRNA molecule influences how many copies can exist at any given time
How are genes arranged in prokaryotes vs. eukaryotes (how many promoters for how many genes?
In prokaryotes, multiple related genes are often grouped together under a single promoter in an operon, meaning one promoter controls the transcription of several genes at once.
In eukaryotes, each gene usually has its own promoter, leading to a more complex arrangement with potentially many promoters for a larger number of individual genes.
prokaryotes have fewer promoters controlling multiple genes, whereas eukaryotes have more promoters controlling individual genes
Describe mRNA processing. Does it occur in prokaryotes or eukaryotes or both? What do the 5’-UTR and 3’-UTR on the mRNA of prokaryotes correspond to on the mRNA of eukaryotes?
mRNA processing, which involves modifications like the addition of a 5’ cap and poly-A tail, as well as the removal of introns through splicing, primarily occurs in eukaryotes and is not a significant feature in prokaryotes; in prokaryotes, mRNA is typically translated directly after transcription without extensive processing due to the lack of a nucleus separating the processes
On the mRNA of eukaryotes, the 5’-UTR and 3’-UTR correspond to the same regions as in prokaryotes, meaning the 5’-UTR is the untranslated region at the 5’ end of the mRNA before the start codon, and the 3’-UTR is the untranslated region at the 3’ end of the mRNA following the stop codon; however, eukaryotic UTRs are often much longer and more complex in structure compared to prokaryotic UTRs, playing a more significant role in post-transcriptional regulation of gene expression in eukaryotes
DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genomic information encoding a particular amino acid or signaling the termination of protein synthesis (stop signals).
Of the 64 codons, 61 code for 20 amino acids
What are codons? How many codons code for one amino acid? How many amino acids can be coded for by one codon?
What does the statement “The genetic code is redundant” mean?
More than one codon may specify a particular amino acid
multiple different codon sequences (combinations of nucleotides) can code for the same amino acid
Why must codons be read in the correct reading frame?
Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced
Know the structural components of tRNAs
75 bases, 50% base paired, 10% modified
anticodon loop
D loop
TYC loop
3’ CCA
Transfer RNAs (tRNAs) are adaptor molecules that play a pivotal role in decoding the genetic code during protein synthesis. It serves as a link between the mRNA and the amino acid sequence that make up a protein. The actual structure of tRNA looks like a clover leaf-shaped structure composed of an anticodon loop, the acceptor arm, the ribosomal binding arm, and the DHU arm. The aminoacyl site (A site ), the peptidyl site ( P site), and the exit site (E site) are the three binding sites for tRNA.
Prokaryotic vs. eukaryotic ribosomes
the main difference between prokaryotic and eukaryotic ribosomes is size, prokaryotic ribosomes are smaller (70S) and composed of smaller subunits (30S and 50S)
eukaryotic ribosomes are larger (80S) which have subunits of 40S and 60S.
Prokaryotic ribosomes have three different rRNA molecules, while eukaryotic ribosomes have four
The 3 sites of ribosomes are
P site- holds the tRNA that carries the growing polypeptide chain
A site- holds the tRNA that carries the next amino acid to be added to the chain
E site- is the exit site, where discharged tRNAs leave the ribosome
How is translation initiated?
A small ribosomal subunit binds with mRNA and a special initiator tRNA
The small subunit moves along the mRNA until it reaches the start codon (AUG)
Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
Describe translational termination
Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome
the A site accepts a protein called a release factor
The release factor causes the addition of a release factor
The release factor causes the polypeptide, and the translation assemble comes apart
What are polyribosomes? Are they present in prokaryotes or eukaryotes or both? How many proteins/polypeptides can be made from one mRNA molecule? From one coding DNA molecule?
polyribosome is a cluster of ribosomes attached to a single messenger RNA (mRNA) molecule, allowing for the simultaneous translation of that mRNA into multiple polypeptide chains, acting as a “factory” for protein synthesis within the cell; it is a key component of the process of translation in both prokaryotic and eukaryotic organisms.
A single mRNA molecule can produce multiple copies of a single polypeptide (protein) because many ribosomes can bind to the mRNA simultaneously, effectively creating a “polysome” where each ribosome translates the same mRNA sequence into a polypeptide chain; essentially, one mRNA can produce hundreds or even thousands of identical proteins depending on the cell type and conditions.
How is translational accuracy maintained?
Accurate translation requires two steps:
- a correct match between tRNA and an amino acid, by aminoacyl-tRNA synthetase
- a correct match between tRNA anticodon and the mRNA codon
Flexible pairing at the third base of a codon is called wobble and allows some tRNAS to bind to more than one codon
What is a wobble? Beneficial how?
Wobbles are flexible pairing at the third base of a codon, and allows some tRNAs to bind to more than one codon.
What does it mean to say “bacterial transcription and translation occur simultaneously”? What benefits does simultaneous transcription and translation offer?
in bacteria, the process of copying genetic information from DNA into mRNA (transcription) and the process of using that mRNA to build proteins (translation) happen at the same time.
unlike in eukaryotes where transcription happens in the nucleus and translation in the cytoplasm.
No nuclear membrane: Bacteria lack a nucleus, allowing the ribosomes to access the newly formed mRNA during transcription, immediately starting translation.
Cytoplasmic location: Both transcription and translation occur in the cytoplasm of the bacterial cell.
Coupling of processes: This close proximity allows for a tight coupling between the two processes, meaning translation can begin even before transcription is fully complete.
At which levels can genes be regulated? Describe.
DNA: transcriptional level of control = noMRNA
mRNA: translational level of control = no protein
Protein: post-translational level of control = protein activated when needed
What are ways to regulate protein synthesis? To regulate mRNA synthesis?
Regulation of Protein Synthesis:
Typically halt transcription
Can stop translation directly
What is an operon? Describe the structure of an operon.
Operon: a genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered along the DNA
Operon Structure:
Promoter
Cluster of structural genes
Additional sequences that control transcription (operator)
Describe how an inducible operon and a repressible operon is regulated. Know the steps in the examples of Trp operon and Lac operon.
Inducible Operon: transcription is usually off and needs to be turned on
Repressible Operon: transcription is normally on and needs to be turned off
Describe positive regulation vs. negative regulation. Are activators or Repressors involved? Where do activators and repressors bind? What are the outcomes in each type?
Positive Regulation: activator is required for transcription; no repressor involved
Negative Regulation: when repressor is present then there is no transcription; requires no repressor and no activator to have transcription
Are regulatory genes always transcribed and translated into regulator proteins? How do they work in repressible vs. inducible operon regulation? What are co-repressors and inducers; and how do they work?
regulatory genes are always transcribed and translated into regulator proteins, as their primary function is to produce the protein that controls the expression of other genes; in a repressible operon, the regulator protein is usually active by default and needs a specific molecule (co-repressor) to bind and repress transcription, while in an inducible operon, the regulator protein is usually inactive and needs a specific molecule (inducer) to bind and activate transcription
A co-repressor is a small molecule that binds to a repressor protein, enhancing its ability to bind to DNA and repress gene transcription, while an inducer is a molecule that binds to a repressor protein, causing a conformational change that prevents it from binding to DNA and thus allows gene transcription to occur; essentially, co-repressors “turn off” gene expression by activating repressors, while inducers “turn on” gene expression by inactivating repressors
What are mutagens? Describe types of mutagens.
Mutagens: agent that causes mutations
Types of Mutations:
Radiation (UV Light):
Ionizing radiation - induces breaks in chromosomes
Non-ionizing radiation - induces thymine dimers
Chemical Mutagens (ethidium bromide, some dyes, base analogs):
Nucleotide analogs - disrupt DNA and RNA replication and cause point mutations
Nucleotide-altering chemicals - result in base-pair substitution mutations and missense mutations
Frameshift mutagens - result in nonsense mutations
