Chapter 6: Nucleic Acid. The Central Dogma Flashcards
What is the central dogma of molecular biology?
DNA → RNA → Protein
How do nucleosomes help DNA?
They help supercoil DNA.
What suggested the mechanism for DNA replication?
DNA structure.
In which direction can DNA polymerases add nucleotides?
3’ end of a primer.
How does DNA replication differ between the leading and lagging strands?
Leading: continuous, 5’ - 3’ towards fork
-> requires 1 primer
Lagging: discontinuous, 3’ - 5’ towards fork (or 5’ - 3’ away from fork)
-> requires many primers
cuz D Pol only attaches to 3’
What is the role of regions of DNA that do not code for proteins?
They have other important functions (regulation, structural, etc.)
What experiment concluded that DNA is the genetic material in bacteriophages?
Hershey and Chase experiment.
What are the three components of a nucleotide?
Nitrogen base, pentose sugar, phosphate group.
What are the four nitrogen bases in DNA?
Adenine, thymine, guanine, cytosine.
What are the four nitrogen bases in RNA?
Adenine, uracil, guanine, cytosine.
What is the structure of RNA?
Single strand of nucleotides.
What type of bonds connect DNA strands?
Hydrogen bonds.
Which nitrogen bases are complementary in DNA?
A-T (2 H-bonds), G-C (3 H-bonds).
What direction do the two strands of DNA run?
Antiparallel (5’→3’ and 3’→5’).
What links the sugar molecules in a strand of DNA?
Phosphodiester bonds.
What are purines and pyrimidines in DNA?
Purines: A, G; Pyrimidines: T, C.
What is a gene?
A DNA sequence coding for one polypeptide.
What causes genetic mutations?
Changes in a gene’s nucleotide sequence.
What are alleles?
Variants of a gene caused by mutations.
Where does DNA replication occur?
In the nucleus.
What enzymes are required for DNA replication?
Helicase, DNA polymerase.
What does helicase do during DNA replication?
Breaks hydrogen bonds.
=> Unwinds DNA at replication fork
What is the role of DNA polymerase in replication?
Forms phosphodiester bonds in the new strand.
What is the semi-conservative model of DNA replication?
Each new DNA has one original strand.
How does bacterial DNA differ from eukaryotic DNA in replication?
Bacterial: circular, one origin, no histone;
Eukaryotic: linear, multiple origins, histone.
What is the function of DNA gyrase?
Stabilizes DNA helix during unzipping.
What produces a primer during DNA replication?
Primase.
What replaces RNA primers with DNA nucleotides?
DNA polymerase I.
What joins Okazaki fragments?
DNA ligase.
In what direction is DNA synthesized?
5’ to 3’ direction.
How is the DNA code carried to ribosomes?
By mRNA.
Where does transcription occur?
In the nucleus.
What strand of DNA is used during transcription?
Anti-sense strand.
What enzyme is key in transcription?
RNA polymerase.
Where does transcription begin and end on DNA?
Begins at promoter, ends at terminator.
How does mRNA compare to the DNA it is transcribed from?
Single-stranded, shorter, complementary to one gene.
Where does translation occur?
Cytosol or rough ER.
What is the role of tRNA in translation?
Brings specific amino acids to ribosomes.
What does the genetic code determine?
Sequence of amino acids in polypeptides.
What is the start codon and its amino acid?
AUG; Methionine.
What are stop codons?
UAA, UAG, UGA.
What does ‘genetic code is degenerate’ mean?
Multiple codons can code for the same amino acid.
What does ‘genetic code is universal’ mean?
Same code in nearly all organisms.
What are ribosomes made of?
2 subunits (large and small), made of rRNA and proteins.
How many bases does a ribosome expose at a time during translation?
Six bases.
What enzyme catalyzes peptide bond formation during translation?
Peptidyl transferase.
What happens when a stop codon is reached during translation?
The polypeptide chain is released.
Why do cells differ if they all have the same DNA?
Different gene expression.
What is gene expression?
Turning on a gene to produce RNA and protein.
At what levels can gene expression be regulated?
Epigenetic, transcriptional, post-transcriptional, translational, post-translational.
How is prokaryotic gene expression regulated?
At the transcriptional level.
How is eukaryotic gene expression regulated?
During transcription, RNA processing, translation, and post-translation.
What is the relationship between histones and DNA?
DNA (negative) binds to positively charged histones.
What is the effect of DNA methylation?
Deactivates gene expression.
What type of DNA is highly methylated?
Inactive DNA.
What are introns and exons?
Introns: non-coding regions; Exons: coding regions.
What happens to introns during splicing?
They are removed.
What is added to mRNA during splicing?
Cap and poly-A tail.
What allows a single gene to produce multiple proteins?
Alternative splicing.
What do transcription factors do?
Bind DNA and regulate RNA polymerase binding.
What are structural genes?
Genes coding for proteins.
What are regulatory genes?
Genes controlling expression of other genes.
What is an operon?
Unit of gene expression in bacteria.
What are the structural genes in the lac operon?
lacZ, lacY, lacA.
What does lacZ code for?
β-galactosidase.
What does lacY code for?
Permease.
What does lacA code for?
Transacetylase.
What is the function of a regulatory gene in the lac operon?
Codes for the repressor protein.
What happens to the lac operon when lactose is absent?
Repressor binds to the operator; no transcription occurs.
What happens to the lac operon when lactose is present?
Lactose binds the repressor, allowing transcription.
What is the shape of bacterial DNA?
Circular.
How many origins of replication are in bacterial DNA?
One.
What is the shape of eukaryotic DNA?
Linear.
How many origins of replication are in eukaryotic DNA?
Thousands.
What enzyme unzips DNA during replication?
Helicase.
What bonds are broken by helicase during DNA replication?
Hydrogen bonds.
What do free nucleotides do during DNA replication?
Pair with template strands.
What is the direction of DNA strand elongation?
5’ to 3’.
What removes primers during DNA replication?
DNA polymerase I.
What connects Okazaki fragments?
DNA ligase.
What are Okazaki fragments?
Short DNA segments on the lagging strand.
What enzyme stabilizes the DNA helix during unzipping?
DNA gyrase.
What is the function of RNA primase in DNA replication?
Produces RNA primers.
What is the template strand in transcription called?
Anti-sense strand.
Where does the RNA polymerase bind to initiate transcription?
Promoter.
What terminates transcription?
Terminator sequence.
What is the first codon in mRNA translation?
AUG.
What amino acid does AUG code for?
Methionine.
How many codons code for stop signals?
Three.
What is the role of tRNA’s anticodon?
Binds to complementary mRNA codon.
How many codons are in the genetic code?
64 codons.
What does epigenetic regulation involve?
Modifying DNA or histones.
What does post-transcriptional regulation include?
Splicing, RNA modification.
What happens in post-translational regulation?
Protein modifications.
What is the role of permease in the lac operon?
Allows lactose to enter the cell.
What is the function of β-galactosidase in the lac operon?
Hydrolyzes lactose into glucose and galactose.
What type of binding sites does the lac operon repressor protein have?
DNA-binding and lactose-binding sites.
What happens when lactose binds to the lac operon repressor?
Repressor shape changes, preventing it from binding DNA.
What is the role of RNA polymerase in the lac operon?
Transcribes structural genes when repressor is inactive.
What is epigenetic modification?
Changes to DNA/histones affecting gene expression.
What effect does histone modification have on DNA?
Alters how tightly DNA is wound.
What group is added during DNA methylation?
Methyl group (-CH3).
What does heavily methylated DNA indicate?
Inactive gene expression.
What does pre-mRNA contain in eukaryotes?
Introns and exons.
What happens during splicing?
Introns are removed, and exons may be rearranged.
What is added to pre-mRNA to form mature mRNA?
A cap and a poly-A tail.
What is the lac operon an example of?
Gene regulation in prokaryotes.
How are transcription and translation coupled in prokaryotes?
They occur simultaneously in the cytoplasm.
Where does eukaryotic transcription occur?
In the nucleus.
Where does eukaryotic translation occur?
In the cytoplasm.
What ensures proper protein folding after synthesis?
Post-translational modifications.
What is the main difference between bacterial and eukaryotic transcription?
Eukaryotes have RNA processing; bacteria do not.
What is the significance of the operator in the lac operon?
Binding site for the repressor protein.
What is the function of transacetylase in the lac operon?
Function is less clear; may detoxify compounds.
Why is the genetic code considered nearly universal?
It is shared by most organisms.
What is the promoter’s role in transcription?
It is where RNA polymerase binds to start transcription.
What regulates RNA polymerase activity in prokaryotes?
Repressor proteins and operator regions.
What happens when a stop codon is exposed during translation?
Translation ends, and the polypeptide is released because no more complimentary anticodon means no more tRNA coming in.
What components are needed for translation?
mRNA, tRNA, ribosome, and amino acids.
How does alternative splicing increase protein diversity?
By rearranging exons to create different mRNA variants.
What is a codon?
A sequence of three nucleotides in mRNA.
What binds to a codon during translation?
tRNA anticodon.
What is the first step of translation?
mRNA binds to the ribosome.
What happens in the elongation step of translation?
Peptide bonds form between amino acids.
What happens in the termination step of translation?
A stop codon signals the end of translation.
What ensures DNA replication accuracy?
Repair enzymes detect and fix errors.
What allows bacterial cells to regulate gene expression efficiently?
Operons like the lac operon.
What are histones?
Proteins that DNA wraps around.
What is chromatin?
DNA-protein complex in the nucleus.
How does RNA differ from DNA structurally?
RNA has ribose and uracil; DNA has deoxyribose and thymine.
What is the role of mRNA?
Carries genetic code from DNA to ribosomes.
What is the role of rRNA?
Forms part of the ribosome’s structure.
What is the role of tRNA?
Brings amino acids to the ribosome.
What is the universal start codon?
AUG.
How are transcription and translation related?
Transcription creates mRNA; translation uses mRNA to make proteins.
What is the primary function of DNA?
Store genetic information.
How are ATPs related to nucleotide adenine?
ATP is basically a nucleotide, but with 2 extra phosphate groups.
hence the name adenosine triphosphate
Why must a purine always link to a pyrimidine?
Big + Small -> Consistent diameter for helix to be stable
What are genes?
DNA segments, a nucleotide sequence doing for one polypeptide chain.
What is DNA replication?
Doubling quantity of DNA, producing an exact copy (daughter DNA)
What are errors in DNA x2 called?
Mutations
In which direction does D pol add nucleotides?
5’ -> 3’
How many types of DNA polymerase contributes in DNA replication?
D Pol I: replaces primer with nucleotide
D Pol II: repair mistakes
D Pol III: add nucleotides onto primer, synthesize new strands
In eukaryotes, D Pol I is RNase H and D Pol III is D Pol α (initiate) and D Pol γ & D Pol ε (lag. & lead. strand extension)
What is topoisomerase?
Top. I: in both proka. and euka., relaxes supercoiling, no ATP.
Top. II:
* Proka: gyrase => negative supercoils (cut a segment and attach back in)
* Euka: similar to gyrase but no NS
Why do EDP only add nucleotides in one direction?
When dNTP binds to nucleotide chain, it binds through α-phosphate, others are released as pyrophospholate
-> release energy
-> form phosphodiester bonds
-> more energy efficient because doesn’t need external energy
dNTP: nucleoside triphosphate
α-phosphate is the phosphate group nearest to sugar
Why must a gene’s promoter region be unique?
Only transcribe a specfific gene when needed.
How is secretory protein synthesized?
rough ER -> vesicle -> Golgi -> exocytosis
Why must there be ribosomes on rough ER when there are ribosomes in cytoplasm already?
Ribosomes on rough ER will synthesize proteins so that they’re in membranes
=> make protein in vesicles (attach to membrane/secrete)
=> no need membranes for ribosomes
Are ribosomes subunits always assembled?
No, only during translation
How are the stop codons special?
They don’t have complementary anticodons.
How is the genetic code specific?
1 amino acid is coded by only 1 codon
Before tRNA brings amino acid to ribosomes, what must be done?
tRNA ligase attaches amino acid to corresponding tRNA (transesterification reaction)
tRNA ligase = aminoacyl - tRNA synthetase
What is the anticodon on the tRNA that brings the first Methionine to ribosome?
5’ UAC 3’
What is the distance that ribosomes move during translation?
1 codon at a time.
Why is the first amino acid always cleaved out after translation?
For diversity, so that not all chains start with Methionine.
What is polysome?
Many ribosomes translating for the same mRNA at the same time
=> Efficiency
hence same polypeptide
Difference in translation between proka. and euka.?
Time:
* Proka: faster, fits with simple needs
* Euka: slower, but more products
Space:
* Proka: both in cytosol at the same time
* Euka: TS in nucleus, TL in cytosol
What are some types of DNA sequences?
- Highly repetitive sequences
- Protein-coding genes
- Structural DNA
or simply coding genes and non-coding genes
Characteristics of highly repetitive sequences?
- Takes up large amount in human DNA
- No coding functions
- Many nucleotides repeated thousands of times
2 types of highly repetitive sequences?
- Satellite DNA: clustered in one area (e.g. telomeres, centromeres)
- Jumping genes/Transposons: transposable elements, can move within a chromosomes (but never detaches) ~45%
What are single-copy genes?
Unique sequence without close copies in a genome
-> 1 in haploid (gametes), 2 in diploid.
-> Critical for survival and study of evolution.
-> Make up exons.
How much of the genome do coding genes take up?
Less than 2%.
What are split genes?
Genes that contain both introns and exons.
What are structural DNA?
Highly coiled sequences with no coding functions
e.g. centromettric DNA, telomeric DNA, heterochromatin
What are 2 types of heterochromatin?
Constitutive: always transcriptionally inactive
Facultative: able to switch to active (euchromatin) if needed through epigenetic regulation
Role of structural DNA?
- Chromosome stability
-
Gene regulation and silencing: packed too tight
-> prevent R Pol * TF to access DNA (epigenetic level) - Facilitate cell division (ensure chromosome is packed, telomeres, etc.)
