BIO 243 - Theme 2: Decoding Genetic Information
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A: Central Dogma B: Transcription C: Translation D: Mutation
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30 Terms
Describe in your own words the genetic code and explain how it related to the central dogma
The genetic code is the set of rules that translate DNA and RNA sequences into proteins. It uses three-letter codons to specify amino acids or stop signals. The code is universal, redundant, and non-overlapping.
It relates to the central dogma, which describes the flow of genetic information:
Transcription: DNA → mRNA
Translation: mRNA → Protein
This process ensures genes are expressed as functional proteins.
What is the central dogma
The central dogma of molecular biology describes the flow of genetic information within a cell. It was first proposed by Francis Crick and states that genetic information moves in one direction:
DNA → RNA (Transcription):
DNA serves as a template to produce messenger RNA (mRNA) through the process of transcription.
This occurs in the nucleus (in eukaryotes) and is catalyzed by RNA polymerase.
RNA → Protein (Translation):
The mRNA is read by ribosomes in the cytoplasm, where transfer RNA (tRNA) brings amino acids to build a protein.
The sequence of nucleotides in mRNA is translated into a chain of amino acids, forming a polypeptide (protein).
This process explains how genetic information stored in DNA is expressed as functional proteins, which perform various roles in the cell. The central dogma is fundamental to molecular biology, though exceptions exist, such as reverse transcription in retroviruses (RNA → DNA).
Explain how the auxotrophic mutants isolated by Beadle and Tatum support the one gene-one polypeptide hypothesis
Beadle and Tatum's experiments with auxotrophic mutants in the bread mold Neurospora crassa provided key evidence for the one gene-one polypeptide hypothesis. Here's how:
1. Creation of Auxotrophic Mutants
Beadle and Tatum exposed Neurospora spores to X-rays, inducing mutations.
They then grew these mutants on complete medium (which supplies all necessary nutrients) and later transferred them to minimal medium (which requires the fungus to synthesize its own nutrients).
2. Identifying Mutants with Metabolic Defects
Some mutants could not grow on minimal medium but could grow when specific nutrients (like amino acids or vitamins) were added.
These mutants were auxotrophic, meaning they had lost the ability to synthesize certain essential compounds due to genetic mutations.
3. Linking Genes to Enzymes in a Pathway
Beadle and Tatum focused on the biosynthesis of arginine, an essential amino acid.
They identified different auxotrophic mutants that could grow only when specific precursors (ornithine, citrulline, or arginine) were provided.
By analyzing the growth patterns, they determined that these mutations affected different steps in the arginine biosynthesis pathway, with each mutant lacking a functional enzyme required for a specific step.
4. Conclusion: One Gene-One Enzyme → One Gene-One Polypeptide
Their work showed that each gene is responsible for making one specific enzyme that catalyzes a biochemical reaction.
Later, scientists refined this idea to the one gene-one polypeptide hypothesis, since some proteins consist of multiple polypeptide chains encoded by separate genes.
Significance
Beadle and Tatum’s findings laid the foundation for understanding gene function and molecular genetics, showing that genes dictate the production of proteins, which in turn control metabolic pathways and cellular functions.
Describe template and coding strands and relate how genes are organized on both DNA strands of a chromosome
In DNA transcription, the two strands of DNA serve different roles:
Template Strand (Antisense Strand)
This is the strand of DNA that is read by RNA polymerase to synthesize mRNA.
It runs in the 3' to 5' direction (since RNA synthesis occurs in the 5' to 3' direction).
The mRNA sequence is complementary to this strand.
Coding Strand (Sense Strand)
This strand is not transcribed but has the same sequence as the mRNA (except that RNA has uracil (U) instead of thymine (T)).
It runs in the 5' to 3' direction.
Gene Organization on Both Strands of a Chromosome
Genes can be present on either strand of DNA, but each gene is transcribed from only one strand at a time.
A gene’s template strand depends on its location and direction.
On one part of a chromosome, the top strand may serve as the template, while in another region, the bottom strand could be the template.
Genes are not always in the same direction; they can be organized in opposite orientations along the chromosome.
Why This Matters
The organization of genes on both strands allows for efficient use of DNA without interference.
Some regions may have overlapping genes, where one gene is read from the top strand and another from the bottom strand.
This structure ensures that transcription can occur in both directions depending on gene location.
Describe the orientation (5’-3’ or 3’-5’) of molecules in the central dogma
1. DNA (Double-Stranded)
DNA strands are antiparallel, meaning one runs 5’ → 3’ while the other runs 3’ → 5’.
During transcription, RNA polymerase reads the template strand in the 3’ → 5’ direction and synthesizes mRNA in the 5’ → 3’ direction.
2. mRNA (Single-Stranded)
The mRNA sequence is complementary to the template strand and identical (except for U replacing T) to the coding strand.
It is always synthesized 5’ → 3’, meaning ribosomes read it in the same direction during translation.
3. Protein (Polypeptide Chain)
The ribosome reads mRNA 5’ → 3’ in sets of three nucleotides (codons).
Translation occurs from the N-terminus (amino end) to the C-terminus (carboxyl end) of the polypeptide.
Describe the origin of the information system
The origin of the information system in biology refers to how genetic information is stored, transferred, and used to produce the molecules necessary for life, specifically proteins. This system underlies the processes of DNA replication, transcription, and translation, which are central to life’s function and inheritance.
1. DNA as the Information Storage Molecule
The genetic code is stored in the DNA (deoxyribonucleic acid), which is composed of long sequences of nucleotides (adenine (A), thymine (T), cytosine (C), and guanine (G)).
The arrangement of these nucleotides in sequences, known as genes, carries the information necessary for building proteins and regulating cellular processes.
2. The Central Dogma
The central dogma of molecular biology describes the flow of information:
DNA → RNA (Transcription): The genetic information in DNA is copied into messenger RNA (mRNA), which serves as a template for protein synthesis.
RNA → Protein (Translation): mRNA is translated into a specific sequence of amino acids, forming a polypeptide (protein).
3. Origins of the Information System
The origin of life and the development of the information system is a complex topic that is still debated. The RNA world hypothesis suggests that early life forms may have used RNA, which can both store genetic information and catalyze reactions (similar to enzymes), as the primary molecule for information storage and transfer. Over time, DNA became the primary information storage molecule due to its stability.
Evolution likely played a key role in refining the information system. Initially, primitive molecules like RNA or even simpler self-replicating molecules could have formed, leading to more sophisticated systems where DNA took over the role of carrying genetic information due to its ability to store information more stably than RNA.
4. Molecular Machines: Enzymes and Ribosomes
The information system is not just about DNA, but also about the molecular machines (like RNA polymerase and ribosomes) that interpret and act upon the genetic code.
RNA polymerase is responsible for transcribing DNA into RNA.
Ribosomes are responsible for translating mRNA into protein by reading the genetic code and linking amino acids in the correct sequence.
5. The Role of Mutation and Natural Selection
Mutations (changes in the genetic code) and natural selection drive the evolution of the genetic code, allowing life forms to adapt and diversify. This is why organisms with similar genetic codes share many biological traits.
In Summary:
The origin of the biological information system is rooted in the development of DNA as a stable and efficient information storage molecule. Over time, molecular mechanisms (transcription and translation) evolved to decode this information and produce the proteins necessary for cellular function, shaping the complexity and diversity of life we observe today.
DNA encodes RNA, which encodes proteins. What is this process called and how does it work?
The process by which DNA encodes RNA, which encodes proteins is called the central dogma of molecular biology. It describes the flow of genetic information from DNA to RNA to protein, and it involves two key processes: transcription and translation.
1. Transcription (DNA → RNA)
DNA contains the genetic instructions for building proteins. The first step is to convert this genetic information into messenger RNA (mRNA), which serves as a temporary copy of the genetic code.
During transcription, the enzyme RNA polymerase reads the DNA sequence on the template strand (3' to 5' direction) and synthesizes a complementary strand of RNA in the 5' to 3' direction.
The resulting mRNA sequence is complementary to the DNA template strand and is identical to the coding strand (except that RNA has uracil (U) instead of thymine (T)).
The mRNA carries the genetic information from the DNA in the nucleus (in eukaryotes) to the cytoplasm, where it can be used to produce proteins.
2. Translation (RNA → Protein)
Translation is the process by which the information in the mRNA is used to build a protein. It occurs in the ribosome, a molecular machine found in the cytoplasm (or rough endoplasmic reticulum).
The ribosome reads the mRNA sequence in sets of three nucleotides called codons, each of which codes for a specific amino acid.
Transfer RNA (tRNA) molecules, which have an anticodon that is complementary to the mRNA codon, bring the correct amino acids to the ribosome.
As the ribosome moves along the mRNA, amino acids are linked together by peptide bonds to form a polypeptide chain (protein).
The process continues until a stop codon is reached, signaling the end of the protein chain.
The newly formed protein then folds into its functional shape and performs its specific role in the cell.
Summary of the Process
Transcription (DNA → RNA):
DNA is transcribed into mRNA by RNA polymerase.
Translation (RNA → Protein):
mRNA is translated into a protein by ribosomes using tRNA to match codons with amino acids.
This process ensures that the information stored in DNA is accurately transferred to RNA and then used to create the proteins that are essential for the structure and function of the cell.
How do RNA viruses reproduce?
RNA viruses reproduce through a process that involves replication and transcription of their RNA genome to produce new viral particles. Unlike DNA viruses, RNA viruses do not rely on the host cell's DNA machinery, but instead use their own or host cell enzymes to replicate and transcribe their RNA. The process varies slightly between different types of RNA viruses (e.g., positive-sense, negative-sense, or retroviruses).
viral RNA needs to be converted into viral DNA in order to integrate into hosts chromosome
the hosts transcription and translation machinery is hijacked to produce viral proteins from the viral DNA
What are properties of information carrying molecule?
Not all DNA codes for proteins—what happens to the other DNA and what is the other DNA?
1. Non-coding DNA that Regulates Gene Expression
Promoters: These are sequences of DNA found near the beginning of genes that act as binding sites for RNA polymerase, the enzyme that starts transcription. Promoters control when, where, and how much of a gene is expressed.
Enhancers and Silencers: These are regulatory elements that can increase (enhancers) or decrease (silencers) the expression of genes. They often work by interacting with transcription factors, which then either facilitate or block the binding of RNA polymerase to the gene.
Introns: In eukaryotic genes, introns are non-coding regions that are transcribed into pre-mRNA but are spliced out during RNA processing. They do not code for proteins, but some introns have important regulatory functions.
2. Structural DNA
Telomeres: These are repetitive sequences at the ends of chromosomes that protect the chromosome from degradation during cell division. Telomeres prevent the loss of important genetic information when the chromosomes are replicated.
Centromeres: These regions of DNA help organize chromosomes during cell division. The centromere is where the spindle fibers attach, ensuring that chromosomes are evenly divided between two daughter cells.
3. DNA that Encodes Non-coding RNA
Not all RNA is translated into proteins. Many non-coding RNAs play crucial roles in cellular processes:
Ribosomal RNA (rRNA): This type of RNA is a structural component of the ribosome, the molecular machine that assembles proteins.
Transfer RNA (tRNA): This RNA carries amino acids to the ribosome during protein synthesis, matching each amino acid to the correct mRNA codon.
MicroRNA (miRNA) and Small Interfering RNA (siRNA): These small RNAs are involved in regulating gene expression by interfering with the translation of mRNA or promoting its degradation.
Long Non-coding RNA (lncRNA): These are involved in regulating gene expression at multiple levels, including chromatin remodeling and transcription.
4. Repetitive and Junk DNA
Satellite DNA: These are highly repetitive sequences that can be found in centromeres and telomeres. They do not code for proteins but may have structural or regulatory functions.
Transposons (Jumping Genes): These are sequences that can move around the genome. While many are inactive, some transposons are involved in the regulation of other genes or could potentially contribute to genetic diversity.
Pseudogenes: These are sequences that resemble genes but have lost their ability to code for functional proteins due to mutations. Some pseudogenes may still play roles in regulating gene expression, while others are considered vestiges of evolutionary processes.
5. Evolutionary and Functional Importance of Non-coding DNA
Evolution: While much of non-coding DNA may not have an immediate function, some can have evolutionary importance, serving as a source of genetic variation. Mutations in non-coding regions can alter gene expression or regulatory mechanisms, influencing traits and disease susceptibility.
Genetic Regulation: Non-coding DNA, especially regulatory elements like enhancers and non-coding RNAs, is essential for fine-tuning the expression of genes. Changes in these regions can lead to significant changes in cellular function and organism development.
Summary
Non-coding DNA makes up a large portion of the genome and includes various types of DNA with important regulatory, structural, and functional roles.
It helps control gene expression, maintains chromosome structure, and is involved in the production of non-coding RNAs.
Though much of non-coding DNA was once considered "junk DNA," research has shown that many of these sequences play vital roles in the regulation of gene activity and the overall function of the cell.
How are genes in DNA encoded into RNA?
The process of encoding genes in DNA into RNA is called transcription, and it involves converting a specific segment of DNA (a gene) into messenger RNA (mRNA) or other types of RNA. Here’s how this process works step by step:
1. Initiation of Transcription
Promoter Sequence: Transcription begins when an enzyme called RNA polymerase binds to a specific region of the gene called the promoter. The promoter is a short sequence of DNA located just upstream (before) the gene.
Transcription Factors: In eukaryotes, additional proteins known as transcription factors help RNA polymerase recognize and bind to the promoter region, ensuring the correct gene is transcribed.
DNA Unwinding: Once RNA polymerase binds to the promoter, the DNA double helix unwinds, exposing the template strand of the gene. This strand will be used as a template for RNA synthesis.
2. Elongation (RNA Synthesis)
RNA Polymerase: RNA polymerase moves along the template strand of the DNA in the 3' to 5' direction, reading the DNA sequence.
Complementary RNA Formation: As RNA polymerase reads the DNA template strand, it synthesizes a complementary strand of RNA in the 5' to 3' direction (opposite to the template strand).
Instead of thymine (T), uracil (U) is used in RNA. For example, where the DNA has adenine (A), RNA polymerase will add uracil (U).
The RNA molecule is an exact copy of the coding strand of the DNA, with uracil replacing thymine.
RNA Chain Growth: RNA polymerase continues to move along the DNA, adding RNA nucleotides to the growing RNA strand, and this process continues as long as the gene is being transcribed.
3. Termination of Transcription
Termination Signal: When RNA polymerase reaches a specific sequence of nucleotides called the terminator (or in eukaryotes, a specific polyadenylation signal), the transcription process stops.
Release of RNA: The RNA molecule is then released from the RNA polymerase, and the DNA re-coils to form the double helix again. The newly synthesized RNA strand is called the primary transcript.
4. RNA Processing (in Eukaryotes)
Before the RNA can be used for protein synthesis (in translation), it may undergo additional processing, especially in eukaryotes:
Capping: A special cap is added to the 5' end of the mRNA molecule. This helps protect the RNA and aids in the process of translation.
Polyadenylation: A poly-A tail is added to the 3' end of the mRNA, which also helps with stability and export from the nucleus.
Splicing: In eukaryotes, the introns (non-coding regions) are removed from the primary RNA transcript, and the exons (coding regions) are joined together. This results in a mature mRNA molecule ready to be translated into a protein.
Summary of Transcription
RNA polymerase binds to the promoter region of the gene.
The DNA unwinds, and the RNA polymerase reads the template strand of DNA.
RNA polymerase synthesizes a complementary RNA strand in the 5' to 3' direction.
Once a termination signal is reached, the RNA molecule is released.
In eukaryotes, the RNA undergoes processing (capping, splicing, polyadenylation) before leaving the nucleus as mature mRNA.
This mRNA now carries the genetic information needed to synthesize proteins, and it will be translated into a functional protein during the process of translation.
Explain how different cells and tissues can form from an identical genome
Describe the main steps of transcription
1. Initiation: mediated by direct interaction of DNA binding proteins to the promoter
RNA polymerase binds to the promoter region of the DNA, which is a specific sequence that signals the start of the gene. signals where transcription begins on the chromosome
promotor is located immediately upstream (5’) of the transcriptional start point
its recognized and bound by the transcription machinery (RNA polymerase)
first the transcription activator proteins bind to enhancer regions distant from the promoter to cause DNA looping bringing the enhancer + RNA polymerase to the promoter resulting in high level of transcription
Transcription factors help RNA polymerase recognize and bind to the promoter.
The DNA unwinds, exposing the template strand that will be used to synthesize RNA.
2. Elongation
RNA polymerase moves along the template strand of the DNA in the 3' to 5' direction.
DNA is unwound in front of the moving RNA polymerase and re-annealed behind the transcription bubble (Contains RNA-DNA hybrid)
As RNA polymerase moves, it synthesizes a complementary RNA strand in the 5' to 3' direction.
Nucleotides are added to the growing RNA chain, with uracil (U) replacing thymine (T) in RNA.
Growing RNA transcript is displaced from the DNA template to allow re-annealing back into double stranded DNA
3. Termination
When RNA polymerase reaches a specific termination sequence on the DNA, it stops synthesizing RNA.
Poly-adenylation sequence in the DNA is transcribed into mRNA (STOP sequence) and it contains a cleavage site that signals the protein complex CPSF to cleave the completed mRNA transcript, which signals to the RNA polymerase to stop transcription
The newly formed RNA strand is released from the RNA polymerase, and the DNA re-coils back into its double helix form.
In eukaryotes, after transcription, the RNA may undergo processing (like capping, splicing, and polyadenylation) to become a mature messenger RNA (mRNA) that is ready for translation into protein.
Describe the structure and function of promoters and enhancers
Promoters Structure:
A promoter is a specific sequence of DNA located near the start of a gene.
It typically includes several key regions:
TATA Box: In many eukaryotic promoters, there's a conserved sequence called the TATA box (approximately -25 to -35 base pairs upstream of the transcription start site). It helps position the RNA polymerase to start transcription correctly.
Core Promoter: This includes the TATA box and other sequences that form the basic binding site for the RNA polymerase and transcription factors.
Transcription Start Site: This is where RNA synthesis begins, typically denoted as +1.
Function:
Initiates transcription: The promoter is crucial for initiating the process of transcription. It is where RNA polymerase binds to start transcribing the DNA into RNA.
Regulates gene expression: The promoter controls when and how much of a gene is transcribed by interacting with transcription factors. These transcription factors can either activate or repress transcription.
In eukaryotes, the promoter works with general transcription factors that help RNA polymerase bind and begin transcription at the right location.
Enhancers Structure:
Enhancers are regions of DNA that can be located far upstream or downstream of a gene, and in some cases, even within the introns of the gene itself.
They often consist of short DNA sequences that bind to specific transcription factors, and they can be located thousands of base pairs away from the promoter.
Enhancers do not have a fixed sequence like promoters but are defined by the binding sites for specific transcription factors.
Function:
Increase transcription levels: Enhancers function to increase the rate of transcription by interacting with the promoter region. When transcription factors bind to the enhancer, they help recruit RNA polymerase or other co-activators to the promoter, thereby facilitating the initiation of transcription.
Can work from a distance: Enhancers can influence transcription even if they are far away from the gene they regulate. This is possible due to the DNA looping, which brings the enhancer region closer to the promoter.
Tissue-specific expression: Enhancers can help ensure that certain genes are activated in specific tissues or at particular stages of development by responding to specific signals or transcription factors that are present only in those cells or at certain times.
Can function in either orientation: Enhancers can work in both the forward and reverse directions (the orientation of the DNA) and still regulate transcription.
Key Differences Between Promoters and Enhancers:
Location: Promoters are typically located immediately upstream of the gene they regulate, while enhancers can be located far away from the gene, even within introns or on other chromosomes.
Function: Promoters are essential for the initiation of transcription, whereas enhancers increase the level of transcription and fine-tune gene expression.
Binding factors: Promoters directly bind RNA polymerase and general transcription factors, while enhancers bind activator proteins and help recruit other factors that enhance transcription.
Explain post-transcriptional regulation of gene expression
5’ capping
modified guanine nucleotide added to the 5’ end of the RNA shortly after transcription begins and helps protect the RNA from degradation by exonucleases + important for exporting the RNA from the nucleus to the cytoplasm, where translation occurs
3’ Poly-adenylation
helps the RNA to be properly exported from the nucleus to the cytoplasm
also helps to terminate the transcription process in some cases by causing RNA polymerase to disassociate from the DNA
splicing
process by which the introns (non-coding regions) of the pre-mRNA are removed and the exons (coding regions) are joined together to form the mature mRNA
process is carried out by large complex called the spliceosome
regulation of expression by small, noncoding RNAs
RNA interference
silencing a gene post-transcription
Explain how transcription is affected by chromatin structure
Chromatin structure affects transcription by controlling accessibility of the DNA to transcription machinery.
Tightly packed chromatin (heterochromatin) is less accessible, making transcription more difficult or preventing it entirely.
Loosely packed chromatin (euchromatin) is more accessible, allowing transcription factors and RNA polymerase to bind and initiate transcription more easily.
Modifications to histones, like acetylation (loosening chromatin) or methylation (tightening chromatin), also regulate gene expression by influencing chromatin structure.
Explain how introns and exons are advantageous in eukaryotes
In eukaryotes, the presence of introns (non-coding regions) and exons (coding regions) provides several advantages:
Alternative Splicing: Introns allow for alternative splicing, a process that enables a single gene to produce multiple proteins by rearranging exons in different combinations. This increases protein diversity and adaptability without requiring additional genes.
Regulation: Introns may play roles in regulating gene expression, such as through the binding of regulatory proteins or by influencing the stability and transport of mRNA.
Evolutionary Flexibility: The presence of introns may contribute to genetic evolution by providing spaces where new functional elements can evolve without disrupting the protein-coding sequence. This allows for easier genetic variation and adaptation.
Overall, introns and exons enhance functional diversity and regulation, making eukaryotic gene expression more flexible and complex.
How does transcription and post transcriptional regulation differ in prokaryotic and eukaryotic organisms?
Transcription and post-transcriptional regulation differ significantly between prokaryotes and eukaryotes due to their structural and organizational differences. Here's a comparison:
1. Transcription
Prokaryotes:
Location: Transcription occurs in the cytoplasm because prokaryotes lack a nucleus.
Speed: Transcription and translation are coupled, meaning translation of mRNA starts while transcription is still happening.
RNA Processing: Prokaryotic mRNA is usually not processed. It does not have a 5' cap, poly-A tail, or splicing.
Eukaryotes:
Location: Transcription occurs in the nucleus, and mRNA must be processed and exported to the cytoplasm for translation.
RNA Processing: Eukaryotic mRNA undergoes extensive post-transcriptional modifications such as 5' capping, 3' polyadenylation, and splicing of introns.
Transcriptional Regulation: Eukaryotes have more complex transcription regulation involving enhancers, silencers, and chromatin remodeling, while prokaryotes typically regulate gene expression through simpler mechanisms like operons.
2. Post-transcriptional Regulation
Prokaryotes:
Minimal Processing: Prokaryotes typically do not have complex post-transcriptional regulation.
mRNA Stability: mRNA degradation is relatively faster in prokaryotes, and regulation often occurs at the level of translation initiation or through mechanisms like operons (e.g., the lac operon).
Eukaryotes:
Extensive Processing: Eukaryotic mRNA undergoes significant post-transcriptional regulation, including:
Splicing (removal of introns)
5' capping and 3' poly-A tail addition for stability, transport, and translation initiation.
Regulation by miRNAs: Eukaryotes utilize microRNAs (miRNAs) and other regulatory RNAs to influence mRNA stability and translation, providing fine-tuned control.
Nuclear Export: Eukaryotic mRNA must be exported from the nucleus to the cytoplasm for translation, which involves regulation at the nuclear pore.
Summary
Prokaryotes: Transcription is simpler and occurs in the cytoplasm, with little to no post-transcriptional modification. Regulation mainly happens at the transcription level through operons.
Eukaryotes: Transcription occurs in the nucleus with extensive post-transcriptional modifications and regulation (capping, splicing, polyadenylation, and miRNA regulation).
How are mRNAs translated into functional proteins?
The process of translating mRNA into functional proteins occurs through translation, which takes place in the cytoplasm. Here's how it works:
1. Initiation
mRNA Binding: The mRNA, now processed and mature, is transported from the nucleus to the cytoplasm.
Ribosome Assembly: The small ribosomal subunit binds to the 5' cap of the mRNA. It moves along the mRNA to find the start codon (AUG).
tRNA Binding: The initiator tRNA (charged with methionine) binds to the start codon on the mRNA. The large ribosomal subunit then attaches to the small subunit, forming the complete ribosome.
2. Elongation
Codon Recognition: The ribosome reads the mRNA in sets of three nucleotides (called codons). Each codon specifies an amino acid.
tRNA Matching: Transfer RNA (tRNA) molecules carry specific amino acids and have anticodons that are complementary to the mRNA codons. Each tRNA matches its anticodon to the codon in the ribosome.
Peptide Bond Formation: The ribosome catalyzes the formation of peptide bonds between adjacent amino acids, extending the growing protein chain.
The ribosome moves along the mRNA, reading each codon, and adding corresponding amino acids to the polypeptide chain.
3. Termination
Stop Codon: When the ribosome reaches one of the three stop codons (UAA, UAG, or UGA) on the mRNA, it signals the end of translation.
Release: A release factor binds to the stop codon, causing the ribosome to release the newly synthesized polypeptide.
Ribosome Disassembly: The ribosome dissociates, and the mRNA is released.
4. Protein Folding and Modification
The newly synthesized polypeptide chain folds into its functional 3D structure. This folding is assisted by chaperone proteins.
Post-translational modifications, such as phosphorylation, glycosylation, or cleavage, may occur to activate the protein or enable it to perform its specific function.
Summary
mRNA is read by a ribosome in the cytoplasm.
tRNA molecules bring amino acids to match the codons on the mRNA.
The ribosome links the amino acids into a polypeptide chain.
The polypeptide folds into a functional protein.
How do processes of translation differ in prokaryotic and eukaryotic organisms?
1. Location of Translation
Prokaryotes: Translation occurs in the cytoplasm, as there is no nucleus to separate transcription and translation. Translation and transcription are coupled, meaning translation begins while the mRNA is still being transcribed.
Eukaryotes: Translation occurs in the cytoplasm, but it is separated from transcription, which occurs in the nucleus. mRNA must first be processed (capping, splicing, and polyadenylation) and exported out of the nucleus before translation can begin.
2. Ribosome Structure
Prokaryotes: The ribosome is smaller with a 70S structure, consisting of a 50S large subunit and a 30S small subunit.
Eukaryotes: The ribosome is larger with an 80S structure, consisting of a 60S large subunit and a 40S small subunit.
3. mRNA Modifications
Prokaryotes: mRNA is typically not modified significantly after transcription. It is often ready for translation immediately and can be translated as soon as it is synthesized.
Eukaryotes: mRNA undergoes extensive post-transcriptional modifications, including:
5' capping
3' polyadenylation
Splicing to remove introns. These modifications enhance mRNA stability, facilitate nuclear export, and help with translation initiation.
4. Initiation of Translation
Prokaryotes: Translation initiation is facilitated by the Shine-Dalgarno sequence, a ribosome-binding site in the mRNA, which helps the ribosome recognize the start codon. The small ribosomal subunit directly binds to the mRNA.
Eukaryotes: Translation initiation is more complex. The ribosome binds to the 5' cap of the mRNA and scans along the mRNA until it finds the start codon (AUG). The small ribosomal subunit associates with initiation factors, and the initiator tRNA carries methionine (in eukaryotes, unlike formylmethionine in prokaryotes).
5. Initiator tRNA
Prokaryotes: The initiator tRNA carries formylmethionine (fMet), which is specific to bacterial translation.
Eukaryotes: The initiator tRNA carries methionine (Met), and there is no formylation.
6. Coupling of Transcription and Translation
Prokaryotes: Transcription and translation are coupled. As soon as mRNA is transcribed, ribosomes can begin translating it because there is no nuclear envelope to separate the two processes.
Eukaryotes: Transcription and translation are uncoupled. Transcription happens in the nucleus, while translation occurs in the cytoplasm after mRNA processing and export.
7. Translation Regulation
Prokaryotes: Translation is mainly regulated at the initiation level, such as through the presence of specific ribosome-binding sites and the availability of translation initiation factors.
Eukaryotes: Translation regulation is more complex and can occur at multiple levels, including initiation, elongation, and through the interaction of regulatory proteins and microRNAs that can block translation or promote mRNA degradation.
8. Speed of Translation
Prokaryotes: Translation is typically faster because the processes are coupled, and the ribosome can begin translating immediately after mRNA synthesis.
Eukaryotes: Translation is generally slower due to the added complexity of post-transcriptional modifications, nuclear export, and the larger size of the ribosome.
Explain what is the genetic code and describe the experiments that led to its discovery?
Characteristics of the Genetic Code
Universal: The genetic code is almost the same in all organisms, from bacteria to humans.
Triplet: Each amino acid is specified by a triplet of nucleotides (codon).
Non-overlapping: Codons are read sequentially, without overlap.
Redundant: More than one codon can code for the same amino acid.
Start and Stop Codons: Certain codons signal the start (AUG) and the end (UAA, UAG, UGA) of translation.
ex. Beadle and Tatum: experiment suggested that one e=gene in the DNA codes for a specific enzyme which was one of the early clues that genes encode proteins
Understand the structure and role of rRNA and tRNA in translation
1. rRNA (Ribosomal RNA) Structure:
rRNA is a type of RNA that is a major component of the ribosome.
The ribosome is made up of two subunits: a large subunit and a small subunit. These subunits are composed of rRNA molecules and proteins.
In prokaryotes, the ribosome has a 30S small subunit and a 50S large subunit, which combine to form a 70S ribosome.
In eukaryotes, the ribosome consists of a 40S small subunit and a 60S large subunit, forming an 80S ribosome.
The rRNA is responsible for the catalytic activity in the ribosome, particularly the peptide bond formation between amino acids during translation.
Role in Translation:
rRNA provides the structural scaffold for the ribosome, ensuring its correct shape and stability.
Catalysis of peptide bond formation: The ribosome’s rRNA catalyzes the formation of peptide bonds between amino acids by bringing the correct amino acids into proximity and facilitating their bonding.
The ribosome reads the mRNA, binding to the mRNA sequence via the small subunit, while the large subunit aids in elongation by adding amino acids to the growing polypeptide chain.
2. tRNA (Transfer RNA) Structure:
tRNA is a small RNA molecule, usually about 70-90 nucleotides long.
It has a cloverleaf structure, with loops and stems, and contains the anticodon loop and the 3' acceptor stem.
The anticodon loop contains a set of three nucleotides (the anticodon) that is complementary to the codon on the mRNA.
The 3' acceptor stem is where the corresponding amino acid is attached, which is catalyzed by an enzyme called aminoacyl-tRNA synthetase.
Role in Translation:
tRNA acts as the adapter molecule in translation, matching the mRNA codon with the appropriate amino acid.
Anticodon-Codon Matching: The anticodon of the tRNA pairs with the complementary codon on the mRNA sequence in the ribosome.
Each tRNA molecule is specific to one amino acid. Once the tRNA’s anticodon binds to the corresponding mRNA codon, the amino acid is added to the growing polypeptide chain.
tRNA carries the amino acid to the ribosome during the elongation phase of translation, facilitating the correct assembly of the protein.
Summary of rRNA and tRNA Roles in Translation
rRNA forms the core structure of the ribosome and catalyzes the formation of peptide bonds between amino acids.
tRNA serves as the adapter molecule that reads the mRNA codons and brings the appropriate amino acids to the ribosome for protein synthesis.
Distinguish between the E, P, and A sites of the ribosome
A site: Where the incoming tRNA carrying the new amino acid binds.
P site: Where the growing polypeptide chain is held and where the peptide bond forms. binds to the tRNA attached to the growing peptide chain
E site: Where the empty tRNA exits after delivering its amino acid.
Know the basic structure of an amino acid and a peptide bond and be able to name the types of amino acids and their main differences
An amino acid consists of a central carbon atom (also known as the alpha carbon, Cα) bonded to:
Amino group (–NH₂): A nitrogen atom attached to two hydrogen atoms.
Carboxyl group (–COOH): A carbonyl group (C=O) attached to a hydroxyl group (–OH).
Hydrogen atom (–H): A single hydrogen atom bonded to the alpha carbon.
Side chain (R group): A variable group that differs for each amino acid and determines the properties and identity of the amino acid. It can range from a simple hydrogen atom (as in glycine) to more complex structures.
Peptide Bond
A peptide bond is a covalent bond that forms between the carboxyl group (–COOH) of one amino acid and the amino group (–NH₂) of another amino acid, releasing a molecule of water (H₂O) in a condensation reaction.
types of amino acids:
nonpolar aa’s
R group usually contains CH2 or CH3 (nonpolar molecules)
uncharged polar aa’s
R group usually contains oxygen (or OH)
charged aa’s
R group that contains acids or bases that can ionize
aromatic aa’s
R group contains a carbon ring with alternating single and double bonds
Special functioning aa’s include:
methionine: first aa in the polypeptide
proline: cause bend in polypeptide chains
cysteine: disulfide bridge contributes to structure of polypeptides
Explain how mutations occur in the genome and the differences between spontaneous and induced mutations and germline and somatic mutations
A mutation is a permanent change in the DNA sequence that can alter the genetic code. Mutations can occur at various levels, including single nucleotide changes (point mutations), insertions or deletions of nucleotides, and larger chromosomal alterations. Mutations can happen during DNA replication, due to damage from external factors, or as a result of errors in cellular processes like repair or recombination.
Spontaneous vs. Induced Mutations1. Spontaneous Mutations
Definition: Spontaneous mutations occur naturally without external influence. They result from normal cellular processes, such as DNA replication or metabolic activities.
Causes:
DNA replication errors: Occasionally, DNA polymerase makes mistakes when copying the DNA, which can lead to incorrect nucleotides being inserted.
Tautomeric shifts: Bases can occasionally shift to alternative forms (tautomers), leading to mispairing during DNA replication.
Depurination and deamination: Spontaneous loss of purine bases (adenine or guanine) or chemical changes in bases (such as cytosine deamination to uracil) can cause mutations.
Frequency: These mutations happen randomly and at a low frequency.
2. Induced Mutations
Definition: Induced mutations are caused by external factors or environmental agents (mutagens) that damage the DNA and lead to changes in the genetic code.
Causes:
Chemical mutagens: Substances that directly alter the structure of DNA, such as base analogs (which can replace natural bases) or alkylating agents (which can add bulky groups to DNA).
Physical mutagens: Forms of radiation such as ultraviolet (UV) light or ionizing radiation (X-rays, gamma rays) can cause breaks in the DNA strands or create thymine dimers.
Biological agents: Some viruses can insert their genetic material into the host genome, causing mutations.
Frequency: Induced mutations tend to have a higher mutation rate because the mutagens are external and can directly damage the DNA.
Germline vs. Somatic Mutations
1. Germline Mutations
Definition: Germline mutations occur in germ cells (sperm or egg cells) and are passed on to the next generation.
Consequences: Because germline mutations affect the DNA in reproductive cells, they can be inherited and passed on to offspring. These mutations may lead to hereditary diseases or genetic disorders.
Example: A mutation in a gene that is responsible for a genetic disorder like sickle cell anemia or cystic fibrosis could be passed down through generations.
2. Somatic Mutations
Definition: Somatic mutations occur in somatic cells, which are all the body cells except for germ cells.
Consequences: These mutations do not get passed to the next generation because they occur in non-reproductive cells. However, somatic mutations can lead to conditions like cancer if they affect genes that regulate cell growth and division.
Example: A mutation in a skin cell that leads to skin cancer or a mutation in a lung cell that causes lung cancer is a somatic mutation.
Explain how mutations can change the amino acid sequence of a polypeptide
Mutations can change the amino acid sequence of a polypeptide by altering the DNA sequence that encodes for the protein. This change in DNA can lead to a different mRNA sequence during transcription, which is then translated into a different amino acid sequence during translation. The effects depend on the type of mutation and where it occurs within the gene. Here’s how mutations can alter the amino acid sequence:
Types of Mutations That Affect Amino Acid Sequences
Point Mutations (Single Nucleotide Changes)
Silent Mutations: A change in the DNA sequence that does not affect the amino acid sequence. This usually happens because of the redundancy in the genetic code (where multiple codons can code for the same amino acid). For example, changing the codon from GAA to GAG still codes for glutamic acid.
Missense Mutations: A change in a single nucleotide that results in the coding of a different amino acid. For example, changing the codon from GAG (glutamic acid) to GTG (valine) leads to a different amino acid being inserted into the polypeptide chain, potentially altering the protein’s structure and function. An example is the mutation causing sickle cell anemia.
Nonsense Mutations: A point mutation that changes a codon into a stop codon, leading to premature termination of protein synthesis. This results in a shortened polypeptide that may be nonfunctional. For example, changing CAA (glutamine) to UAA (stop codon) will prematurely stop translation.
Frameshift Mutations (Insertions or Deletions of Nucleotides)
Insertion: Inserting one or more nucleotides into the DNA sequence shifts the reading frame of the codons during translation. This alters the amino acid sequence from that point onward. For example, inserting a single nucleotide into a sequence may change ATG (start codon) into ATTG, resulting in a completely different sequence of amino acids from that point on.
Deletion: Removing one or more nucleotides also shifts the reading frame, leading to a different amino acid sequence after the mutation. If one nucleotide is deleted, the entire sequence of codons following the deletion may encode different amino acids. For example, deleting a nucleotide in a codon like ATG could change it to AG, altering the amino acid encoded.
How Mutations Change the Amino Acid Sequence
DNA Sequence Change: Mutations in the DNA sequence (whether point mutations or frameshifts) lead to changes in the mRNA sequence during transcription.
mRNA Sequence: During translation, the mRNA is read in triplets of nucleotides (codons), each specifying a particular amino acid.
A missense mutation causes a different amino acid to be incorporated into the protein.
A nonsense mutation causes early termination, producing a truncated protein.
A frameshift mutation alters the reading frame, which can result in a completely different amino acid sequence.
Consequences of Mutations on Protein Function
Change in Structure: If the mutation alters an amino acid that is critical for the protein’s 3D structure (such as in the active site of an enzyme), it can affect the protein's function.
Nonfunctional Proteins: Premature stop codons or frameshift mutations often lead to incomplete or nonfunctional proteins.
Gain of Function: In some cases, mutations can lead to a protein with a new function, which might be beneficial or harmful.
Explain how creating mutants in genetic model systems can help us infer the function of genes
Creating mutants in genetic model systems helps us infer gene function by allowing scientists to observe the effects of specific genetic changes on an organism. By introducing mutations, researchers can:
Loss-of-function mutations: Inactivate genes to study the absence of function.
Gain-of-function mutations: Make genes overactive to observe abnormal traits.
Model organisms: Use organisms like fruit flies or mice to study gene function in a controlled environment.
Genetic complementation: Introduce a wild-type gene to rescue a mutant phenotype, confirming gene function.
Forward genetics: Induce random mutations and observe resulting phenotypes.
Reverse genetics: Deliberately mutate known genes to study the effects.
Conditional mutants: Control gene expression under specific conditions.
Gene interactions: Study how different mutations interact to understand gene pathways.
Define alleles and describe the types of alleles and their affects on gene function
Alleles are different versions of the same gene that exist at a specific location (locus) on a chromosome. They can vary slightly in their DNA sequence and lead to differences in the traits an organism expresses.
Types of Alleles:
Dominant Alleles:
Effect on gene function: A dominant allele expresses its trait even when only one copy is present (heterozygous). It can mask the effect of a recessive allele.
Example: The allele for brown eyes (B) is dominant over the allele for blue eyes (b), so individuals with at least one B allele will have brown eyes.
Recessive Alleles:
Effect on gene function: A recessive allele only expresses its trait when two copies are present (homozygous). Its effect is masked if a dominant allele is present.
Example: The blue eye allele (b) only results in blue eyes if an individual has two copies (bb).
Co-dominant Alleles:
Effect on gene function: Both alleles are expressed equally in a heterozygous individual. Neither allele is dominant or recessive.
Example: In blood type inheritance, an individual with one A allele and one B allele (AB) will have both A and B antigens on their red blood cells.
Incomplete Dominance:
Effect on gene function: The heterozygous phenotype is a blend of the two alleles, with neither allele being fully dominant over the other.
Example: In some flowers, crossing a red-flowered plant (RR) with a white-flowered plant (WW) results in pink flowers (RW).
Impact on Gene Function:
Dominant and recessive alleles affect gene expression by determining which trait is visible.
Co-dominant alleles and incomplete dominance lead to different expressions of traits in heterozygous individuals.
Mutations in alleles can also cause diseases or disorders by altering the function of the protein the gene encodes.
How do we determine the function of genes
We determine the function of genes through various experimental approaches:
Gene Mutations:
Loss-of-function mutations: Disrupting a gene to study its absence and observe resulting phenotypic changes.
Gain-of-function mutations: Activating a gene to see what happens when it’s overexpressed.
Gene Knockout/Knockdown:
Knockout: Removing or inactivating a gene in an organism to study the effects on development or health.
Knockdown: Reducing gene expression (e.g., using RNA interference) to observe changes in phenotype.
Gene Editing (CRISPR/Cas9):
Using CRISPR to precisely alter or delete genes to study their roles.
Gene Overexpression:
Introducing extra copies of a gene to see how increased expression affects the organism.
Gene Complementation:
Inserting a wild-type gene into a mutant organism to see if the phenotype is restored, confirming the gene’s function.
Reporter Genes:
Fusing a gene of interest with a reporter gene (like GFP) to track its expression and localization.
Gene Expression Analysis:
Measuring RNA levels (e.g., using qPCR or RNA-seq) to understand when and where a gene is active.
Protein Function Analysis:
Studying the protein product of a gene, including its activity, interaction with other proteins, and its role in cellular processes.
How do we characterize mutations
Duplication: A segment of DNA is copied and inserted elsewhere in the genome, potentially leading to gene overexpression.
Inversion: A segment of DNA is reversed, which may disrupt gene function.
Translocation: A segment of DNA is moved from one chromosome to another, potentially disrupting genes.
Note 
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