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level: Level 1

Questions and Answers List

level questions: Level 1

QuestionAnswer
DNA and proteins? Stages of Gene Expression?- The DNA inherited by an organism leads to​ specific traits by dictating the synthesis of proteins​ - Proteins are the links between genotype and phenotype​ - Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation​
Finding how genes dictate phenotypes- In 1902, British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions​ - He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme​ - Cells synthesize and degrade molecules in a series of steps, a metabolic pathway​ - Experiments were made that used mutants and found that they lacked different enzymes that were needed for synthesizing a certain molecule - The results of the experiments provided support for the one gene–one enzyme hypothesis​ - The hypothesis states that the function of a gene is to dictate production of a specific enzyme​ - Not all proteins are enzymes, so researchers later revised the hypothesis: one gene–one protein​, and after realizing that proteins are made of several polypeptides (polymer for protein, each has their own gene) they revised the hypothesis to the one gene - one polypeptide hypothesis - but it is common to refer to gene products as proteins rather than more precisely as polypeptides​
Transcription- Transcription is the synthesis of RNA using information in DNA​ - Transcription produces messenger RNA (mRNA)​ - One per gene - Think "A copy of something else" - Transcription is the first stage of gene expression​
Translation- Translation is the synthesis of a polypeptide (polymer for proteins), using information in the mRNA​ - Think: "Translation like languages, always happens after transcription" - Ribosomes are the sites of translation​ (Think: "Ribosomes are the Readers") - In prokaryotes, translation of mRNA can begin before transcription has finished​ - In a eukaryotic cell, the nuclear envelope separates transcription from translation ​ - Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA​ - Its like the Eukaryotic RNA is editing the information a bit - RNA processing allows mRNA to fit through the nuclear envelope. Bacteria RNA doesn't need this because everything is just floating in the cytoplasm. [reference image!]
Primary transcriptA primary transcript is the initial RNA transcript from any gene prior to processing​
Central dogmaThe central dogma is the concept that cells are governed by a cellular chain of command: ​ DNA → RNA → protein​
Codon (triplet code)- Codon = set of 3 nucleotides (like words in a sentence [which is the polypeptide chain] that ribosomes read) - The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words​ - The words of a gene are transcribed into complementary nonoverlapping three-nucleotide words of mRNA​ - These words are then translated into a chain of amino acids, forming a polypeptide​ - 1 gene = 1 polypeptide chain
Template strand- One of the two DNA strands, the template strand, provides a template for ordering the sequence of complementary nucleotides in an mRNA transcript​ - The template strand is always the same strand for a given gene​ - However, further along the chromosome, the opposite strand may be the template strand for a different gene​ - Specific DNA sequences associated with the gene direct which strand is used as the template​ - The mRNA molecule produced is complementary to the template strand​ - During translation, the mRNA base triplets, called codons, are read in the 5′ → 3′ direction​
Coding strand- The nontemplate strand is called the coding strand because the nucleotides of this strand are identical to the codons, except that T is present in the DNA in place of U in the RNA​ - Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide​
Reading frame- Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation​ - The genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid​ - Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced​
Is the genetic code universal?- yep, it is nearly universal, shared by the simplest bacteria and the most complex animals - Genes can be transcribed and translated after being transplanted from one species to another​
RNA polymerase- RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and joins together the RNA nucleotides​ - The RNA is complementary to the DNA template strand​ (they pair up) - RNA polymerase does not need any primer​ - RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine​ - RNA polymerase is more functionable than DNA polymerase - it can both open DNA strands and join RNA nucleotides
PromoterThe DNA sequence where RNA polymerase attaches is called the promoter​
TerminatorIn bacteria, the sequence signaling the end of transcription is called the terminator​
Transcription unitThe stretch of DNA that is transcribed is called a transcription unit​
Three stages of transcription- Initiation - Elongation - Termination
Transcription Initiation (start point, transcription factors, transcription initiation complex, TATA box)- Promoters signal the transcription start point and usually extend several dozen nucleotide pairs upstream of the start point​ - Transcription factors help guide the binding of RNA polymerase and the initiation of transcription​ - The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex​ - A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes​
Transcription Elongation- As RNA polymerase moves along the DNA, it untwists the double helix - Nucleotides are added to the 3′ end of the growing RNA molecule​ - ​A gene can be transcribed simultaneously by several RNA polymerases​
Transcription Termination- In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification​ - In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence​
What happens in RNA processing? cap and tail?- Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm​ - During RNA processing, both ends of the primary transcript are altered​ - Also, in most cases, certain interior sections of the molecule are cut out and the remaining parts spliced together​ - Each end of a pre-mRNA molecule is modified in a particular way​ (The 5′ end receives a modified nucleotide 5′ cap​, The 3′ end gets a poly-A tail​) - Functions of these modifications: They seem to facilitate the export of mRNA to the cytoplasm, They protect mRNA from hydrolytic enzymes​, They help ribosomes attach to the 5′ end​
RNA splicing- Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions​ - These are removed through RNA splicing ​
IntronsThe noncoding segments in a gene are called intervening sequences, or introns​ - intron = get spliced out, "int"ervening
ExonsThese regions are eventually expressed, usually translated into amino acid sequences - exons = "ex"pressed
Spliceosomes- The removal of introns is accomplished by spliceosomes​ - Spliceosomes consist of a variety of proteins and several small RNAs that recognize the splice sites​ - The RNAs of the spliceosome also catalyze the splicing reaction​ [don't need to worry about details]
RibozymesRibozymes are catalytic RNA molecules that function as enzymes and can splice RNA​ [don't need to worry about details]
Three properties of RNA enable it to function as an enzyme​- It can form a three-dimensional structure because of its ability to base-pair with itself​ - Some bases in RNA contain functional groups that may participate in catalysis​ - RNA may hydrogen-bond with other nucleic acid molecules​
alternative RNA splicing​- Some introns contain sequences that regulate gene expression and many affect gene products​ - Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing​ - This is called alternative RNA splicing​ - Consequently, the number of different proteins an organism can produce is much greater than its number of genes​ - this helps add more diversity
Domains- Proteins often have a modular architecture consisting of discrete regions called domains​ - In many cases, different exons code for the different domains in a protein​ - Exon shuffling may result in the evolution of new proteins by mixing and matching exons between different genes​ [don't need to worry too much about this]
Where does translation occur?Ribosomes (RNA gets processed and goes to ribosomes, which makes proteins)
Transfer RNA (tRNA)- A cell translates an mRNA message into protein with the help of transfer RNA (tRNA)​ - tRNAs transfer amino acids to the growing polypeptide in a ribosome​ - Each tRNA molecule enables translation of a given mRNA codon into a certain amino acid​ - Each carries a specific amino acid on one end​ - Each has an anticodon (opposite complementary part for codon) on the other end; the anticodon base-pairs with a complementary codon on mRNA​
Visuals for tRNA and anticodon structureCan be represented by a clover leaf structure or a sock-like structure (or a ribbon structure, but don't worry about that one) ~~ see image ~~
Accurate translation requires two instances of molecular recognition​- First: a correct match between a tRNA and an amino acid​ - Second: a correct match between the tRNA anticodon and an mRNA codon​
ribosomal RNAs (rRNAs)​- Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis​ - The two ribosomal subunits (large and small) are made of proteins and ribosomal RNAs (rRNAs)​ part of ribosome :)
Ribosome has three binding sites for tRNA​- The P site holds the tRNA that carries the growing polypeptide chain​ (polypeptide holding site) - The A site holds the tRNA that carries the next amino acid to be added to the chain​ (they get dropped off) - The E site is the exit site, where discharged tRNAs leave the ribosome​ /look at image + understand process ~! /
Three stages of translation- Initiation - Elongation - Termination
Translation Initiation- The initiation of translation starts when the small ribosomal subunit binds with mRNA and a special initiator tRNA​ - The initiator tRNA carries the amino acid methionine​ - Then 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​
"AUG"- Start amino acid - mRNA
"Met"- name of the codon that is complementary to AUG - UAC - tRNA
Translation Elongation- During elongation, amino acids are added one​ by one to the C-terminus of the growing chain​ - Each addition involves proteins called elongation factors - Elongation occurs in three steps: codon recognition, peptide bond formation, and translocation​ - Empty tRNAs released from the E site return to the cytoplasm, where they will be reloaded with the appropriate amino acid​​
Translation Termination- Elongation continues until a stop codon in the mRNA reaches the A site ​ - The A site accepts a protein called a release factor​ - The release factor causes the addition of a water molecule instead of an amino acid​ - this is because the release factor uses hydrolysis (breaking) to release the polypeptide, and that type of reaction has water as a byproduct - This reaction releases the polypeptide, and the translation assembly comes apart​
Post-Translation polypeptide modification- Polypeptide chains are modified after translation or targeted to specific sites in the cell​ - During synthesis, a polypeptide chain begins to coil and fold spontaneously into a specific shape: a three-dimensional molecule with secondary and tertiary structure - During synthesis, a polypeptide chain begins to coil and fold spontaneously into a specific shape: a three-dimensional molecule with secondary and tertiary structure​​ - Post-translational modifications may be required before the protein can begin doing its particular job in the cell​
Free and Bound Ribosomes? Cytosol?- Two populations of ribosomes are evident in cells: free ribosomes (in the cytosol) and bound ribosomes (attached to the ER)​ - Free ribosomes mostly synthesize proteins that function in the cytosol ​ - Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell​. A majority of ribosomes are on the rough ER (bound ribosomes) - Ribosomes are identical and can switch from free to bound​ - Polypeptide synthesis always begins in the cytosol​ - Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER​
Overall Transcription + Translation imageSee image, keep in mind: - Each part and process - RNA polymerase = ca unzip and match base pairs (its the multitasker) - want Exons - Introns get spliced out - pre-mRNA = before getting processed and modified - A = adding amino acids - P = polypeptide (hold them) - E = exit - polypeptide chain (the string of shapes) shifts as anticodons go in and out in order to stay in the middle - AUG: start codon - hydrolysis is used to get the polypeptide chain out of the "P" area, with a water molecule as a byproduct
Overall Gene DefinitionA gene can be defined as a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule​
Mutations? Point mutations?- Mutations are changes in the genetic information of a cell ​ - Point mutations are changes in just one nucleotide pair of a gene​ (two categories: Single nucleotide-pair substitutions​, Nucleotide-pair insertions or deletions​) - The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein​ - If a mutation has an adverse effect on the phenotype of the organism, the condition is referred to as a genetic disorder or hereditary disease​ - Different mutations can occur in different ways
Frameshift mutation​- Insertions and deletions are additions or losses of nucleotide pairs in a gene​ - These mutations have a disastrous effect on the resulting protein more often than substitutions do ​ - Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation​ - Insertions or deletions outside the coding part of a gene could affect how the gene is expressed​
Spontaneous mutationsSpontaneous mutations can occur during errors in DNA replication or recombination​
Mutagens- Mutagens are physical or chemical agents that can cause mutations​ - Chemical mutagens fall into a variety of categories​ - Most carcinogens (cancer-causing chemicals) are mutagens, and most mutagens are carcinogenic​
CRISPR-Cas9- Biologists who study disease-causing mutations have sought techniques for gene editing–altering genes in a specific way​ - The powerful technique called CRISPR-Cas9 is transforming the field of genetic engineering​ - In bacteria, the protein Cas9 acts together with a guide RNA to help defend bacteria from viral infection​ - The Cas9 protein will cut any sequence to which it is targeted ​ - Scientists can introduce a Cas9–guide RNA complex into a cell they wish to alter​ - The guide RNA is engineered to target a gene​ - Can disable (or "knock out") genes to see what the gene does in an organism for studies - Can be used to find the causes of diseases - Can treat genetic diseases (introduce a normal copy of the gene to be corrected, allows for edits to the defective gene and corrections) - Biologists need to be cautious though, there may be unintended effects on other genes and also ethical dilemmas