| 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 transcript | A primary transcript is the initial RNA transcript from any gene prior to processing |
| Central dogma | The 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 |
| Promoter | The DNA sequence where RNA polymerase attaches is called the promoter |
| Terminator | In bacteria, the sequence signaling the end of transcription is called the terminator |
| Transcription unit | The 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 |
| Introns | The noncoding segments in a gene are called intervening sequences, or introns
- intron = get spliced out, "int"ervening |
| Exons | These 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] |
| Ribozymes | Ribozymes 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 structure | Can 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 image | See 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 Definition | A 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 mutations | Spontaneous 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 |
