DNA & Protein Synthesis

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课程笔记

The Genome and Proteome

The genome is the complete set of genes present in a cell.
The full genome is present in every cell of an organism, but not every gene is expressed; the genes expressed depend on the cell type.
The proteome is the full range of proteins that a cell can produce.
The proteome is usually larger than the genome due to post-translational modification of proteins (often in the Golgi apparatus).
Each gene can produce multiple different proteins via alternative splicing.
Processes such as alternative splicing and protein modification increase the complexity of the proteome from the genome.

Structure of RNA

RNA is a polynucleotide made of many nucleotides linked in a long chain.
RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose) and the bases adenine, guanine, cytosine and uracil (never thymine).
RNA molecules are single-stranded; each strand has a sugar-phosphate backbone and exposed unpaired bases.
mRNA is a transcript copy of a gene that encodes a specific polypeptide; it carries the genetic code from DNA in the nucleus to ribosomes.
tRNA has a folded shape and is single-stranded, but hydrogen bonds between some complementary bases hold the strand together in certain regions.
tRNA has an anticodon complementary to a specific triplet (codon) on mRNA, and a site for a specific amino acid.

Transcription

Protein synthesis occurs in two stages: transcription (DNA is transcribed to produce mRNA) and translation (mRNA is translated to produce an amino acid sequence).
Transcription occurs in the nucleus; a section of DNA unwinds and hydrogen bonds break, catalysed by helicase, exposing the gene.
Free activated RNA nucleotides pair with complementary bases on the template strand via hydrogen bonds.
The non-template (non-transcribed) strand has the same base sequence as the mRNA transcript, but with uracil replacing thymine.
RNA polymerase bonds the sugar-phosphate groups of RNA nucleotides to form the sugar-phosphate backbone of mRNA.
RNA polymerase moves along the template strand in the 3' to 5' direction, so mRNA grows in the 5' to 3' direction.
When transcription is complete, hydrogen bonds between mRNA and DNA break, the DNA re-forms its double helix, and mRNA leaves the nucleus via a nuclear pore.

Eukaryotic and Prokaryotic Transcription

Eukaryotic genomes contain non-coding DNA: non-coding multiple repeats between genes and introns within genes.
Eukaryotic transcription produces pre-mRNA, which contains both introns and exons.
Splicing removes non-coding sections (introns) and joins coding sections (exons) before the pre-mRNA exits the nucleus.
The resulting mature mRNA contains only exons and exits the nucleus to join a ribosome for translation.
Alternative splicing joins different combinations of exons from the same pre-mRNA, so a single eukaryotic gene can code for more than one polypeptide.
In prokaryotes, transcription produces mRNA directly from the DNA template because prokaryotic genes do not contain introns; there is no pre-mRNA stage.
In prokaryotes, transcription and translation are coupled because both occur in the cytoplasm, allowing rapid protein synthesis.

Translation

Translation occurs in the cytoplasm; mRNA attaches to a ribosome after leaving the nucleus.
Free tRNA molecules in the cytoplasm bind with their specific amino acids and bring them to the mRNA on the ribosome.
The anticodon on each tRNA pairs with a complementary codon on the mRNA molecule.
Two tRNA molecules fit onto the ribosome at any one time, bringing their amino acids side by side.
A peptide bond forms between the two amino acids; this requires energy in the form of ATP, provided by mitochondria.
Translation continues until a stop codon on mRNA is reached, signalling termination; the completed amino acid chain forms the final polypeptide.

The Genetic Code and Amino Acid Sequences

The four RNA bases (A, U, C, G) can form 64 different codons, but only 20 amino acids are coded for, so the genetic code is degenerate.
Multiple mRNA codons can encode the same amino acid (e.g., UGU and UGC both code for cysteine), so a change in the genetic code does not necessarily change the amino acid sequence.
The START codon (AUG, coding for methionine in eukaryotic cells) initiates translation at the correct location.
STOP codons (e.g., UAA) terminate translation and do not code for any amino acid.
The genetic code is non-overlapping: each base is read only once in the codon it is part of.
Each amino acid is coded for by a triplet (codon) of 3 nucleotides; the last codon is a STOP codon that does not code for an amino acid.
To calculate the number of amino acids from coding mRNA nucleotides: divide by 3, then subtract 1 for the STOP codon.
To derive an amino acid sequence, convert the DNA template sequence into mRNA codons using complementary base pairing, then use a codon table to translate each codon.

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练习题

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1.What is meant by the term genome?
Easy
- AThe full range of proteins that a cell can produce
- BThe complete set of genes present in a cell
- CAll the mRNA molecules present in a cell at a given time
- DThe complete set of enzymes coded for by a cell
2.Which statement about the proteome is correct?
Easy
- AThe proteome is usually smaller than the genome
- BThe proteome is always identical in every cell of an organism
- CThe proteome is usually larger than the genome because of post-translational modification and alternative splicing
- DThe proteome contains only proteins coded for by exons
3.Which of the following are true of RNA nucleotides? (select all that apply)
Medium
- AThey contain the pentose sugar ribose
- BThey contain the nitrogenous base thymine
- CThey contain the nitrogenous base uracil
- DThey contain the nitrogenous base adenine
- EThey are always double-stranded
4.tRNA is a single-stranded molecule that is folded into a shape held together by hydrogen bonds between some complementary bases.
Easy
True or false?
5.The proteome of a cell is always smaller than its genome.
Easy
True or false?
6.Which enzyme is responsible for forming the sugar-phosphate backbone of mRNA during transcription?
Easy
- ADNA polymerase
- BHelicase
- CRNA polymerase
- DLigase
7.What is the role of RNA polymerase in transcription?
Medium
- AIt breaks hydrogen bonds between DNA strands
- BIt joins RNA nucleotides together to form the sugar-phosphate backbone of mRNA
- CIt joins amino acids together to form a polypeptide
- DIt removes introns from pre-mRNA
8.Which of the following correctly describes a difference between transcription in prokaryotic and eukaryotic cells?
Medium
- AProkaryotic transcription produces pre-mRNA that requires splicing
- BEukaryotic transcription produces mRNA directly without a pre-mRNA stage
- CProkaryotic transcription produces mRNA directly because prokaryotic genes do not contain introns
- DEukaryotic transcription occurs in the cytoplasm

复习笔记

## The Genome & Proteome - **Genome** = the complete set of genes present in a cell. The full genome is present in every cell, but not every gene is expressed — which genes are expressed depends on cell type. - **Proteome** = the full range of proteins a cell can produce. It is usually **larger than the genome** because of post-translational modification (often in the Golgi apparatus) and because each gene can produce multiple proteins via **alternative splicing**. ## The Structure of RNA - RNA is a **polynucleotide** — many nucleotides linked in a long chain. - RNA nucleotides contain the bases **A, G, C and uracil (U)** — never thymine (T) — and the pentose sugar **ribose** (not deoxyribose). - RNA molecules are **single-stranded**: a sugar-phosphate backbone with exposed unpaired bases projecting sideways. - **mRNA** is a transcript copy of a gene that encodes a specific polypeptide; it carries the genetic code from DNA in the nucleus to the ribosomes. - **tRNA** has a folded shape; despite looking double-stranded it is single-stranded, held together in regions by hydrogen bonds between complementary bases. It has an **anticodon** (triplet of unpaired bases) at one end and a site for a specific amino acid at the other. There are at least 20 types. ## Transcription - Occurs in the **nucleus**. A section of DNA unwinds — hydrogen bonds between complementary base pairs break ('unzipping'), catalysed by **helicase**. - Free activated RNA nucleotides pair (via hydrogen bonds) with complementary DNA bases on the **template strand**. The other strand is the **non-template (non-transcribed) strand**; its base sequence is the same as the mRNA transcript, but with uracil replacing thymine. - **RNA polymerase** bonds the sugar-phosphate groups together to form the mRNA backbone. It moves along the template strand **3' to 5'**, so mRNA grows **5' to 3'**. - mRNA leaves the nucleus via a pore in the nuclear envelope. ## Eukaryotic & Prokaryotic Transcription - Eukaryotic genomes contain non-coding DNA: **multiple repeats** between genes and **introns** within genes. - Eukaryotes transcribe the whole gene to make **pre-mRNA** (introns + exons). Before leaving the nucleus, **splicing** removes non-coding sections and joins coding sections (exons) — this mature mRNA carries only exons. - **Alternative splicing**: exons can be spliced in different combinations from the same pre-mRNA, so one gene can code for more than one polypeptide. - Prokaryotes: **no pre-mRNA stage** (genes have no introns, so no splicing); transcription produces mRNA directly. Transcription and translation are **coupled** — translation can begin while transcription is in progress (both occur in the cytoplasm), allowing rapid protein synthesis. ## Translation - Occurs in the **cytoplasm** at the **ribosome**. - tRNA molecules bind their specific amino acids and bring them to the mRNA. The anticodon pairs with a complementary **codon** on mRNA. - Two tRNA molecules fit on the ribosome at once, bringing amino acids side by side; a **peptide bond** forms between them (requires **ATP**, provided by mitochondria). - Continues until a **stop codon** is reached; the amino acid chain then forms the final polypeptide. ## Nucleic Acid & Amino Acid Sequence Comparison - 4 bases form **64 codons** but only **20 amino acids** — so the genetic code is **degenerate** (e.g. UGU and UGC both code for cysteine). - **START codon** = AUG, codes for methionine in eukaryotic cells, initiates translation. **STOP codons** (e.g. UAA) terminate translation and code for no amino acid. - The code is **non-overlapping** — each base is read once. - Each amino acid is coded for by a triplet of 3 nucleotides; the last codon is a STOP codon. - **Number of amino acids** = (coding nucleotides ÷ 3) − 1. - To derive an amino acid sequence: convert DNA to mRNA codons by complementary base pairing, then read the codon table left to right.

Genome: The complete set of genes present in a cell.
Proteome: The full range of proteins that a cell can produce.
Transcription: DNA is transcribed, and an mRNA molecule is produced.
Translation: mRNA is translated, and an amino acid sequence is produced.
Template strand: The strand of the DNA molecule that is transcribed.
Non-template (non-transcribed) strand: The strand of the DNA molecule that is not transcribed; its base sequence is the same as the mRNA transcript, but with uracil replacing thymine.
RNA polymerase: The enzyme that bonds the sugar-phosphate groups of RNA nucleotides together to form the sugar-phosphate backbone of the mRNA molecule.
Pre-mRNA: The molecule produced during transcription in eukaryotic cells; it contains the introns and exons of a certain gene.
Splicing: The non-coding sections are removed and the coding sections are joined together.
Alternative splicing: Different combinations of exons are joined together from the same pre-mRNA transcript, meaning a single eukaryotic gene can code for more than one polypeptide chain.
mRNA: A transcript copy of a gene that encodes a specific polypeptide; it carries the genetic code from DNA in the nucleus to the ribosomes.
tRNA: A folded, single-stranded RNA molecule with an anticodon at one end and a site for a specific amino acid at the other; it brings amino acids to the mRNA during translation.
Anticodon: A triplet of unpaired bases on a tRNA molecule, complementary to a specific triplet of bases on an mRNA molecule.
Codon: A triplet of bases on an mRNA molecule that codes for an amino acid.
Degenerate (genetic code): Multiple mRNA codons can encode the same amino acid; e.g. UGU and UGC both code for the amino acid cysteine.
START codon: Marks the start of the protein and initiates translation from the right location; always the amino acid methionine in eukaryotic cells, coded for by the codon AUG.
STOP codons: Cause translation to terminate at the end of the protein and do not code for any amino acids, e.g. UAA.
Non-overlapping (genetic code): Each base is only read once in the codon that it is part of.

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