CHAPTER 1: PROTEIN SYNTHESIS Flashcards
what are nucleic acids
- biomolecules found in all organisms
- two kinds:
- DNA: deoxyribose nucleic acid
- RNA: ribonucleic acid
- provides information and is involved in protein synthesis
- are polymers, made up of monomers
nucleotide
is a monomer of DNA and RNA
- bond between adjacent nucleotides is a phosphodiester bond
- each nucleotide has
- a 5 carbon (pentose) sugar (deoxyribose or ribose)
- a phosphate
- a nitrogenous base
DNA vs RNA
- both are made of nucleotides
- DNA
- double stranded
- sugar: deoxyribose
- adenine, guanine, thymine, cytosone
- RNA
- single stranded (usually)
- sugar: ribose
- adenine, guanine, uracil, cytosine
DNA
- codes for proteins : vital for structure and function of an organism
- passed on/replicated in cell division
- runs anti-parallel
- 5’ end is phosphate end
- 3’ end is hydroxyl end of sugar
what is mRNA
messenger RNA
- carries genetic message from DNA in the nucleus to ribosomes
- involved in transcription and translation
what is rRNA
ribosomal RNA
- works with other proteins to make ribosomes in cytosol
- Subunits that allow for the interaction of mRNA and tRNA. Allows for the growing peptide chain to be created.
what is tRNA
transfer RNA
- carry SPECIFIC amino acids to ribosomes to be used to construct proteins
DNA code is…
- is universal and redundant
- universal: essentially the same across all organisms - bacteria, plants, animal
-
redundant: different triplets of bases can code for the same amino acid
- provides an element safety to ensure that not all mutations result in abnormal proteins being created.
- unambiguous → the same codon will always code for the same amino acid
steps in transcription
- RNA polymerase, attaches to a specific promoter sequence of DNA in the upstream region of the template strand
- DNA of the gene unwinds and exposes the bases of the template strand.
- template strand guides the building of a complementary copy of the mRNA sequence
- RNA polymerase moves along DNA template in a 3’to 5’direction.
- as it moves, complementary nucleotides are brought into place and joined to form an RNA chain → added to the growing 3’ end
- after the RNA polymerase moves past the coding region and into the downstream region of the gene, transcription stops and the pre-mRNA is released from the template.
template strand is not the same as the coding strand
coding strand is the complementary strand of DNA (not used as the template in making mRNA)
would have the same sequence as the mRNA with the exception of Ts -> Us
RNA processing
- turns pre-mRNA to mRNA
- capping of the 5’ end with a methyl cap
- protects mRNA from degradation
- help attach mRNA to ribosome
- addition of a poly-A tail on the 3’ end
- helps protect mRNA from degradation
- facilitates export of mRNA from nucleus
- introns are removed and exons are spliced together
- introns: sections that aren’t expressed → don’t provide code for amino acid
- exons: sections that are expressed → provides the code for amino acids
- capping of the 5’ end with a methyl cap
steps in translation
- mRNA moves to the ribosome, where it is read in groups of three known as codons.
- amino acids are brought to the ribosomes by tRNA. At one end of each tRNA molecule are three bases that make up an anticodon. At the other end is a region that attaches to a specific amino acid
- The ribosome continues to move along the mRNA and tRNA molecules to deliver the appropriate amino acid. As amino acids are added, they are joined by peptide bonds to form a polypeptide chain
- codon representing STOP is reached and the polypeptide chain is released from the ribosome.
the stop codon doesn’t produce an amino acid
promoter region
- short DNA segment in the upstream region of template strand
- contains particular base sequences → TATA box (A’s and T’s bases)
- where RNA polymerase binds to initiate transcription
prokaryotic cells - gene structure
have operons and operators
operon
- related genes found in a cluster on a chromosome, under the control of a single promoter
- transcription and translation occurs all at once so more than one protein is created
- operon is transcribed as a single entity with one long mRNA strand being produced
operator
- short DNA segment found between promoter and gene to be transcribed
- provides a binding site for a repressor to prevent transcription
structural genes
code for proteins that become part of the structure or function of cells
regulatory genes
- encodes for proteins that control the expression of other genes (known as transcription factors)
- example are repressors
- act in 2 ways
- directly:
- produces DNA binding proteins that binds to regions in DNA near genes to directly turn them on or off
- indirectly:
- produces signalling proteins that bind to cell receptors and trigger a series of reactions that lead to gene being turned on or off
- directly:
what is tryptophan
- an amino acid (trp)
- bacteria e-coli can ingest it from surroundings or produce it when required
- trp synthesis uses enzymes encoded by 5 genes (trp operon)
presence of tryptophan - repression
- trp binds to the repressor protein causing a configurational change in its shape → allows it to be active
- enables the repressor to bind to the operator
- RNA polymerase is unable to bind to the promoter and transcription does not occur
- operon is turned off
- trp isn’t made
absence of tryptophan - repression
- repressor is unable to bind to the operator (in an inactive form)
- rna polymerase can bind to the promoter and start transcription of the structural genes
- operon is on
- trp can be made
attenuation
- leader sequence is located before the coding region on an operon
- codes for a protein contain 14 amino acids
- leader mRNA sequence has 4 regions that can form different base paired ‘hairpin’ structures → terminator
- these can fold in different ways
- the active tryptophan repressor that blocks RNA polymerases access to the operator and the downstream structural genes is not 100% effective.
- It will occasionally disconnect and allow RNA polymerase to access and transcribe the structural genes and therefore produce tryptophan.
- To overcome this the LEADER SECTION (trp L) AND ATTENUATORS (hair pin folds) are used.
When trp is high the ribosome does not need to pause in the trp L region The allows a terminator hairpin loop to form between the 3 /4 region. The hairpin causes the ribosome to disengage from the mRNA and trp is not produced.
- when cell has a lot of trp, mRNA is translated quickly and the mRNA folds into a terminator hairpin
- ribosome does not need to pause in the trp L region
- allows a terminator hairpin loop to form between the 3 /4 region
- this hairpin causes the ribosome to disengage from the mRNA and trp is not produced.
- transcription stops and no enzymes to make more trp are made
-
the genes are not transcribed as they are after the leader sequence (transcription stops at the leader section)
- terminator hairpin loops causes the RNA polymerase to detach from the DNA
- when the cell is low in trp, the mRNA is translated slowly and the mRNA folds into an anti-terminator
- Translation occurs just behind transcription
- te ribosome will pause at the TWO ADJACENT trp codons to wait for tryptophan tRNA to become available.
- During this wait the mRNA folds to create a hair pin loop (2/3 region).
- This loop allows the ribosome to complete translation and produce trp.
- transcription can continue and the cell is able to make more trp
NOTE IN PROKARYOTES, TRANSCRIPTION AND TRANSLATION OCCUR SIMULTANEOUSLY (NO SEPARATE PROCESSES BC THERE IS NO NUCLEUS)
why does gene regulation need to occur
- by expressing only the genes that are required, organisms can conserve their energy and resources
- also enables cells to make substances required when none are available from the environment
amino acid structure
- amino acids vary only in the R-group
- this gives amino acids its chemical properties
- hydrophobic, hydrophilic, positively charged, negatively charged
- the amino group and carboxyl group remains the same
condensation polymerisation
- the process of joining amino acids together
- condensation → water/smaller
- polymerisation → making a polymer
- amino acids join using energy and water is released
- carboxyl groups bind with the amino group
- OH of carboxyl group joins w/ H of the amino group to form water
why is the shape of a protein important to its function
the structure of a protein is important as the shape of a protein allows it to perform its particular role or function
primary structure
- linear sequence of amino acids linked together
- called a polypeptide chain
- NOT FUNCTIONAL
secondary structure
- consists of alpha helices
- beta pleated sheets
- random coils
- the folding and coiling is caused by interactions of the R-group
tertiary structure
- irregular 3D folding held together by ionic or hydrogen bonds forming a complex shape
- involves the way the secondary structures fold in respect to each other
- the shape is held in place by chemical bonds
- A FUNCTIONAL STRUCTURE
3D STRUCTURE COMPOSED OF SECONDARY STRUCTURES
quaternary structure
the bonding of two or more polypeptide chains
example of proteins and their roles
- enzymes: speed up (catalyse) reactions
- antibodies: fight pathogens in your body
- haemoglobin: in blood cells → carries oxygen and carbon dioxide
proteome
the complete array of proteins produced by a single cell or an organism in a particular environment
why is it useful to study proteins together
- It is useful to study proteins together as many influence other proteins.
gene regulation
the process of controlling a gene’s expression, turning genes on or off
polymers
- a large substance made up of smaller subunits
- eg. DNA (nucleotides) and proteins (amino acids)
nucleus
role in synthesis and export of proteins
codes for the proteins (makes mRNA) which goes to the ribosome on the rough endoplasmic reticulum
rough endoplasmic reticulum
role in synthesis and export of proteins
the ribosome uses the mRNA code to make a protein, which is then folded and modifies in the rough endoplasmic reticulum
transport vesicles
role in synthesis and export of proteins
the proteins are placed into a transport vesicle which then moves to the golgi apparatus
golgi apparatus + secretory vesicles
role in synthesis and export of proteins
the golgi apparatus further modifies the proteins and packages it into a secretory vesicle for export out of the cell through exocytosis
plasma membrane
role in synthesis and export of proteins
the secretory vesicles move to the plasma membrane and expel its contents through exocytosis
exocytosis
- exocytosis causes the plasma membrane gets slightly larger
- the secretory vesicle fuses with the plasma membrane
endocytosis
- Products produced from other cells or molecules that are necessary for effective cellular communication need to enter the cell.
- To do this a small portion of the cellular membrane is pinched off.
- The vesicle is then broken down by a lysosome to free the cellular product.
vesicle transport
- All internal transport within the cell requires vesicles.
- All vesicles are composed of phospholipids.
- All vesicles are composed of a double layer of phospholipids.
- The double layer allows for the creation of an internal aqueous environments.
how can the same gene code for different proteins
- exon shuffle: exons can be shuffled around to have diff orders
- alternate folding: can fold in different ways in the ER
- golgi modification: golgi modifies the exons
- different post-transcriptional modification or modifications of the pre-mRNA
- different exons are joined or alternative splicing
- different nucleotide sequences/mRNA sequences, code for a different protein
- post-translational changes to the protein; for example, alternative folding
advantage and disadvantage of using an operon
advantage
* operons allow protein synthesis to be controlled in response to the needs of a cell
* By producing proteins only when they are required, the cell can conserve energy and resources
* multiple genes with similar functions are transcribed at the same time, resulting in the same number of proteins being produced
* increases the number of genes on a chromosome due to less promoters
disadvantage
* if mutations occur (in regulatory gene, promoter, operator or leader, it can cause none of the genes to be expressed which can result in cell death
eukaryotic gene structure
- Flanking regions
- Coding region
- Upstream and downstream
- Direction of transcription
why we have introns and exons
- The final mRNA can have different sequences of mRNA
- provide more variety through exon splicing
