Protein Synthesis Flashcards
DNA Structure
Deoxyribonucleic acid (DNA) is a double-stranded helix made of chemical building blocks called nucleotides. Nucleotides are made of sugar (deoxyribose), phosphate, and nitrogenous bases.
Nitrogenous Bases
There are four nitrogenous bases:
Adenine
Thymine
Cytosine
Guanine
A pairs with T and C pairs with G—this is the complementary base-pairing rule. This is due to the different number of hydrogen bonds needed for each pair. A and T bond with two hydrogen bonds, C and G bond with three hydrogen bonds.
Adenine and guanine are purines (contain two nitrogen/oxygen compounds) and are bigger. Thyme and cytosine are pyrimidines (contain one nitrogen/oxygen compound) and are smaller.
DNA: The Blueprint for Organisms
DNA is the set of instructions for initiating and maintaining life processes. DNA carries information for producing specific proteins in the sequence of nucleotide bases found in specific stations called genes. Different versions of genes (alleles) carry information for producing different proteins. Different proteins lead to different visible traits (phenotypes).
DNA is found inside the cell’s nucleus. It is usually coiled into long strands called chromatin (except during S phase, when DNA replication occurs).
Definitions
Gene - section of DNA that codes for a specific protein
Allele - alternate version of a gene
Genotype - collection of an organism’s genes/alleles/possible proteins
Phenotype - physical characteristics of an organism
Gene expression - the process by which the instructions in our DNA are converted into a functional protein product, which leads to specific phenotypes
Ribosomes
Ribosomes are made of 2 subunits (large and small) that come together. The small subunit decodes genetic messages, and the large subunit activates peptide bond formation. Each subunit is made of ribosomal RNA (rRNA) and protein. The ribosome’s function is to produce polypeptide chains/proteins (long chains of amino acids) by reading genetic instructions. It is found on the rough endoplasmic reticulum or free-floating in the cytoplasm.
Ribosomes get the information they need to produce proteins from the DNA in the nucleus. Each protein/polypeptide chain is made using coded information from the DNA and the available amino acids.
Transporting Genetic Information
DNA is a very large and important molecule as it holds all the genetic information inside a cell. Any damage to the DNA can be very harmful for the organism, so the DNA must be kept safe inside the nucleus at all times. But we need the information to make the proteins in the ribosomes. DNA is also more stable. To get the information from nucleus to ribosomes in the cytoplasm, DNA is copied into RNA.
RNA
Ribonucleic acid (RNA) is single-stranded. RNA molecules are short ‘copies’ of single genes on the DNA strand that can leave the nucleus but degrade quickly.
In RNA, thymine is replaced with uracil (U). A pairs with U with two hydrogen bonds just like T—this prevents genetic information from changing.
There are three types:
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- Ribosomal RNA (rRNA)
Comparison - DNA vs. RNA
Structure - DNA is double-stranded, RNA is single-stranded
Sugar - DNA has deoxyribose sugar, RNA has ribose sugar
Bases - DNA (A T C G), RNA (A U C G)
Length - DNA is 20,000 genes long, RNA is 1 gene long
Location - DNA is in the nucleus, RNA is in the nucleus and the cytoplasm
Purpose - DNA holds all the genetic information for life processes (MRS C GREN), RNA carries genetic information out of the nucleus for protein synthesis
Proteins
Proteins play many roles in the structure and function of organisms. They are considered the building blocks of life on Earth. They are the basis of living tissues, catalyse reactions as enzymes, transport crucial molecules around the body such as oxygen, transport messages from cell to cell as hormones, etc.
Proteins are polymers (long chains) of amino acids that have specific shapes and functions linked to their shape. Functional units made up of one or more polypeptide chains. The expression of the genotype (the phenotype) is due to the protein coded for by the gene.
Amino Acids
These are the building blocks of protein. There are 20 amino acids found in the body—11 are made by the body, but the other 9 can’t be so they must come from diet. Amino acids are held together in long chains by peptide bonds. These chains are called peptide or polypeptide chains.
(Picture the structure here)
All amino acids have this same structure; the only thing that changes is the R group (side chain) which makes each amino acid unique.
Different R groups have different chemical properties, which affects the bonds that they make with each other (e.g. acidic or basic, hydrophobic or hydrophilic). The different properties cause different shapes of proteins when R groups interact with each other.
Levels of Protein Structure
There are 4 levels - primary, secondary, tertiary and quaternary.
Primary Structure (1º):
This is a simple polypeptide chain—amino acids connected by peptide bonds.
Secondary Structure (2º):
This is the initial folding of the polypeptide chain into alpha-helix coils or beta-pleated sheets due to hydrogen bonds between amino acids.
Tertiary Structure (3º):
The polypeptide chain folds further into a complex 3D shape due to more interactions between amino acids (e.g. bonds, electrostatic attraction, etc.). This can be the final shape for some proteins.
Quaternary Structure (4º):
Multiple polypeptide chain subunits already folded into their tertiary shapes combine together to make a large 3D shape held together by bonds between amino acids on the different chains. This can be the final shape for some proteins.
Shape of Proteins
The final shape of a protein (3º or 4º) is dependent on the primary structure: the specific order of amino acids. Folding of proteins into their correct structure is key to their function (shape of protein = function). If the order of amino acids is incorrect, the protein will not fold correctly. Failure to fold properly produces inactive or toxic proteins that malfunction and cause a number of diseases. If one amino acid in a protein sequence is changed, the protein could change its function or become non-functional.
Globular Proteins:
3º and 4º structure is critical to the function. The polypeptide chains fold into a spherical shape. They are soluble and so are easily transported throughout the body.
Functions are catalytic, signalling and communication, and transport.
Fibrous Proteins:
1º and 2º structure is critical to the function. Long strings of parallel polypeptide chains have high strength. These are used for structural support and movement.
Protein Synthesis Definition
This is the creation of a protein in a cell using transcription and translation.
Transcription - the creation of an mRNA transcript from DNA
Translation - the creation of a polypeptide chain from an mRNA transcript using a ribosome
Protein Synthesis - Transcription
This is the process of converting the DNA template strand into an mRNA transcript. It occurs in the nucleus. The molecules involved are the DNA template strand, RNA polymerase, and RNA nucleotides (A, U, C, and G).
Transcription has three stages—initiation, elongation, and termination.
Initiation:
RNA polymerase attaches to the promoter region of the gene and unwinds the DNA double helix to expose the nitrogenous bases. The promoter region is a sequence of DNA that is used to signal/initiate the start of transcription. The template strand is copied during transcription.
Elongation:
RNA polymerase moves down the coding region of the DNA template strand, reading the exposed DNA bases and attaching free RNA nucleotides using the complementary base-pairing rule. The mRNA strand produced is complementary to the template strand but identical to the coding strand. RNA polymerase reads 3’ to 5’, so the mRNA is built 5’ to 3’.
Termination:
RNA polymerase reaches the terminator region of the gene, at which point it detaches and releases the mRNA strand (and the DNA double helix rewinds). The newly synthesised mRNA strand leaves the nucleus via the nuclear pore and into the cytoplasm where the ribosomes are.
Purpose of Transcription
- To make a copy of the genetic instructions that can be damaged, used, or destroyed without permanently altering the DNA.
- Take genetic instructions out of the nucleus into the cytoplasm where ribosomes are located for protein synthesis.
- Make multiple copies of a single protein-producing gene to allow simultaneous production of many protein products at once.
The Genetic Code - Triplets, Codons, Anticodons
DNA nucleotides are organised into groups of three called triplets, which are then transcribed into groups of three RNA nucleotides called codons. In tRNA, the groups of three are called anticodons. Each different codon tells the ribosome which amino acid to use when it is making the protein. The sequence of bases (A, U, C, G) determines the order of amino acids. The genetic code is read codon by codon.
The ribosomes need to know when to start and stop reading the RNA strand, otherwise the ribosome could start anywhere and make a protein that is non-functional. So the RNA has START and STOP codons to signal when protein synthesis begins and ends.
- START codon in mRNA → AUG, codes for methionine
- STOP codon in mRNA → UAA, UAG, and UGA, doesn’t code for any amino acids
Triplets are used because we need to provide unique combinations for the 20 unique amino acids. Having two-base codons would not give enough combinations with the 4-base alphabet to code for 20 amino acids.
Protein Synthesis - Translation
This is the process of converting the mRNA transcript made during transcription into a polypeptide chain. A polypeptide chain is built from amino acids, guided by the sequence of codons on the mRNA. It occurs via ribosomes in the cytoplasm.
The molecules involved are mRNA, tRNA (which carries amino acids), ribosomes (made from rRNA), and amino acids.
Translation also has the same three stages; initiation, elongation, and termination.
tRNA:
The ribosome ‘reads’ the mRNA that is going into it in groups of three. Transfer RNA (tRNA) brings amino acids to the ribosome for protein production. To make sure that the amino acids are added to the protein in a specific order, the tRNA reads the codons from the mRNA.
The three base anticodon on the tRNA ‘matches up’ with the right mRNA codon inside the ribosome. If the bases are complementary to each other, the amino acid carried by the tRNA is released, and they can form bonds.
Initiation:
Translation begins when the ribosome binds to the AUG codon on the mRNA strand. AUG (START codon) signals the start of translation, and therefore the beginning of the polypeptide forming. AUG codes for the amino acid methionine (Met), which is brought by the tRNA molecule. The ribosome moves from the 5’ to 3’ end of the mRNA strand.
Elongation:
The tRNA anticodon binds to the complementary mRNA codon. If the codon and the anticodon match, the tRNA deposits its attached amino acid. Amino acids are added to the polypeptide chain one by one by tRNAs as the ribosome reads the mRNA codons. They are joined together by peptide bonds. The tRNA leaves the ribosome and can be reused to pick up another amino acid.
Termination:
The ribosome reaches a STOP codon on the mRNA. The stop codon does not code for a specific amino acid, it codes for the ribosome to release the formed polypeptide. The newly released polypeptide can fold into its specific protein structure. The ribosome and tRNA can be reused with multiple copies of the mRNA strand to make many polypeptides at once.
Purpose of Translation
- Turn genetic instructions into a sequence of accurate amino acids to build a desired protein product.
- Allow the synthesised protein to fold into the correct shape for its function.
- Enable life processes (MRS C GREN)
