5.3 - Polypeptide Synthesis Flashcards
DNA in prokaryotes
Pro: circular DNA, a strand
- Located in the nucleoid, a region slightly denser than the rest of the cytoplasm
- Large circular simple chromosome - no histone proteins
- Sometimes accompanied by plasmids - smaller rings of DNA that contain limited genes
Plasmid
Provide selective advantages (antibiotics or resistance to external selective pressure) as it replicates independently of chromosomes.
It can be integrated into the main DNA structure if neded for replication
DNA in Eukaryotes
What is structure, and mtDNA
In eukaryotes, DNA is coiled in a histone protein framework chromosome
Often have DNA in organelles, such as mitochondria and the chloroplast.
A prominent example: mtDNA located in the mitochondria:
- mtDNA is formed in small circular rings genes resembling plasmids, genetic code for producing ATP.
- mtDNA is inherited from a single maternal lineage as all cytoplasmic organelles are inherited from the mother’s ovum (sperm has almost no cytoplasm). However, in forming a zygote half the nuclear DNA comes from the sperm and half from the ovum
Compare DNA in prokaryotes and eukaryotes
They differ in packaging and quantity, although the base molecule remains the same (same enzymes for DNA replication)
Similarities: same complementary bases and backbone of sugar and phosphate
- Supercoiling occurs for efficient packaging (in nucleus/nucleoid) and DNA processes (DNA transcription and replication)
Prokaryotes:
- Same purpose: gene expression through protein synthesis.
- A (single, most of the time) circular chromosome with no telomeres
- Can be found in the form of plasmids, circular molecules (DNA is DNA no matter the organism)
- Less DNA than eukaryotes (thousands to millions of bases)
- Fewer genes (thousands)
- Less non-coding DNA (introns)
- Genes cluster into functional groups, operating together in operon regions
Eukaryotes:
- Linear thread-like with telomeres
- Other DNA can be found in organelles (chloroplast, mitochondria)
- More DNA (million to billion bases)
- More genes (tens of thousands)
- More introns
- Genes coding for functionally similar proteins can be physically apart or on different chromosomes. This is possible as they are more evolutionarily complex and can express these genes at the same time.
When answering this question, ensure that you discuss features of the DNA, not the cell features (organelles etc.) or location
Phenotype
examples to come
Expression of the genotype: physical appearance, physiology, behaviours.
It is determined partly by environment as it influences how a gene is expressed; the genetic makeup provides potential for traits, and environmental conditions such as diet, stress and temperature influence gene expression. Note: genes determine how phenotypes are expressed under genetic conditons.
Genotype
Genetic code specific to an individual
Phenotype example: temperature-sensitive expression
There are 2
Himalayan rabbits
The Himalayan rabbit has a gene that codes for a pigment enzymes that is only active at cooler temperatures (below 20C). This enzyme is inactive at higher temperatures (above 30C). As the ears, nose, feet and tail are cooler than the rest of the body the enzyme is activated, resulting in darker pigmentation.
Australian bearded dragon lizard has genotypic sex determined by the presence of sex chromosomes. However, if eggs are incubated at high temepratures, genotypically male embryos will undergo sex-reversal into females. 2 genes are turned on under heat stress that override the sex chromosomes and trigger sex reversal
Proteins
A group of molecules that drive all processes in the body. Functions:
- Control all metabolic processes as enzymes
- Some send intracellular or intercellular signals (e.g. control release of insulin)
- Antibodies are involved in the adaptive immune system’s response to foreign pathogens in the body
- Transmembrane proteins alter cell membrane permeability (e.g. aquaporins and channel proteins)
- Some proteins build structure and mechanics of an organism, e.g. collagen and keratin
Proteins determine our phenotype with influence from the external environment
Phenotype example: alkalinity-sensitive expression
Hydrangeas
In acidic soil with pH < 6, aluminium ions in the soil become more available to the plant. The ions are absorbed, resulting in blue or purple flowers.
In neutral to alkaline soil ph 6+, aluminium ions are less accessible. The low absorption of these ions causes the flowers to be pink or red.
Amino acids
- Organic compounds containing amine and carboxyl functional groups, as well as a side chain (called an R group) which is determines the shape and structure of a polypeptide chain (aka a protein)
- Amino acids in a polypeptide chain are attracted to one another by intermolecular forces. Analogy: a necklace made of broken magnets. When released, the components will spontaneously form a particular shape.
- Shapes give the protein its specific role in the body.
Phenotype example: epigenetics
PKU disorder
It increases the levels of amino acid phenylalanine (phe) in the blood, and can lead to brain damage. The expression of phe can be prevented early in life if babies diagnosed with the PKU gene are placed on a continuously low-phe diet. This causes the PKU gene to not be expressed.
Secondary structure proteins
Local folded structures formed within a polypeptide due to interactions between atoms in the R-group
- 2 most common types of structures in this level are alpha-helix and beta-pleat
- Alpha-helix is a helical shape, single stranded unlike DNA (like RNA)
- Beta-pleat is like accordion folds
- These structures are held in shape by hydrogen bonds between the carbonyl O of one amino acid and the amino H of another.
Easy def: when sequence of amino acids are linked together by hydrogen bonds, forming alpha helix or beta pleats.
Tertiary structure proteins
Overall 3D structure of a polypeptide, occurs when certain attractions are present between alpha helics and pleated sheets
- Affected by interactions between R-groups of the amino acids that make up the protein
Protein structures
Polypeptides can form different structures
Primary, secondary, tertiary, quaternary
Quaternary structure proteins
Many proteins don’t reach this stage of structural complexity, but some do. The quaternary sturcture is when protein subunits, which are made up of multiple polypeptide chains, come together.
- Example: haemoglobin protein is made of a combination of alpha-chains and beta-chains and iron to carry oxygen molecules.
- Multiple polypeptide chains → subunits → quaternary structure protein
Protein consisting of more than one amino acid chain
RNA
Ribonucleic acid
- Thymine is replaced with uracil
- Single stranded, leaving nucleotides exposed on one side → more susceptible to mutations than DNA. E.g. COVID (sobs)
- Contains ribose sugar instead of deoxyribose
- RNA can bond with itself: parts of the RNA molecule with corresponding bases can fold and bond with itself through hydrogen bonding to form an intrastrand
- Intrastrand bonding allows the RNA to fold into shapes that have similar functions to proteins. It is less rigid, specific and effective, but can cataylse some basic metabolic processes
- RNA can do a bit of what proteins and DNA can do, but not as effectively in the specialist functions of either one
Primary structure proteins
A sequence of amino acids in a polypeptide chain
- Order and positioning of functional R-groups in the polypeptide determines its other, higher structures.
Intrastrand
An RNA molecule that bonds with itself by folding and forming hydrogen bonds between base pairs.
Polypeptide synthesis
Transcription (mRNA) and translation
Ribosomes makes proteins, information in the nucleus. To link these, Pre-mRNA is formed (transcription)
Pre-mRNA has exones and intrones - intrones are removed forming mRNA. This leaves the nucleus to the ribosomes, where translation occurs to form a polypeptide.
Protein structure 4 levels
- Primary
- Secondary
- Tertiary
- Quaternary
Transcription
Occurs in the nucleus:
- The enzyme RNA polymerase unwinds and unzips the double helix, from 5’ to 3’
- Complimentary RNA nucleotides are connected to the DNA, in which uracil connects with adenine instead of thymine
- The RNA nucleoids polymerise to form a strand, which takes the coded message outside the nucleus to be translated.
- mRNA leaves the nucleus through nuclear pores.
Coding vs template strand
- As DNA is a double helix, the strands are complimentary.
- RNA should have the same base pairs as the coding strand, so it is synthesised on the template (complimentary) strand. Therefore, the base it forms will be identical to the coding strand.
Codons in transcription
- 3 base pairs
- DNA has a start and stop codon that tells RNA Polymerase to start or stop synthesising.
- This is important as not the whole genome is read, only a small portion to form a protein.
- The code carried by mRNA is just one gene, for one protein polypeptide.
Processing mRNA
Before mRNA leaves the nucleus it is matured
Spliceosome cuts out introns to mature the mRNA
- Intron to spliced out, extrons joined back together.
- Then leaves the nucleus, to ribosomes floating in the nucleus or the rough ER
Ribosomes
Ribosomes are 40% ribosome RNA and 60% protein by mass
They are made of two subunits, that lock around mRNA and read it.
Translation - ribosomes, tRNA
- tRNA brings amino acids to the ribosome to create a polypeptide.
- tRNA have anit-codons, complimentary to the codon on the mRNA. They have an amino acid attached to the other end.
- Two subunits come together locking the mRNA. According to this code, different tRNA come to
- Elongation factors bring tRNA to the ribosome.
tRNA in translation
tRNA molecules move in turn along the mRNA as it is strung through the ribosome, initiated by the start codon. The amino acids polymerise through condensation reactions and exit the ribosomes as a polypeptide.
- Incoming tRNA bound to an amino acid.
- Translation occurs, adds to the growing amino acid chain.
- Outgoing tRNA is empty
Comparison of protein synthesis across euk/prokaryotes
Prokaryotes don’t have nucleus - so transcription and translation occurs at the same time.
However in eukaryotes, this is a process.
- Linear/circular
- single/whole genome of chromosomes
Start codon
mRNA: AUG
DNA: TAC
Gene expression
Gene expression is the process by which the information encoded in a gene is turned into a function, such as directing the assembly of a protein molecule. As proteins act as enzymes (metabolic processes), structural features and other functions, this influences the phenotype.
DNA Transciption v. DNA replication
Similarities:
- Uses a DNA template to guide the synthesis of a new strand (DNA in replication, RNA in transcription).
- Directionality in the 5’ to 3’ direction
- Both require specific enzymes (DNA replication: DNA polymerase, Transcription: RNA polymerase)
- Both rely on complementary base pairing: (In replication: A-T and G-C. In transcription: A-U and G-C.)
Differences:
- Template use: DNA replication uses both strands as template, and involves the whole genome; transcription only uses the template strand, and only specific genes or regions of DNA.
- Forms: Double-stranded DNA. Single-stranded RNA.
- Purpose: produce identical DNA for cell division. To synthesize RNA for protein synthesis
Phenotyphic expression - skin colour
There are several genes that determine the amount of melanin produced (skin pigmentation). However, exposure to UV rays stimulates melanin production.
What happens if there is a mutation in DNA (mRNA)
If on exon, the codon is different -> could be different amino acid/stop codon
* Changes polypeptide change, altering its function or rendering completely dysfunctional
