biology unit 3 aos 1

structure of an amino acid

central carbon, amino group, carboxyl group, r-group

primary structure of a protein

the sequence of amino acids in a polypeptide chain

bonds present in primary structures

peptide bonds

secondary structure of a protein

formed when a polypeptide chain folds and coils either alpha helices, beta-pleated sheets and random coils

bonds present in a secondary protein structure

hydrogen bonds

tertiary protein structure

overall functional 3D shape of a protein, formed when secondary structures further fold by forming interactions and bonds between amino acids and R groups of different sections

bonds present in tertiary protein structure

disulphide bonds

quarternary protein structure

formed when 2 or more tertiary structures join together

structure of a nucleotide

phosphate group, pentose sugar, nitrogenous base

bonds joining nucleotides

phosphodiester bonds formed via condensation reactions

similarities between dna and rna

contain adenine, guanine and cytosine, has a sugar-phosphate backbone, follow complementary base pairing rule

differences between dna and rna

dna nucleotides have a deoxyribose sugar whereas rna nucleotides have a ribose sugar

dna has thymine whereas rna has uracil

dna is double stranded whereas rna is single stranded

dna is inherited whereas rna is synthesised and temporary

properties of the genetic code

universal, unambiguous, degenerate

universal (genetic code)

nearly all living organisms use the same codons to code for specific amino acids

unambiguous (genetic code)

each codon is only capable of coding for one specific amino acid

degenerate (genetic code)

each amino acid may be coded for by multiple different codons

gene structure

promoter region, introns, exon, termination sequences and operator regions

promoter region of a gene

upstream binding site for rna polymerase, in eukaryotes its often the TATA box

introns

regions of non coding dna that dont code for proteins, spliced during rna processing. only found in eukaryotes

exons

regions of coding dna, which are transcribed and translated into the final protein. found in both eukaryotes and prokaryotes

termination sequence

represents a sequence of dna that signals for the end of transcription

operator

serves as the binding site for repressor proteins which can then inhibit gene expression. typically only found in prokaryotic genes as eukaryotes have different regions for regulating gene expression

rna polymerase

the enzyme responsible for constructing a pre-mrna sequence from a dna sequence during transcription. initiates transcription by binding to the promoter region of a gene

stages of gene expression

transcription (nucleus) , rna processing (nucleus), translation (ribosome in either cytosol or attached to rough er)

transcription

rna polymerase binds to promoter region of gene, signals for hydrogen bonds to break exposing 2 strands of dna as they unwind and unzip

rna polymerase runs along template strand, reading the nucleotide sequence and using free-floating nucleotides to produce pre-mrna molecule. synthesised in a 5-3 direction, complementary to template strand and identical to coding strand

transcription ends when rna polymerase reaches the termination sequence of a gene. once reached, rna polymerase detaches, releasing pre-mrna molecule and dna molecule winds back into a double helix

rna processing

only in eukaryotes. adds 5’ methyl-g cap and 3’ poly-a tail, removal of introns and splicing of exons together

alternative splicing

different exons can be removed during splicing process, meaning single pre-mrna strant can produce many different mrna molecules depending on which exons are spliced out or kept. allows for a single gene to give rise to many different mrna strands and code for many different proteins

translation

5’ end of the mrna molecule binds to ribosome and is read until the start codon (AUG) is recognised. trna molecule with a complementary anticodon binds to the ribosome, commencing translation

ribosome continues to read the mrna molecule allowing for codons to be matched with trna anticodons, bringing amino acids to the chain. the amino acids bind to adjacent amino acids through peptide bonds made through condensation reactions

process occurs until a stop codon is reached, signalling for the end of translation. this releases the polypeptide chain as a primary structure of protein

regulatory genes

segment of dna responsible for the production of regulatory proteins such as repressor proteins, which can inhibit or decrease the expression of structural genes

structural genes

responsible for producing proteins that are involved in the structure or function of a cell

gene regulation

the process of either inhibiting or activating gene expression, helps organisms prevent the unnecessary production of gene products, thereby conserving energy. also ensures cells produce the appropriate proteins

trp operon

regulates the expression of structural genes which code for the production of tryptophan

high levels of trp = transcription stopped

low levels of trp = transcription started

trp operon repression

high levels of trp - 2 trp bind to repressor protein inducing conformational change to its shape which enables it to bind to the operator region. this inhibits transcription of trp as rna polymerase’s path is blocked

low levels of trp - there is insufficent quantity of intracellular tryptophan molecules to bind to repressor protein, causing repressor protein to become inactive and detach from operator region which allows rna polymerase to transcribe trp structural genes so levels of trp can increase. as it accumulates it will bind to repressor protein and repression will happen again

mechanisms keep the amount of trp avaliable within the cell at a relatively constant level to ensure energy and resources are expended appropriately

trp operon attenuation

occurs in response to the amount of trna bound trp

transcription of structural genes begins but is stopped early before any actual proteins are made

must remember: transcription + translation occur simultaneously and close to eachother within the cytoplasm of prokaryotes, leader region sitting just before 5 trp structural genes is pivotal to attenuation

trp operon attenuation process HIGH LEVELS OF TRP

1. transcription + translation occur simultaneously

2. ribosome involved in translation arrives at the two tryptophan codons in a row. trna bound trp is present travels to ribosome and is added to the protein being made

3. causes the mrna molecule being read by the ribosome to fold in a specific way via hydrogen bonds and form a terminator hairpin loop

4. the folding of the terminator hairpin causes the mrna molecule to separate from the template dna at the attenuator sequence

5. rna polymerase detaches from the dna, causing transcription to stop before any structural genes are transcribed. without these structural genes, new trp cant be synthesised

trp operon attenuation process LOW LEVELS OF TRP

1. transcription + translation begin and occur simultaneously

2. ribosome involved in translation arrives at the two trp codons in a row. due to there being no trna bound trp in the cell, when the ribosome involved in translation arrives at the attenuator sequence that codes for 2 trp amino acids it pauses. meanwhile, rna polymerase continues along the dna

3. causes mrna molecule to fold in a specific way via hydrogen bonds and form an antiterminator hairpin loop

4. antiterminator hairpin doesnt cause mrna to separate from template strand at attenuator sequence

5. rna polymerase continues to read the dna template strand, continuing transcription and therefore translation

exocytosis

the process whereby the contents of a vesicle are released from a cell

stages of exocytosis

1. vesicle containing secretory proteins is transported to plasma membrane

2. membrane of the vesicle fuses with the plasma membrane

3. secretory products are released from the cell into extracellular environment

protein secretory pathway

1. ribosome (synthesises proteins)

2. rough er (folds and transports proteins)

3. transport vesicle (transports proteins)

4. golgi apparatus (modifies and packages proteins)

5. secretory vesicle (transports proteins)