AOS1 Flashcards
Biomacromolecule
Proteins are biomacromolecules;
- A large organic molecule (in organisms) and are composed of smaller subunits.
Polymer
Proteins can also be defined as a polymer.
- A polymer is a large molecule composed of a chain of repeating similar smaller molecules (monomers)
Monomers
A simple molecule with 2 or more binding sites (to form a macromolecule).
Proteome
Is more diverse than a genome.
- It is the entire complement of proteins in a cell or organism.
Amino acid subgroups:
- Amino group (2 hydrogens + a nitrogen).
- Central carbon (H - C).
- R group (changes)
- Carboxyl group (C =O - O - H)
Polymerisation of amino acids:
- The hydroxyl group is broken off the carboxyl of one amino acid to form a covalent bond with the hydrogen from the other amino group to form a water molecule.
- Amino acid residues are joined together in a peptide bond. (condensation reaction).
( 100 or more chain = poly peptide )
( 20 or less = peptide )
4 levels of protein structure
- Primary.
- Secondary.
- Tertiary.
- Quaternary.
Primary
The sequence of amino acids in a protein.
Secondary
3D form of segments of a polypeptide chain; due to the interactions between nearby amino acids including the Alpha Helices and Beta Pleated Sheets.
Tertiary
The overall 3D shape of a protein (polypeptide).
(The shape of the protein determines its function).
- Folded into shape by chaperone proteins.
- When folded it is held by a hydrogen bond or a disulfide bond between cysteine amino acids.
Quaternary
- Only occurs if the protein is made of more than 1 polypeptide chain.
- When a polypeptide joins to another biomacromolecule.
Purines:
2 nitrogen-containing carbon ring.
- Adenine.
- Guanine.
Pyrimidines:
1 nitrogen-containing carbon ring.
- Cytosine.
- Thymine.
- Urical.
Proteins
Biomacromolecule made up of amino acid chains folded into a 3D shape.
Nucleic acids:
Information molecules that encode instructions for the synthesis of proteins.
- Pentose (5 carbon) sugar.
- Nitrogenous-containing base.
- Phosphate group.
3 main forms of RNA:
- Messenger RNA.
- Transfer RNA.
- Ribosomal RNA.
Messenger RNA
(mRNA).
Carries genetic code from DNA in the nucleus to the ribosome.
Transfer RNA
Carries specific amino acids from the cytoplasm to the ribosome and pairs with complementary code carried by mRNA.
Ribosomal RNA
The main structural component of ribosomes within cells.
RNA polymerisation.
RNA built by enzyme; RNA polymerase.
- Polymerase built on a 5’-3’ direction adding new nucleotides to 3’ end.
Structure of genes:
Exons, Introns, promoter and operator regions
Introns
Contain non-coding DNA.
- Transcribed regions of eukaryotic genes that are REMOVED from RNA before translation.
(Occurs in RNA processing).
- Not found in prokaryotic
Exons
Are EXPRESSED
- Transcribed regions of a gene that are translated.
- Coding DNA.
5’ UTR (untranslated region).
3’ UTR
“the leader”
- upstream; front of gene.
“the trailer”
- downstream.
Promoter
Ahead of gene
- the binding site for RNA polymerase.
- TATAAA
Activator/Repressor
Increase/Decrease
Enhancer/Silencer
Increases/Decreases the rate of transcription (rate of RNA subscribed).
Operator region
A binding site for repressor proteins which can inhibit gene expression.
- Interacts with a repressor to alter the transcription of an operon.
Termination sequence
Sequence of DNA that signals for the end of transcription.
Anticodon
Negative-sense sequence of 3 unpaired nucleotides in tRNA.
- Non-coding strand.
Codon
Positive-sense sequence of 3 nucleotides in mRNA and the coding strand of DNA.
Gene expression
The production of functional gene products.
Process of gene expression.
Transcription: copying of DNA –> pre mRNA.
Rna Processing: Modifies pre-mRNA to produce mRNA.
Translation: Decoding of mRNA strand into polypeptide chain.
Transcription:
Occurs in the NUCLEUS
- RNA polymerase enzyme runs along template (non-coding) strand, 3’-5’ unwinding and unzipping DNA, building a complementary strand of RNA, 5’-3’
RNA processing:
Occurs in the NUCLEUS
- Pre-mRNA; introns are cut out and exons join together (splicing).
- Methyl-g cap added to 5’
- Poly-A tail added to 3’
Translation
Occurs in the RIBOSOME
- Anticodon of tRNA pairs with a complementary codon in RNA.
- Amino acids carried to the ribosome this way are linked by peptide bonds.
Gene regulation
To save cells energy, by inhibiting and activating gene expression. (cells can be switched off)
–> In eukaryotic cells; makes it possible for cells to differentiate for particular functions.
Gene regulation by transcription repression; Low levels
Insufficient quantity of tryptophan causes the repressor protein to become inactive and detach from the operator region, allowing RNA polymerase to transcribe the trp structural genes so that the level of tryptophan can increase.
Gene regulation by transcription repression
- High levels of tryptophan
- Tryptophan binds to the repressor (conformational) changing its shape.
- Repressor protein changes into its active form.
- Binding to operator region and blocking path of RNA polymerase, stopping production of tryptophan
Gene regulation by attenuation
Attenuation: reduce the effect
mRNA transcript contains 4 domains capable of binding to the next.
- Domain 1; 2 tryptophan codons.
- Between domains 1 and 2 there is a STOP codon.
- Attenuator at 3’ of mRNA, containing U-A bonds; weak bonds.
Gene regulation by attenuation; tryptophan
When tryptophan is present, the ribosome runs pasts tryptophan codons and stops at the stop codon (1-2).
- Preventing domain 2 from pairing with 3, making 3 pair with 4, forming a hairpin.
- Putting tension on the attenuator, so mRNA pulls away from DNA ending transcription. (stopping production of tryptophan).
Gene regulation by attenuation; NO tryptophan
- Ribosome pauses at the 2 tryptophan codons waiting for a tRNA carrying.
- Allowing domain 2 to pair with 3, preventing 3 from pairing with 4, creating a hairpin.
- Due to being far away from the attenuator, mRNA does not pull away from DNA, and the ribosome continues along transcribing genes of the operon.
Trp Operon
series of genes within certain species of bacteria that encode for the production of the amino acid tryptophan.
High tryptophan levels: Attenuation.
1 The processes of transcription and translation of the trp operon begin and occur simultaneously.
2 The ribosome (in translation) arrives at the two tryptophan codons in a row.
The tRNA-bound tryptophan present in the cell travels to the ribosome and is added to the protein that is being made by the ribosome.
3 This 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 loop 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 tryptophan
cannot be synthesised
Low levels of tryptophan: Attenuation.
1 The processes of transcription and translation of the trp operon begin and occur simultaneously.
2 The ribosome involved in translation arrives at the two tryptophan codons in a row. Due to there being no tRNA-bound tryptophan in the cell, when the ribosome involved in translation arrives at the attenuator sequence that codes for two tryptophan amino acids it pauses. Meanwhile, the RNA polymerase involved in transcription continues along the DNA.
3 Causing the mRNA molecule to fold in a specific way via hydrogen bonds and form an antiterminator hairpin loop.
4 The antiterminator hairpin loop does not cause the mRNA to separate from the template strand at the attenuator sequence.
5 RNA polymerase continues to read the DNA template strand, transcribing the
structural genes for proteins involved in the synthesis of tryptophan and translation
can continue
The protein secretory pathway (PSP)
Involves various different organelles that produce, fold, modify, and package proteins, eventually exporting them from the cell via the process of exocytosis.
- Rough endoplasmic reticulum, Golgi apparatus, transport and secretory vesicles, ribosome.
Ribosome PSP
Synthesises proteins; Assemble polypeptide chains from amino acids by translating mRNA.
Rough endoplasmic reticulum PSP
Folds and transports proteins; folding of newly formed polypeptide chain before passing to the Golgi apparatus.
Transport Vesicle
Transports proteins; buds off rough ER and travels to the Golgi body.
Golgi Apparatus
Modifies and packages proteins; Proteins have chemical groups that are either added or removed in the golgi body, where they are packaged into secretory vesicles for export into cytosol.
Secretory Vesicle
Transports proteins; Buds off Golgi (containing proteins), travels through cytoplasm and fuses with the plasma membrane, releasing protein contained within into the extracellular environment through exocytosis.
Proteome
The complete array of proteins produced by a single cell or an organism in a particular environment
Role of enzymes
Catalyse reactions by lowering the activation energy for a chemical reaction to start.
Catabolic
A chemical reaction that breaks a big molecule into smaller molecules. (Exergonic) No energy- releases energy
Anabolic
Reaction builds a bigger molecule from small molecules. (Endergonic) Absorbs Energy