Proteins and Genes (chapters 2-3) Flashcards
Exogonic
High energy to low energy
Endogonic
Low energy to high energy
3 Stages of Transcription
- Initiation
- Elongation
- Termination
Transcription - Initiation
- RNA polymerase binds to DNA at promoter region
- Promoter region contains TATA box - recognised by ‘TATA’ sequence
- Once bound, RNA polymerase unzips two DNA strands
Transcription - Elongation
- RNA polymerase moves along template strand to form RNA strand
- RNA synthesized in 5’ to 3’ direction
Transcription - Termination
- RNA polymerase detaches from DNA
- Transcription stops, DNA strands return to normal double helix formation
3 Stages of Translation
- Initiation
- Elongation
- Termination
Translation - Initiation
- 5’ end of mRNA molecule binds to ribosome, read until start codon (AUG) is recognised
- tRNA with complementary anticodon (UAC) binds to ribosome, delivers amino acid methionine
Translation - Elongation
- mRNA molecule is fed through the ribosome so that the next codon can be matched to its complementary tRNA anticodon
- complementary tRNA molecules deliver specific amino acids to the ribosome, which bind to adjacent amino acids with a peptide bond via a condensation reaction
Translation - Termination
- Translation occurs until stop codon found
- The polypeptide chain is then released by the ribosome into the cytosol or endoplasmic reticulum.
Gene Expression 3 Stages
- Transcription
- RNA processing
- Translation
RNA Processing
Making mRNA from pre-mRNA
- Introns cut out, exons join together
- methyl cap added to 5’ end of pre-mRNA, poly-A tail added to 3’ end
- Once all this happens, becomes mRNA
Trinucleotide
Sequence of 3 adjacent nucleotides
pre-mRNA
unmodified RNA molecule
Exporting Proteins - Rough Endoplasmic Reticulum
Has ribosomes ‘rough’
- Makes proteins to be exported from the cell
- Proteins synthesized at ribosomes on Rough E.R.
Exporting Proteins - Golgi Aparatus
Stack of 4-8 flattened membrane sacs called Cisternae
- Modify and package proteins for export outside of the cell
- Proteins move from Rough E.R. to Cisternae in the Golgi Body, where proteins are modified by resident enzymes
- Modifications are necessary to target proteins to intended desination
Exporting Proteins - Vesicles
- Proteins released from Golgi in vesicles that bud off from the trans face
- Cargo proteins bind to specific membrane bound receptor proteins within the vesicle
- Cargo proteins change shape of receptors, telling vesicles where to go
Tryptophan
Rarest naturally occuring amino acid
Trp Operon
A series of genes within certain species of bacteria that encode for the production of the amino acid tryptophan
- ONLY IN PROKARYOTES
Attenuate
To reduce the effect of something
Leader
5’ untranslated region between promoter and operon genes
Domain
Distinct region of complex molecule
Surplus of Tryptophan
- When tryptophan is present, it binds to the repressor protein
- Repressor protein binds to the operator, blocking RNA polymerase from carrying out its function, therefore preventing transcription
Deficit of Tryptophan
- Insufficient quantity of tryptophan to bind to the repressor
- Causes the repressor protein to detach from operator region
- Allows RNA polymerase to transcribe trp structural gens
Proteome
all the proteins that are expressed by a cell or organism at a given time
Enzyme
an organic molecule, typically a protein, that catalyses (speeds up) specific reactions
Antibody
A protein produced by plasma cells during the adaptive immune response that is specific to an antigen and combats pathogens in a variety of ways.
Also known as immunoglobulin
Amino Acid Structure
composed of a central carbon atom, a carboxyl group, an amino group, an R-group,
and a hydrogen atom.
monomer
a molecule that is the smallest building block of a polymer
polymer
a large molecule that is made up of small, repeated monomer subunits
Peptide Bond
the chemical bond linking two amino acids
Levels of Protein Structure
- the sequence of amino acids (primary)
- arrangement into alpha-helices, beta-pleated sheets, or random coils (secondary)
- functional 3D shape of the protein (tertiary)
- bonding of multiple polypeptide chains together (quaternary).
Primary Protein Structure
the first level of protein structure, which refers to the sequence of amino acids in a polypeptide chain
Secondary Protein Structure
the level of protein structure where the amino acid chain forms either alpha-helices, beta-pleated sheets, or random coils
tertiary protein structure
the functional 3D shape of a polypeptide chain
quaternary protein structure
the level of protein structure where multiple polypeptide chains bond together, or other non-protein groups are added to form a fully functional protein
Carboxyl Group (Amino Acid Structure)
the functional group on amino acid molecules that contains a hydroxyl group (OH) and an oxygen doublebonded to a carbon atom
Amino Group (Amino Acid Structure)
the functional group on amino acid molecules that is made up of one nitrogen and two hydrogens (NH2)
R-Group (Amino Acid Structure)
the variable portion of an amino acid molecule. It can be one of twenty variations and determines the identity of the amino acid
Nucleic Acid
the class of macromolecule that includes DNA and RNA. All nucleic acids are polymers made out of nucleotide monomers
Nucleotide
the monomer subunit of nucleic acids. Made up of a nitrogen-containing base, a fivecarbon sugar molecule (ribose in RNA and deoxyribose in DNA), and a phosphate group
DNA
a double-stranded nucleic acid chain made up of nucleotides.
carries instructions for proteins required for cell and organism survival
RNA
a singlestranded nucleic acid chain made up of nucleotides
- tRNA
- mRNA
- rRNA
Nucleotide Structure
- Phosphate Group
- 5 Carbon Sugar
- Nitrogen-containing base
Phosphodiester Bonds
a strong covalent bond linking a five-carbon sugar to a phosphate group
joins nucleotides together
Chromosome
a structure made of protein and nucleic acids that carries genetic information
Gene
a section of DNA that carries the code to make a protein
Genome
the complete set of DNA housed within an organism
DNA Structure
DNA is composed of two polynucleotide chains which run antiparallel to each
other
Composed of:
- Phosphate Group
- deoxyribose sugar
- Nitrogenous Base (A,T,G,C)
Nuclear DNA
DNA located in the nucleus of a cell
Messenger (mRNA)
RNA molecules that are produced during transcription and carry genetic information from the nucleus to the ribosomes
Transfer (tRNA)
RNA that recognises specific codons on the mRNA strand and adds the corresponding amino acid to the polypeptide chain during protein synthesis
Ribosomal (rRNA)
RNA that is a key structural component of ribosomes, which assemble proteins
RNA Structure
Single Strander
Composed of:
- Phosphate Group
- Ribose Sugar
- Nitrogenous Base (A,U,G,C)
Transcription Summary
the process whereby a sequence of DNA is used as a template to produce a complementary sequence of mRNA
Translation Summary
the process where an mRNA sequence is read to produce a corresponding amino acid sequence to build a polypeptide
codon
the sequence of three nucleotides in mRNA coding for one amino acid
Start Codon
the sequence of three nucleotides in mRNA that signals the start of translation
Stop Codon
the sequence of three nucleotides in mRNA that signals the end of translation
Gene Structure
Genes can be composed of many different components, including a promoter region,
introns, exons, termination sequences, and operator regions.
Promoter
the sequence of DNA to which RNA polymerase binds
RNA Polymerase
the enzyme responsible for constructing a pre-mRNA sequence from a DNA sequence during transcription
Introns
non-coding regions of DNA that do not code for proteins. They are spliced out during RNA processing
Exons
regions of DNA that code for proteins and are not spliced out during RNA processing
Termination Sequence
a sequence of DNA that signals the end of transcription
*is there a difference between termination sequence and stop codon?
Operator
a short region of DNA that interacts with repressor proteins to alter the transcription of an operon
Leader Region
the segment of DNA or mRNA that immediately precedes the coding region. Also known as the leader segment or leader sequence
Catalyst
a substance capable of increasing the rate of a reaction without being used up
Substrate
the reactant of a reaction catalysed by an enzyme
active site
the part of an enzyme where the substrate binds
activation energy
the energy required to initiate a reaction
Biochemical Pathway
a series of enzyme-catalysed biochemical reactions in which the product of one reaction becomes the substrate of the next reaction
Factors affecting enzymes - Temperature
- If enzymes get too hot, they run the risk of denaturing - when the bonds that create the tertiary and quartenary structures break down
- If enzymes denature, it is irreversible
- If enzymes get too cold, molecules move more slowly, and collide less frequently, and can eventually freeze
- Is reversible
Denature
the disruption of a molecule’s structure by an external factor such as heat
Factors affecting enzymes - pH
If pH becomes either too acidic, or too basic, enzymes can denature
- Acidic have low pH (<7)
- Basic have high pH (>7)
Factors affecting enzymes - Concentration
- if concentration of substrate increases, while enzyme concentration remains same, rate of reaction will increase
Saturation Point
the point at which a substance (e.g. an enzyme) cannot receive more of another substance (e.g. a substrate)
Limiting Factor
a factor that prevents the rate of reaction from increasing
Limiting Reagent
a reactant that prevents the rate of reaction from increasing
Enzyme inhibitor
a molecule that binds to and prevents an enzyme from functioning
Competitive Inhibition
the hindrance of an enzyme by blocking the active site and preventing the substrate from binding
Allosteric Site
a region on an enzyme that is not the active site
Factors affecting enzymes - Competitive v Non Competitive Inhibition
Enzymes can be hindered by molecules known as competitive inhibitors that impede
enzymes by blocking their active site,
or by non-competitive inhibitors that interfere with enzymes by binding to a site other than the active site and inducing a conformational change.
Factors affecting enzymes - Reversible and irreversible inhibition
Enzyme inhibitors can also be classified according to if their effects are permanent or
temporary.
Reversible inhibitors bind weakly to an enzyme, allowing for the bonds to
be broken and overcome. Irreversible inhibitors form strong bonds with an enzyme that cannot be broken
Non competitive inhibition
the hindrance of an enzyme by binding to an allosteric site and changing the shape of the active site to prevent the substrate from binding
Reversible Inhibition
enzyme inhibition that involves weaker bonds that can be overcome
Irreversible Inhibition
enzyme inhibition that involves stronger bonds that cannot be broken
Factors affecting enzymes - Coenzymes
Coenzymes assist enzymes in catalysing reactions. The cycling of coenzymes is integral to many biochemical processes.
Coenzyme
a non-protein organic cofactor that assists enzyme function. They release energy and are recycled during a reaction
Cofactor
any organic or inorganic molecule, such as a coenzyme or metal ion, that assists enzyme function
ATP
adenosine triphosphate,
a high energy molecule that, when broken down, provides energy for cellular processes
ADP
adenosine diphosphate,
the unloaded form of ATP
