proteins Flashcards
enzymatic proteins
catalysts in cellular reactions
hormonal proteins
Coordinate organism’s activities by triggering responses
immunological proteins
Protect against disease by recognising foreign bodies and microbes and activating immune cells
contractile and motor proteins
Aid muscle contractions and motor proteins are responsible for the movement of cilia and flagella
structural proteins
Provide support by forming structural components and assist in contractile functions
transport proteins
Act as protein channels or carrier proteins
receptor proteins
Assist the cell in responding to a chemical stimuli
storage proteins
Storage of metal ions and amino acids
what is a proteome?
proteome: the complex and complete set of proteins expressed by the genome of an individual cell or organism.
Varies between cell type, developmental stage and environmental conditions.
A cell has the entire genome but only some genes are switched on making sure it produces the right proteins.
what is proteomics?
Large scale study of the structure, function and interactions of proteins.
Might examine the proteins produced by cells in different conditions.
Important in the production of medications and early detection of diseases using protein biomarkers.
how does the synthesis of proteins work?
Proteins are made of amino acids, joined by peptide bonds.
Then coiled into proteins.
what is the amino acid structure? how to the amino acids change?
An amine group (NH2)
A carboxyl group (COOH)
A variable R group (or side chain)
There are 20 different standard (or canonical) amino acids, each with a different R group.
The varies of the R group (polar, non-polar, charged, non-changed etc.) determine the protein made
what is condensation polymerisation? how does it work?
Amino acids are joined by peptide bonds in a condensation polymerisation reaction which involves the removal of water (dehydration)
The hydrogen and oxygen from the carboxyl group of one amino acid join with the hydrogen atom of the amine group of another amino acid and produce water and a dipeptide (two amino acids linked) is synthesised with a peptide bond holding the amino acids together.
The backbone of a peptide chain is repeated amine and carboxyl groups.
The R groups are off the side
With folding and modification, a protein is formed.
primary structure? length and differences? what info do they form? how can we learn from them?
Linear sequence of amino acids in a polypeptide chain
Unique to each protein
Shorter than 50 amino acid sequences are called peptides
Length varies
Provides information on how the protein will fold
Functional and non-functional sequences are compared to see what causes a lack of function
Can be compared between proteins to see the evolutionary history
secondary structure? three types?
The folding or the coiling of the polypeptide chain.
Folding occurs due to the formation of hydrogen bonds between amine and carboxyl groups that are close together.
This results in the secondary structures: alpha helix, beta-pleated sheets and random coil
Alpha helix: hydrogen bonds form between adjacent amine and carboxyl groups, forming a helical shape
Beta-pleated sheets: hydrogen bonds form between amine and carboxyl groups in different parts of adjacent chains, causing the chains to fold back on each other
Random coil: it looks random, but eg. All insulin proteins will have the same random coils.
tertiary structures?
The further folding to form more stable, globular or fibrous 3D shapes
Usually the combination of alpha helices and beta-pleated sheets along with other folded areas.
Occurs due to different types of bonds, such as the disulphide bridge and the hydrogen bridge between the R groups.
3D structure is essential to functioning
Small chains fold due to chemical environment but more complex ones need specialised proteins to fold them and to refold them if the unravel or denature
This can be the final stage for some proteins
quaternary structure?
Two or more polypeptide chains or prosthetic groups (inorganic compound that is involved in protein structure or function) join together to make a single functional protein.
The polypeptides may be identical or different.
A protein with a prosthetic group is known as a conjugated protein.
chaperonins? how do they work?
Protein molecules that aid in the folding of other proteins.
It provides a sheltered space away from influences of the environment for a protein to fold.
It also stops newly synthesised polypeptide chains and submits form becoming non-non-functional due to high heat.
two types of proteins classification?
Fibrous proteins Elongated Insoluble Little or no tertiary folding eg. Collegen
Globular porteins Compactly folded Have tertiary or quaternary structures Usually Soluble Core is hydrophobic Outer hydrophilic region Most enzymes and hormones
what are the factors that affect proteins?
Temperature
pH
Concentration of ions or molecules that act as cofactors
denaturation and renaturation
Denatured when the bonds that cause its tertiary structure are broken and the protein changes shape
It is inactive
If it is partially affected, it may be able to renature if there are appropriate conditions
temp on proteins
At high temperatures they denature (40 degrees hydrogen bonds break)
At below 35 degrees the bonds are not flexible enough to allow the conformational changes
Optimal temperatures
pH on proteins
They have differing optimum pHs
They may denature if the pH gets too high or too low
effect of cofactors on protein function?
Some proteins need non-protein chemical compounds (cofactors) to function.
The presence and concentration of salts, specific elements or organic molecules has a significant role in the folding and function.
what is a nucleic acid?
large biomolecules that store and transmit hereditary information. They also encode instructions for the synthesis of proteins. DNA and RNA are the types.
what do nucleotides contain? numbering?
Phosphate group
Five carbon (pentose) sugar
- deoxyribose in DNA
- Ribose in RNA
A nitrogenous base
Carbons are numbered 1’ to 5’
Phosphate is on 5’ and base of 1’
what are the nitrogenous bases and their groups?
Adenine Guanine Cytosine Thymine (in DNA only) Uracil (in RNA only)
Groups:
Purines: (A and G) two rings
Pyrimidines: (T, U, C) one ring
how does the condensation polymerisation of nucleotides work? what is formed?
Firstly two join to form a dinucleotide
OH on 3’ of sugar joins with a phosphate and water is produced
Nucleotides can be continuously added forming a long sugar-phosphate-sugar-phosphate backbone (polynucleotide)
Nucleotides are joined by phosphodiester bonds (strong covalent)
Strands have a free phosphate group on the 5’ carbon (5’ end) and a free OH on the 3’ carbon (3’ end)
DNA and RNA are formed this way and are polynucleotides
what is the structure of DNA and its base pairing?
Two strands are coiled into a helix
Hydrogen bonds between bases
The strands run antiparallel
Complementary base pairing:
Purine A with pyrimidine T held with 2 weak H bonds
Purine G pairs with pyrimidine T with 3 weak H bonds
what is the structure of RNA and what is the base pairing?
Usually a single strand
Sometimes folded onto itself
Shorter than DNA
Uracil is more stable with single strands
Complementary pairs:
U with A
C with G
what is the role of DNA in protein synthesis? what is a gene?
Order of nucleotides determines what is synthesised
Mainly makes proteins but also functional RNA
gene: region of DNA that contains information to produce a protein or a functional RNA molecule
mRNA how is it formed? what does it do?
Formed in nucleus by transcription
Carries a DNA sequence that codes for a protein
In transcription, pre-mRNA is made with the enzyme RNA polymerase
Pre-mRNA is then processed (post-transcription modification) to have a single stand of DNA
Binds to ribosomes for translation
where is rRNA made? how Is it made? what does it make?
Synthesised in the nucleolus
Based on nucleotide sequence of DNA
With proteins it forms ribosomes
what is tRNA? how many? how many codons? what does it do?
Transfer amino acids to ribosomes to be joined to form polypeptide chains based on the arrangement of nucleotides in mRNA
61 tRNA molecules that only combine with one amino acid
64 codons which each represent an amino acid
3 are stop codons which tRNA does not recognise (translation is stopped)
3 places for tRNA to bind with ribosomes: exit site, peptidyl side or the aminoacyl.
At the other end of tRNA molecule there is a sequence of nucleotides called antocodon
Anticodon recognises particular sequences of nucleotides in mRNA which enables amino acids to be positioned in the correct space on a protein
what is a gene? how many nucleotides can they have?
Gene: region of DNA that may be translated into a polypeptide or an RNA molecule.
Genes can be millions of nucleotides in length
what is genetic code?
Genetic code: set of rules that defines how the information in nucleic acids is translated into proteins and functional RNA.
what is a triplet?
: 3-letter code of nucleotides in DNA and RNA
what is a codon?
codon: a DNA triplet that has been transcribed into mature mRNA.
Each one codes for an amino acid.
May ‘start translation’ or ‘stop translation’
what does it mean that genetic code is universal?
Genetic codes are the same for all organisms.
what is degeneracy? what does this protect against?
Genetic code degenerates
Degenerate: more than one codon can can code for the same amino acid
Differences in codons usually occur in the 2nd or 3rd base
Genetic code uses 4 nucleotides and 3 code for an amino acid, the combination of nucleotides make 64 possible codons to code for 20 amino acids.
Protects against gene mutation in that a single change in base may not lead to a change in amino acid.
what are the structure of genes?
Stop and start triplet sequences
Promoter regions: an upstream binding region for the enzyme that is involved in the encoding process (RNA polymerase)
Exons: DNA regions that are the coding segments
Introns (spacer DNA): non-coding segments
what are the stop and start instructions?
Start codon: AUG (for most functional proteins)
AUG codes for amino acid methionine
Some rare exceptions that do not begin with AUG
Stop codon: UAA, UAG, UGA (does not code for amino acid)
what is the promoter region? which end of the gene is it at? what is it usually coded by?
Where RNA polymerase will begin Identifies which DNA will be transcribed Identifies end Identifies direction At 5’ end of a section of gene Usually coded by TATAAA (TATA box)
what are introns and exons?
what is gene expression Exons are express as proteins or RNA (make up mRNA)
Introns are non-coding and are spliced out
what is gene expression and what are the three stages? how is it managed?
Gene expression: the process by which the information stored in a gene is used to synthesise a functional gene product (protein or RNA)
Managed so only what is needed is produced
Three stages:
Transcription
RNA processing
Translation
what does transcription achieve? where does it occur? what is the unit?
Produces mRNA from DNA
Occurs in nucleus
Transcription unit: DNA segment undergoing transcription
initiation of transcription?
RNA polymerase combines to the promoter region
RNA polymerase unwinds and unzips the DNA molecule by breaking hydrogen bonds and creating two strands
elongation of transcription?
RNA polymerase covers an area of about 30 base pairs
A segment of about 15 base pairs is uncoiled which forms a transcription bubble
DNA strands behind the bubble coil again
A template strand of DNA is used to produce the mRNA strand
mRNA is synthesised 5’ to 3’ direction with new nucleotides added to the 3’ end
Primary mRNA transcript is produced
termination of transcription?
RNA polymerase reaches a termination point (stop codon)
Stop codon releases factors that signal termination
RNA polymerase detaches and mRNA is released allowing DNA to reform
what is the template stand?
strand of DNA that is transcribed
what is the coding strand?
other complementary strand
mRNA contains same base sequence as coding strand except with U
what happens in RNA processing?
methyl cap, poly-A tail and splicing
methyl cap?
A methyl cap is added to the 5’ end of pre-mRNA
cap aids in ribosome binding
Provides some stability and prevent degrading
poly-A tail
Up to 250 adenines are added to 3’
Increase stability, prevent degrading
splicing
Introns are cut out Forms mature mRNA Spliceosome (made of protein and RNA) splices Not all exons are included Exits the nucleus through nuclear pores
alternative splicing
Some exons are removed
Splicing means that more proteins can be made from the same gene
what is translation? what does it form? where does it occur?
Codons on mRNA are translated into a sequence of animal acids resulting in a Polypeptide
Occurs on ribosomes
Ribosomes bind to mRNA and act as docking stations for tRNA to deposit the specific amino acids
The anticodon of the tRNA recognises and binds to the codon on the mRNA by complementary base pairing
tRNA carries a specific amino acid related to the codon to which it binds
initiation of translation
A small Ribosomal subunit attaches to 5’ end and moves along until AUG (start codon)
tRNA molecule with the anticodon UAC then brings the amino acid
Anticodon and codon join together by complementary base pairing
A large ribosomal subunit attaches to the tRNA and the small ribosomal subunit which causes the formation of three special sites for tRNA to bind: aminoacyl site (A site), peptidyl site (T site) and exit site (E site).
Attachment of tRNA to corresponding amino acids happens in the cytosol
elongation of translation
The next tRNA anticodon joins to the next codon, adding the specific amino acid and growing the polypeptide chain
Condensation polymerisation joins the amino acids
Ribosome releases tRNA and moves along the mRNA
tRNA can be reused when it picks up a new amino acid
termination of translation
Amino acids stop being added when stop codon is reached
Polypeptide chain is released into cytoplasm or the ER
gene regulation in eukaryotes: how controlled? when can it occur?
Highly controlled
Can occur during transcription (inhibited), RNA processing (inhibited), mRNA export (degraded), translation (inhibited) and the final protein (broken down)
gene regulation in prokaryotes? where does it happen? when does it happen?
Gene expression has only transcription and translation and happens in the cytoplasm
Transcription and translation occur at almost the same time
Regulated during transcription
what are constitutive genes?
always switched on; transcribed continually
Other genes have transcription induced or repressed by transcription factors when the cell needs them
what are regulatory genes?
code for transcription factors which in term controls the expression of structural genes.
what are transcription factors?
proteins that control gene expression at the transcription stage.
Bind to DNA close to promoter region or to RNA polymerase to induce or repress the expression of specific genes.
structural genes?
code for proteins and RNA not involved in gene regulation. eg. enzymes, protein channels, tRNA etc.
where is the LAC Operon found?
Prokaryote model
Found in E.coli and some other bacteria
what is an operon?
unit of DNA under regulation of a single promoter that codes for several proteins.
is the lac operon always on? what does it express? what does it form?
Lac operon is an inducible operon (switched on or off)
Expresses three structural genes that make three enzymes in the presence of lactose
Lactose breakdown into lactose and galactose
Would waste energy if enzymes were made constituently especially as E. Coli does to use lactose as main energy source
what features does the lac operon have?
Promoter region- binding site for RNA polymerase
An operator- binding site for transcription factors (repressor in this case)
Three structural genes- lac Z, Y and A
how does the lac operon work?
Adjacent to the lac operon is lacI which makes the lac repressor
lacI gene is constituent (repressors always present)
Repressor binds to lac operon operator preventing RNA polymerase from binding and therefore producing enzymes
When lactose is present, lactose binds to the lac repressor inhibiting the transcription factor from binding ti the operator
RNA polymerase can bind and transcribe the genes, making enzymes to breakdown lactose
prokaryotes: number of chromosomes, type of chromosomes, amount of DNA, amount of genes, amount of non-coding DNA, type of DNA, packaging of DNA, operon regions?
One chromosome per cell Circular chromosome without telomeres Much less DNA Fewer genes Less non-coding DNA Contains plasmids- small circular DNA DNA is not packaged into an organelle Genes cluster into functional groups known as operon regions
eukaryote:
number of chromosomes, type of chromosomes, amount of DNA, amount of genes, amount of non-coding DNA, type of DNA, packaging of DNA, operon regions?
Multiple chromosomes per cell Linear chromosomes Much more DNA More genes more non-coding DNA No plasmids but chloroplasts and mitochondria have DNA DNA is tightly packaged No operon region
what similarities do prokaryotes and eukaryotes have in genetic material?
Both have double-stranded DNA made up of nitrogenous bases
Both have mRNA
The way mRNA codons are translated into aa is similar
