Proteins: Functions, Structure and Synthesis Flashcards
What are the main functions of proteins?
-Carry out enzymatic functions
-Generating movements of cells
-Carrying signals from cell to cell and within individual cells
-Providing support to cells and tissues
What are the main features of proteins?
- Proteins are linear chains of amino acids arranged in a 3D structural hierarchy
- Diversity of structures, resulting in a wide range of functions. Functions depend on the 3D protein structure. Its 3D structure is determined by a proteins amino acid sequence.
Without its normal conformation (native folding), the protein loses its biological activity.
What are IDSs? Intrinsically disordered Proteins?
Are proteins that have lost their native, functional folding, resulting in an insoluble aggregation in many organs (causing many diseases)
What can the accumulation lead to?
the neurotoxic effects in neurodegeneration diseases: Beta amyloid protein is one of the IDPs associated with neurodegenerative diseases like Parkinsons, prion disease and Alzheimers diseases.
What are amino acid monomers?
- Proteins are assembled essentially from a set of 20 different amino acids
- Amino acids have in common: Carbon a(alpha), amino (-NH2) and carboxyl (-COOH) functional groups
- R group or side chain is specific for each amino acid
What makes up an amino acid?
-Alpha carbon, amino and carboxyl
What are peptide bonds between amino acids called?
Polypeptides
What do the peptide bonds between amino acids do? diagram
- In a protein, amino acids are linked together by covalent peptide bonds formed between carboxylic acid and amino groups of two consecutive amino acids.
- The continuous peptide bonds between amino acids form linear, unbranched polypeptides and the backbone of the protein.
- The R groups are protruding the outside
- Every proteing has a unique sequence of amino acids with a carboxyl end (C-term) and an amino end (N-term)
What is the four level protein structure?
he architecture of proteins has four levels of organisation: Primary, Secondary, Tertiary and Quaternary
What is the Primary structure of proteins?
- The unique sequence of amino acids in a polypeptide chain, with no folding
Based on the length of the sequence:
- Peptide=short chain(<50 amino acids)
- Protein=longer chain (>50 amino acids)
Also referred to polypeptides. Both are composed of repetition of amino acids.
What is the Secondary Structure of proteins?
- Secondary structure consists of stable spatial coils and folds of segments within a polypeptide chain. They are formed by H-bonds between the backbone amino and carbonyl groups and often involving repeating structural patterns (helices and sheets)
- Typical secondary structures are:
-Coil called (alpha a) helix
-Folded structure called B (beta) pleated sheet related to its amino acid sequence
What is the Tertiary Structure of Proteins ?
- Tertiary structure is the three-dimensional folding pattern determine by interactions among various side chains. It determines the overall folding/conformation of a polypeptide chain subunit.
- It is stabilised primarily by:
-Hydrophobic interactions (weak and reversible) between non-polar side chains
-Ionic bonds and strong covalent bonds called disulfide bridges (of cysteines) between non-polar side chains.
-Hydrogen bonds involving polar side chains and backbone amino/carboxyl groups
What is the Quaternary Structure of Proteins?
- Quaternary structure is the result of the association of two or more polypeptide chain subunits into a closely packed arrangement. For example:
1) Haemoglobin, to transport oxygen in red blood cells, consisting of four polypeptide chains: two a (alpha) and two (B beta)
2) Tubulin, the component of microtubules, consisting of 2 polypeptide chains: a (alpha) and B(beta)
How do you recognise DNA structure?
deoxyribose lacking OH-at 2’, nucleotide sugar (Pentose)
-double stranded
How do you recognise RNA structure?
RNA-Ribose having OH- at 2’’, nucleotide sugar (Pentose)
-single stranded
What is protein synthesis in Eukaryotic cells?
Protein synthesis (or gene expression) consists in two phases-transcription and translation (separated by the RNA maturation in the eukaryotic cells)
Where does Transcription take place?
Where does Translation take place?
What is Transcription?
The process of converting DNA (double stranded) to mRNA(single stranded)
-It occurs in the nucleus
Why does Transcription take place inside the nucleus?
DNA is too large to leave the nucleus (RNA can pass through the nuclear pores)
What is the process of Transcription?
RNA polymerase uses one of DNA strands as a template to produce pre-messenger RNA (pre-mRNA-codes for proteins) with a complementary sequence to DNA.
- It adds nucelotides (complementary base pairing -U INSTEAD OF T) in the 5’-3’ direction.
- Only 1 strand of the 2 strands of DNA is transcribed.
- DNA transcription consists of 3 stages
What are the 3 stages of Transcription?
-Initiation
-Elongation
-Termination
DNA Transcription -Initiation
Initiation step - RNA polymerase, with the help of transcription factors, binds to a specific sequence of DNA (promoter-just before the start site of a gene). Each gene has its own promoter. This ensures that the genetic region will be transcribed into RNA.
- RNA polymerase separates the double strands and use a single strand as a template
- 2 initial RNA nucleotides are joined together to begin the complementary RNA strand synthesis
DNA transcription -strand elongation and termination steps
Elongation step - RNA polymerase moves along the DNA coding sequence in 5’-3’ direction. It melts duplex DNA whilst it adds ribonucleotides to the growing RNA (by phosphodiester)
Termination step- The RNA polymerase encounters a specific termination sequence (stop site). This releases the RNA strand. The newly RNA transcript is a precursor of mRNA (or pre-mRNA)
What RNA complementary strand will be made from the following sequence?
DNA- TAC GCA TGA CTA ACT
RNA -AUG CGU ACU GAU UGA
What are the complementary base pairs for DNA,
T, A, C, G
-T with A
-C with G
What are the complementary base pairs from a DNA sequence to an RNA sequence?
T,A,C,G ? U?
-Use U instead of T
-U with A
-C with G
What is RNA Processing ?
The pre-mRNA must undergo RNA processing steps, before it can be exported to the cytosol
What are the 3 RNA processing steps?
- Capping at 5’ end
- Polyadenylation at 3’ end
- splicing
What is Capping at 5’ end?
A modified nucleotide 5’ cap, a 7-methylguanylate is added to the ribonucleotide at 5’ by a usual 5’-5’ triphosphate linkage (this will allow the attachment to the ribosome later)
What is Polyadenylation?
- A repetition of poly-A (100-250bp of ribonucleotide A) is added to the 3’ end
- Its functions includes: increasing the stability of mRNA molecules (preventing its degradation) and facilitates its migration to the cytosol
What is splicing?
Splicing is a large assembly of RNA and protein (spliceosome) excises (cuts out) introns and exons are joined together.
Splicing - What are INTRONS ?
internal sequences that do not code for proteins, junk RNA
Splicing - What are EXONS?
segments that DO code for proteins, expressed.
What happens after RNA processing?
After RNA processing, pre-mRNA becomes a mature mRNA and is exported to the cytoplasm to start the translation.
What is Translation?
- (RNA to protein) is the conversion of the information from RNA (4 nucleotides) into protein (20 amino acids).
-It occurs in the cytoplasm on the ribosomes.
Where does Translation occur?
In the cytoplasm on the ribosomes.
During the process of Translation what does the mRNA do?
mRNA carries information from DNA in groups of these consecutive nucleotides, Codons. Each Codon specifies one amino acid (Universal Genetic Code), except stop codons.
What is RNA made up of?
RNA is made of 4 different nucleotides, 64 combinations of three nucleotides are possible for 20 amino acids. Some amino acids being specified by more than one codon.
-Which is why we use a codon table
What are the steps of Translation?
What is a STOP codon?
What is a codon table ? How do I read it ? diagram / practise
What are tRNA molecules ?
adaptors between amino acids and codons
- A charged tRNA carrying the next amino acid binds to A site on the ribosome and interacts with the mRNA codon.
- The C-term of the polypeptide chain forms a peptide bond to the NH2 group of the amino acid at A site
- mRNA is translated in the 5’ to 3’ direction
- The protein is growing from N-term to C-term direction
- The ribosome translocates along the mRNA to the next codon
- The spent tRNA is ejected and A site is open to bind the next charged tRNA
- -Short RNA folded into a 3D structure
- Adaptors between codons of mRNAs and the corresponding amino acid
- ensure that the genetic code is applied
-Two structures to mediate this adaption: Anticodon, 3 nucleotides that bind the complentary mRNA codon.
-3’ end (acceptor stem) attached to the specific amino acid that matches the codon
- Some amino acids are linked to >tRNA
- Many tRNAs can pair with >1 codon (’wobble’ base pairing - non perfect complementary)
What is a codon?
What is an Anticodon?
Ribosomes as Protein Synthesising machines
- Machinery to synthesise proteins
- In eukaryotes, ribosomes (80S) consist of a small (40S) and a large subunit (60S)
- Each subunit contains three binding sites for tRNA molecules A, P and the E site.
- During Translation, tRNAs move through sites A to P to E.
What is A site?
Where the incoming charged tRNA bind to mRNA
What is P site?
Binds to the tRNA holding the growing polypeptide chain of amino acids
What is the E site?
Where the spent tRNA is ejected
What is a ribosomal subunit ? diagram
What are the 3 phases of Translation?
- Initiation
-Elongation
-Termination
What is translation Initiation ?
the ribosome gets together with the mRNA and the first tRNA.
- tRNA carrying methionine (linked to the start codon) binds the small subunit
- Ribosomes bind to the mRNA 5’ end by recognising the 5’ GTP cap 9RNA processing)
- Ribosomes slide along the mRNA (direction 5’-to-3’) until the start codon (AUG), which matches the anticodon of the linked tRNA
- The large subunit attaches to the small one so that the tRNA is aligned on site P, completing the formation of an 80S initiation complex
Translation Elongation step
amino acids are brought to the ribosome by tRNAs and linked together to form a chain.
- A charged tRNA carrying the next amino acid binds to A site on the ribosome and interacts with the mRNA codon.
- The C-term of the polypeptide chain forms a peptide bond to the NH2 group of the amino acid at A site
- The ribosome translocates along the mRNA to the next codon
- The spent tRNA is ejected and A site is open to bind the next charged tRNA
- mRNA is translated in the 5’ to 3’ direction
- The protein is growing from N-term to C-term direction
Translation - Termination step
1) Translation halts at a stop codon (UAA, UAG, and UGA)
2) The stop codons are not recognised by a tRNA and do not specify an amino acid
3) Release factors bind to any stop codons that reached the A site
4) The ribosome releases the mRNA and dissociates into its two subunits
Proteins exert a variety of what?
Essential biological functions within human cells
Each protein has a unique what? which determines?
Unique amino acid sequence, which determines both its three-dimentional shape and its biological activity. The correct folding is essential for their activities.
DNA is transcribed into what? and where?
pre-mRNA in the nucleus
Pre-mRNA is processed where ? and matured into what?
In the nucleus (RNA processing) and matured into mRNA, in order to leave the nucleus and enter the cytoplasm.
mRNA is transcribed to what? and where?
Proteins (translation process) in the cytoplasm on ribosomes following the genetic code
