Module 5: Protein Structure, Function & Synthesis Flashcards
Proteins are ___, ___, &___
ubiquitous, diverse and versatile
Many of the cellular activities and reactions that are involved in cellular function are ___ by ____
mediated by proteins
3 Models of Protein Structure
- ball- and - stick model
- ribbon model
- space-filling model
Proteins are linear polymers of a combination of ____
20 amino acids
Protein function…
is related to structure.
Amino acids are the…
and made up of…
(4 components)
building blocks of proteins
Four components (each component is bound to the alpha carbon):
1. carboxyl group (-)
2. amino group (+)
3. hydrogen
4. side chain/ R group
- make each amino unique
- responsible for chemical and physical properties of each amino acid monomer
Amino Acid Classification
R groups are grouped according to their properties
Based on:
- how they interact with water (hydrophobic or hydrophilic)
- basic or acidic
- polar or non polar
Hydrophobic Amino Acids
- tend to buried in interior of folded proteins
- hydrophobic R groups aggregate together away from the water
- Weak van der Waals forces help with stability by causing hydrophobic R groups to be attracted to each other
Hydrophilic Amino Acids
- contain EN elements like N and/or O
- results in unequal charge, allows R groups to interact with each other or with H2O via H-bonding
- Basic AA tend to be + charged
- Acidic AA tend to be - charged
- charged groups can form ionic bonds with one another and other charged molecules
- typically found on “outer” surface of proteins
Glycine
Gly, G
- has H as R group
- not asymmetric
- small and nonpolar, allows free rotation around C-N bond
- this increases the flexibility of the polypeptide backbone
Proline
Pro, P
- makes a pentagon with 3 CH2s
- linkage restricts rotation of the C-N bond, limits amount of protein folding around proline
Cysteine
Cys, C
- CH2 bonded to SH for R group
- allows two cysteines to form a S-S disulfide bond, forms a cross bridge
- the cross-bridges can connect different parts of the same protein or different proteins together
Linking Amino Acids
- adjacent amino acids are joined by peptide bond (between amino of one AA and carboxyl of another AA)
- this is a dehydration (or condensation) reaction
– releases H2O - free AA group at end of peptide forms the N- terminus
- carboxyl group at end is C-terminus
A polymer of AA connected by peptide bonds is a ____, used synonymously with ____
polypeptide
protein
Protein Structure
amino acid in a protein gives the structure and thus the function
- proteins fold a certain way based on sequence of AA and the order of the R groups
- 4 levels of organization:
primary, secondary, tertiary, quaternary
- the three-dimensional structure of a protein is the protein conformation, this is described by 2’, 3’, 4’
Primary Structure
- specific linear sequence of amino acids that make up the polypeptide chain, from amino to carboxyl end
- most polypeptides contain many amino acids, these are coded for by the genome
- primary structure determines 2’, 2’, 4’ structure of the protein
- sequence of primary structure can be written either as three letter or one letter abbreviations
- R groups alternate position on either side of the chain of amino acids
– this affects protein folding and interaction of R group
Secondary Structure
- describes conformation of portions of the polypeptide chain
- two types, alpha helix & beta sheet
- results from H-bonding between neighbouring amino acids of the polypeptide backbone, occur between functional groups
- R groups are not involved
Alpha Helix
- very stable structure
- right handed helices, let molecules that are not nearby in main structure interact with one another
- forms due to H-bonds to the 4th amino acid neighbour above and below in the spiral
- the carbonyl group of the one AA and the amide group of the 4th AA
Beta Sheet
- segments of the polypeptide lying side by side, assumes a pleated (folding) conformation
- can be parallel and antiparallel
- structure is stabilized by H-bonds formed between carbonyl groups in one chain and amide groups in the other chain within the same polypeptide
Tertiary Structure
- describes the conformation of the entire protein, single polypeptide chain folded into 3’ structure
- ultimately this is how the regions of 2’ conformations are oriented
- results in its functional form, unless part of protein with multiple subunits
- structure determined by:
– spatial distribution of hydrophilic and hydrophobic R groups
– chemical bonds and interactions that form between R groups
– H-bonds, hydrophobic, ionic, disulfide bonds - overall shape of (3’) functional protein may result in areas of protein that form active sites for enzymes, exterior R groups may impact how protein interacts with other molecules or proteins
Quaternary Structure
- Many proteins are made up of more than one polypeptide chain, subunit
- the spatial arrangement of these subunits is the 4’ structure
- these arise due to the same bonds as found in 3’ structure
- polypeptide chains in each subunit may be:
– identical - Homodimer
– non-identical - heterodimer
In transcription the sequence of DNA is used as…
a template, it makes the mRNA
In translation the sequence of bases in mRNA is used to…
specify the order of amino acids to be added to the growing polypeptide, its the final stage of the central dogma
Components of Translation:
- mRNA (messenger)
- Ribosome
- tRNAs (transfer)
- Aminoacyl tRNA synthetases
- Initiation factors, elongation factors & release factors
Ribosomes
- protein factories
- this is where translation takes place
- complex structure of RNA and protein
– consist of small subunit and large subunit - eukaryotic ribosomes are larger than prokaryotic ribosomes
- the mRNA is bound by the large and small ribosomal subunits, then moves through center of ribosome
- 5’ to 3’ reading individual codons to incorporate the appropriate amino acids
What is a codon?
- a nucleotide combination that specifies the placement of an amino acid (codes for it)
- Read in groups of 3
- reading frame is where the ribosome begins reading the sequence of nucleotides
Where does translation begin?
- does not begin with the first 5’ RNA base on the mRNA
- begins with start codon AUG
- codes for methionine
Ribosome Sites
3 functional sites
1. the aminoacyl tRNA is accepted in the A site
2. the peptide bond formation happens in the P site
3. the tRNA exits the ribosome in the E site
Transfer RNAs
- translation needs the transfer RNA molecule, i.e. tRNA
- small molecules containing 70 -90 nucleotides (know are small)
- each tRNA bonds with itself, forms base pairs
- results in a structure that looks like a cloverleaf
- two important sites on each tRNA
– the 3’ hydroxyl site on the 5’-CCA-3’ end of the tRNA is where the specific amino acid attaches
– three bases in the anticodon loop make up the anticodon
How are amino acids attached to the tRNA?
specific amino acids area connected to specific tRNA molecules by enzymes called aminoacyl tRNA synthetases
- a tRNA without an amino acid attached is uncharged
- a tRNA with an amino acid attached is charged
- tRNA synthetases are very accurate
The Genetic Code
- during translation, the anticodon of the tRNA base pairs with the codon on the mRNA
- base pairing is the specificity of DNA-RNA or codon-anticodon interactions
- anticodons of tRNA base pair in antiparallel fashion
– so first base of codon pairs with last base of anti-codon - genetic code has 20 amino acids but specified by 64 codons
- many amino acids are specified by more then one codon, makes the genetic code redundant or degenerate
- bases read 5’ to 3’ on mRNA chart
Translation Stages
Has 3 stages
1. Initiation
- AUG codon is recognized and Met is the first amino acid
2. Elongation
- each successive amino acid is added to the growing polypeptide chain
3. Termination
- adding amino acids stops and the polypeptide chain is released from the ribosome
Eukaryotic Translation Initiation
- steps 2 & 3 of translation are similar between prokaryotes and eukaryotes
– step 1 is different - in eukaryotes the initiation complex forms at the 5’ cap of the mRNA
– the small ribosome and initiation factors will then “scan” the mRNA for the start codon on the mRNA -AUG - once start codon is reached the large ribosomal subunit is then recruited and translation can start
- initiation factors are released
Translation Elongation
- after the ribosome is assembled, a new tRNA enters the A site, allows peptide bond to form
- amino acid on the tRNA in the P site transfers to the tRNA in the A site during elongation
- the reaction is catalyzed by an rRNA molecule in the large ribosomal subunit
- ribosome then shifts one codon to the right
- this moves uncharged tRNA (Met) to the E site
- the peptide bearing tRNA moves to the P site
- this frees the A site for the next charged tRNA in line to come in based on the next codon
Translation Termination
- process continues until one of 3 codons are reached
- UAA, UAG, UGA these are stop codons, they don’t code for an amino acid
- a protein release factor binds to the A site of the ribosome at the stop codon
- causes bond that’s connected to polypeptide of the tRNA to break
- creates the carboxyl terminus of the polypeptide, completes the chain
Prokaryotic Translation Initiation
- prokaryotes don’t have 5’ cap
- initiation complex is formed at one or more internal sequences present in mRNA, Shine-Dalgarno sequence
- elongation and termination are like in euks
Regulating Protein Synthesis
- not all genes are expressed in the cell all the time
- many levels of regulation in cell
– DNA accessibility
– transcription factors
– RNA processing
– post-translational modifications
Protein Sorting in Eukaryotes
- mRNA is bound to a ribosome in the cytosol, where translation begins
-what happens to the protein post translation depends on how its going to be sorted, specific signal sequences - no signal, stay in cytosol
- amino terminal signal sends to chloroplast or mitochondria
- internal signal sends to nucleus
Some proteins have a specific amino terminal signal sequence for transport to the ____
ER
- it is bound by the signal recognition particle, SRP
- the ribosome with associated mRNA and newly formed polypeptide are transported to the ER
Proteins produced by ribosomes on the rough ER could be found:
- embedded in the ER membrane, inserted as it is synthesized
- within the lumen of the endomembrane system
- secreted out of the cell
