Chapter 4 - Translation & Protein Structure Flashcards
What is different between amino acids?
their side chains
What is the structure of an amino acid?
central alpha carbon atom, connected by covalent bond to an amino group (NH2) a carboxyl group (COOH), a hydrogen atom (H) and a variable side chain denoted by R.
What happens to the amino group in a cellular environment?
it gains a proton to become NH3^+ and carboxyl group loses a proton to become COO^-
how many different amino acids are most commonly found in proteins?
20
What are hydrophobic amino acids?
they do not readily interact with water or form hydrogen bonds
most have a non polar R group of hydrocarbon chain or uncharged carbon rings
How does the bonding work in hydrophobic amino acids?
water molecules in cell hydrogen bond with each other
hydrophobic R groups aggregate each other but stabilised by weak Van der Waals forces
Where do hydrophobic amino acids tend to reside?
buried within interior folds of proteins
how does bonding work in hydrophilic amino acids?
form hydrogen bonds with water
R group gains proton becomes positively charged
Where are hydrophilic amino acids usually found?
in surface of folded protein molecules
can bind to other charged particles - allows for association with macromolecules like DNA
What are the 3 amino acids with special properties?
glycine, proline, cysteine
What is the R group of glycine?
H
What does glycine’s R group allow for?
small size allows for freer rotation around C-N bond
What does freer rotation enabled by glycine enable?
increases the flexibility of the polypeptide backbone, can be important in the folding of protein
What is special about the R group of proline?
is linked back to the amine group linkage creates a kink or bend in the polypeptide chain and restricts rotation of C-N bond
What does the linkage of amine group in proline cause?
constraints on protein folding in its vicinity
What is the R group of Cysteine?
SH
What can happen when 2 cysteine molecules come close together? what does it allow/mean?
they can react to form a disulfide bond, which covalently joins the side chains = stronger than ionic interactions and form cross bridges that can connect different parts of the same protein or even different proteins
What bonds connect successive amino acids?
peptide bonds
where do peptide bonds form in amino acids? and what is released when they form?
forms between carboxyl group and amino group of amino acid
a molecule of water is released
What is the C=O group in amino acid chain bond?
Carbonyl
What is the N-H group in amino acid chain bond?
amide
how do electrons behave in peptide bond?
they are more attracted to C=O group because of greater electronegativity of oxygen atom.
What are some characteristics of a double bond?
shorter
not free to rotate
What is a polymer of amino acids called?
polypeptide
What is the longest polypeptide?
muscle protein titin at 34,350 amino acids
what are amino acid residues?
amino acids incorporated into proteins
What is primary structure?
sequence of amino acids
What is secondary structure?
interaction between stretches of amino acids
What is tertiary structure?
longer range interactions between secondary structures
What is quaternary structure?
several individual polypeptides that interact with each other
how do secondary structures form?
result from hydrogen bonding in the polypeptide backbone
Who conducted the X -ray crystallography experiment?
Liam Pawling & Robert Corey in 1950s
What was the X-Ray crystallography experiment?
x rays through crystal forms a series of spots = position of arrangement of atoms in a molecule
What are alpha helices?
twisted tightly with right handed coil - 3.6 amino acids per complete turn
What are beta pleated sheets?
folds back and forth with hydrogen bonds
forms chains that are antiparallel = more stable
What are tertiary structures formed by?
interactions between R groups and spatial distribution of hydrophobic or hydrophilic amino acids
loops or turns in the backbone allow R groups to sit near each other
Who experimented with ribonuclease?
Christian Anfinsen in 1961
What did Christian Anfinsen prove?
that the sequence of amino acids, in itself, determines the way the chain folds itself and that no additional genetic information is required in the process
What are quaternary structures formed from?
polypeptide subunits can come together and bind
they can be identical or different polypeptides
How can the subunits affect each other?
they can influence each other’s behaviour
e.g. in haemoglobin when binds with oxygen, other subunits change and increase affinity for oxygen
What are Chaperones?
they help protect slow-folding or denatures proteins until they can attain their proper 3D structure
How do Chaperones work?
they bind with non polar R groups to shield them from inappropriate aggregation. in repeated cycles of bind and release give polypeptides time to find shape
What are ribosomes?
complex structures of rRNA and protein that bind with mRNA and are the site of translation
What do ribosomes consist of?
a small subunit and a large subunit each composed of 1 to 3 types of rRNA and 20 t0 50 types of ribosomal protein
What does the large subunit have to allow for translation?
3 binding sites for molecules of tRNA called the A (aminoacyl) site, the P (peptidyl) site, and the E (exit) site.
What is the role of the ribosome?
making sure mRNA is read in successive, non-overlapping groups of 3 nucleotides
What is each non-overlapping trio of nucleotides called?
a codon
What does each codon code for?
an amino acid
What are reading frames?
different places to start, synthesis of the mRNA nucleotide sequencing (only correct if translated into the proper reading frame
What is tRNA?
small RNA molecules of 70-90 nucleotides. Each has a self-pairing structure can be drawn as a clover leaf
What is an anticodon?
3 nucleotides that undergo base pairing with the corresponding codon. each tRNA has the nucleotide sequence CCA at its 3’ end and the 3’ hydroxyl of the A is the attachment site for the amino acid corresponding to the anticodon
What connects specific amino acids to specific tRNA molecules?
enzyme aminoacyl tRNA synthetase
What is a tRNA with no attached amino acids called?
uncharged
What is a tRNA with attached amino acids called?
charged
What do codons specify for?
an amino acid according to genetic code
What is the codon at which translation occurs called?
initiation codon
What amino acid does the codon AUG specify?
Met (methionine)
When initiated what does met form?
amino end of polypeptide, in many cases is cleaved off, also AUG codon specifies the incorporation of met at internal sites within polypeptide chain
What does the position of the codon establish?
the reading frame that determines how the downstream codons are to be read (non-overlapping bases of groups of 3 after AUG codon)
When does the process of translation stop?
when a stoop codon is reached - polypeptide is finished and released into cytosol
How many amino acids in humans? specified by how many codons?
20 amino acids specified by 61 codons
When an amino acid is coded by more than 1 codon what is it considered?
redundant
What are the patterns of redundancy?
results almost exclusively from the 3rd codon position
When an amino acid is specified by 2 codons, they differ either whether the 3rd position is a U or C, or an A or G
When an amino acid is specified by 4 codons the identity of the 3rd codon does not matter
Who conducted experiment to decipher the genetic code?
Har Gobind Khornana
What did Har Gobind Khornana do?
constructed synthetic RNAs with predetermined sequences, added to solution for translation - manipulated the repeating sequences to determine the reading frames and identify what bases produced which amino acids
What are the 3 stages of translation?
initiation, elongation, termination
what is initiation?
initiator AUG codon recognised, met = first amino acid. translation starts
What is elongation?
successive amino acids added
what is termination?
addition of amino acids stops and completed polypeptide chain released from ribosome
why do we need elongation factors?
ribosome movement along mRNA and peptide bonds require energy
What are the 3 stop codons?
UAA, UAG, or UGA
In prokaryotes what does translation start at?
Shine-Dalgarno sequence
What is a operon?
when functionally related genes located in a line along the DNA are transcribed in a single unit from one promoter
What does a operon result in?
formation of polycistronic mRNA
What is a protein family?
a group of proteins that are structurally and functionally related as a result of their shared evolutionary history
what is a folding domain? (proteins)
region of a protein that folds in a similar way relatively independently of the rest of the protein
What can amino acid evolution through mutations and selection allow for?
allows for complex proteins to evolve against seemingly long odds
What is a mutation?
a change in sequence of the gene (can affect function)
What is selection? (mutations)
in a population of organisms, random mutations are retained or eliminated through the process.
based on individuals ability to survive and reproduce (most are eliminated)
