Protein Stuff

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Protein Stuff
2013-08-24 11:49:50

Exam 1; crossover between chp. 3 & 4
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  1. tRNA is made up of 4 parts:
    • 1) acceptor stem: CCA nucelotides on the 3' end are found universally; attachment of an amino acid to the A at the 3' end yields an aminoacyl-tRNA
    • 2) D loop: mostly contains a dihydrouridine
    • 3) TΨCG loop: contains ribothymidine and pseudouridine are present here
    • 4) anticodon loop: the triplet at the tip = anticodon (base pairs to corresponding codon in mRNA)
  2. polypeptides exhibit directionality:
    • -N-terminus is usually on the left and is composed of unlinked amino group
    • -C-terminus is on the right and is composed of a free carboxyl group; during translation amino acids are added to the C-terminus end of a growing polypeptide chain
  3. start codons
    AUG (some bacteria use GUG or CUG); start of all polypeptides begins with amino acid methionine
  4. stop codons
    UAA, UGA, or UAG; don't code for amino acids just code for stop
  5. aminoacyl-tRNA synthetase
    (20 different kinds) an enzyme that catalyzes the esterification of an amino acid to any of its compatible tRNAs (there can be more than 1) to form an aminoacyl-tRNA; once this happens, a ribosome can transfer the amino acid from the tRNA onto a growing peptide
  6. peptide bond
    forms by the joining of N-terminus and C-terminus via dehydration reaction; covalent bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule; resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide (4-atom functional group -C(=O)NH- = peptide link)
  7. initiation factors (IFs)
    mediate initiation phase of translation; help small/large ribosomal subunits assemble around mRNA that has tRNA positioned at its start codon
  8. eIF1, eIF1A, & eIF3
    all bind to the ribosome subunit-mRNA complex; implicated in preventing 60S from binding to 40S before elongation should start; eIF3 uses the eIF4F complex to position the mRNA strand near the exit site of the 40S ribosome subunit, promoting assembly of the pre-initiation complex
  9. key steps of elongation (summarized)
    • 1) entry of each succeeding aminoacyl-tRNA with an anticodon complementary to next codon on mRNA
    • 2) formation of a peptide bond
    • 3) the movement of the ribosome one codon at a time along the mRNA
  10. Eukaryotic elongation factors
    carry out elongation in eukaryotes via two elongation factors; eEF-1 and eEF-2; are very similar to those in prokaryotes
  11. eEF-1
    eukaryotic elongation factor that has two subunits, α and βγ; α meadiates entry of the aminoacyl tRNA into a free site of the ribosome (counterpart to prokaryotic EF-Tu); βγ serves as the guanine nucleotide exchange factor for α, catalyzing the release of GDP from α (counterpart to prokaryotic EF-Ts)
  12. eEF-2
    eukaryotic elongation factor that catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation; (counterpart to prokaryotic EF-G)
  13. Kozak Sequence
    A_ _AUGG

    this sequence on an mRNA molecule is recognized by ribosome as the translational start site; ribosome requires this sequence to initiate translation; a purine (adenine or guanine) is three bases upstream of the start codon (AUG), which is then followed by another G
  14. protein release factors (RF's, two types)
    eRF1: shape is similar to a tRNA and works by binding to A and recognizing stop codons

    eRF3 (+ GTP): works with eRF1 to promote cleavage of the peptidy-tRNA, therefore releasing the polypeptide chain
  15. proteins are important for/function as:
    • -organization of the genome
    • -organization of other proteins
    • -organization of lipid bilayer membranes
    • -organization of the cytoplasm
    • -regulation (control of protein activity)
    • -signaling (monitoring the environment/transmitting information
    • -transport (moving molecules across membranes)
    • -enzymatic activity (catalysis)
    • -generating force for movement (motor proteins)

    -all of these function evolve from specific binding interactions/conformational changes
  16. primary structure
    linear arrangement (sequence) of amino acid residues; peptides = 20-30 residues, while polypeptides = 200-500 residues
  17. secondary structure
    staple spatial arrangements of segments of a polypeptide chain held together by hydrogen bonds; the main 3 types are alpha helix, beta sheet, and the beta turn

    -in the average protein 60% of the chain exists as alpha helices and beta sheets
  18. irregular structure
    used to describe a protein that lacks the classic 3 defined types of secondary structures but still have a well-defined stable shape
  19. alpha helix
    when the backbone of a segment of a polypeptide forms a spiral structure where the carbonyl Oxygen atom of each peptide bond is hydrogen-bonded to the amide Hydrogen atom of the amino acid FOUR residues along the chain

    -there's a complete turn of the spiral every 3.6 RESIDUES (.54nm per turn)
  20. beta sheet
    consists of laterally packed strands 5-8 residues long; hydrogen-bonding occurs between backbone atoms in separate but adjacent beta strands
  21. beta turn
    composed of 4 residues, are sharp bends on the surface of a protein that reverse the direction of the polypeptide backbone (often toward a protein's interior); glycine and proline are often found in beta turns; turns help large proteins fold into compact shape
  22. tertiary structure
    refers to the overall conformation of a polypeptide chain; primarily stabilized by hydrophobic interactions between nonpolar side chains; tertiary structure of a protein is NOT RIGID because it depends on the environment within which a protein is found in
  23. depending on their tertiary structure, proteins can be classified into 3 categories:
    1) fibrous proteins: large, elongated, stiff molecules often composed of tandem copies of a short sequence that forms a single repeating secondary structure (ex: collagen); usually play a structural role or help with movement

    2) globular proteins: water-soluble, compactly folded structures, often spherical that comprise a mixture of secondary structures

    3) integral membrane proteins: embeded within phospholipid bilayer of cell membranes

    these aren't mutually exclusive!
  24. coiled coil
    structural motif when alpha helices from multiple (1-4) polypeptide chains coil around each other ('coil of coils'); individual helices bind tightly to each other because of aliphatic (aka hydrophobic) side chains that merge together like the teeth of a zipper (leucine and valine are often represented, which is why these are also called leucine zippers)
  25. EF Hand
    two helical structures connected by a loop; used to detect calcium levels in the cell; depending on the concentration conformational changes in the protein can be induced
  26. zinc finger
    contains 3 secondary structures: an alpha helix and 2 beta sheets (oriented nonparallel); the combination forms a finger-like bundle held together by a zinc ion
  27. same structural motif in different proteins with similar functions indicates:
    that the conservation of such secondary structures has been evolutionarily beneficial
  28. domains (3 types)
    1) functional: a region of protein that exhibits a particular activity characteristic of the protein

    2) structural: 40 or more amino acids arranged in a stable, distinct secondary or tertiary structure that often can fold into its characteristic structure independently of the rest of the protein

    3) topographical: regions of proteins that are defined by their distinctive spatial relationships to the rest of the protein
  29. basic helix-loop-helix
    structural motifs are used for protein binding to DNA and subsequently the regulation of gene activity
  30. multimeric proteins
    proteins that consist of two or more polypeptide chains or subunits
  31. quaternary structure
    describes the number (stoichiometrically) and relative positions of the subunits in multimeric proteins
  32. oligomerization
    the assembly of individual proteins into a multimeric protein; permits proteins that act sequentially in a pathway to increase their efficiency of operation
  33. homologs
    proteins that have a common ancestor; main evidence for homology among proteins = similarity in sequence or structure
  34. native state
    the most stably folded form of the molecule; in terms of thermodynamics, native state = conformation with the LOWEST free energy
  35. chaperones
    proteins that catalyze the 3D folding of newly synthesized polypeptide chains
  36. nonsense suppression
    when a mutation that converts a codon that normally codes for an amino acid into a stop codon is suppressed by the subsequent matching notation in a the corresponding tRNA molecule; formation of the polypeptide chain progresses as planned
  37. two ways a cell can increase the rate at which it synthesizes a protein:
    • 1) by translating an mRNA strand using multiple ribosomes (simultaneously); [polyribosomes]
    • 2) rapidly recycling ribsomal subunits after they disengage from the 3' end of an mRNA
  38. molecular chaperones
    bind and stabilize unfolded/partially folded proteins, preventing said proteins from aggregating and then being degraded
  39. chaperonins
    form a small folding chamber into which an unfolded protein can be kept separate from interfering elements, giving it time and an appropriate environment to fold properly
  40. example of chaperonin folding mechanism: GroEL
    • 1) partially folded/misfolded peptide is inserted into the cavity of the barrel-like GroEL
    • 2) protein binds to inner wall and folds into native conformation
    • 3) ATP-dependent step: GroEL undergoes conformational change and releases folded protein after GroES caps an open end of GroEL (ATP converted to ADP + Pi)
  41. protein misfolding causes disease:
    misfolded proteins not only can't function properly, but are marked for degredation; when degredation is incomplete or can't keep up with the number of misfolded proteins, insoluble protein plaques form and contribute to degenerative diseases (Ex. parkinson's, alzheimer's, mad cow's)