MB PRELIM LEC 4: PROTEINS Flashcards
- Products of transcription & translation of nucleic acids
- Polymers of amino acids
- Manifest the phenotype directed by the nucleic acids
PROTEINS
AMINO ACIDS STRUCTURE
a. Carboxyl group (COO-)
b. Amino group (NH2 group bonded to C atom)
c. R (radical) group/side chains
d. Central C atom
amino acids become
completely +/- charged at certain pH
levels
pK values
pH where amino acids are
neutral
pI values
covalent C-N bonds that
connect amino acids in proteins
Peptide bonds
polymer of few amino acids
Peptide
Sequence of amino acids in proteins
which determines the nature & activity
of that protein
PRIMARY STRUCTURE
Local interactions between amino acid side chains
Ordered beta/ beta pleated sheets and less-ordered alpha helices, or random coils
SECONDARY STRUCTURE
Further folding secondary structures of
proteins
TERTIARY STRUCTURE
Protein structure consisting of more than one polypeptide
QUATERNARY STRUCTURE
CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Only amino acids
EX: Albumins, globulins, histones
SIMPLE PROTEINS
CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Proteins and nonprotein component
(prosthetic group)
EX: Lipoprotein (Low density lipoproteins), glycoproteins (mucin), metalloproteins (ferritin & hemoglobin)
CONJUGATED PROTEINS
CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Simple (conjugated proteins having been partially hydrolyzed by acids,
enzymes or alkalis
EX: Proteases, fibrin
DERIVED PROTEINS
CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Spherical
- Enzyme, messengers, transporters, regulators, & sometimes structural
EX: Hemoglobin
GLOBULAR PROTEINS
CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Sheet-like filamentous
- Protection, structural role
EX: Collagen
FIBROUS PROTEINS
CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Intermediate to fibrous to globular
- Blood clotting
EX: Fibrinogen
INTERMEDIATE PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Act as catalysts
EX: Nucleases
ENZYMES
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Transport substance across biological membrane
EX: Channel proteins (sodium ion channels)
TRANSPORT PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Reserves of metal ions and amino acids
EX: Ferritin
STORAGE PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Generate movement
EX: Myosin
MOTILITY PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Maintain cell shape
EX: Collagen
STRUCTURAL PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Protection against harmful agents
EX: Antibodies
DEFENSIVE PROTEINS
CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Regulate different processes and activities
EX: Enzymes
REGULATORY PROTEINS
- Ordered sequence of nucleotides on a
chromosome that encodes a specific functional protein - Fundamental physical & functional unit of inheritance
- 1 st studied by tracking mutations
GENES
GENES COMPOSITION:
- coding sequence of a gene
STRUCTURAL SEQUENCES
GENES COMPOSITION:
- does not code for proteins, they regulate transcription of a gene
EX: promoter
REGULATORY SEQUENCES
THE GENETIC CODE
Gene’s nature was further clarified
Deciphered by
Francis Crick,
Marshall Nirenberg,
Philip Leder,
Gobind Khorana,
& Sydney Brenner
A dictionary to translate the 4-nucleotide sequence information in DNA to the 20- amino acid sequence information in proteins
1965:
3-nucleotide code: 43 = 64 Triplets were assigned to amino acids
Redundant (all except 2 methionine &
tryptophan, have more than 1 codon)
Wobble in the 3rd position - Triplets coding for the same amino acid often differing in the 3rd base of the triplet
Nonsense codons - Terminate protein synthesis: UAG, UAA, UGA
GENETIC CODE
“There must be a molecular factor that can recognize components for both nucleic acid & protein sequences.” > tRNA (over 50 in humans & 40 in bacteria)
Adaptor hypothesis
START OF PROTEIN SYNTHESIS:
- activation of the amino acids by covalent attachment to tRNA & catalyzed by 20 aminoacyl tRNA synthetases
tRNA charging
START OF TRANSLATIONS
Classes of aminoacyl tRNA synthases:
- act on the 2’ OH of the tRNA
acceptor stem
CLASS I OR II?
CLASS I
START OF TRANSLATIONS
Classes of aminoacyl tRNA synthases:
- act on the 3’ OH
CLASS I OR II?
CLASS II
Site of protein synthesis
RIBOSOMES
80S ribosomes
- 60S large subunit (2.7 million daltons) = 5S rRNA + 5.8S rRNA + 28s rRNA + 40 ribosomal proteins
- 40S small subunit (1.3 million daltons_ = 18S rRNA + 30 ribosomal proteins
PROKARYOTES OR EUKARYOTES?
EUKARYOTES
70S ribosomes
- 50S large subunit (1.8 million daltons) = 5S rRNA + 23S rRNA + 34 ribosomal proteins
- 30S small subunit (1 million daltons) = 16S rRNA + 21 ribosomal proteins
- mRNA & initiating factors
PROKARYOTES OR EUKARYOTES?
PROKARYOTES
TRANSLATION PROCESS:
BEGINNING of translation, when the small ribosomes subunit assembles with mRNA & then the large ribosomal subunit
INITIATION
TRANSLATION PROCESS:
BINDING of charged tRNAs & formation of the peptide bond producing growing polypeptide
ELONGATION
TRANSLATION PROCESS:
ENDING of translation, occurs when the complex encounters a nonsense codon
TERMINATION
- SMALL RIBOSOMAL SUBUNIT first BINDS TO INITIATION FACTORS 3 (IF-3) & then to specific sequences near the 5’ end of mRNA (ribosomal binding site)
- GUIDES THE START CODON (AUG) to the proper place in the ribosomal subunit - INITIATION FACTOR 2 (IF-2) BOUND TO GTP & the INITIATING tRNAMet (eukaryotes) / tRNAfmet (bacteria, mitochondria, & chloroplasts), then joins the complex
- LARGE RIBOSOMAL SUBUNIT associates w/ HYDROLYSIS OF GTP resulting to formation of the initiation complex
tRNAmet (eukaryotes)/ tRNAfmet (bacteria, mitochondria, & chloroplasts) is situated & can only bind to the peptidyl site (P site)
All other tRNAs bind to
TRANSLATION: INITIATION
accepts an incoming tRNA bound to an amino acid
A SITE
holds a tRNA that carries a growing
polypeptide (first amino acid added is methionine
(Met)
P SITE
- Trna carrying the next amino acid binds to the A site in a complex
- 1st formation of peptide bond between amino acids in A & P sites by transfer of the 1st amino acid to the next, generating a dipeptidyl-trna in A site (catalyzed by PEPTIDYL TRANSFERASE)
- Dipeptidyl-trna shifts from A site to P site (translocation) with the release of the “empty trna” from the E site
During translation, the growing
polypeptide begins to fold into its mature conformation
- Assisted by molecular chaperons
TRANSLATION: ELONGATION
TRANSLATION: TERMINATION
Signaled by 1 of the 3
stop/nonsense/termination codons:
UAA, UAG, or UGA
hydrolysis of the finished polypeptide from the final trna > release of the final trna from the ribosome > dissociation of large and small ribosomal subunits
TERMINATION/RELEASE FACTORS
