MB PRELIM LEC 4: PROTEINS Flashcards by Sunwoo's Berry

Products of transcription & translation of nucleic acids
Polymers of amino acids
Manifest the phenotype directed by the nucleic acids

PROTEINS

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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

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amino acids become
completely +/- charged at certain pH
levels

pK values

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pH where amino acids are
neutral

pI values

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covalent C-N bonds that
connect amino acids in proteins

Peptide bonds

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polymer of few amino acids

Peptide

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Sequence of amino acids in proteins
which determines the nature & activity
of that protein

PRIMARY STRUCTURE

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 Local interactions between amino acid side chains
 Ordered beta/ beta pleated sheets and less-ordered alpha helices, or random coils

SECONDARY STRUCTURE

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Further folding secondary structures of
proteins

TERTIARY STRUCTURE

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Protein structure consisting of more than one polypeptide

QUATERNARY STRUCTURE

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CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Only amino acids
EX: Albumins, globulins, histones

SIMPLE PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Proteins and nonprotein component
(prosthetic group)
EX: Lipoprotein (Low density lipoproteins), glycoproteins (mucin), metalloproteins (ferritin & hemoglobin)

CONJUGATED PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON COMPOSITION
- Simple (conjugated proteins having been partially hydrolyzed by acids,
enzymes or alkalis
EX: Proteases, fibrin

DERIVED PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Spherical
- Enzyme, messengers, transporters, regulators, & sometimes structural
EX: Hemoglobin

GLOBULAR PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Sheet-like filamentous
- Protection, structural role
EX: Collagen

FIBROUS PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON STRUCTURE
- Intermediate to fibrous to globular
- Blood clotting
EX: Fibrinogen

INTERMEDIATE PROTEINS

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CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Act as catalysts
EX: Nucleases

ENZYMES

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CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Transport substance across biological membrane
EX: Channel proteins (sodium ion channels)

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TRANSPORT PROTEINS

CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Reserves of metal ions and amino acids
EX: Ferritin

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STORAGE PROTEINS

CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Generate movement
EX: Myosin

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MOTILITY PROTEINS

CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Maintain cell shape
EX: Collagen

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STRUCTURAL PROTEINS

CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Protection against harmful agents
EX: Antibodies

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DEFENSIVE PROTEINS

CLASSIFICATION OF PROTEINS BASED ON FUNCTIONS
- Regulate different processes and activities
EX: Enzymes

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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

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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

1. 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 2. INITIATION FACTOR 2 (IF-2) BOUND TO GTP & the INITIATING tRNAMet (eukaryotes) / tRNAfmet (bacteria, mitochondria, & chloroplasts), then joins the complex 3. 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

1. Trna carrying the next amino acid binds to the A site in a complex 2. 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) 3. 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

MB PRELIM LEC 4: PROTEINS Flashcards

(44 cards)