RELEVANT TOPICS TO BE COVERED:

I. BIOMOLECULAR STRUCTURE: PROTEIN AND DNA

II. HOW DNA IS MADE

III. HOW PROTEINS ARE MADE

IV. COMPUTER RESOURCES

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I. BIOMOLECULAR STRUCTURE: PROTEIN AND DNA

PROTEINS ARE LIKE BIG MASS OF SPAGHETTI NOODLES. THE SPAGHETTI NOODLE REPRESENTS A CHAIN OF AMINO ACIDS CALLED A POLYPEPTIDE.

ONE PROTEIN CAN BE ONE POLYPEPTIDE CHAIN, HOWEVER, ONE PROTEIN CAN BE MADE UP OF MORE THAN ONE POLYPEPTIDE CHAIN. IF THE PROTEIN HAS 2 POLYPEPTIDE CHAINS, THEN IT IS SAID TO HAVE
"SUBUNITS."

THE TYPICAL PROTEIN IS AN ENZYME; OTHERS ARE STRUCTURAL PROTEINS (MAKE UP TENDONS, ETC.).

MOST PROTEINS ARE SPHERICAL (CALLED "GLOBULAR") WHEREAS OTHERS ARE SHAPED LIKE A ROD (ROD-LIKE OR FIBROUS PROTEINS). ALL ENZYMES ARE SPHERICAL WHEREAS COLLAGEN (A STRUCTURAL PROTEIN) IS FIBROUS.

IN ONE AREA ON THE SURFACE OF ENZYMES (CALLED THE ACTIVE SITE), A MOLECULE CALLED A SUBSTRATE IS BOUND.

THROUGH THE FORMATION OF NEW CHEMICAL BONDS BETWEEN THE ENZYME AND THE SUBSTRATE, THE ENZYME "TUGS" ON THE SUBSTRATE AND SPEEDS UP ITS BREAKDOWN (THERE ARE MANY MECHANISMS FOR ENZYMES).

THE 3-D SHAPE OF THE PROTEIN (CONFORMATION) IS CRUCIAL TO SET UP THE CORRECT FIT WITH THE SUBSTRATE. THE CONFORMATION OF THE PROTEIN (HOW THE SPAGHETTI NOODLE IS ARRANGED IN SPACE) IS DUE TO MANY WEAK BONDS BETWEEN VARIOUS PARTS OF THE PROTEIN. STRONG BONDS ARE BETWEEN MONOMERS OF THE CHAIN.

SEE KID'S TOY; STRONG BONDS ARE LIKE WOODEN STICKS WHEREAS WEAK BONDS ARE LIKE RUBBER BANDS.

WEAK BONDS ARE:

1. HYDROGEN BOND (BETWEEN HYDROGEN ATOM AND TYPICALLY OXYGEN ATOM),
2. WEAK IONIC BOND (OR ELECTROSTATIC INTERACTION) BETWEEN + AND - CHARGES
3. HYDROPHOBIC INTERACTION (NONPOLAR AMINO ACIDS CLUMP TOGETHER; SEE DEFN BELOW FOR NONPOLAR AMINO ACIDS).

THERE IS ONE STRONG BOND THAT CAN HELP MAINTAIN 3-D SHAPE OF A PROTEIN: IT IS CALLED THE DISULFIDE BRIDGE AND OCCURS BETWEEN THE R GROUPS OF TWO CYSTEINE AMINO ACIDS.

SOME POLYPEPTIDE CHAINS CAN SPONTANEOUSLY FOLD INTO THE PROPER CONFORMATION BUT OTHERS REQUIRE THE HELP OF "CHAPERONES."

SINCE DNA AND PROTEINS ARE POLYMERS (MADE UP OF MONOMERS); THEY ARE LIKE CHAINS MADE UP OF LINKS.

THEY ARE MADE BY ADDITION OF ONE MONOMER AT A TIME BY A REACTION CALLED DEHYDRATION SYNTHESIS OR CONDENSATION SYNTHESIS.

THERE ARE 20 DIFFERENT AMINO ACIDS USED IN MAKING A PROTEIN.

SOME AMINO ACIDS ARE CHEMICALLY MODIFIED AFTER THE PROTEIN IS MADE.

WHEN ANALYZING PROTEIN AMINO ACIDS, ONE TECHNIQUE CANNOT TELL THE DIFFERENCE BETWEEN GLUTAMINE (GLN) AND GLUTAMIC ACID (GLU), SO THE ANALYZER REPORTS "GLX." THE ANALYZER ALSO CANNOT TELL THE DIFFERENCE BETWEEN ASPARAGINE (ASN) AND ASPARTIC ACID (ASP); SO IT REPORTS "ASX."

AMINO ACIDS HAVE A "BACKBONE" PART THAT FORMS THE ACTUAL CHAIN, THIS PART IS THE SAME FOR ALL 20 AMINO ACIDS. BUT THERE IS ANOTHER PART CALLED THE "R GROUP." THIS R GROUP STICKS OFF AT A RIGHT ANGLE FROM THE BACKBONE PART AND IS DIFFERENT FOR ALL 20 AMINO ACIDS.

THE R GROUP STICKS OFF THE BACKBONE AND CAN CHEMICALLY INTERACT WITH OTHER R GROUPS IN THE SAME PROTEIN, OR WITH R GROUPS OF OTHER PROTEINS, WITH SUBSTRATE'S EQUIVALENT OF "R GROUPS" OR WITH THE SURROUNDING WATER.

IT IS THE WEAK BONDS BETWEEN R GROUPS OF ONE PROTEIN THAT SETS THE PROTEIN'S CONFORMATION.

BASED ON THE R GROUP PRESENT, THERE ARE THREE TYPES OF AMINO ACIDS:

SEE FIGURE 3-2 SHOWING TYPES OF AMINO ACIDS.

IN GENERAL, PROTEINS KEEP THE NONPOLAR AMINO ACIDS ON THE VERY INSIDE (AWAY FROM POLAR WATER SINCE THEY DO NOT INTERACT WELL WITH WATER).

THE SURFACE OF THE ENZYME TYPICALLY HAS POLAR OR CHARGED AMINO ACIDS THAT INTERACT WELL WITH THE SURROUNDING WATER

THE "FRONT" END OF A PROTEIN (WHERE THE NUMBER ONE AMINO ACID IS LOCATED) IS CALLED THE N TERMINUS. THE BACK END IS WHERE THE LAST AMINO ACID IS LOCATED AND IS CALLED THE "C TERMINUS." THIS IS ALSO HOW THE PROTEIN IS MADE.

THE TYPICAL PROTEIN IS 500 AMINO ACIDS LONG.

BY FULLY UNDERSTANDING PROTEIN STRUCTURE, WE WILL BE ABLE TO MAKE A SYNTHETIC PROTEIN WITH A SPECIFIC FUNCTION TO CURE A DISEASE.

LEVELS OF PROTEIN STRUCTURE:

1. PRIMARY

THIS IS A SIMPLE LIST OF AMINO ACIDS FROM THE N TERMINUS TO THE C TERMINUS. THERE IS A STRONG (COVALENT) BOND CALLED A PEPTIDE BOND BETWEEN MONOMERS; THIS STABILIZES PRIMARY STRUCTURE.

CHANGE ONLY ONE AMINO ACID OUT OF THE 146 AMINO ACIDS IN HEMOGLOBIN, HEMOGLOBIN DOES NOT FUNCTION (SICKLE CELL ANEMIA). CHANGE ONE AMINO ACID IN PROTEIN RAS, GET A CANCER CAUSING PROTEIN.

2. SECONDARY STRUCTURE

THE CHAIN FOLDS BACK ON ITSELF IN TWO SPECIFIC WAYS (FIG. 3-7):

A. ALPHA HELIX (LIKE A CORKSCREW- _KNIFE)

B. BETA PLEATED SHEET (LIKE A PLEATED CURTAIN)

NOTE THAT ONLY HYDROGEN BONDS (BETWEEN THE R GROUPS) STABILIZE SECONDARY STRUCTRURE.

SECONDARY STRUCTURE PATTERNS:

NOTE ALPHA HELIX CAN BE REPRESENTED BY A SPIRAL OR A CYLINDER. FOR BETA SHEETS, THE ARROW POINTS IN THE DIRECTION OF THE C TERMINUS.

FIG. 3-8. MOTIFS ARE COMBINATIONS OF SECONDARY STRUCTURE (BETA SHEETS AND/OR HELICES) COMMONLY FOUND IN DIFFERENT PROTEINS. TYPICALLY, LESS THAN 50 AMINO ACIDS ARE INVOLVED ("DOMAIN" REFERS TO COMMON STRUCTURES INVOLVING MORE THAN 50 AMINO ACID AND TERTIARY STRUCTURE). FOR EXAMPLE, THE HELIX TURN HELIX MOTIF IS USED BY DIFFERENT PROTEINS TO BIND DNA. IT IS LIKE TAKING A CARBURETOR FROM A FORD MUSTANG AND PUTTING IT INTO A PONTIAC GRAND PRE.

NOTE THAT "RANDOM COIL" IS THE TERM USED FOR BITS OF POLYPEPTIDE THAT CONNECT THE SHEET OR HELIX.

SILK FIBROIN IS A PROTEIN THAT HAS A LOT OF BETA PLEATED SHEET. THE MOST COMMON AMINO ACIDS IN THIS PROTEIN ARE: GLYCINE, ALANINE, AND SERINE. THESE AMINO ACIDS HAVE SMALL R GROUPS AND PACK TOGETHER BETTER THAN AMINO ACIDS WITH LARGE R GROUPS. THIS MAXIMIZES THE HYDROGEN BONDS IN THE BETA PLEATED SHEET. THE EXTENSIVE WEAK BONDING (HYDROGEN BONDS) IS LIKE VELCRO (EACH BOND IS WEAK BUT THERE ARE SO MANY OF THEM) AND THIS MAKES SILK STRONG.

LEUCINE, METHIONINE AND GLUTAMATE ARE STRONG "HELIX FORMERS."

ISOLEUCINE, VALINE, PHEYLALANINE ARE STRONG BETA SHEET FORMERS.

GLYCINE AND PROLINE ARE "HELIX BREAKERS" AND ARE FOUND LARGELY IN TURNS AND BENDS OF THE POLYPEPTIDE CHAIN (IN THE "RANDOM COIL" SECTIONS). BENDS AND TURNS OCCUR LARGELY AT THE SURFACE OF THE PROTEIN.

3. TERTIARY STRUCTURE

R GROUPS TYPICALLY LOCATED A GREAT DISTANCE FROM EACH OTHER (ON THE SAME POLYPEPTIDE CHAIN) WILL INTERACT. THIS CREATES LARGE LOOPS IN THE PROTEIN (VS. THE SMALL "LOOPS" CREATED IN SECONDARY STRUCTURE'S HELIX OR SHEET).

WEAK BONDS (HYDROGEN BOND, HYDROPHOBIC INTERACTION, WEAK IONIC BOND) AND THE DISULFIDE BRIDGE MAINTAIN TERTIARY STRUCTURE.

DOMAINS: A UNIT OF TERTIARY STRUCTURE. TYPICALLY, A STRETCH OF 50-350 AMINO ACIDS THAT HAS A SPECIFIC FUNCTION (SUCH AS BINDING A SPECIFIC ION LIKE CALCIUM OR CHROMIUM). SMALLER PROTEINS HAVE ONLY ONE DOMAIN, WHEREAS LARGER GLOBULAR PROTEINS HAVE MULTIPLE DOMAINS. DIFFERENT PROTEINS THAT BIND THE SAME ION HAVE A COMMON DOMAIN.

4. QUATERNARY STRUCTURE

DOES THE PROTEIN HAVE SUBUNITS? IF SO, THE PROTEIN HAS QUATERNARY STRUCTURE AND IS CALLED "MULTIMERIC." HEMOGLOBIN HAS FOUR SUBUNITS OF TWO DIFFERENT TYPES (SO HEMOGLOBIN IS TYPE1₂TYPE2₂).

BONDS THAT STABILIZE TERTIARY STRUCTURE ALSO OCCUR BETWEEN POLYPEPTIDE CHAINS OF A MULTIMERIC PROTEIN.

LOOK AT COLLAGEN (MADE UP OF THREE CHAINS OF ALPHA HELICES): DOES IT HAVE ALL LEVELS?

NOTE THAT FIBROUS PROTEINS LIKE COLLAGE HAVE EXTENSIVE SECONDARY STRUCTURE.

DNA IS A NUCLEIC ACID THAT IS LOCATED IN THE NUCLEUS AND KEEPS THE GENETIC INFORMATION (SUCH AS THAT FOR RED HAIR, THIN OR FAT, ETC.). IT IS MADE UP OF 4 MONOMERS CALLED "NUCLEOTIDES."

A NUCLEOTIDE CONSISTS OF THREE PARTS CONNECTED BY STRONG BONDS: A SUGAR, A PHOSPHATE AND ONE NITROGENOUS BASE.

DNA CONSISTS OF TWO CHAINS OF NUCLEOTIDES KEPT TOGETHER BY HYDROGEN BONDS. AS WITH PROTEINS, WITHIN EACH NUCLEOTIDE CHAIN, THERE ARE STRONG BONDS TO KEEP THE MONOMERS TOGETHER. THE TWO STRANDS ARE IN A HELIX; SO DNA IS A "DOUBLE HELIX."

NUCLEOTIDES FOUND IN DNA ARE: A, T, C, G.

RNA IS A SINGLE STRAND OF NUCLEOTIDES. ONE MAJOR TYPE FUNCTIONS TO CARRY THE GENETIC INFORMATION FROM THE NUCLEUS TO THE CYTOPLASM. ALL RNA IS MADE FROM DNA.

NUCLEOTIDES FOUND IN RNA ARE: A, U, C, G (NOTE T IS SUBSTITUTED BY U).

DNA STRUCTURE: FIG. 3-18. NOTE THAT HYDROGEN BONDS ONLY OCCUR BETWEEN CERTAIN NUCLEOTIDE PAIRS: G AND C, AND A AND T.

IN NUCLEIC ACID, THE 5' END IS THE FRONT END, AND THE BACK END IS THE 3' END. SO THE TWO STRANDS ARE ORIENTED IN OPPOSITE DIRECTIONS.

JUST LIKE WITH POLYPEPTIDES, THERE IS A BACKBONE (IN DNA, MADE UP BY PHOSPHATE-SUGAR), AND SOMETHING STICKS OFF THE BACKBONE (THE NITOGENOUS "BASES" PART OF THE NUCLEOTIDE).

HOW DO YOU GET FROM DNA TO A PROTEIN?

DNA MAY HAVE TGAAC

ACTTG

WHEREAS THE PROTEIN HAS THE AMINO ACIDS: ILE-GLY

CENTRAL DOGMA: DNA HOLDS THE CODE (GENES) AND STAYS IN THE NUCLEUS. THEN THE CODE IS TRANSCRIBED TO MESSENGER RNA. MESSENGER RNA CARRIES THE CODE FROM THE NUCLEUS TO THE CYTOPLASM. IT BINDS TO A RIBOSOME WHICH ACTUALLY USES THE CODE TO MAKE THE PROTEIN.

DNA HAS TO UNWIND TO MAKE SINGLE STRANDED mRNA.

THE CODE IS THE SERIES OF BASES (OR NUCLETODIES) FOUND IN THE DNA. THIS CODE IS KNOWN AS A CODON (WHEN FOUND IN mRNA; DNA HAS ANTICODON).

USING THE DICTIONARY OF THE GENETIC CODE, YOU CAN DETERMINE WHAT AMINO ACID DERIVES FROM A CODON.

TRANSCRIPTION- GIVING THE CODE TO mRNA

TRANSLATION; MAKING THE PROTEIN

MOVIES (SciRen CD) and Protein structure with Kinemage

IT IS USUALLY EASIER TO DETERMINE DNA NUCLEOTIDE SEQUENCE ("GENE") THAN PURIFY AND ANALYZE AMINO ACID SEQUENCE OF A PROTEIN. SO, ONCE A DNA NUCLEOTIDE SEQUENCE HAS BEEN DETERMINED, YOU CAN THEN INFER THE AMINO ACID SEQUENCE OF THE PROTEIN.

YOU CAN USE WEB SITES TO COMPARE EITHER DNA NUCLEOTIDE SEQUENCE TO OTHER "GENES" OR COMPARE AMINO ACIDS.

RELATED PROTEINS HAVE SIMILAR SEQUENCE. FOR EXAMPLE, A PRIMITIVE PROTEIN EVOLVED INTO TWO DIFFERENT PROTEINS. INSULIN-LIKE GROWTH FACTOR NUMBER ONE AND TWO EVOLVED RATHER RECENTLY FROM INSULIN.

PROTEINS OF APE ARE VERY SIMILAR TO HUMAN PROTEINS.

HOWEVER, SOME PROTEINS STAY PRETTY MUCH THE SAME THROUGHOUT EVOLUTION; A COUPLE OF PROTEINS (CYTOCHROMES) IN BACTERIA ARE VERY SIMILAR TO HUMAN PROTEINS.