- WELCOME TO PART ONE OF THE VIDEO TUTORIALS
ON PROTEINS AND ENZYMES,
A VERY IMPORTANT AND INTERESTING CLASS OF BIOMOLECULES,
ESPECIALLY A CHEMIST
BECAUSE THEY'RE THE CATALYSTS FOR MANY REACTIONS.
LET'S GET STARTED.
SO, THE MAJOR BUILDING BLOCK
OF PROTEINS AND ENZYMES IS AMINO ACIDS.
AND WE WILL ABBREVIATE THAT AA QUITE A BIT,
SO KIND OF SAVE SOME PEN STROKES,
AND SPECIFICALLY, THEIR ALPHA-AMINO ACIDS.
SO, WHAT THAT MEANS IS WE HAVE THIS CARBON
THAT WE CALL THE ALPHA CARBON.
AND SO THE CARBOXYLIC ACID
AND THE AMINE ARE BOTH BONDED TO THAT SAME CARBON,
THE ALPHA CARBON.
NOW, THESE FEATURES ARE THE SAME FOR EVERY AMINO ACID.
SO, THIS PART IS IMPORTANT TO KNOW ABOUT.
AND WE'LL LOOK AT THE CHEMISTRY HERE.
BUT IT'S THE R GROUP.
THIS IS THE PART THAT CREATES THE IDENTITY OF AN AMINO ACID.
SO, IT SEPARATES VALINE FROM ALANINE FROM PHENYLALANINE,
SO IT CREATES THE IDENTITY OF AN AMINO ACID, ALL RIGHTY.
SO, IT'S IMPORTANT TO GET THAT OUT OF THE WAY.
AND THEN REMEMBER, RIGHT,
THAT CARBON ALWAYS WANTS FOUR BONDS,
SO THERE'S AN UNDERSTOOD HYDROGEN THERE.
WE JUST WANT TO KEEP THAT IN OUR AWARENESS.
HOWEVER, THESE--
NORMALLY IS THERE ARE LOTS OF CHEMISTRY
THAT CAN HAPPEN HERE BUT JUST WITHIN OUR BIOLOGICAL FLUIDS,
WE HAVE CARBOXYLIC ACIDS, WHICH ARE A WEAK ACID,
AND AMINES THAT ARE WEAK BASES.
AND SO WHEN WE LOOK AT THIS AMINO ACID
AT A PHYSIOLOGICAL PH,
WE WILL SEE THAT IT FORMS A ZWITTERION,
THAT WE HAVE TWO CHARGES ON THE SAME ION, RIGHT?
SO, A ZWITTERION IS SIMPLY AN ION WITH TWO CHARGES.
THE INTERESTING THING
ABOUT AMINO ACIDS IS THAT SOME OF THEM WE ARE NOT ABLE
TO PRODUCE INSIDE OUR BODY SIMILAR TO LIKE VITAMIN C,
LIKE-- SO HUMANS AND GUINEA PIGS ARE ABOUT THE ONLY MAMMALS
THAT CAN'T SYNTHESIZE VITAMIN C. SO,
THERE ARE AMINO ACIDS THAT WE'RE NOT ABLE
TO PRODUCE INSIDE OUR BODY.
AND SO FOR THESE AMINO ACIDS,
WE MUST GET THEM FROM OUR FOOD.
AND SO IT'S JUST ANOTHER EXAMPLE
OF HOW IMPORTANT IT IS TO PAY ATTENTION
TO WHAT WE'RE EATING AND PUTTING IN OUR BODY.
SO, LET'S LOOK A LITTLE MORE CLOSELY AT THESE AMINO ACIDS.
NOW, I DON'T EXPECT YOU TO MEMORIZE THEM ALL.
I WILL GIVE YOU A LIST, NOT QUITE THIS FORM.
THIS FORM GIVES A LITTLE BIT TOO MUCH INFORMATION,
BUT YOU'LL ALWAYS HAVE A LIST OF THE AMINO ACIDS.
SO, WE WANT TO NOTICE SOME CHARACTERISTICS, RIGHT?
SO, IT'S ALL ABOUT LOOKING AT THE R GROUP.
AND THERE IS ONE TYPO ON THIS HANDOUT RIGHT HERE,
THAT THE R GROUP WAS--
ONE CARBON WAS OVERLOOKED.
AND SO WHAT'S BEEN BOXED HERE ARE THE R GROUPS.
SO, FOR THIS GROUP, THE R GROUPS ARE ALL NONPOLAR,
EVEN HERE WHERE WE HAVE A NITROGEN OR A SULFUR,
AND HERE'S ANOTHER NITROGEN.
THESE ARE STILL CONSIDERED NONPOLAR.
THIS IS AN AROMATIC RING.
AND THAT'S WHY WE DON'T RECOGNIZE THAT POLARITY THERE.
AND THEN WHERE I COPIED THIS TABLE FROM, THEY BROKE--
THEY TOOK THIS OTHER GROUP OF AMINO ACIDS
AND IT CALLED THEM ALL POLAR.
NOW, I DON'T REALLY LIKE THAT CLASSIFICATION.
WE'RE GOING TO GO WITH POLAR DOWN HERE WHERE THEY'RE NEUTRAL.
SO, IF WE LOOK AT ALL OF THESE R GROUPS,
WE SEE HYDROXYL GROUPS AND THIOL GROUPS AND AMINES.
SO, WE WILL DESCRIBE THESE R GROUPS AS POLAR.
HOWEVER, FOR THESE R GROUPS HERE,
NOTICE WE'RE GOING TO DO ACIDIC.
NOTICE THAT THEY ALL HAVE A CARBOXYLIC ACID, RIGHT,
AS PART OF THE R GROUP,
OR THEY HAVE BASIC.
THERE'S AN AMINE PRESENT.
AND THEN OF COURSE FROM THE PREVIOUS PAGE--
OH, I PROBABLY-- WE SHOULD RECOGNIZE OF COURSE
THAT THERE'S ACID-BASE CHEMISTRY GOING ON THERE.
SO, WE WANT TO TRAIN YOUR EYE
TO RECOGNIZE THAT EVERY AMINO ACID IS GOING TO HAVE AN AMINE
AND A CARBOXYLIC ACID.
AND THEN THERE'S OUR ALPHA CARBON.
SO, THE ALPHA CARBON IS THE HUB.
ALL BONDS, YOU KNOW,
ALL PARTS OF THE AMINO ACID LEAD TO THE ALPHA CARBON,
THE AMINE, THE CARBOXYLIC ACID, AND THE R GROUP.
THEN YOU WANT TO BE ABLE TO RECOGNIZE THE R GROUPS
AND CLASSIFY THEM AS POLAR,
ACIDIC, BASIC, OR NONPOLAR.
AND ONE LAST THING, SO ON THE PREVIOUS PAGE,
I MENTIONED THE AMINO ACIDS.
SO, LOOKING AT THIS LIST HERE,
THE ESSENTIAL AMINO ACIDS ARE ALL INDICATED BY A STAR,
IF YOU'RE CURIOUS WHO THEY ARE.
AND A LOT OF BOOKS MAKE A BIG DEAL
ABOUT THEM BEING ALPHA-AMINO ACIDS,
AND THEN A COUPLE PAGES INTO THE CHAPTER,
IT GETS OMITTED BECAUSE AT THAT POINT,
EVERYONE'S SUPPOSED TO KNOW IT.
SO, DON'T LET THAT PRESENCE OR ABSENCE OF AN ALPHA FOOL YOU.
IF WE'RE TALKING ABOUT BIOCHEMISTRY,
WE'RE TALKING ABOUT ALPHA-AMINO ACIDS.
AND THEN I JUST WANTED TO SPEND
A LITTLE BIT MORE TIME EXPLORING THESE ACIDIC AMINO ACIDS.
PART OF THE CHALLENGES
OF THIS COURSE ARE THAT YOU ARE LEARNING BIOCHEMISTRY
WITH ABOUT THE MINIMUM AMOUNT OF CHEMISTRY BACKGROUND POSSIBLE,
AND SO AS YOU READ DOCUMENTS,
NOT EVERYBODY IS GOING TO BE SENSITIVE
TO YOUR BEGINNER QUALITY.
AND SO I WANTED TO POINT OUT
TO YOU A COUPLE THINGS LINGUISTICALLY,
IS FOR EXAMPLE HERE,
I HAVE REPRODUCED THE TWO ACIDIC AMINO ACIDS,
AND WE CAN SEE THEIR CARBOXYLIC GROUPS.
SO, EVEN THIS--
SOMETIMES THIS BUGS STUDENTS, THIS HAS A ASPARTIC ACID
BUT THERE ARE NO PROTONS PRESENT OR A GLUTAMIC ACID,
AND THERE'S NO PROTONS PRESENT.
SO, AS YOU'RE READING DOCUMENTS,
REMEMBER THE ACID-BASE CHEMISTRY.
AND SO IF WE LOOK HERE,
WE SEE HERE'S OUR ALPHA-AMINO ACID,
NOTICE THERE'S BEEN A LITTLE BIT
OF ROTATION AROUND THAT ALPHA-AMINO ACID,
BUT THAT'S OKAY BECAUSE WE KNOW ABOUT CONFIRMATIONS.
AND WHAT WE CAN SEE
HERE THEN IS THERE'S OUR CARBOXYLIC ACID AND AMINE,
SO HERE'S OUR R GROUP.
AND SO IF WE LOOK AT THESE TWO AMINO ACIDS,
WE RECOGNIZE THEM AS ASPARTIC ACID.
SO WE'LL USE THE ACID TERM WHEN PROTONATED, RIGHT?
AND THEN THE CORRECT TERM IN--
WHEN IT'S DEPROTONATED WOULD BE ASPARTATE.
AND SO THE MAIN REASON FOR THIS PAGE
AND THE NOTES IS FOR YOU JUST TO RECOGNIZE
THAT THIS ACID-BASE REACTION HAS A VERY LOW ACTIVATION ENERGY,
IT HAPPENS VERY QUICKLY.
AND SOMETIMES, AUTHORS ARE NOT--
THEY DON'T EXHIBIT PROTON AWARENESS.
SO, EVEN THOUGH THIS FEELS LIKE IT'S NAMED INCORRECTLY,
AT THIS POINT,
YOU KNOW ENOUGH CHEMISTRY,
YOU'RE SUPPOSED TO BE ABLE TO OVERLAY YOUR KNOWLEDGE
OF ACID-BASE CHEMISTRY ON THE AMINO ACIDS.
SO, IN A SIMILAR FASHION,
IF WE LOOK AT THIS R GROUP FOR GLUTAMIC ACID,
WE LOOK HERE AND WE RECOGNIZE THIS AS THE R GROUP.
AND SO THE MOST CORRECT TERM
WOULD BE TO DESCRIBE THIS AMINO ACID AS GLUTAMATE.
AND THEN WHEN IT'S FULLY PROTONATED,
WE CALL IT GLUTAMIC ACID.
SO, JUST REMEMBER, RIGHT,
THAT HERE IN BIOLOGICAL PH,
THEY'RE SHOWING UP AS CARBOXYLATES.
AND IN THEIR NEUTRAL FORM,
THEY WOULD BE PROTONATED AND HAVE THE ACID.
AND LINGUISTICALLY,
YOU CAN ALWAYS INTERCONVERT TO EITHER FORM.
ALL RIGHTY.
SO, THIS CONCLUDES OUR INTRODUCTION TO AMINO ACIDS.
NOW WOULD BE A GREAT TIME TO WORK A FEW HOMEWORK PROBLEMS
TO REINFORCE YOUR UNDERSTANDING.