Notesale: Turn your study into money

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Introductory Biology, Fall 2018
MIT OpenCourseWare
Barbara Imperiali: "We have a small class this year because of changes in the institute with
pass/fail types of things
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Ray and I consider this to be a special
opportunity for us to run the course a little bit differently with a few more quirks and surprises
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Study biology in the 21st century is a fabulous opportunity
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Biology
would not be where it is today in the absence of science , engineering to promote it and to
support progress in biology
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So there 's a common molecular logic of very complex
processes
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You look at the molecules and you
see how form fulfills function , which is something I 'm really excited about
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People believe that the building blocks of life came together from things like
hydrogen cyanide , or sulfide
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They 're photosynthetic
bacteria
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Evolution of homo sapiens can
be thought of as something that we can keep track of a bit through fossil records over the last
five million years
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Then the humanoids gradually became
different, evolved
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Human and neanderthal diverged from the chimpanzee a certain time ago based on the
molecular clock that's available
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Despite this huge breadth of sizes and huge differences in organisms, the building
blocks are the same
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Watson and
Crick had no clue how the DNA could encode and program the synthesis of a protein
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8 meters of DNA in it
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Cells are different in size
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Professor Martin: We 'll talk about the importance in
model organisms in discovering new biology
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One topic that I 'll start on when I start lecturing either at the end of
this month or beginning of October is genetics
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In addition to considering single
cells, we also want to understand how entire organisms and tissues work
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And this changes three hours into development
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It goes from being a single layer to now having
multiple layers
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We can
study this in fruit fly embryos or many other model systems in order to try to understand
mechanistically how this happens
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And a
breakdown of this control is important in the progression of cancer
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I find that students are a little hesitant to come to my office
hours
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And so if you like to run, you can just meet there
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10 Angstrom equals 1
nanometer
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The course will
literally do this take you from one end of the scale to the other
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noncovalent bonding is what gives us
dynamics
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and then today, we 'll talk about lipids and membranes
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If we did n't have the membrane bilayer, once again, we wouldn't have life in the
same way that we have it now
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They make up 98% of the cellular mass
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and then last of
all, there are some rogue ones that there 's even smaller amounts in physiologic systems
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all the information that
you need has been condensed
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the most important thing about hydrogen,
carbon, nitrogen, oxygen,, phosphorus and sulfur is they love to make covalent bonds
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the side chain
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phosphorus and sulfur are a little tricky,, but there is some good news
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Functional groups are oftentimes where chemistry happens or biochemistry happens
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the carboxylate group is important because it loses a proton
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It 's often ionized can form an electrostatic interaction between themselves
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and then the composite groups that I want to mention to you in particular are the
amide and the ester
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noncovalent bonding is synonymous with dynamics forces

that can be readily broken and reassembled
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it takes a
lot to break those bonds
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them at will to go and do some biological
activity
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carbonhydrogen, carboncarbon bonds are at the higher
end about 100 kilocalories per mole
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the next most important bond is the hydrogen bond
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hydrogen bonding is very important to form the threedimensional
structures of proteins
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two
types of interactions are the hydrophobic interactions and Van der Waals forces
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There is the Van der Wals force
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What do you need to be
able to do is understand them and recognize them in complex
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Proteins are the largest molecules in cells
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And amino acids are made of peptides
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All of these
things are made of smaller molecules
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"Proteins have a lot of interesting properties
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This is
what allows them to interact with other molecules and do their jobs in cells
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This is what allows them to do their jobs in
cells
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This is what allows them to
carry out their functions in cells
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Proteins have a lot of noncovalent forces
between their atoms which allows them to interact with other molecules and do their jobs in

cells
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This section will be about the building blocks of your protein macromolecules
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They comprise 50% of all the macrumolecules
that have a lot of different functions
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There is a side chain that dictates the properties
of the amino acids
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The next most abundant type of amino acids have hydrophobic side chains
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But in an amino acid such
as tyrosine, it's likely to be charged
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The building blocks are not functional themselves
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The order in which amino acids appear is dictated by the order of the amino acids
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Amino acids are assembled in a unique linear polymer of defined order
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Proteins can be 1,000, 1,500, or thousands of amino
acids
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When nature bonds all these amino acids together, it carries out a condensation reaction to
form a peptide bond between these two components of the amino acid, the amine and the
carboxylic acid
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All of these show freedom of
rotation
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So it's
as if you've got a linear polymer but every third bond has kind of stuck in a particular orientation
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When I condense three amino acids,
I spit out two molecules of water and I put in place two amide or peptide bonds
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There're nuances of the structure
that may be lit for good for a later discussion
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Enzymes & Metabolism

MIT OpenCourseWare
A protein variant that is the cause of sickle cell anemia is a heterotetrameric protein
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We'll talk about why those things
cause changes
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The proteins stretch out into their denatured state
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Salts and organics
may slip into a hydrophobic core and break them up
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A defect in a transport protein that carries
oxygen around the body is a defect in hemoglobin
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So these are tiny changes in the protein that cause dramatic
changes in its structure and function of the protein
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The iron heme complex is responsible for the red color of your blood cells
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There are four proteins, beta
globin, alpha globin, and beta globins, that are 146 amino acids long in each of them
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One change in beta globin means two changes in the structure of the whole
structure of hemoglobin
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Sickle red blood
cells have evolved to move smoothly through your capillaries
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And when you
have the defect where all of your hemoglobin is messed up with this variation, it is incredibly
painful
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This is a dimer of tetramers
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So what I can do is I can show you
everything as a cartoon and get rid of all those little lines
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Phenylalanine and leucine are both
hydrophobic, providing a patch on the one tetramer where the valine from the other tetramer

combined
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And there's one you can't see that's tucked
behind
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But the people who were healthy, normal homozygotes for the right hemoglobin, were
infected with plasmodium falciparum
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And there are other bloods tested which shows the same correlation
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Typical enzymes take a substrate to a product
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It just depends on the transformation that you're doing
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h is the enthalpy t is the
temperature in kelvin
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In a chemical transformation, we care about delta g
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How fast the reaction goes is described in a different
part of this diagram
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So the higher that
mountain is, the slower the reaction will be because it is a much harder transformation to go
through
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Enzymes are the ultimate green reagents
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So catalysts do change
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And we'll talk about how
they do that the end
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You want to
think about the reactions and then just think about ways in which an enzyme could contribute to
that
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There are loads and loads of different principles
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The last type of inhibitors that are important are the ones that bind at different
sites on the enzymes
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So these are the way small molecules
work
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Carbohydrates and Glycoproteins
MIT OpenCourseWare
" The professor is discussing how enzymes are important in catalysis, and how defects in
enzymes can lead to disorders
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both of these families have a nitrogen atom in the middle
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now, what
happens when we add a phosphate? the phosphate is attracted to the nitrogen and then it forms
a bond with the nucleobase
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it 's not like a covalent bond
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this bond is like a pi bond
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now, another important
component of nucleic acids is the sugar
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phosphodiesters are made up of two molecules of sugar
connected by a phosphorus atom
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what happens when we add another nucleobase from one of these families? well, now we
have a molecule that has four rings
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now, there are other sugars that can be found in nucleic
acids glucoses and galactoses but we will only be talking about glucose for this lecture
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now, what does this mean for our understanding of dna? well, first of all,

glycosidic bonds are very stable they don't break down easily
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finally, glycosidic bonds also allow for
the attachment of proteins to DNA which is why they are so important in molecular biology
In nature, we use the nucleotide building blocks or the nucleotides in many different ways
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And so here, I'm showing you some really important nucleotide that
are found in nature
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There are five
nucleobases in DNA, two purines and three pyrimidines
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There are reasons for these differences, and I'll nudge into some of
those chemical differences in a moment
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And there are glycosidases that cleave the bond from the base to the sugar
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In the biosynthesis of DNA, you keep on adding new nucleotides to the 3 prime end
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But we also build them n to c
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As long as a u in there, you know RNA
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The
noncovalent structure of nucleic acids is the most exciting part of this entire endeavor
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That data actually gave a clue to some of the dimensions of the
double-stranded DNA structure
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Pauling's model came about from his worry about other things and not focusing on the DNA
structure
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So, let's
try to explain Chargaff's data by looking at the nucleobases and thinking about how they might
come together
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The antiparallel orientation is important for the thermodynamic stability and the

optimum hydrogen bonding interaction of all those bases that are pairing
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And it turns out, though, when you try to pair the two
strands in a parallel orientation, they're very uncomfortable
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So you can get two daughter double
strands from a single parent double strand
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RNA forms various structures, so much more irregular structures than DNA
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RNA is the message that you make transiently to
program a protein being made and then you want to get rid of it
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They called this process "dna origami" because you can build up complex structures by
folding DNA into shapes
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The components of nucleic acids are
organized in an antiparallel orientation, so one end runs 5 prime to 3 prime
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The goals of the next four classes are to show you how the structures of nucleic acids really are
purposed for the sorts of processes that they undergo
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Isotopes are elements that share the same number
of protons and electrons, but they differ in the number of neutrons
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