Notesale: Turn your study into money

Document Preview

Extracts from the notes are below, to see the PDF you'll receive please use the links above

---

1st class (27-09):
The seven chemical groups most important in biological processes are the hydroxyl,
carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups
...
of these six, all except the sulfhydryl group are
also hydrophylic and thus increase the solubility of organic compounds in water
...
the hydrogen on this
group can dissociate and this is why molecules with a carboxyl group are acids
...


pH vs pKa is like a battle between solution and molecule for a proton
...
If the pKa is higher than the pH, the molecule
wins the proton
...


Most of the glucose monomers in starch are joined by 1-4 linkages (number 1
carbon to number 4 carbon), like the glucose units in maltose
...
These two ring
forms for glucose are called alpha (a) and beta (b), respectively
...
The glucose
monomers of cellulose are all in the beta configuration, making every glucose
monomer "upside down" with respect to its neighbors
...


Chitin is similar to cellulose, with beta linkages, except that the glucose
monomer of chitin has a nitrogen-containing attachment
...


Introdução às Ciências Biológicas

5

The carbon at one end of the skeleton of a fatty acid is part of a carboxyl group
(COOH)
...

In saturated fats (which lacks double bonds) their flexibility allow the fat
molecules to pack together tightly
...


In phospholipids, the third hydroxyl group of glycerol is joined to a phosphate
group, which has a negative eletrical charge in the cell
...
Choline
is one such molecule
...
However,
the phosphate group and its attachments form a hydrophilic head that has an
affinity for water
...


Steroids are lipids characterized by a carbon skeleton consisting of four fused
rings
...
It is a common
component of animal cell membranes and is also the precursor from which
other steroids, such as the vertebrate sex hormones, are synthesized
...
A high level of cholesterol in the blood may contribute to
atherosclerosis, although some researchers are questioning the roles of
cholesterol and saturated fats in the development of this condition
...
Usually it's a chiral carbon, except on glycine (where the R group is

Introdução às Ciências Biológicas

6

only an H atom)
...

Its four different partners are an amino group, a carboxyl group, a hydrogen
atom, and a variable group symbolized by R
...

18 out of the 19 chiral aminoacids exist in their (s)-absolute configuration form
...
youtube
...


The aminoacids are grouped according to the properties of their side chains
...
Basic amino acids have amino groups in their side chains that are
generally positive in charge
...


Introdução às Ciências Biológicas

8

The pH of the solution in which the aminoacid is determines whether or not the
amino group and carboxyl group are protonated or deprotonated
...
The
dipolar form is also know as the zwitterion form: The amino group is
protonated (it has a full positive charge, NH3+) and the carboxylic group is
deprotonated (it has a full negative charge, COO-)
1) At the low pH of 1, the carboxylic acid group is protonated
...
At around pH=2, the H found in the carboxylic acid group begins to
dissociate->deprotonates, loses the H atom and gains that full negative charge
...
At this basic pH,
the low [H+] causes the amino group to deprotonate losing its hydrogen,
thereby forming a negatively-charged species (NH2 is neutral and COO- is
negative)

The type of bond that holds our amino acids together is a special type of
covalent bond known as a peptide bond or an amide bond
...
To actually
form a peptide bond we have to use ATP molecules as a result of the fact that
the reactants are thermodynamically more stable than our products
...

One end of the polypeptide chain has a free amino group, while the opposite
end has a free carboxyl group
...


Even though the reaction from the products to the reactants is
thermodynamically favorable it is not kinetically favorable what that means is we

Introdução às Ciências Biológicas

9

have to input a lot of energy to actually overcome this reverse activation barrier
and we simply don't have that much energy under normal conditions inside our
cell at a pH of 7 and at the normal body temperature
...


There are hydrophobic amino acids which means that their non-polar side
chains tend to pack together rather than interact with water
...

Phenylalanine contains an unreactive and highly non-polar aromatic ring
...

Tryptophan contains a NH group, making it slightly reactive
...

Cysteine is structurally similar to serine, except it has a thiol group
...

Asparagine and glutamine contain polar carboxamide groups
...
It is achiral and can fit into either
hydrophobic or hydrophilic environments
...
The five-membered ring
of proline makes it structurally restrictive, allowing it to greatly influence the
structure of proteins
...
This makes them highly hydrophilic
Lysine has a relatively long side chain group that is capped by a primary
amino group
...

pKa=10 (if the pH is equal to the pKa that is the point at which half of the
molecules are deprotonated and half of them are protonated) —>Basic
aminoacid
Arginine also has a relatively long side chain group
...
5
...
Histidine can exist in its protonated or deprotonated state at
neutral pH
...
Histidine is
very commonly found in the active sites of many different enzymes
...
1
...
1 these groups are very likely to be protonated but above 4
...
At a physiological pH of around 7 the
carboxylate ion groups will exist in their deprotonated state so they will bear
a full negative charge and that full negative charge will be delocalized
among the two electronegative oxygen atoms and that will be a stabilizing
effect
...

Likewise in its deprotonated state we call glutamate but in its protonated state
we call it glutamic acid

Seven of the 20 amino acids that exist inside our body have sidechain groups
that are readily ionizable and what that means is at certain pH values these
ionizable sidechain groups will be able to exchange hydrogen atoms, they can
donate and accept hydrogen atoms and that gives them the ability not only to
participate in as the base reactions but to also form ionic bonds
...

Every single one of our amino acid contains an alpha carboxyl group that exists
in the carboxylate ion form because the pH of 7 is above the pH of 3
...
0
...
1 so
what that means is if we're at 4
...
At the normal physiological pH because that is higher than
4
...
0
...
3
...
At
the normal physiological pH these three amino acids will always exist in the
acid form
...
At the
normal physiological pH tyrosine will act as a very hydrophobic molecule
and so it will be found inside the protein structure because usually on the
outside we have the polar water molecules and this will observe the
hydrophobic effect

NUCLEIC ACIDS:
A nucleotide, in general, is composed of three parts: a five-carbon sugar (a
pentose), a nitrogen-containing (nitrogenous) base, and one to three phosphate
groups
...

The beginning monomer used to build a polynucleotide has three phosphate
groups, but two are lost during the polymerization process
...


There are two families of nitrogenous bases: pyrimidines and purines
...
The
members of the pyrimidine family are cytosine (C), thymine (T), and uracil (U)
...

The purines are adenine (A) and guanine (G)
...
Adenine, guanine, and cytosine are found in both DNA and RNA;
thymine is found only in DNA and uracil only in RNA
...
This bonding results in a repeating pattern of sugarphosphate units called the sugar-phosphate backbone
...


In both DNA and RNA molecules, each nucleotide consists of a linear backbone
that consists of repeating sugar phosphate units
...


ISOELECTRIC FOCUSING
Since proteins consist of different combinations of readily ionizable amino acids
what that means is they will have different net charge values at some specific
pH value for example they will have different net charges at the physiological
pH of around 7
...
All the charges on all our amino acids on that
protein will exactly cancel one another out
...
Some proteins consist of
the same exact combination of ionizable amino acids so they will have the
same isoelectric point
...
A gel with a pH gradient is
set-up (on one side we're going to have a low pH acidic environment and on the
other end a high pH basic environment)
...
Each protein will move
due to the presence of electric field
...
When they reach the isoelectric point, their net charge of zero will
cause them to stop
...

Examples of a non-ionized amino acid is glycine, valine, alanine, leucine,
isoleucine, etc
...
At some specific temperature value the pKa of this particular
Alpha amino group is 8
...
1
at that same temperature condition
...
1)/2= 5
...

We have aspartate and glutamate
...
1
...
1+3
...
6
...
6 the two negative charges will cancel
out the positive charge found on the terminal alpha amino group and
so at this particular pH value this will have a net charge of zero
...


Introdução às Ciências Biológicas

15

We take the average of the pKa values of the terminal alpha amino
group and the side chain
...
8 and the PKa value of the alpha
amino terminal group is 8
...
8 + 8)/2=9
...
4 the two positive charges will exactly cancel out the negative
charge that is found on the Alpha carboxyl group
Fourth case: If we have an ionizable sidechain group but it is neither basic
nor acidic
Exists two amino acids and they are cysteine and tyrosine
...

Tyrosine has an ionizable sidechain group but it is neither basic nor acidic
...
9, 3
...
0
...
0
...
(8
...
1)/2= 5
...


When we take a molecule to somewhere to the right of the pI value this
molecule will tend to want to move back in the direction of the pI and that's
because anywhere in this region this molecule will have on net negative charge
...


How to determine what the pI value is for a specified
polypeptide?
1- Estimate the pH at which the net charge on the protein would be zero
...

(exemplo no tablet)

Introdução às Ciências Biológicas

16

Given 3 pKa values, when you protonate the R group or the amino acid sidechain you have two outcomes:
If the atom that gets protonated is oxygen or sulfur, you're going to get a
neutral protonated group; seen in acidic amino acids aspartic acid and
glutamic acid; seen in non acidic basic ionizable side-chains, cysteine and
tyrosine
...
In this case we use upper 2 pKa values
...
For histidine, arginine and lysine
we're going to use the pKa of the amine group and the side-chain
...


SDS-POLYACRYLAMIDE GEL ELECTROPHORESIS
Another important method by which we can purify proteins is gel
electrophoresis
...

Inside a structure we have a gel and we connect the entire apparatus to a
voltage source in such a way so that the top portion becomes negatively
charged and the bottom portion becomes positively charged
...

Proteins always move from the negatively charged to the positively charged
(from the top to the bottom)

What are all the forces that are acting on the protein as it
moves down along the gel?

Introdução às Ciências Biológicas

17

We have two forces (three if we consider the force of gravity but because the
force of gravity is so much smaller than the other forces we can neglect it)
...
It points downward
in the direction of motion; the other force is the frictional force that exists as a
result of the gel that is in the way of this protein and then that gel exerts a force
that pushes opposite to the direction of motion
...


From electromagnetism we know that if we have a charge that is inside a
constant electric field then the force our charge feels is simply that electric field
E multiplied by the quantity of charge on that molecule (Q is the charge)
The drag force is equal to the coefficient of friction f multiplied by V, the velocity
of that object
...

V is equal to the product of the electric field and the charge Q divided by the
coefficient of friction f
...

Polyacrylamide is essentially a polymer that intertwines and folds and makes
many pores and channels that allows the protein to move across
...
That's an important property because as the protein
travels along the gel we don't want that protein to react and change its
chemical nature and that's why polyacrylamide is used most often
...
It contains a carbon
chain, at the end it contains a negatively charged sulfate group and it is
connected to a sodium molecule
...

When the protein is denatured, SDS anions attach onto the side chains of
amino acids at a rate of about one SDS anion per two residues
...
After we have these many
anions attached onto our protein the entire net charge of that protein becomes
negative so even if the protein before this process had a native positive charge
that protein gains a net negative charge, allowing to move from the top (from
the negative side) to the bottom (to the positive side) in our electric field
...
Therefore
both small and large proteins will have a net negative charge but the larger
protein will have a greater net negative charge
...
But we know that is not true, in fact the opposite is true: Smaller
proteins move along the gel quicker with the greater velocity
...
Larger proteins will be higher up along that slab than
smaller proteins over that same time interval
...

In gel electrophoresis all of the proteins in the mixture are forced to move
through the pores gel but in the case of gel filtration chromatography only the
small proteins are actually forced to move through the beads that are composed
of that porous gel
...

In gel electrophoresis the large molecules remain at the top but in gel filtration
chromatography the large molecules go to the bottom but the small ones
remain at the top
...

A mixture of proteins is first exposed to isoelectric focusing
...
If two or more proteins have the same pI value, they will be
found in the same band
...

The proteins now begin to move in a perpendicular direction downward
...


2nd class (28-09):
glicocalyx: outer coating of many prokaryotes, consisting of a capsule or a slime
layer
...


cytoskeleton reinforces cell's shape; functions in cell movement; components are
made of proteins
...
made of
a protein called tubulin
...
The
cell's main microtubule organizing center is called centrosome
...


central vacuole: prominent organelle in older plant cells; functions include storage,
breakdown of waste products, and hydrolisis of macromolecules; enlargement of
the vacuole is a major mechanism of plant growth
plasmodesmata: cytoplasmic channels through cell walls that connect the
cytoplasms of adjacent cells
...
Except at the pores, the nuclear side of
the envelope is lined by the nuclear lamina, a netlike array of protein filaments (in
animal cells, called intermediate filaments) that maintains the shape of the nucleus
by mechanically supporting the nuclear envelope
...

Most of the proteins made on free ribosomes function within the cytosol; Bound
ribosomes generally make proteins that are destined for insertion into membranes,
for packaging within certain organelles such as lysosomes, or for export from the
cell (secretion)
...


Introdução às Ciências Biológicas

21

Functions of Smooth ER: synthesis of lipids (oils, steroids, new membrane
phospholypids), metabolism of carbohydrates, detoxification of drugs and poisons,
and storage of calcium ions
...


Functions of Golgi Apparatus: Products of the ER, such as proteins, are modified
and stored and then sent to other destinations (the golgi apparatus is especially
extensive in cells specialized for secretion); it also manufactures some
macromolecules, like polysaccharides
...


Lysosomes: membranous sac of hydrolytic enzymes that many eukaryotic cells
use to digest (hydrolyze) macromolecules
...
Hydrolytic enzymes
and lysosomal membrane are made by rough ER and then transferred to the Golgi
apparatus for further processing
...

Membrane repair, cell signaling and metabolism
...
Some peroxisomes use oxygen to break fatty acids down into smaller
molecules that are transported to mitochondria and used as fuel for cellular
respiration
...
The H2 O2
formed by peroxisomes is itself toxic, but the organelle also contains an enzyme
that converts H2 O2 to water
...
:
A functional protein is not just a polypeptide chain, but one or more polypeptides
precisely twisted, folded, and coiled into a molecule of unique shape
...
)

Introdução às Ciências Biológicas

22



---