Pcom Survey Biochem_Class 7 & 8

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Three major nitrogen-containing building blocks:

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1. Amino Acids
2. Porphyrins
3. Nucleotides

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Amino Acids BASICS:
specific amines that build proteins;
they are the subunit/monomers of proteins. A protein is a long, unbranched chain of linked amino acids.

Back 2

Cells build proteins; proteins are built from amino acids,
small nitrogen-containing molecules with an NH2 amino
group, a carboxyl group, and an R-group.

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Glutathione

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Amino acid: a cell’s major antioxidant molecule

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Glutathione

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It functions in the cytoplasm
of all cells to relieve oxidative stress from
cellular processes and toxins. The thiol
(sulfhydryl) group – SH – is the active
oxidant scavenger.
It is the most abundant molecule in the
cytoplasm of cells besides water —
speaking to the importance of this
molecule, and to the amount
of oxidative stress in cells.

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How many amino Acids are used for making proteins?

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In humans, there are 20 specific amino acids
that are used in making proteins

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How many amino acids do human have that their genetic code/enzymes can synthesize?.
How many do they need to require from food proteins

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Humans have the genetic code/enzymes to
synthesize 12 of these, but needs to acquire 8 of
these from food protein — and these 8 are
properly called essential amino acids.

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What 8 are properly called essential amino acids.

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the 8 needed to be acquired from food.

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Like many organic molecules, amino acids
are found with enantiomeric and chiral
conformations.

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Like many organic molecules, amino acids
are found with enantiomeric and chiral
conformations.

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In animal systems what can form enantiomer amino acids and what type of amino acids are incorporated into proteins?

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In animal systems, only the L- form enantiomer
amino acids
only α- chiral amino acids are
incorporated into proteins.
Enzymes may or may not convert the D- and
β􀀎 forms to L- and α􀀎 forms for utilization in
protein synthesis. Therefore, the L- α form of
an amino acid is the only conformation
incorporated into proteins.

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Important once a protein chain is formed; these
properties give multiple, diverse possibilities for
protein conformation (folding).

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Sulfur-containing aminos: cysteine and methionine
are important in protein folding and integrity by forming disulfide bridges
– Charged or uncharged molecules: net charge on
aminos can be negative, neutral, or positive — this
causes attraction and repulsion when the polypeptide folds into a protein.
– Some aminos will more readily form hydrogen bonds between each other than others, again affecting the conformation and stability of the resulting protein.
– Hydrophobic and hydrophilic aminos will be attracted or repulsed with each other as the protein folds

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diverse and important to life. This is a short list.

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– Enzymes — catalyze a myriad of biochemical
processes
– Structural proteins — connective tissue, skin, collagen
– Movement — tendon, muscle (actin, myosin)
– Messengers/hormomes/regulatory molecules —
especially in metabolism regulation (insulin, glucagon)
– Transport — provide product transport in the blood
(hemoglobin); plasmalemma transport and channel
proteins
– Defense — immunoglobulins, or B-cell mediated
(humoral) immunity
– Nutrient storage — milk protein, albumin

Front 12

What are important in sulfur containing amino acids?

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Sulfur-containing aminos: cysteine and methionine
are important in protein folding and integrity by forming disulfide bridges

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Primary structure (or conformation ) (1°)

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A polypeptide produced by a ribosome is a linear, unfolded chain of amino acids linked with peptide bonds.

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secondary structure (2°)

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secondary structure (2°) forms as hydrogen
bonding between specific amino units begins the folding
process.

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The tertiary structure (3°)

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folds the polypeptide
even further, as disulfide bonds, charge attractions/
repulsions, and hydrophobic/hydrophilic attractions are lined up. Most proteins are complete at this stage.

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Quaternary structures (4°)

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Quaternary structures (4°) are created when 2 or
more tertiary proteins form similar weak bonds between
each other, creating often massive, multi-protein
molecules. Hemoglobin in blood is one such quaternary
structure. Immunoglobulins (antibodies) are another.

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Example of a tertiary structure (3°)

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Cyclooxygenase II — manufactures Prostaglandin H2
— Tertiary structure

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Active Sites:

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Enzymes, as folded 3-dimensional proteins, have an
active site or sites within the macromolecule where
the catalytic work of the enzyme takes place — a
cavity in the enzyme where the desired reaction takes
place.

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What are substrates

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Substrates are the molecules that will be acted upon by the enzyme. There can be one substrate or multiple substrates. These substrates enter the active site to be worked upon. Splitting or joining molecules and flipping conformation occur in active sites

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The rest of the enzyme molecule supports the activity of the active site. Coenzymes and cofactors like ATP,
vitamins, ions and prophyrins are often part of or
introduced into the site, facilitating reactivity..

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The rest of the enzyme molecule supports the activity of the active site. Coenzymes and cofactors like ATP,
vitamins, ions and prophyrins are often part of or
introduced into the site, facilitating reactivity.

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Proteins from foods are catabolized by?

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Proteins from food are catabolized in the stomach and intestines by proteases — enzymes that hydrolyze proteins and release amino acids into the bloodstream via small intestine absorption.

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Porphyrins

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Porphyrins are complex
heterocyclic amine molecules
with important roles in enzymes
and enzyme-related processes.
They are noted for their ability
to chelate metal ions onto their
structure, and hence utilize the
electron cloud properties of the
captured metal ion. They are
found in the active site of
enzymes.

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Porphyrins; This is one variation of Vitamin B-12,

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cyanocobalamin. Its chelate is cobalt, a metal ion that has numerous valence states, and is polychromatic.

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Nucleotides and Nucleic Acids

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The fourth major class of biological molecules are
the Nucleic Acids. “Nucleo-” is used because the
genetic material found in the nucleus of cells is
nucleic acid. The building blocks of nucleic acids
are nucleotides.

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Nucleotides form a chain composed of

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a phosphate-sugar backbone of either
ribose or deoxyribose sugars and phosphate (PO4).
This unbranched chain is called a nucleic acid.

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The two types of nucleic acids are

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Ribonucleic acid — RNA, utilizing ribose,
and
Deoxyribonucleic acid — DNA utilizing deoxyribose.

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What are the 3 subunits that Nucleotides complex molecules composed of ?

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a nitrogenous base,
a sugar, and
a phosphate group.

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What 2 types of bases does a nucleotide have?

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either a purine or pyrimidine

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What types of sugar does is a nucleotide compose of?

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monosaccharide (simple sugar)

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Tell me what nucleotides form

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RNA and DNA chains, or as
monomers as in ATP, or dimers, as in NADH or FAD.

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Where are nucleotides manufactured?

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Nucleotides are manufactured in the cell nucleus, and
float freely so they can be used anytime there is
duplication, transcription, or vitamin/cofactor needs.
There are deoxyribonucleotides (DNA) and
ribonucleotides (RNA) depending on the type of
monosaccharide used.

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Tell me more about the nitrogenous base?

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Nitrogenous bases are heterocyclic amines. There are 5 specific bases used by DNA and RNA.
Purines and pyrimidines are the two nitrogen containing structures of nitrogenous bases

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Nucleotides: Pyrimidine bases have how many rings

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one

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Name three Pyrimidine

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Thymine , cytosine and Uracil (CUT)

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Purine has how many rings

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TWO

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Name two Purines

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Guanine and Adenine

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NAme the sugars in nucleotides and nucleosides

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Ribose ( RNA)
deoxyribose ( DNA )

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What about the phosphate group

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double bonded and high energy

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name other notable Purines

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Adenosine ( base for ATP, NADH and cAMP, ADP, ) and CAffine

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Nucleosides

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Nucleosides are the second step in building
nucleotides. They are a nitrogenous base plus a ribose
or deoxyribose

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Phosphorylation

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Phosphorylation of nucleosides by bonding a
phosphate group completes the formation of
nucleotides from nucleosides.

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Adenosine

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Adenosine is used as a base for some of the most
important molecules in the cell — ATP (adenosine
triphosphate), NADH, and cAMP (cyclic adenosine
monophosphate). Adenosine diphosphate (ADP)
and adenosine monophosphate (AMP) are
intermediaries of ATP in metabolism.

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cAMP

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cytoplasm, regulating cell metabolism by stimulating
energy use. It is a modified adenosine molecule
that in higher concentrations causes the cell’s
metabolism to increase, and in
lowered concentrations slows cellular
metabolism.

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WHat enzyme brakes down cAMP?

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phosphodiesterase, Caffeine inhibits
this enzyme

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What are linear unbranched chains of bonded nucleotides?

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RNA and DNA

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What 4 nucleotides are used in DNA and RNA?

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There are 4 nucleotides used in each of RNA and DNA
— 2 purine nucleotides and 2 pyrimidine nucleotides.
These molecules are called bases. The nucleotides
are bonded between their sugar and phosphate
moieties, forming a sugar-phosphate backbone

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What forms a Double Helix — 3 dimensional form

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DNA

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Pairing of Nitrogenous Bases

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The 4 bases pair with each other in DNA, forming
hydrogen bonds between the two bases. The
bases pair very specifically:
DNA:
Adenine with Thymine (AT)
Thymine with Adenine (TA)
Cytosine with Guanine (CG)
Guanine with Cytosine (GC)
RNA
Adenine with Uracil (AU)
Uracil with Adenine (UA)
Cytosine with Guanine (CG)
Guanine with Cytosine (GC)

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When nuclear DNA needs to be repaired or
duplicated. What happens??

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free-floating nucleotides are paired up
with the original DNA, and carefully recoded into
intact, exact duplicate strands of DNA by the action
of REPAIR ENZYMES. There can be mistakes that are
not correctable in this process, and hence,
mutations get into the genetic code.

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RNA

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RNA (containing uracil) is a single strand nucleic acid, and does not form any 2-stranded
macromolecules, though it can double back and
hydrogen-bond to itself as in this example.

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DNA and RNA both help code for proteins.
DNA has one function:

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as a storage molecule for
genetic data.

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DNA and RNA both help code for proteins.
DNA has one function: as a storage molecule for
genetic data.
RNA has multiple functions in the cell, and is found
in 3 distinct types:

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rRNA – ribosomal RNA
tRNA – transfer RNA
mRNA – messenger RNA

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RNA is the workhorse of nucleic acids.

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It is always a
single-strand molecule though it can fold onto itself
and have hydrogen bonding between pairs. rRNA
and tRNA structures are usually folded and
hydrogen bonded. mRNA on the other hand, exists
as an open, unbonded strand.

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rRNA — Ribosomal RNA

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Ribosomal RNA is made in the cell nucleus.
Several forms of rRNA are used in the cell and
have enzymatic properties. Ribosome
organelles are made in the nucleus, and
structured with about half rRNA and half
enzymatic protein. The active site of the
ribosome is composed of rRNA. Other rRNA
structures are pure rRNA, and are called
ribozymes RIBOZYMES, as their roles in the cell are
exactly like an enzyme.

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Messenger RNA — mRNA

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Messenger RNA is a single-strand nucleic acid, hundreds of nucleotides long. It is transcribed from DNA in the nucleus, and is an sense copy of one (antisense) strand of the double-stranded DNA. mRNA carries the protein code
from the nucleus to the cell’s manufactories as information packets called codons.

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tRNA Transfer RNA

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Transfer RNA is a short nucleic acid, an oddly folded, single strand of RNA bases. The job of tRNA is to carry amino acids into the protein synthesis process in the ribosome. There are twenty different tRNAs which code for each of the 20 amino acids used in human protein. Therefore, there is a specific tRNA for each amino acid used for proteins. The anticodon is the 3-base portion of the chain which matches up to the codon on messenger RNA.

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EnZYmES
Enzymes work on biological molecules in 3 basic ways:

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a.) building larger molecules (anabolism),
b.) breaking down larger molecules (catabolism), and
c.) rearranging atoms and molecules within the molecule
being acted upon — enantiomers and chiral formations.

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Enzymes catalyze biological reactions in two ways:

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specificity and reaction rate.

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Catalysts work to

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lower the activation energy of
chemical reactions.

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By reducing the activation energy of
biological reactions,

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the reaction rate is greatly
accelerated. Without enzymes, most reaction rates
would be at or near zero (reactions per second), and life
systems would not function. Enzymatic reaction rate is
between 1x106 to 1x109 times as fast if molecules were
left alone to react.

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Enzyme specificity

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Enzymes have an amazing discriminatory ability
to work on or select the exact molecules or atoms
they are designed for —

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Substrate

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Substrate is the generic name for a molecule that
will be worked on by an enzyme; eg. starch is the
substrate of amylase enzymes — amylases break
down starches.

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Many drugs and herbs “fool” the specificity of
enzymes. This is often caused by

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Many drugs and herbs “fool” the specificity of
enzymes. This is often caused by competitive
inhibition of the active site. There are both positive
and negative consequences in artificially interfering
with the active site and specificity of an enzyme

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Enzymes are made of

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Enzymes are made of protein, but also incorporate
cofactors of many sorts — coenzymes, vitamins,
porphyrins and mineral ions to facilitate their
functioning. rRNA as in ribosomes would be another
factor which cooperates with enzymes.

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Enzyme activity is affected by many external
factors

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– Presence or absence of substrates
– pH changes or other ionic factors
– Temperature range
– Availability of nutrients: ATP, cofactors,
coenzymes, and ions
– The functionality of the enzyme — is it damaged
and not yet replaced?
– Molecules may be present causing competitive
inhibition of the active site — drugs, herbs,
toxins, organisms

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Classification and Nomenclature
Enzymes are typically classified by the chemical nature of the
reactions they catalyze. “ase” always indicates an enzyme

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– Oxidoreductases – remove molecules or atoms from substrates
– Transferases – transfer functional groups from one molecule to
another, such as moving a phosphate group
– Hydrolases – add water to substrates
– Lyases – work with double bonds
– Isomerases – change the isomeric status of a molecule
– Ligases – join or release carbon bonds and requires ATP
Enzymes are also named for the substrate upon which they
work, such as a urease working upon a urea molecule, or a
dehydrogenase which removes water from a molecule. Few
retain their old names given before naming conventions came
about – the digestive enzymes trypsin and pepsin.

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The term enzyme cascade

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The term enzyme cascade is commonly used to signify
that a number of enzymes work on substrates in a specific
order — an orderly chain of events facilitated by different
enzymes. For example, glycolysis, which we looked at in
Lecture 5 on carbohydrates, is a typical enzyme cascade.

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Cofactors, Coenzymes, Ions, Vitamins'
Many enzymes are dependent for proper function on
several non-protein molecules called cofactors. When an
enzyme does not have its cofactors present, it is called an

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apoenzyme and is not functional

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An enzyme with
cofactors and fully functioning is

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a holoenzyme.

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Cofactors

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Cofactors — A cofactor is a non-protein molecule that has
either a tight or loose affinity to an enzyme and is required
for enzymatic action. Biochemists classify 2 types —
prosthetic groups and coenzymes

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1. Prosthetic Groups — Porphyrin groups, vitamins and
metallic ions are common prosthetic groups. These groups
are often the limiting factor in nutrition and energy
generation. Deficiency in vitamins and minerals slows the
overall metabolism in the organism because the cellular
enzymes revert back to apoenzyme status.

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1. Prosthetic Groups — Porphyrin groups, vitamins and
metallic ions are common prosthetic groups. These groups
are often the limiting factor in nutrition and energy
generation. Deficiency in vitamins and minerals slows the
overall metabolism in the organism because the cellular
enzymes revert back to apoenzyme status.