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Biology 112 Chapters 3-4 study guide
Terms in this set (78)
What do proteins do?
Defense: Proteins act as antibodies and complement proteins attack to destroy viral pathogens as well as bacteria.
Motor proteins with contractile proteins help with movement of cell as well as transportation of large cargo. These includes actin and myosin.
Catalyze (speed up) reactions by acting as enzymes. Example is blood carbonic anhydrase which catalyzes reactions to maintain blood pH.
Peptide hormones are able to bind to receptor proteins on certain cells and create a cascade of reactions and mechanisms to transmit signals.
Are able to help give cells their specific shape and support.
Proteins help bring in and take out particular molecules within cells.
Are the building blocks of proteins.
Every amino acid contains:
a carboxyl group, amino group, and a side chain.
Every amino acid has a carbon linked to:
a hydrogen, an amino group, a carboxyl group, and an R group.
Amino acids can be
hydrophobic (do not mix in water) or hydrophilic (mix well in water)
Compounds made of same molecular formula but the atoms are bonded in a different arrangement in them.
Same atoms in the compound but have different order of bonds in compound
Same atoms in the compound but have different arrangement of atoms or groups on different sides of double bonds.
Same atoms in the compound but differ in the atom arrangement around a carbon with four different attached groups.
Amino acids are viewed as monomers
when joined together form a long polymeric structure through a process known as polymerization. Formed proteins are macromolecules (polymer)
Water is removed to add a monomer to a polymer chain.
Water is added to break a monomer off of a polymer chain.
A bond connecting the amino group from one amino acid to the carboxyl group on the other amino acid via condensation.
When amino acids gets joined together as residues via peptide bonds they form
a polypeptide molecule.
Less than 50 amino acids linked is:
an oligopeptide or peptide.
More than 50 amino acids is
The unique sequence of amino acids bonded to one another via peptide bonds.
Created by hydrogen bonding between carboxyl oxygen on one amino acid and the hydrogen on amino groups on another amino acid. Secondary structure are formed into either alpha helix or beta sheets.
Results from the interaction of the side groups present on amino acids in their peptide backbone. Each interaction causes the shape of the molecule to bend in a certain way making the three dimensional folding structures of a polypeptide.
A combination of more than one polypeptide (tertiary structure) together forming a single structure. The polypeptides are held together by interactions among side groups on the amino acids.
The folding and structure of a protein
is extremely important in determining its function.
Unfolding of a protein into its primary structure by breaking hydrogen and tertiary structure interactions. Denaturing a protein causes it to not function properly anymore.
Specific proteins which help folding the denatured protein back into its original structure to function properly.
Misfolded proteins which act as infectious disease-causing agents leading to disease such as mad cow disease "sponge-brain illness".
Most important function of proteins is to
act as enzymes to catalyze and speed up reactions.
Enzymes are effective because
they bring reactant molecules (substrates) together in the necessary orientation to react, and have enough kinetic energy to overcome repulsion between electrons which come into contact as a bond is made.
Part of a chemical reaction where old bonds are being broken and new bonds formed simultaneously.
Amount of free energy that is needed for a reaction to reach transition state.
Reactions only happen when
they have enough kinetic energy to reach the transition state, which is at the peak of the reaction and requires the most energy
Any substance that lowers the activation energy of a reaction and increase the rate of that very reaction.
Substrates first bind to the active site on
an enzyme which is the site where catalysis occurs.
Upon binding of the substrate to the active site the enzyme will...
undergo a conformational change known as an induced fit. This induced fit prevents anything else from binding to that enzyme on its active site.
Enzyme catalysis occurs in 3 steps:
Initiation, Transition state-Facilitation, and Termination.
Enzyme orients reactants as precisely as possible to bind at active site location.
Binding causes a transition state to occur; leading to interactions between substrate and side groups on enzyme active site. This lowers the activation energy needed for the reaction allowing more reactants to have enough kinetic energy to proceed past transition state into products.
Products are formed with less affinity for the active site as their substrates counterparts and the binding ends returning the enzyme to original conformation.
Atom or molecule not part of the enzyme primary structure which is required and needed for the enzyme to function normally.
Metal Ions (zinc or magnesium) + coenzymes.
Most cases the cofactor binds directly onto the
active site and plays a key role in stabilizing the transition state during the reaction.
Catalysis is inhibited when a molecule same size and shape as the substrate binds to the active site of the enzyme.
Regulatory molecule binds to location other than active site.
When substate concentrations are low
reactions speeds increase linearly. Increasing substrate concentrations causes a decrease in reaction speed till it reaches a max speed.
Enzyme activities are sensitive to
pH and temperature.
Nucleic acids are
polymers that are created with monomers known as nucleotides.
Nucleotides are made up of
a phosphate (PO4) group, a sugar, and a nitrogenous (nitrogen containing) base.
The sugar component of a nucleotide can either be a
ribose or deoxyribose They both differ in a single atom which is the -OH group.
are known as Cytosine (C), Uracil (U), and Thymine (T).
are known as Guanine (G) and Adenine (A).
is only in RNA
In bonding of DNA...
the Adenine (A) base pairs with the Thymine (T) base
Guanine (G) base...
ALWAYS pairs with the Cytosine (C) base.
Polymerization occurs by
a phosphodiester linkage (condensation) between the phosphate group on one nucleotide and the hydroxyl (-OH) group on the sugar of another nucleotide.
When the bonds occur between ribose bases in the monomer nucleotides the polymer is known as...
ribonucleic acid (RNA)
When the bonds occur between deoxyribose bases instead the polymer is known as...
deoxyribonucleic acid (DNA).
Bonding in the nucleic acid is
directional, meaning that DNA and RNA is read in ONE direction. Typically read in a direction known as 5 prime (5') to 3 prime (3'). (Fifth, or 3rd carbon on the sugar part of the nucleotide)
The 5' end has an
unlinked carbon while the 3' end has an unlinked carbon as well. While growing a strand, bases get added at the 3' end of the strand.
Writing the sequence of DNA is written in single letter abbreviations
Both DNA and RNA have
sugar-phosphate backbone structure
In 1953 James Watson and Francis Crick presented a model for DNA structure that represented what was known as a
double helix structure
They discovered that in a DNA sample the...
total number of purines and pyrimidines are the same. Also, the numbers of T's and A's in a DNA sample are equal and the number of C's and G's are equal.
When a double helix structure of DNA is made one strand...
it is ran in the 5' to 3' direction. The second strand which is known as an exact complement of the first strand is antiparallel and ran in the 3' to 5' direction.
Between the joining of the two DNA strands there are multiple
hydrogen bonds occurring that help stabilize the structure and align the bases in a certain way as well.
Energy for polymerization comes from the
phosphorylation of the nucleotides.
an Information-Containing Molecule (contains biological information!)
Complementary base pairing provides a
simple mechanism for DNA replication - each strand can serve as a template for the formation of a new complementary strand.
DNA replication requires two steps:
1. Separation of the double helix
2. Hydrogen bonding of deoxyribonucleotides with complementary bases on the original template strand, followed by phosphodiester bond formation to form the complementary strand
DNA's stability makes it a
reliable store for genetic information - it is less reactive than RNA but more resistant to chemical degradation.
Stable molecules such as DNA
make poor catalysts.
DNA is always more stable than
Like DNA, RNA has a primary structure consisting of
sugar-phosphate backbone formed by phosphodiester linkages and, extending from that backbone, a sequence of four types of nitrogenous bases: A,U,G,C
The primary structure of RNA differs from DNA in two ways:
1. RNA contains uracil instead of thymine.
2. RNA contains ribose instead of deoxyribose.
The presence of the -OH group on ribose makes RNA...
much more reactive and less stable than DNA.
are enzyme-like RNAs; the discovery of ribozymes showed that there was a possibility that RNA molecules could create copies of themselves.
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