FINAL TERM Flashcards
Class of Protein
Structural, Contractile, Transport, Storage, Hormone, Enzyme, and Protection
Class of Protein that regulate body metabolism and nervous system
Hormone
Class of protein that catalyze biochemical reactions in the cells
Enzyme
Class of protein that recognizes and destroy foreign substances
Protection
-are the building blocks of proteins
-contain a carboxylic acid group and an amino group
-on the alpha (α) carbon
-are ionized in solution
-each contains a different side group (R)
Amino acids
Types of Amino acids
Polar, nonpolar, acidic, and basic
Type of amino acids with hydrocarbon
side chains (hydrophobic)
-has an R group that is H, an
alkyl group, or aromatic.
Nonpolar
Type of amino acids with polar
or ionic side chains
(hydrophilic)
-has an R group that is alcohol,
thiol, or amide.
Polar (neutral)
Type of amino acids with
–NH2 side chains
(hydrophilic)
-with an amino R group (NH3+)
Basic
-are chiral except glycine, which has two H atoms
-attached to the alpha carbon atom
-have Fischer projections that are stereoisomers
-that are L isomers are used in proteins
Amino acids
-has an equal number of —NH3+ and COO– groups
-forms when the H from —COOH in an amino acid
transfers to the —NH2
Zwitterion
-are the pH at which zwitterions
have an overall zero charge
-of nonpolar and polar (neutral)
amino acids exist at pH values
from 5.1 to 6.3
Isoelectric points (pI)
the zwitterion accepts a proton
(H) to form a positively charged ion.
Acidic solution
-In solutions that are more acidic than the pI,
-the COO– in the zwitterion accepts a proton
-the amino acid has a positive charge
Zwitterions in Acidic solutions
-In solutions that are more basic than the pI,
-the NH3+ in the zwitterion loses a proton
-the amino acid has a negative charge
Zwitterions in basic solutions
the -NH3+ of the zwitterion loses a
proton, and a negatively charged species is formed.
Basic solution
-a polar (acidic) amino acid,
-has a pI of 2.8
-forms a zwitterion at pH 2.8
-forms negative ions with charges 1– and 2– at pH
values greater than pH 2.8
Aspartic acid
-an electric current is used to
separate a mixture of amino acids, and
-the positively charged amino acids move toward the
negative electrode
-the negatively charged amino acids move toward the
positive electrode
-an amino acid at its pI does not migrate
-the amino acids are identified as separate bands on the
filter paper or thin layer plate
Electrophoresis
-is an amide bond
-forms between the carboxyl group of one amino acid
and the amino group of the next amino acid
-contains an N (free H3N+) terminal written on the left
-contains a C (free COO –) terminal written on the right
Peptide bond
-a yl ending for the N-terminal (free H3N+) amino acid
-the full amino acid name of the free carboxyl group
(COO–) at the C-terminal end
Dipeptide
The primary structure of a protein is
-the particular sequence of amino acids
-the backbone of a peptide chain or protein
-have similar primary structures
-differ only in the amino acids at positions 3 and 8
Nonapeptides oxytocin and vasopressin
-was the first protein to have
its primary structure
determined
-has a primary structure of
two polypeptide chains
linked by disulfide bonds
-has an A chain with 21
amino acids and a B chain
with 30 amino acids
Insulin
-a coiled shape held in place by hydrogen bonds
between the amide groups and the carbonyl groups
of the amino acids along the chain
-hydrogen bonds between the H of an —NH group
and the O of C═O of the fourth amino acid down
the chain
Alpha helix (α-helix)
is a secondary structure that consists of polypeptide chains arranged side by side
-has hydrogen bonds between chains
-has R groups above and below the sheet
-is typical of fibrous proteins such as silk
Beta-pleated sheet (β-pleated sheet)
-consists of three alpha helix
chains woven together
-contains large amounts of
glycine, proline, hydroxyproline,
and hydroxylysine that contain
–OH groups for hydrogen
bonding
-is found in collagen, connective
tissue, skin, tendons, and
cartilage
Triple helix
are the ten amino
acids not synthesized
by the body
must be obtained from
the diet
are in meat and diary
products
are missing (one or
more) in grains and
vegetables
Essential amino acids
gives a specific three-dimensional shape to the
polypeptide chain
involves interactions and cross-links between
different parts of the peptide chain
is stabilized by:
hydrophobic and hydrophilic interactions
salt
bridges
hydrogen bonds
disulfide bonds
Tertiary structure
Interactions between nonpolar groups
Hydrophobic interactions
Attraction between polar and ionized groups and water on the surface of the tertiary structure
Hydrophilic interactions
Ionic interactions between ionized acidic and basic amino acids
Salt bridges
Occur between H and O or N
Hydrogen bonds
Strong covalent links between sulfur atoms of two cysteine amino acids
Disulfide bonds
have compact,
spherical shapes
carry out synthesis,
transport, and
metabolism in the cells
such as myoglobin
store and transport
oxygen in muscle
Globular proteins
consist of long, fiber-like
shapes
such as alpha keratins make
up hair, wool, skin, and nails
such as feathers contain
beta keratins with large
amounts of beta-pleated
sheet structures
Fibrous proteins
is the combination of two or
more tertiary units
is stabilized by the same
interactions found in tertiary
structures
of hemoglobin consists of two
alpha chains and two beta
chains with heme groups in
each subunit that pick up
oxygen for transport in the
blood to the tissues
Quaternary structure
splits the peptide bonds to give smaller peptides
and amino acids
occurs in the digestion of proteins
occurs in cells when amino acids are needed to
synthesize new proteins and repair tissues
Protein hydrolysis
the disruption of bonds in the secondary, tertiary,
and quaternary protein structures
heat and organic compounds that break apart H
bonds and disrupt hydrophobic interactions
acids and bases that break H bonds between polar R
groups and disrupt ionic bonds
heavy metal ions that react with S—S bonds to form
solids
agitation, such as whipping, that stretches peptide
chains until bonds break
Denaturation
an egg is cooked
the skin is wiped with alcohol
heat is used to cauterize
blood vessels
instruments are sterilized in
an autoclave
Denaturation
are proteins
that
catalyze nearly all the
chemical reactions taking
place in the cells of the
body
increase the rate of
reaction by lowering the
energy of activation
Enzymes
Classification of enzymes
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
Add or remove groups without hydrolysis or oxidation that may result in a double bond
Lyases
Join molecules using ATP energy
Ligases
is a region within an
enzyme that fits the
shape of the reacting
molecule, called a
substrate
contains amino acid R
groups that bind the
substrate
releases products when
the reaction is complete
Active site
a substrate attaches to
the active site
an enzyme–substrate
(ES) complex forms
reaction occurs and
products are released
an enzyme (E) is used
over and over
enzyme-catalyzed reaction
Enzymes may recognize and catalyze
a single substrate
a group of similar substrates
a particular type of bond
Enzyme specificity
Catalyze one type of reaction for a single substrate
Absolute
Catalyze one type of reaction for similar substrates
Group
Catalyze one type of reaction for a specific type of bond
Linkage
the active site has a rigid shape
only substrates with the matching shape can fit
the substrate is the key that fits that lock
Lock-and-key model
enzyme structure is flexible, not rigid
shapes of enzyme and substrate adjust for best fit at
the active site to improve catalysis of reaction
substrate specificity increases
Induced-fit model
The active site is
1) the entire enzyme
2) a section of the enzyme
3) the substrate
2
In the induced-fit model, the shape of the enzyme
when substrate binds
1) stays the same
2) adapts to the shape of the substrate
2
catalyze the same reaction in different tissues in
the body
can be used to identify the organ or tissue involved
in damage or disease
such as LDH have one form more prevalent in
heart muscle and another form in skeletal muscle
and liver tissue
Isoenzymes
determine the
amount of damage in
tissues
that are elevated
may indicate damage
or disease in a
particular organ
Diagnostic enzymes
are most active at an
optimum temperature
(usually 37°C in
humans)
show little activity at
low temperatures
lose activity at high
temperatures as
denaturation occurs
enzymes
Enzymes in the body have an optimum pH of about
7.4
are molecules that cause a loss of catalytic activity
prevent substrates from fitting into the active sites
Inhibitors
Types of Inhibition
Reversible and Irreversible
Types of Reversible Inhibition
Competitive and noncompetitive
has a structure that is
similar to that of the
substrate
competes with the
substrate for the active
site
has its effect reversed by
increasing substrate
concentration
Competitive inhibitor
has a structure that is much
different than the substrate
distorts the shape of the
enzyme, which alters the
shape of the active site
prevents the binding of the
substrate
cannot have its effect
reversed by adding more
substrate
Noncompetitive inhibitor
A molecule that forms a covalent bond to a part of the active site, permanently preventing substrates from occupying ir.
Irreversible Enzyme Inhibitor
is a competitive
inhibitor of succinate
dehydrogenase
has a structure that is
similar to succinate
inhibition is reversed
by adding succinate
Malonate
Identify each description as an inhibitor that is
1) competitive or 2) noncompetitive.
A. increasing substrate reverses inhibition
B. binds to enzyme surface but not to the active site
C. structure is similar to substrate
D. inhibition is not reversed by adding more substrate
Identify each description as an inhibitor that is
1) competitive or 2) noncompetitive.
1 A. increasing substrate reverses inhibition
2 B. binds to enzyme surface but not to the active site
1 C. structure is similar to substrate
2 D. inhibition is not reversed by adding more
substrate
are inactive forms of enzymes
are activated when one or more peptides are removed
Zymogens
produced as zymogens in one organ and transported
to another, such as the pancreas, when needed
activated by removing small peptide sections
Digestive enzymes
an enzyme in a reaction sequence that binds a
regulator substance
Allosteric enzyme
when it enhances the binding
of substrate and accelerates the rate of reaction
Positive regulator
when it prevents the binding
of the substrate to the active site and slows down
the rate of reaction
Negative regulator
a product acts as a regulator
an end product binds with the first enzyme (E1) in
a sequence when sufficient product is present so
shuts down the reaction
Feedback control
it binds to threonine deaminase, the first enzyme in
the pathway from threonine to isoleucine
a change in the shape of threonine deaminase blocks
the binding of threonine
Isoleucine
is an active enzyme that
consists only of protein.
Simple enzyme
is a cofactor that is a small organic
molecule such as a vitamin.
coenzyme
Identify each enzyme as
1) a simple enzyme
2) an enzyme that required a cofactor
A. requires Mg2+ for hydrolysis of phosphate esters
B. requires vitamin B3 to transfer an acetyl group
C. is active with four polypeptide subunits
Identify each enzyme as
1) a simple enzyme
2) an enzyme that required a cofactor
2 A. requires Mg2+ for hydrolysis of phosphate esters
2 B. requires vitamin B3 to transfer an acetyl group
1 C. is active with four polypeptide subunits
soluble in aqueous solutions
cofactors for many enzymes
not stored in the body
water-soluble vitamins
was the first B vitamin identified
is part of the coenzyme thiamin pyrophosphate (TPP)
is used to decarboxylate α-keto carboxylic acids
has a recommended daily allowance (RDA) of 1.2 mg;
deficiencies include fatigue, poor appetite, weight loss,
nerve degeneration, and heart failure
Thiamin (Vitamin B1)
is found in the coenzymes flavin adenine dinucleotide
(FAD) and flavin mononucleotide (FMN)
is needed for good vision and healthy skin
has an RDA of 1.2–1.8 mg; deficiencies include
dermatitis, dry skin, tongue inflammation, and
cataracts
Riboflavin (Vitamin B2)
is part of the coenzyme
nicotinamide adenine
dinucleotide (NAD+) involved in
oxidation–reduction reactions
has an RDA of 14–18 mg
deficiency can result in
dermatitis, muscle fatigue, and
loss of appetite
Niacin (Vitamin B3)
is part of coenzyme A needed for energy
production
is involved in glucose and cholesterol synthesis
has an RDA of 5 mg
deficiency can result in fatigue, retarded growth,
cramps, and anemia
Pantothenic acid (Vitamin B5)
two forms of vitamin B6, which are converted to the
coenzyme pyridoxal phosphate (PLP)
required in the transamination of amino acids and
decarboxylation of carboxylic acids
has an RDA of 1.3–2.0 mg; deficiency may lead to
dermatitis, fatigue, and anemia
Pyridoxine and pyridoxal
consists of four pyrrole rings
with a Co2+
is a coenzyme for enzymes
that transfer methyl groups
and produce red blood
cells
has an RDA of 2.0–2.6 μg
deficiencies are pernicious
anemia, nerve damage, and
malformed red blood cells
Cobalamin (Vitamin B12)
is required in collagen
synthesis and healing of
wounds
has an RDA of 60–95 mg
deficiencies are scurvy,
weakened connective tissue,
slow-healing wounds, and
anemia
Ascorbic acid (Vitamin C)
is a coenzyme for enzymes that transfer
carboxyl groups
has an RDA of 30 μg
deficiencies include dermatitis, loss of hair,
fatigue, and anemia
Biotin
consists of pyrimidine, p-aminobenzoic acid, and
glutamate
forms the coenzyme THF used in the transfer of
methyl groups and is involved in the synthesis of
nucleic acids
has an RDA of 400 μg
deficiencies are abnormal red blood cells,
anemia, and poor growth
Folic acid (Folate)
vitamins A, D, E, and K
soluble in lipids but not in aqueous solutions
stored in the body
important in vision, bone formation, antioxidants, and
blood clotting
Fat-soluble vitamins
is needed for retinol (vision); synthesis of RNA
has an RDA of 800 μg
deficiencies include night blindness, immune system
repression, and slowed growth
Retinol (Vitamin A)
is synthesized in skin
exposed to sunlight
regulates the absorption of
phosphorus and calcium
during bone growth
has an RDA of 5–10 μg
deficiency includes
weakened bones
Cholecalciferol (Vitamin D)
is an antioxidant in cells
may prevent the oxidation of unsaturated fatty acids
is found in whole grains and vegetables
has an RDA of 15 mg
deficiencies are hemolysis and anemia
Tocopherol (Vitamin E)
Vitamin K1 in plants has a
saturated side chain.
Vitamin K2 in animals has a
long unsaturated side chain.
Vitamin K2 is needed for the
synthesis of zymogens for
blood clotting.
Vitamin K has an RDA of
90–120 μg.
Deficiencies are prolonged
bleeding time and bruising
Menaquinon (Vitamin K)
Identify each of the following as a water-soluble vitamin
(WS) or fat-soluble vitamin (FS).
A. folic acid
B. retinol (vitamin A)
C. vitamin C
D. vitamin E
E. niacin
Identify each of the following as a water-soluble vitamin
(WS) or fat-soluble vitamin (FS)
WS
A. folic acid
FS
B. retinol (vitamin A)
WS
C. vitamin C
FS
D. vitamin E
WS
E. niacin
Identify the vitamin associated with each
1) riboflavin (B2)
2) vitamin A
3) vitamin K
4) vitamin D
5) ascorbic acid
A. collagen formation
B. part of the coenzymes FAD and FMN
C. absorption of phosphorus and calcium in bone
D. vision
E. blood clotting
Identify the vitamin associated with each
1) riboflavin (B2)
2) vitamin A
3) vitamin K
4) vitamin D
5) ascorbic acid
5 A. collagen formation
1 B. part of the coenzymes FAD and FMN
4 C.absorption of phosphorus and calcium in bone
2 D. vision
3 E. blood clotting
molecules that store information for cellular growth
and reproduction
deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA)
Nucleic acids
large molecules consisting of long chains of
monomers called
nucleotides
Nucleotides are consist of
base with nitrogen
pentose sugar
phosphoryl group
The bases in DNA and RNA are
pyrimidines C, T, and U
purines A and G
in RNA is ribose
in DNA is deoxyribose, with
no O atom on carbon 2′
has carbon atoms numbered
with primes to distinguish them
from the atoms in the bases
Pentose sugar
has a base linked by a
glycosidic bond to C1′ of
a sugar (ribose or
deoxyribose)
is named by changing
the end of the base
name to osine for
purines and idine for
pyrimidines
nucleoside
has a phosphoryl group
attached to the C5′ —OH
group of a nucleoside
is named using the name
of the nucleoside followed
by
-5′-monophosphate
nucleotide
nucleotides are joined by phosphodiester bonds
the 3′ —OH group of the sugar in one nucleotide
forms an ester bond to the phosphate group on the
5′ carbon of the sugar of the next nucleotide
Primary structure of nucleic acids
has a free 5′-phosphate
group at one end and a free
3′ —OH group at the other
end
is read from the free 5′ end,
using the letters of the
bases
segment shown here is read
as:
5′—A—C—G—T—3′
nucleic acid polymer
is a single strand of
nucleotides
consists of the bases A,
C, G, and U linked by
3′—5′ ester bonds
between ribose and
phosphate
Primary structure of RNA
the percentage of adenine (A) is the same as the
percentage of
Thymine
the percentage of guanine (G) is the same as the
percentage of
Cytosine
Adenine is always linked by ____ hydrogen bonds to
thymine (A−T)
two
guanine is always linked by ______ hydrogen bonds
to cytosine (G−C)
Three
consists of two strands of
nucleotides that form a double
helix structure like a spiral
stair case
has hydrogen bonds between
the bases A–T and G–C
has bases along one strand
that complement the bases
along the other
Double helix
involves unwinding the DNA
pairing the bases in each
strand with new bases to
form new complementary
strands
producing two new DNA
strands that exactly
duplicate the original DNA
DNA replication
from the hydrolysis
of each nucleoside
triphosphate
is used to form a
phosphodiester
bond to each new
nucleotide on the
complementary
strand
Hydrolysis energy
at each open DNA section (called a __________),
DNA polymerase catalyzes the formation of 5′–3′ ester
bonds of the leading strand
Replication fork
the lagging strand (growing in the 3′–5′ direction) is
synthesized in short sections called
Okazaki fragments
Match the following:
1) helicase
2) DNA polymerase
3) replication fork
4) Okazaki fragments
A. short segments formed by the lagging strand
B. the starting point for synthesis in unwound DNA
sections
C. the enzyme that unwinds the DNA double helix
D. the enzyme that catalyzes the formation of
phosphodiester bonds of complementary bases
Match the following:
1) helicase
2) DNA polymerase
3) replication fork
4) Okazaki fragments
4 A. Short segments formed by the lagging strand.
3 B. The starting point for synthesis in unwound DNA
sections.
1 C. The enzyme that unwinds the DNA double helix
2 D. The enzyme that catalyzes the formation of
phosphodiester bonds of complementary bases
transmits information from DNA to make proteins
RNA
carries genetic information from DNA to the ribosomes.
Messenger RNA (mRNA)
brings amino acids to the ribosome to make the protein.
Transfer RNA (tRNA)
makes up 2/3 of ribosomes where protein synthesis takes place.
Ribosomal RNA (rRNA)
mRNA is formed from a gene on a DNA strand
Transcription
tRNA molecules bring amino acids to mRNA to build a protein
Translation
moves along the DNA template in
the 3′–5′ direction to synthesize the corresponding
mRNA
the mRNA is released at the termination point
RNA polymerase
DNA contains _______ that code for proteins and
_______ that do not code for proteins
exons, introns
in which the end products
speed up or slow the synthesis of mRNA
Feedback control
in which high levels of a
reactant induce the transcription process to
provide the necessary enzymes for that reactant
Enzyme induction
consists of a control site and
structural genes that produce mRNA for lactose
enzymes.
lactose operon
is a sequence of nitrogenous bases in an mRNA that
determines the amino acid order for the protein
consists of sets of three bases (triplets) along the
mRNA called codons
has a different codon for all 20 amino acids needed
to build a protein
contains codons that signal the “start” and “end” of a
polypeptide chain
Genetic code
occurs when a synthetase
uses energy from ATP
hydrolysis to attach an
amino acid to a specific
tRNA
prepares each tRNA to
use a triplet called an
anticodon to complement
a codon on mRNA
activation of tRNA
an mRNA attaches to a ribosome
the start codon (AUG) binds to a tRNA with
methionine
the second codon attaches to a tRNA with the next
amino acid
a peptide bond forms between the adjacent amino
acids at the first and second codons
Initiation
the first tRNA detaches from the ribosome
the ribosome shifts to the adjacent codon on the
mRNA
a new tRNA/amino acid attaches to the open
binding site
a peptide bond forms, and the empty tRNA
detaches
the ribosome shifts down the mRNA to read the
next codon
Translocation
a polypeptide with all the amino acids for a protein
is synthesized
the ribosome reaches a “stop” codon: UGA, UAA,
or UAG
there is no tRNA with an anticodon for the “stop”
codons
the polypeptide detaches from the ribosome
Termination
Match the following:
1) activation
2) initiation
3) translocation
4) termination
A. Ribosomes move along mRNA, adding amino acids
to a growing peptide chain.
B. A completed peptide chain is released.
C. A tRNA attaches to its specific amino acid.
D. A tRNA binds to the AUG codon of the mRNA on the
ribosome.
Match the following:
1) activation
2) initiation
3) translocation
4) termination
3 A. Ribosomes move along mRNA, adding amino
acids to a growing peptide chain.
4 B. A completed peptide chain is released.
1 C. A tRNA attaches to its specific amino acid.
2 D. A tRNA binds to the AUG codon of the mRNA on
the ribosome.
alters the nucleotide sequence in DNA
results from mutagens such as radiation and
chemicals
produces one or more incorrect codons in the
corresponding mRNA
produces a protein that incorporates one or more
incorrect amino acids
causes genetic diseases that produce defective
proteins and enzymes
Mutation
a different base substitutes for the proper base in DNA
there is a change in a codon in the mRNA
the wrong amino acid may be placed in the polypeptide
Substitution mutation
an extra base adds to or is deleted from the normal
DNA sequence
the codons in mRNA and the amino acids are incorrect
from the base change
Frame shift mutation
Identify each type of mutation as a substitution (S) or
frame shift (F).
A. Cytosine (C) enters the DNA sequence.
B. One adenosine is removed from the DNA
sequence.
C. A base sequence of TGA in DNA changes to TAA.
Identify each type of mutation as a substitution (S) or
frame shift (F).
F A. Cytosine (C) enters the DNA sequence.
F B. One adenosine is removed from the DNA
sequence.
S C. A base sequence of TGA in DNA changes to
TAA.
a DNA fragment from one organism is combined
with DNA in another
restriction enzymes are used to cleave a gene from
a foreign DNA and open DNA plasmids in Eschericia
coli
DNA fragments are mixed with the plasmids in E.
coli and the ends are joined by ligase
the new gene in the altered DNA produces protein
recombinant DNA
restriction enzymes cut a DNA sample into smaller
fragments (RFLPs)
the fragments are sorted by size
a radioactive isotope that adheres to certain base
sequences in the fragments produces a pattern on
X-ray film, which is the “fingerprint”
the “fingerprint” is unique to each individual DNA
DNA fingerprinting
produces multiple copies of a DNA in a short time
separates the sample DNA strands by heating
mixes the separated strands with enzymes and
nucleotides to form complementary strands
is repeated many times to produce a large
sample of the DNA
polymerase chain reaction (PCR)
are small particles of DNA or RNA that require a
host cell to replicate
cause a viral infection when the DNA or RNA
enters a host cell
are synthesized in the host cell from the viral
RNA produced by viral DNA
Viruses
a retrovirus, which contains viral RNA but no viral
DNA, enters a cell
the viral RNA uses reverse transcriptase to
produce a viral DNA strand
the viral DNA strand forms a complementary DNA
strand
the new DNA uses the nucleotides and enzymes
in the host cell to synthesize new virus particles
Reverse transcription
is a retrovirus that infects
T4 lymphocyte cells
decreases the T4 level,
making the immune
system unable to destroy
harmful organisms
is associated with an
increased chance of
developing pneumonia
and skin cancer
associated with AIDS
HIV-1 virus
Match the following:
1) virus
2) retrovirus
3) protease inhibitor
4) reverse transcription
A. a virus containing RNA
B. small particles requiring host cells to replicate
C. a substance that prevents the synthesis of viral
proteins
D. using viral RNA to synthesize viral DNA
Match the following:
1) virus
2) retrovirus
3) protease inhibitor
4) reverse transcription
2 A. a virus containing RNA
1 B. small particles requiring host cells to replicate
3 C. a substance that prevents the synthesis of viral
proteins
4 D. using viral RNA to synthesize viral DNA
