Exam 1 Flashcards
All biological systems are composed of
cells containing the same types of chemical molecules and employing similar principles of organization at the cellular level
All living organisms descended from a common
ancestral cell
___ and ___ gave rise to new organisms during evolution
gene duplications; mutations
Tree branch relationships were assigned by similarities in
organismal morphological features and in DNA and protein sequences
Mitochondria and chloroplast organelles were formed from
bacteria incorporated as endosymbionts into precursor eukaryotic cells
Which came first: mitochondria or chloroplast?
mitochondria
What are some features that cells share?
DNA, plasma membrane
How do cells differ?
differ in morphology, ability to move, internal organization (prokaryotes vs. eukaryotes), and metabolic activities
Eubacteria and Archaea have ___ genes than single-cell and multicellular eukaryotes
fewer
What is the use of E.coli?
E.coli is a model organism that is used to investigate common cell activities such as gene regulation and membrane transport found in other organisms
Diversity of function and morphology at the cellular and organismal levels, respectively, arises through
complex interactions of cellular products that have multiple functions (e.g. proteins, molecules, RNAs, etc.)
All cellular life is connected to a large degree as the result of
genetic conservation
What are the major cellular macromolecules?
- amino acids
- nucleic acids
- carbohydrates
- lipids
What are amino acids involved with?
proteins
What are nucleic acids involved with?
RNA and DNA
What are carbohydrates involved with?
structure or source of energy
What are lipids involved with?
structure (cell membranes) or energy source (fatty acids)
What are some important small molecules?
- carbon-based molecules- carbon dioxide
- water
- ATP
- ions and minerals
- many others…
Prokaryote refers to
bacteria and archaea
Which came first: prokaryotic or eukaryotic cells?
prokaryotic; gave rise to eukaryotic
What does the Endosymbiont Theory state?
organelles in eukaryotic cells (mitochondria and chloroplasts) evolved from smaller prokaryotic cells
What are the two domains of prokaryotic cells?
Domain Archaea and Domain Bacteria
What types of organisms are in the Domain Archaea?
- methanogens
- halophiles
- acidophiles
- thermophiles
What is included in the Domain Bacteria?
- mycoplasma (smallest known cells)
- cyanobacteria (some photosynthetic bacteria; gave rise to green plants and an oxygen rich atmosphere)
Archaea are often referred to as
extremophiles (because of the environment they live in and the materials they utilize for energy (sugar, ammonia, sulfur, hydrogen, metals))
What is characteristic of methanogens?
oxygen is poisonous to them
What is characteristic of halophiles?
live in high salt environments
What is characteristic of thermoacidophiles or thermophiles?
can’t survive at “low temperatures (55 C = 131 F)
Plasma cell contains prominent endoplasmic reticulum and Golgi complex organelles involved in
synthesizing antibodies secreted by the cell
What are some features of eukaryotic cells?
- complex cytoskeletal system
- organizations of DNA
- DNA segregated in nucleus
- specialized organelles for aerobic respiration and photosynthesis (mitochondria and chloroplasts)
What is the function of the complex cytoskeletal system in eukaryotic cells?
- gives cell mechanical strength
- controls cell shape
- organizes cytoplasm
- drives and guides movements
What is characteristic of the organization of DNA in eukaryotic cells?
- long linear strands associated with proteins
- capable of condensing into mitotic chromosomes
What is characteristic of mitochondria and chloroplasts?
- contain own DNA and protein synthesizing machinery
- divide to increase number
- believed to have come from prokaryotic cells engulfed by eukaryotic ancestor
What is the major difference in features of prokaryotic and eukaryotic cells in reference to cell membranes?
- Bacteria and Eukaryotes: made of D-glycerol phospholipids
- Archaea: made of L-glycerol phospholipids with branching chains
What is the major difference in features of prokaryotic and eukaryotic cells in reference to cell walls?
- Bacteria: made of peptidoglycan (combination of sugars and amino acids)
- Archaea: made of S-layer, surface-layer proteins or pseudomurein (pseudopeptidoglycan)
- Eukaryotes: cellulose (plants) or chitin (fungi)
Prokaryotes have ___ flagella while eukaryotes have ___ flagella
simple; complex
Prokaryotes move by
rotation
Eukaryotes move by
whip-like undulation
How is the rotating movement of bacteria different than that of archaea?
In bacteria, a proton gradient drives rotation; in archaea rotary motors are powered by ATP
What is another difference in bacteria, archaea, and eukaryotes?
- Bacteria have a single circular DNA chromosome and no histone proteins
- Archaea have a single circular DNA chromosome and histone-like proteins
- Eukaryotes have multiple linear DNA chromosomes and histone proteins
A circular chromosome contains all necessary genes for
life function and replication
Plasmids contain extra genes that can
benefit survival
Archaea and eukaryotic histones share a common ancestry and
bind and wrap DNA similarly using conserved residues
What is the difference between eukaryotes and bacteria and archaea in reference to sexual reproduction?
Eukaryotes: sexual reproduction involving meiosis and fertilization
Bacteria and archaea: capable of exchanging pieces of DNA (conjugation) but no true sexual reproduction
Eukaryotes undergo
mitosis (nuclear division)
-utilizes a microtubule-containing spindle to separate duplicated chromosomes
Bacteria and archaea undergo
binary fission
-duplicated DNA separated by growth of cell membrane
What does phylogenetics state?
that many proteins in archaea are more closely related to eukaryotes than bacteria
Unicellular eukaryotic organisms range from relatively ___ (yeast) to perhaps the most ___ of all cells (protozoa and algae)
simple; complex
How many different cell types are found in the human body?
around 200
Multicellularity requires ___ and ___ adhesions
cell-to-cell; cell-to-matrix
Hox genes in conserved clusters encode highly conserved Hox protein master transcription factors, which control
the activities of other genes that direct the development of different segments along the head-to-tail axis in both protostomes and deuterostomes
Molecular complementarity enables proteins with complementary shapes and chemical properties to form
bimolecular interactions
Small molecule building blocks form
larger cellular structures and polymers such as DNA
T or F? Chemical reactions are reversible
T
What is K(eq)?
the ratio of forward (K(f)) and reverse (K(r)) reaction rate constants
What does K(eq) reflect?
the relative amounts of products and reactants at equilibrium
The energy driving many cellular activity reactions is derived from
hydrolysis of the high energy phosphoanhydride bond linking the beta and gamma phosphates in the ATP molecule
What does hydrophilic mean?
refers to molecules that readily dissolve in water; related to the polarity of the molecule (partial or full charge)
What does hydrophobic refer to?
molecules that of not readily dissolve in water; non polar molecules (can dissolve in organic solvents (non polar solvents))
What does amphipathic refer to?
biomolecules that exhibit both hydrophilic and hydrophobic regions
Bonds between atoms with shared pairs of electrons are called
covalent bonds
Stable combinations of atoms held together by covalent bonds
molecules
Molecules with more than one type of atom
compounds
Electrons are present around an atom’s nucleus in
“clouds” or orbitals that are roughly defined by their boundaries
A primary determinant of the chemical properties of an element
the number of outer-shell electrons
In covalent bonds, energy is released during
formation
T or F? Covalent bonds are stable under most conditions
T
The amount of energy required to break a bond is ___ as the amount of energy released when the bond is formed
the same
How many unpaired electrons are in carbon’s outer orbital?
4
Carbon can form ___ covalent bonds
4
In covalent bonds, the number of shared pairs contributes to
the shape of the molecule
The atoms around single bonds
rotate
The atoms around double or triple bonds
don’t rotate
Are polar bonds hydrophilic or hydrophobic?
hydrophilic
Polar molecules have ___ distributions of electrical charge
asymmetric
Are non polar bonds hydrophilic or hydrophobic?
hydrophobic
Non polar molecules lack
polarized bonds
Amphipathic molecules have both ___ and ___ regions
polar and nonpolar
What are some examples of amphipathic (having both polar and non polar regions) molecules?
proteins and phospholipids
Polarity or non polarity of biomolecules is determined by
the presence or absence of electronegative atoms within the molecular structure
What is electronegativity?
the ability of an atom to attract electrons towards itself forming a polar covalent bond
Hydrogen has one electron to share and forms __ covalent bond
1
Oxygen usually forms two covalent bonds but has
two additional pairs of electrons that can participate in non covalent interactions
Sulfur has up to __ electrons to share
6
Sulfur forms __ covalent bonds in hydrogen sulfide
2
Sulfur forms __ covalent bonds in sulfuric acid
6
Nitrogen has __ electrons to share
5
In ammonia (NH3), the nitrogen forms __ covalent bonds; the pair of electrons around the atom not involved in a covalent bond take part in ___
3; non covalent interactions
In the ammonium ion (NH4+), nitrogen forms 4 covalent bonds, which have a ___ geometry
tetrahedral
Phosphorous has __ electrons to share
5
Phosphorous commonly forms __ covalent bonds, as in phosphoric acid (H3PO4) and its phosphate derivatives
5
Phosphoric acid (H3PO4) and its phosphate derivatives
form the backbone of nucleic acids, high energy bonds in ATP, and covalently phosphorylate amino acid OH groups to regulate proteins activity
Carbon forms __ covalent bonds in many biologically relevant molecules
4
Carbon forms ___ in other non relevant molecules
‘unsaturated’ double bonds
What are functional groups?
groups of atoms giving organic molecules different characteristics and properties
What does the hydroxyl functional group look like?
-OH
What does the acyl functional group look like?
O
||
–C–R
What does the carbonyl functional group look like?
O
||
–C–
What does the carboxyl functional group look like?
O
||
–C–O^-
What does the sulfhydryl functional group look like?
–SH
What does the amino functional group look like?
–NH2 or –NH3+
What does the phosphate functional group look like?
O
||
--O--P--O^-
|
O^-What does a pyrophosphate functional group look like?
O O
|| ||
--O--P--O--P--
| |
O^- O^-What does the ester functional group look like?
||
–C–O–C–
|
What does the ether functional group look like?
|
–C–O–C–
| |
What does the anide functional group look like?
O
||
–N–C–
|
Covalent bond electrons are shared unequally between atoms with different
electronegativities
What is a dipole moment?
when covalent bond electrons are shared unequally between atoms with different electronegativities
In a non polar covalent bond between atoms
the bonding electrons are shared equally between two atoms with similar electronegativity
(ex: C-C and C-H bonds)
In polar covalent bonds between atoms with different electronegativities,
shared electrons spend more time closer to the more electronegative atom resulting in partial negative and positive charges on each end of the molecule
Shared electrons stay closest to the nucleus with the highest
electronegativity
What is the extent of dipole charge separation?
dipole moment
A dipole moment is the product of
the partial charge on each atom and the distance between the two atoms
Bond strength/energy is
the energy required to break/make a particular type of bond
Covalent bonds are much __ and more __ than non covalent bonds
stronger; stable
Multiple non covalent interactions can combine to form strong associations in
macromolecules and structures such as DNA and membranes
The energy in the “high-energy” phosphoanhydride bonds in ATP used to power numerous cellular processes is __ than the energy associated with single (C-C) and double (C=C) bonds
less
Noncovalent bonds are __ than covalent bonds
much weaker
Non covalent are responsible for
the transient interaction between cellular macromolecules
What does multipoint contacts additive do?
- produce stable structures
- provide specificity in molecular interactions
- selectivity in biological associations
- conformation of macromolecules
- formation of complexes between macromolecules
What are ionic bonds?
attractions between charged atoms
T or F? Ionic bonds are weakened in the presence of water
T
In solid crystals, cations and anions form neatly ordered arrays in which
the positive and negative charges counterbalance each other
The energy released in formation of ion hydration shells (energy of hydration) is greater than
the lattice energy that stabilizes the crystal
Increasing ion concentration can
compete for, weaken, or even disrupt the ionic interactions holding biomolecules together
When do hydrogen bonds occur?
when covalently bonded hydrogen has a partial positive charge and attracts electrons of a second atom
H-bonds determine
the structure and properties of water
Water forms hydrogen bonds with alcohols and amines, which
solubilizes compounds
The peptide group and ester group, which are present in many biomolecules form __ with water or other polar groups to stabilize molecular structures and interactions
hydrogen bonds
What are Van der Waals interactions?
hydrophobic attractions between non polar molecules that are due to transient dipole formation
Where do Van der Waals interactions take place?
between atoms that are close enough for electrons of one atom to overlap and perturb electrons of the other atom
Transient dipoles in the electron clouds of all atoms give rise to weak attractive forces between
a partial negative charge and a partial positive charge
What are hydrophobic interactions?
occurs when non polar molecules associate and minimize their exposure to polar molecules
Molecular complementary of two protein surface shapes, charges, polarity, and hydrophobicity permit multiple weak interactions that combined can form
specific, weak to strong, transient to stable interactions
What is Kd?
bonding dissociation constant
Induced fit binding of one molecule changing conformation of the other increases
molecular complementarity
What are the macromolecule polymers and their monomer subunits?
proteins-amino acids
nucleic acids-nucleotides
polysaccharides-monosaccharides
Differences in size, shape, charge, hydrophobicity, and reactivity of the 20 common amino acid side chains determine
protein chemical and structural properties
What are polysaccharides?
hexoses (glucose and others) linked by two types of bonds
What do nucleic acids do?
store and transmit genetic information
What do carbohydrates include?
simple sugars and sugar polymers
Lipids are a diverse group of __
non polar molecules
Fats are made of
glycerol linked by three ester bonds to three fatty acids
What causes a dehydration reaction?
the polymerization of two monomers by forming a covalent bond
What is the result of a dehydration reaction?
the loss of water
What are hydrolysis reactions responsible for?
the breakdown or cleavage of a covalent bond by incorporating water
Major types of biological macromolecules are assembled by __ __ of multiple small identical or similar molecules (monomers): amino acids-proteins, nucleotides-nucleic acids, and monosaccharides-polysaccharides
covalent (dehydration) polymerization
What are the components of amino acids?
- an alpha carbon
- an amine group
- a carboxyl group
- a variable R group
Amino acids are linked together by
peptide bonds into a polypeptide chain to make a protein
What determines the characteristic properties of each amino acid and is the basis for grouping the 20 common amino acids into three main categories: hydrophobic, hydrophilic, and special
The side chain (R group) of the amino acid
When an amino acid is hydrophobic what does that mean?
they have a non polar R group
What does it mean when an amino acid is labeled hydrophilic?
it has a polar R group and its ionic groups are charged at pH 7
What are examples of special amino acids?
- C with reactive sulfhydryl group that can form disulfide bonds
- G with single H that can fit into small spaces in proteins
- P with cyclized R group that forms rigid kinks in proteins
Humans can synthesize __ amino acids, but __ essential amino acids must be consumed in diet
11;9
Amino acids in proteins may be
modified
Peptide bonds form between the __ and the __ of participating amino acids
alpha-carbonyl; alpha-amino
Amino acids differ in the __ attached to one of the bonds of the alpha-carbon
R group
R groups of amino acids can be
polar charged, polar uncharged, nonpolar
Polar charged contain R groups that
act as stronger organic acids, bases; can form ionic bonds
What are characteristics of polar charged amino acids?
- almost always fully charged at pH 7; side chains are relatively strong organic acids and bases
- Can form ionic bonds due to charges; histones with arginine (+- charge) bind to negatively charged phosphate groups of DNA
- Histidine- usually only partially charged at pH 7; often important in enzyme active sites due to its ability to gain or lose a proton in physiologic pH ranges
Polar uncharged amino acids contain
R groups that are weakly acidic or basic; not fully charged at pH 7
Polar uncharged amino acids can
form hydrogen bonds with other molecules like water since they have atoms with a partial negative or positive charge
What is characteristic of non polar amino acids?
- R groups hydrophobic
- generally lack O and N
- can’t interact with water or form electrostatic bonds
- vary primarily in size and shape
- allows them to pack tightly into protein core
Non polar amino acids associate with one another via
hydrophobic and van der Waals interactions in protein core
What is unique about glycine (R=H)?
small R group makes backbone flexible and able to move so it is useful in protein hinges; small R group allows 2 backbones (of same or different protein) to approach closely
What is unique about proline?
R group forms ring with amino group (imino acid); hydrophobic amino acid that does not readily fit into orderly secondary structure (alpha-helix)
What is unique about cysteine?
R group has a reactive –SH; forms disulfide (-S-S-) bridge with other cysteines often at some distance away in polypeptide backbone
Glycine has only __ as its R group and is small
–H
The alpha-carbon of __ is part of a ring, creating kinks in the protein
proline
Cysteine forms __ __ (-S-S-) with other cysteines
disulfide bridges
The nature of the __ determines the function of the protein
R groups
Each nucleotide consists of what three parts?
- 5 carbon sugar
- a phosphate group
- a nitrogenous base
- bases are either purines or pyrimidines
A phosphate group is linked to the 5’ C in a pentose (five-carbon) sugar by
a phosphoester bond
A pentose (five-carbon) sugar is linked through its __ to a nitrogenous base
1’ C
The pentose sugar in RNA is
ribose
The pentose sugar in DNA is
deoxyribose
What are examples of purines?
adenine and guanine
What are examples of pyrimidines?
cytosine
Thymine is only found in
DNA
Uracil is only found in
RNA
Purine means
pair of fused rings
Pyrimidines means
single ring
Nucleic acids can be polymerized by the formation of __ to produce single-stranded polymers
phosphodiester bonds
The long chains of deoxynucleotides in the double helix of DNA are linked by
hydrogen bonds
To link A to T, __ hydrogen bonds are needed
2
To link G to C, __ hydrogen bonds are needed
3
GC-rich DNA is
more stable
Nucleosides consist of a nitrogenous base covalently attached to
a sugar
Nucleotides consist of a nitrogenous base covalently attached to
a sugar (ribose or deoxyribose) and one to three phosphate groups
Carbohydrates include
simple sugars and sugar polymers
Carbohydrates serve as
energy storage molecules or structural molecules
What is the chemical structure of carbohydrates?
(CH2O)n
T or F? The sugars of carbohydrates can be linear but sometimes form ring structures
T
Ketose sugars
have a carbonyl (C=O) on an internal carbon
Aldose sugars
have a carbonyl (C=O) on a terminal carbon
Carbohydrates have a backbone of carbon linked by
single bonds
Usually __ and __ are attached to each carbon in the backbone of a carbohydrate
H; OH
Glycosidic bonds are __ links between sugars
-C-O-C-
Disaccharides are used as
a source of readily available energy
Where are oligosaccharides found?
bound to cells surface proteins and lipids
Oligosaccharides may be used
for cell recognition
Storage polysaccharides are
polymers of sugars joined by glycosidic bonds linked by alpha(1-4) linkage with branches consisting of alpha(1-6) linkages
Glycogen is
an animal product
Glycogen is made of
branched glucose polymers
Starch is
a plant product
Starch is made of
both branched and unbranched glucose polymers
What is cellulose?
structural polysaccharides comprised of beta(1-4)-linked glucose units
What is chitin?
structural polysaccharides found in the exoskeleton of invertebrates
Lipids are a diverse group of
non polar molecules
Fats may be made of
glycerol linked by three ester bonds to three fatty acids
Fatty acids are
unbranched hydrocarbons with one carboxyl group that are amphipathic
Saturated fatty acids
lack C=C double bonds and are solid at room temperature
Unsaturated fatty acids
have one or more C=C double bonds and are liquid at room temperature
Steroids are
animal lipids derived from cholesterol
Phospholipids are
amphipathic lipids that are a major component of cell membranes
Diacylglycerols consist of
- glycerol backbone
- 2 fatty acids
- phosphate group
- small polar group
- nomenclature based on polar group
K(eq) = product/reactant ratio when forward and reverse rates are
equal
Cell linked reactions are at a steady state, not
equilibrium
The dissociation constant (K(d)) is a measure of
non covalent interactions
The pH range of cytoplasm is
7.2-7.4
The pH of some organelles such as lysosomes is
4.5
Acids __ protons (H+)
release
Bases __ protons (H+)
bind
Biological systems use weak acid/base buffers to
maintain pH in narrow ranges
The __ and __ at which chemical reactions proceed determine the chemical composition of cells
extent; rate
Chemical reactions are
reversible
Initial forward and reverse reaction rates depend on the
initial concentrations of reactants and products
The net forward reaction rate __ as the concentration of reactants decreases
slows
The net reverse reaction rate __ as the concentration of products increases
increases
What is characteristic of equilibrium?
the rates of the forward and reverse reactions are equal, and the concentrations of reactants and products remain constant
What is the equilibrium constant (K(eq))?
the ratio of product to reactant concentrations at equilibrium and the ratio of forward to reverse rate constants
Equilibrium constant depends on what?
temperature and pressure
A catalyst can increase reaction rate but has no effect on
equilibrium constant (K(eq))
When K(eq) = 1,
the reaction is at equilibrium
Cells must maintain a __ __ for the biochemical reactions
steady state
Equilibrium results in
cell death
The concept of equilibrium also applies to the binding of one molecule to another without __ __ to either molecule
covalent changes
The dissociation constant K(d)) is the __ of the equilibrium constant
reciprocal
The dissociation constant (K(d)) is a measure of
the bonding affinity the two molecules have for one another
The lower the dissociation constant (K(d)), the __ the bonding affinity between two molecules
stronger
The higher the dissociation constant (K(d)), the __ the bonding affinity between two molecules
weaker
Macromolecules can have distinct __ __ for multiple ligands
binding sites
Acids __ protons
release
Bases __ protons
accept
Amphoteric molecules can act as
either acids or bases
What is the formula for pH?
pH = pKa + log([A-]/[HA])
Biological processes are sensitive to
pH
Changes in pH affect the __ __ and __ of proteins
ion state; function
__ in living systems resist changes in pH
buffers
What is the formula for pKa?
pKa = -logKa
What is the pKa of an acid?
the pH at which half the molecules are dissociated and half are neutral (undissociated)
pH is the major factor in determining if a macromolecule will be predominantly __, which in turn influences the types of __ interactions that may occur
ionized; noncovalent
If pKa - pH = 0, then
50% of the molecule is ionized and 50% is non-ionized
For weak acids, if the pH is higher than the pKa, then
more of the molecule is ionized than non-ionized
For weak acids, if the pH is lower than the pKa, then
less of the molecule is ionized than non-ionized
For weak bases, if the pH is lower than the pKa, then
more of the molecule is ionized than non-ionized
For weak bases, if the pH is higher then the pKa, then
less of the molecule is ionized than non-ionized
Ionized molecules can form
ionic bonds
Non-ionized molecules can form
hydrogen bonds or hydrophobic interactions
How do weak acids differ from weak bases?
-for weak acids:
pKa - pH = log ([nonionized]/[ionized])
-for weak bases:
pKa - pH = log ([ionized]/[nonionized])
Buffering capacity depends on
concentration of the buffer and the relationship between its pKa value and the pH
Buffers are best when they’re __ unit above or below pKa value
1
What does deltaG measure?
reaction change in free energy
-deltaG reactions are
thermodynamically favorable
+deltaG reactions are
not thermodynamically favorable
What is the equation for deltaG?
-2.3RTlogK(eq)
Rate of reaction depends on
activation energy
Rate of reaction lowered by a
catalyst
What is the ultimate source of all cell energy?
sunlight energy captured by photosynthesis
What is bioenergetics?
the study of the various types of energy transformations that occur in living organisms
What is energy?
capacity to do work, or the capacity to change or move something
What is thermodynamics?
the study of the changes in energy that accompany events in the universe
Kinetic energy is the energy of
movement
What is thermal energy?
the flow of energy from a region of higher temp to lower temp
Is thermal energy a major player in cellular activity?
no
What is radiant energy?
kinetic energy of photons or waves of light
e.g. photosynthesis
What is mechanical energy?
the major form of kinetic energy in biology
e.g. reorganization of the cytoskeleton
What is electric energy?
energy of moving electrons or charged particles
e.g. transport of charged ions across the cell membrane, electrically active neurons
Potential energy is
stored energy
What is chemical potential energy?
energy stored in bonds connecting atoms in molecules
e.g. conversion of glucose to ATP and NADH
What are concentration gradients?
potential energy created by storing molecules on one side of a membrane and allowing them to flow across the membrane barrier spontaneously
e.g. oxidative phosphorylation
What is electric potential energy?
potential energy produced by separating differently charged ions on opposite sides of the membrane, e.g. membrane potential
What does the first law of thermodynamics state?
energy can neither be created nor destroyed
The first law of thermodynamics is called
the law of conservation of energy
What is transduction?
conversion of energy from one form to another
What is an example of transduction?
conversion of sunlight into chemical energy
The universe can be dividd into
system and surroundings
What is the system?
a subset of the universe under study
What are the surroundings?
everything that is not part of the system
The energy of the system is called
internal energy (E)
The change of the energy of the system during a transformation is called
deltaE
What is the equation for the first law of thermodynamics?
deltaE = Q - W
E: internal energy
Q: heat energy
W: work energy
When there is energy transduction (deltaE) in a system, heat content may
increase or decrease
Reactions that lose heat are
exothermic
Reactions that gain heat are
endothermic
The first law predicts whether an energy change will be positive or negative
F
What does the second law of thermodynamics state?
events in the universe tend to proceed from a state of higher energy to a state of lower energy toward equilibrium
When an event is spontaneous, it means that
it can occur without the input of external energy
Loss of available energy during a process is the result of
a tendency for randomness to increase whenever there is a transfer of energy
Events progress from
an ordered state to a disordered state
What is entropy?
a measure of the randomness of disorder
Every event is accompanied by __ __ in the entropy of the universe
an increase
Entropy is associated with
random movements of particles or matter
Living systems maintain
a state of order, or low entropy
T or F? Entropy is energy not available to do additional work
T
What is the equation for loss of available energy?
TdeltaS
deltaS: change in entropy
Entropy (disorder) will increase until
the system reached equilibrium
Spontaneous reactions are thermodynamically
favorable
The second law of thermodynamics is only absolute in
a closed system
Catabolic pathways are
metabolic pathways that break down molecules into smaller units and release energy
Anabolic pathways are
metabolic pathways that construct molecules from smaller units and require energy
Cellular metabolism is __ metabolism
non-equilibrium
Cells are __ thermodynamic systems
open
Cellular metabolism exists in a
steady state
What are the characteristics of a steady state?
- concentrations of reactants and products remain constant, but not at equilibrium
- New substrates enter and products are removed
What is the difference between equilibrium and steady-state metabolism?
maintaining a steady state requires a constant input of energy, whereas maintaining equilibrium does not
What is the equation of enthalpy?
deltaH (enthalpy) = deltaG + TdeltaS
Free energy, deltaG is
the energy available to do work
The spontaneity of a reaction is
deltaG
If deltaG is <0, then the reaction is
exergonic
If deltaG is >0, then the reaction is
endergonic
Spontaneity depends on both
enthalpy and entropy
What is Gibbs equation?
deltaG = deltaH -TdeltaS
- deltaG: change in free energy of system
- deltaH: change in enthalpy; total energy content of a system
- T: temp
- deltaS: change in entropy; an increase in disorder
A reaction is energetically favorable if deltaG is
negative
A reaction that is -deltaG
will proceed spontaneously
A reaction with a negative deltaG is an ___ reaction
exergonic
A reaction with a negative deltaG is thermodynamically
favorable
In a reaction with a negative deltaG
total free energy of the reactants is greater than the total free energy of the products
The greater the deltaG of a reaction,
the farther the reaction is from equilibrium and the more work that can be performed by the system
If a reaction has a positive deltaG, it is energetically
unfavorable
A reaction with a positive deltaG is an ___ reaction
endergonic
Reactions with a positive deltaG
require the input of energy to proceed
In exergonic reactions (spontaneous), the free energy of the products is
less than that of the reactants and energy is released as the reaction proceeds
In endergonic reactions (not spontaneous), the free energy of the products is
greater than that of the reactants and requires an external energy source
In the equation deltaG = deltaH - TeltaS, if deltaH is positive (+) and deltaS is negative (-), the reaction is
not spontaneous and energetically unfavorable
In the equation deltaG = deltaH - TdeltaS, if deltaH is negative (-) and deltaS is positive (+), the reaction is
spontaneous and energetically favorable
In the equation deltaG = deltaH - TdeltaS, if BOTH deltaH and deltaS are negative (-), the reaction is
not spontaneous
In the equation deltaG = deltaH - TdeltaS, if BOTH deltaH and deltaS are positive (+), the reaction is
not spontaneous
The rates of chemical reactions are proportional to
the concentration of reactants
At equilibrium, the free energies of the products and reactants are
equal (deltaG = 0)
Reactions with a Keq > 1 have a __ deltaG
negative
Reactions with a Keq < 1 have a __ deltaG
positive
Reactions with a Keq = 1 have a delta G of
0
deltaG is influenced by
the concentration of molecules in the reaction
Equilibrium constant (K(eq)) equals
[products]/[reactants]
If K(eq) > 1
forward reaction favored
If K(eq) < 1
reverse reaction favored
If K(eq) = 1
forward and reverse reactions are equally favored (equilibrium)
How does a catalyst increase the speed of a reaction?
lowers the activation energy of the reaction
Catalysis does not influence the __ of a reaction
thermodynamics
Cellular reactions with a positive (+) deltaG occur because
- the ratio of reactants to products is kept low enough to drive forward reaction
- input of energy; coupled reactions
- use activated carrier molecules
NADH, NADPH, and FADH2 are
electron carriers
Redox reactions involve the
transfer of electrons from one molecule (oxidation) to another molecule (reduction)
In a redox reaction, electrons move spontaneously toward atoms or molecules having
more positive reduction potentials
Non equilibrium conditions are maintained because
cell is an open system
The exceptional conformational flexibilities of disordered proteins contribute to
their multiple functions
Homologous proteins
- evolved from a common ancestor
- have similar sequences, structures and functions
- can be classified into families and superfamilies
The human genome has __ protein-encoding genes
20,000-23,000
What is the primary structure of proteins?
linear sequence of amino acids linked by peptide bonds
What is the secondary structure of proteins?
folding of the polypeptide chain into local alpha-helices or beta-sheets
What is the tertiary structure of proteins?
peptide 3D shape
- structure of a peptide composed of secondary structural elements and various loops and turns
- may form distinct, independently stable domains
What is the quaternary structure of proteins?
association into multipoeptide complexes
-some functional proteins are composed of more than one polypeptide
What is characteristic of supramolecular complexes?
can be very large, consisting of tens to hundreds of subunits
Protein functions depend on
specific binding interactions and conformational changes in the structure of a properly folded protein
How are proteins involved in structure?
they are involved in organizing the genome, organelles, cytoplasm, protein complexes, and membranes in 3D space
How are proteins involved in regulation?
the control protein activity
How are proteins involved in signaling?
they monitor the environment and transmit information
How are proteins involved in transport?
they move small molecules and ions across membranes
How are proteins involved in enzyme activity?
they catalyze chemical reactions
How are proteins involved in motors?
they generate force for movement
The 3D structure of a protein is determined by
the amino acid sequence and intramolecular non covalent interactions
How is a peptide bond formed?
a dehydration reaction linking one amino acid C-terminus to another amino acid N-terminus
What is characteristic of a polypeptide?
linear polymer has a free amino end (N-terminus) and a free carboxyl end (C-terminus)
Peptide bonds link
the amino nitrogen atom of one amino acid with the carbonyl carbon atom of an adjacent amino acid in the chain
If there is a change in an amino acid due to a point mutation, the affect on the structure depends on
the nature of the side chain
- may have little or no affect if side chain has similar properties
- more affect if side chain has different properties
A change in an amino acid has a greater impact if
the change causes a change in the 3D structure or properties
Secondary structure riders to the conformation of adjacent amino acids into
an alpha-helix, beta-sheet, hinges, turns, loops, or finger-like extensions
What is a secondary structure?
stable spatial arrangement od polypeptide chain segments held together by hydrogen bonds between backbone amide and carbonyl groups
A polypeptide backbone (ribbon) folds into a spiral/helix with
3.6 amino acids per turn
An alpha-helix is stabilized by
hydrogen bonds between backbone oxygen and hydrogen atoms (more bonds-more stable)
R groups project outward from the surface of the alpha-helix and
determine the chemical nature of helix faces
Pralines can’t participate in hydrogen bonding and are usually excluded from
an alpha-helix
What is a beta sheet?
laterally packed beta strands, each of which is a nearly fully extended polypeptide segment
A three-stranded beta sheet is made of
antiparallel beta strands with connection loops
-alternate R groups project above and below the plane of the sheet
Three-stranded are stabilized by
hydrogen bonds between backbone oxygen and hydrogen atoms in amino acids on different strands
Alpha carbon bond angles produce
a pleated polypeptide backbone contour
A parallel beta strand sheet is composed of
the same N-to-C strand orientations with connecting loops
What is the structure of a beta turn?
- composed of four residues
- reverses direction of a polypeptide chain (180 U-turn)
- Calpha carbons of the first and fourth resides are usually less than 0.7nm apart and are linked by a hydrogen bond
- glycine (smallest R group) and proline (built in bend) are commonly found in beta turns
Structure dictates
function
Beta turns facilitate
the folding of long polypeptides into compact structures
Tertiary structure is the conformation of
the entire polymer
Tertiary structures are stabilized by
- hydrophobic and Van der Waals interactions between non polar side chains
- hydrogen bonds involving polar side chains and backbone amino and carboxyl groups
Proteins can be
fibrous or globular
Hydrophobic residues of a tertiary structure
cluster together like drops of oil in the folded protein core, driven away from the aqueous surrounding by the hydrophobic effect
Charged and uncharged polar side chains of the tertiary structure
form stabilizing interactions with surrounding water and ions on the protein surface
Disulfide bonds between cysteine residues can also play a role in
stabilizing tertiary structure
The formation of non covalent bonds results in
a release in energy and a more stable macromolecular structure (lower energy state)
Proteins fold into a 3D shape that
requires the least amount of energy to maintain
What are characteristics of globular proteins?
- generally water-soluble
- compactly folded structure
- often but not exclusively spheroidal in shape
What are characteristics of fibrous proteins?
- large
- elongated
- often stiff molecules
What is characteristic of integral membrane proteins?
embedded within the phospholipid bilayer of membranes
Globular, fibrous, and integral membrane proteins are all
well-ordered proteins
What are characteristics of intrinsically disordered proteins?
- do not have well ordered structures in their native states
- polypeptide chains are very flexible with no fixed conformation
- interact with multiple partner proteins
- only fold into a well-defined conformation during specific interaction with other protein partners
What is characteristic of induced fit?
the interaction between two molecules results in conformational changes that allow the molecules to interact with greater affinity for one another
Calpha backbone traces depict
how the polypeptide is tightly packed into a small volume
Ball-and-stick representations reveal
locations of all atoms
Ribbon diagrams emphasize
how beta-strands and alpha-helices are organized in the protein
Water-accessible surface models reveal
protein surface topology with positive charge and negative charge regions
What are structural motifs?
regular combinations of secondary structures usually with a specific type of function
Structural motifs can be encoded by
a highly conserved sequence motif
What is a coiled-coil motif?
two alpha helices wound around each other
What is an EF hand?
a type of helix-loop-helix motif in many proteins, including many calcium-binding and DNA-binding regulatory proteins
Zinc-finger motifs are present in
many DNA-binding proteins that help regulate transcription
Domains occur when
proteins are composed of two or more distinct regions
What are the three main classes of protein domains?
functional, structural, and topological domain
What is the functional domain of a protein?
region of protein that exhibits a specific activity, usually independent of other regions of the protein
What is the structural domain of a protein?
region of >40 amino acids arranged in a single, stable, distinct structure often comprised of one or more secondary structures
What is the topological domain of a protein?
regions of proteins defined by their spatial relationship to the rest of the protein; e.g., membrane spanning proteins have extracellular, membrane embedded and cytoplasmic domains
Well-ordered proteins easily fold into their
proper 3D shape
75% of eukaryotic proteins have multiple
structural domains
What is epidermal growth factor (EGF) precursor generated by?
proteolytic cleavage
Proteolytic cleavage generates multiple
EGFs (epidermal growth factors)
What is Neu?
EGF domain plus other domains
What is Tissue plasminogen activator (TPA)?
EGF domain plus other domains
Quaternary structure refers to proteins composed of
subunits
Quaternary structure refers to
the manner in which subunits interact
Different proteins can become physically associated to form
a multiprotein or supramolecular complexes
Protein amino acid sequence determines its
3D structure and function
ATP-dependent molecular chaperones and chaperonins assist
protein folding in vivo
Misfolded/denatured proteins can form well-organized amyloid fibril aggregates that can
cause diseases
Polypeptide chain on either side of the peptide bond can be oriented in either a __ or __ configuration relative to the peptide bond
trans; cis
99.97% of the peptide bonds that have any residue other than proline at P2 are in the __ configuration
trans
Planar peptide bonds limit
the shapes into which proteins can fold
In peptide bonds, the carbonyl carbon and amide nitrogen must
lie in a fixed plant
-little rotation of the peptide bond is possible
The only flexibility in a polypeptide chain is
rotation of the fixed planes of adjacent bonds
Proteins may assume their __ conformation through a series of steps
native
What is the monomeric protein folding hierarchy?
primary –> secondary –> tertiary –> structure
Formation of small structural motifs appears to precede formation of __ and the __
domains; final tertiary structure
Domain folding is usually independent of
other regions of the protein
What is the native state of a protein?
usually the conformation with the lowest free energy (G)
What are molecular chaperones?
“helper proteins” that prevent nonselective interactions during protein folding to achieve proper 3D conformation
What do molecular chaperones do?
bind to a short segment of a protein substrate and stabilize unfolded or partly folded proteins, preventing aggregation or degradation
Chaperonins allow
large new proteins to assemble without interference from other macromolecules
Chaperonins process up to __ of the cells’ proteins
15%
The Hsp70 chaperone protein cycle
binds transiently to a nascent polypeptide as it emerges from a ribosome or to a protein that has unfolded
What is the first step of the Hsp70 chaperone protein cycle?
Hsp70 binds unfolded protein in rapid equilibrium to the open conformation of the substrate-binding domain and ATP in the nucleotide-binding domain
What is the second step of the Hsp70 chaperone protein cycle?
Co-chaperone accessory proteins (DnaJ/Hsp40) stimulate ATP hydrolysis inducing a large conformational change in the substrate-binding domain that locks the unfolded protein region into the substrate-binding domain- proper folding is facilitated
What is the third step of the Hsp70 chaperone protein cycle?
exchange of ATP for the bound ADP stimulated by other accessory co-chaperone proteins (GrpE/BAG1)
What is the fourth step of the Hsp70 chaperone protein cycle?
Releases the properly folded substrate, regenerating the open conformation
What are the steps of the Hsp90 molecular chaperone cycle?
- no nucleotide bound to the nucleotide-binding domain- dimer in a very flexible, open configuration that can bind a client
- rapid ATP binding causes conformational change- nucleotide-binding domains dimerize and the substrate-binding domains move together
- intermediate state
- closed conformation
- ATP hydrolysis- conformational change in Hsp90 that may include a highly compact form, folding of the client, and client protein release
- release of ADP regenerated the initial flexible open state
What are chaperonins?
folding chambers into which all or part of an unfolded protein can be bound in an appropriate environment, giving it time to fold properly
Proline isomerases catalyze
the cis/trans isomerization to facilitate protein folding
Cis/trans isomerization of a single proline
- alters structure of a protein domain
- can influence a protein’s activity
- proline isomerases may act as switches that regulate protein activity
T or F? All amino acids are in every protein
F
The defined and predictable structure of proteins based on
- nature of amino acids in protein
- order of amino acids
- environment
Misfolded proteins/proteolytic fragments can accumulate as __ inside or outside of cells in various organs including joints between bones, the liver, and the brain
aggregates or plaques
Many diverse proteins can aggregate into amyloid (well-ordered) __ that have a common structure and can cause amyloidoses diseases such as Alzheimer’s, Parkinson’s, and “mad cow” disease
fibrils
Protein function depends on
binding other molecules (ligands)
Enzymes accelerate rate of cellular reactions by
lowering activation energy and stabilizing transition-state intermediates
Enzymes often use __ mediated by one or more amino acid side chains
acid-base catalysis
Metabolic pathway enzymes may be associated as
- domains of a monomeric protein
- subunits of a multimeric protein
- components of a protein complex assembled on a common scaffold
What is a ligand?
molecule to which a protein binds
Ligand binding often results in
a conformation change in the protein’s 3D shape
What is specificity?
the ability of a protein to bind one molecule or a small group of molecules in preference to all other molecules
What is affinity?
refers to the tightness or strength of binding determined by the ligand-binding site
Low Kd = __ affinity
high
High Kd = __ affinity
low
__ __ is required for specificity and affinity
molecular complementarity
What are CDR’s? What are they responsible for?
complementarity-determining regions; responsible for the specificity of ligand binding
Enzymes are almost always
proteins
What are ribozymes?
RNA molecules with enzymatic activity
Enzymes may be conjugated with
non-protein components
What are cofactors?
inorganic enzyme conjugates (e.g., metals)
What are coenzymes?
organic enzyme conjugates
K(eq) and deltaG don’t predict the rates of reactions, only the
direction
Enzymes are
biological catalysts
Enzymes are present in cells in
small amounts
Enzymes are __ altered during a reaction
reversibly
Enzymes enter and exit a reaction
in the same condition
T or F? Enzymes can only be used once in a reaction
F; can be used over and over
Enzymes have __ effect on thermodynamics of reaction
no
Enzymes increase __ of reaction
velocity
Enzymes are highly specific for their particular reactants called
substrates
Enzymes produce only
appropriate metabolic products
T or F? Enzymes can be regulated to meet the needs of the cell
T
Thermodynamically favorable reactions don’t proceed on their own at relatively rapid rates
in the absence of enzymes
T or F? Kinetic stability and thermodynamic stability are not interdependent
T
What is activation energy?
the energy that must be overcome for a chemical reaction to occur
Chemical transformations require the breaking of
covalent bonds
Reactants must contain sufficient __ to overcome activation energy and reach an activated state to achieve the atomic rearrangements necessary for a reaction to occur
kinetic energy
The geometry and electron distribution of atoms around bonds are
distorted
Shape of molecule distorted to
break the covalent bonds
What is a transition state?
the point at which reactants reach the energy crest and are ready to be converted into products
T or F? Activation energy isn’t required if the reaction is energetically favorable
F
The activation energy required to reach the transition state is not a fixed value but varies with
the particular reaction mechanism utilized
An enzyme interacts with its substrate to form
an enzyme-substrate (ES) complex
The substrate binds to a portion of the enzyme called the
active site
The active site and the substrate have ___ shapes that allow substrate specificity
complementary
Enzymes catalyze reactions by making or breaking
substrate covalent bonds
What does the substrate-binding pocket do?
binds specific substrates
What does the catalytic site contain?
side chains of the catalytic amino acids that alter covalent bonds
Catalytic and substrate-binding sites may
overlap or be in two structurally distinct regions
Amino acids lining the side-chain-specificity pocket determine its
shape and charge and binding properties
What does Trypsin do?
binds substrate (+) charged arginine and lysine side chains
What does Chymotrypsin do?
binds large, hydrophobic side chains such as phenylalanine
What does Elastase do?
binds small side chains such as glycine and alanine
What are some mechanisms of enzyme catalysis?
substrate orientation, changing substrate reactivity, inducing strain in the substrate
What is substrate orientation?
multiple substrates brought together in correct orientation to catalyze reaction
What happens when you change substrate reactivity?
substrate influenced by amino acid side chains at active site that alter chemical properties (e.g., charge) of substrate
What happens when you induce strain in the substrate?
enzyme changes conformation of substrate to bring closer to conformation of transition state
- shifts in the conformation cause an induced fit between enzyme and substrate
- covalent bonds of the substrate are strained
What are the steps of the schematic model of an enzyme’s reaction mechanism?
- enzyme’s substrate-binding site and catalytic site cooperate in multistep reaction to convert substrate to product
- enzyme binds substrate molecules at a fixed enzyme active site
- Enzyme-substrate (ES) complex:
- in equilibrium with the unbound enzyme and substrate
- intermediate step in the conversion of substrate to product (P)
Describe enzyme catalysis in multiple discrete steps
- initial formation of an ES complex
- conversion via a single transition state to the free enzyme and product
- activation energy for each step is significantly less than the activation energy for the uncatalyzed reaction, enhancing the reaction rate
What is kinetics?
the study of rates of enzymatic reactions under various experimental conditions
Rates of enzymatic reactions increases with __ until the enzyme is saturated
increasing substrate concentrations
At saturation, every enzyme is working at
maximum capacity
The velocity at saturation is called
maximal velocity (V(max))
What is the turnover number?
the number of substrate molecules converted to product per minute per enzyme molecule at V(max)
What is Michaelis constant (K(m))?
the substrate concentration [S] that yields a half-maximal reaction rate; depends on affinity of enzyme for substrate
Maximal reaction velocity (V(max)) depends on
number of enzymes
What happens when you quadruple enzyme concentration?
- V(max) increases proportionally
- K(m) remains the same
Acid-base catalysis is __ dependent
pH
Catalysis requires a particular ionization state (protonated or nonprotonated) of
one or more amino acid side chains in the catalytic site
Enzyme activity is influenced by
temp
How can temperature affect an enzyme?
- introduce energy to the system and increase kinetic activity
- affect the 3D structure of the enzyme since high temperatures can disrupt ordered structures in proteins
What do enzyme inhibitors do?
slow the rates for enzymatic reactions
Irreversible inhibitors bind __ to the enzyme
tightly
Reversible inhibitors bind __ to the enzyme
loosely
Competitive inhibitors compete with the enzyme for
active sites
Competitive inhibitors usually resemble the __ in structure
substrate
Competitive inhibitors can be overcome with
high substrate/inhibitor ratios
Noncompetitive inhibitors bind to
sites other than active sites and inactivate the enzyme
With noncompetitive inhibitors the maximum velocity of enzyme molecules
can’t be reached
T or F? Noncompetitive enzymes can be overcome with high substrate/inhibitor ratios
F
Competitive inhibition increases K(m) without affecting
V(max)
Noncompetitive inhibition reduces V(max) without affecting
K(m)
Coupling by a scaffold protein overcomes
slow substrate diffusion in a metabolic pathway
Describe the sequential action enzymes by which reaction pathways convert substrate into final products
- enzymes free in solution: reaction intermediates diffuse from one enzyme to the next, which may be inherently slow
- multisubunit enzyme complex formed by a scaffold protein minimizes or eliminates substrate diffusion time
- some enzymes are fused at the genetic level, becoming domains in a single polypeptide chain-also minimizes or eliminates substrate diffusion time
Proteins may be regulated at the level of
- protein synthesis (transcription/translation)
- protein degradation
- through non covalent or covalent interactions
Proteins marked for destruction with a polyubiquitin tag by ubiquitin ligases are degraded in
proteasomes
Several allosteric mechanisms act as switches, reversibly turning __ on and off
protein activity
Higher-order regulation includes
the intracellular compartmentation of proteins (sub cellular localization)
What is covalent modification of a protein?
a molecule is covalently attached to the protein, thereby changing its chemical composition and altering the 3D structure of the protein
What are examples of covalent modification?
- phosphorylation
- glycosylation
- ubiquitination
What is allosteric modification of a protein?
a molecule non-covalently interacts with the protein, thereby producing modest changes in the 3D conformation of the protein, resulting in a change in activity or interaction with other macromolecules
What are some examples of allosteric modification?
interaction with metal co-factors or nucleotide
What are post-translational modifications (PTMs)?
alterations to the side chains of the amino acids after their incorporation into a polypeptide chain
Post-translational modifications (PTMs) can occur in
- the cytoplasm
- golgi apparatus
- endoplasmic reticulum
Post-translational modifications (PTMs) allow a single polypeptide to exist as
a number of distinct biological molecules
What are three common forms of PTMs?
- phosphorylation
- glycosylation
- ubiquitination
PTMs are specific to
different amino acids
In phosphorylation-dephosphorylation regulation of protein activity, kinases
transfer terminal phosphate group from ATP to specific Serine/Threonie or Tyrosine OH groups
In phosphorylation-dephosphorylation regulation of protein activity, phosphatases
hydrolyze phosphate group off protein
Kinases and phosphates work in pairs to regulate
protein activity
Enzymes can be regulated by phosphorylation/dephosphorylation by
having the covalent modification alter the shape of the enzyme to regulate substrate-binding specificity
Transcription factors can be regulated by phosphorylation/dephosphorylation by
having the covalent modification alter the shape of the protein to regulate sub cellular localization
Protein degradation regulates
life spans of intracellular proteins- vary from as short as a few minutes for mitotic cyclins to as long as the age of an organism for proteins in the lends of the eye
Protein degradation removes
damaged proteins
The proteasome molecular machine
degrades targeted proteins
What is polyubiquitinylation?
the addition of a polymeric chain of ubiquitins, usually marks protein for degradation
What is monoubiquitinylation?
attachment of a single ubiquitin to a protein, alters protein function or sub cellular localization
What is multiubiquitinylation?
addition of multiple, single ubiquitins; alters protein function or sub cellular localization
Non-covalent binding of regulatory molecule to allosteric site
changes the conformation of a protein
Allosteric switches control
protein activity
What is Calmodulin?
a widely distributed cytosolic protein; contains four EF hand Ca2+ binding sites
-(helix-loop-helix motif; Kd of 10^-6 M)
GTPase superfamily proteins exist in two forms/conformation, what are they?
GTP-bound and GDP-bound
GTPases hydrolyze __ to __
GTP; GDP
What is the conformation of the GTP-bound form of GTPase?
active “on” conformation
The GTP-bound form of GTPase can
interact with target proteins to regulate their activities
What is the conformation of the GDP-bound form of GTPase?
inactive “off” conformation
What does guanine nucleotide exchange factor (GEF) do?
stimulates replacement (exchange) of the bound GDP (off) with a GTP (on)
What does GTPase-activating protein (GAP) do?
stimulates GTP (on) hydrolysis to GDP (off)
What are the four basic molecular genetic processes?
- transcription
- RNA processing
- translation
- DNA replication
What happens in transcription?
the four-base DNA code specifying the amino acid sequence of a protein is copied (transcribed) into a precursor messenger RNA (pre-mRNA) by the polymerization of ribonucleoside triphosphate monomers (rNTPs)
What happens in RNA processing?
removal of noncoding sequences and other modification to pre-mRNA to make mRNA, which is transported to the cytoplasm
What happens in translation?
in ribosomes, tRNAs base pair with mRNA codons to position specific amino acids where they are linked into proteins
What happens in DNA replication?
OCCURS ONLY IN CELLS PREPARING TO DIVIDE; deoxyribonucleoside triphosphate monomers (dNTPs) are polymerized to yield two identical copies of each chromosomal DNA molecule, one for each daughter cell
DNA replication only occurs in cells
preparing to divide
In DNA, two phosphoester bonds (phosphodiester bond) link
adjacent nucleotides
Polynucleotides are synthesized in the __ to __ direction
5’ to 3’ (left to right)
In the DNA double-helical structure, there are __ percentages of A=T and G=C
equal
Interaction with a protein can __ DNA
bend
The conserved C-terminal domain of the TATA box- binds to
the minor groove of specific DNA sequences rich in A and T
-this untwists and sharply bends the double helix
Transcription of most eukaryotic genes requires participation of
TBP
Which is more stable, DNA or RNA?
DNA
Because DNA is more stable than RNA, it is a better carrier of
genetic information
Why is RNA less stable than DNA?
because the 2’ hydroxyl group in RNA (absent in DNA) can act as a nucleophile, attacking the phosphodiester bond and breaking the strand
The G/C content of DNA affects
melting temp
DNA strands unwind and separate during replication and transcription by
breaking the hydrogen bonds between base-paired bases
DNA denaturation/melting can be induced experimentally by
raising temp
What is T(m)?
“temp of melting”; temp at which half the double-stranded DNA bases have melted/denatured
The greater the G+C percentage, the higher the
T(m)
What are some characteristics of RNA?
- has a hydroxyl at 2’
- uracil base instead of thymine
- usually single-stranded
Ribozyme RNAs have catalytic activity based on
tertiary structures formed by base pairing
Base pairing between distant complementary segments of an RNA molecule forms
- hairpins (5-10 nucleotide loop
- stem-loops (11-100s of nucleotide loop)
- other structures including pseudo knots that contribute to tertiary structure
RNA is synthesized
5’ –> 3’
One gene DNA strand is template for __ by pairing complementary bases
transcription of an RNA
RNA polymerase begins transcription at gene nucleotide designated
+1
The RNA polymerase travels “downstream” toward the __ end on the DNA, and downstream bases are designated with __ numbers
3’; positive
“Upstream” bases are designated with __ numbers
negative
What important gene features lie upstream of the transcription start site?
promoting sequences recognized by transcription factors that recruit RNA polymerase to the gene
DNA strand being transcribed is the __
template strand
The complement to the template strand is the
nontemplate strand
RNA synthesized is complementary to the __ strand and is therefore identical with the nontemplate strand sequence, except with uracil in place of thymine
template
Regulation of eukaryotic gene transcription is __ compared to regulation in prokaryotes
much more complex
The promoter region of eukaryotic genes contain
enhancers
What are enhancers?
short DNA sequence motifs to which specific transcription factors bind to recruit the molecular machinery necessary to transcribe mRNA
What is combinatorial control?
eukaryotic gene regulation is in response to many integrated signals, activating numerous transcriptional regulators that converge on multiple enhancers within a single gene to differentially regulate activation or repression of gene expression
What are the 3 stages of transcription?
initiation, elongation, termination
What is initiation of transcription?
RNA polymerase melts DNA duplex to form a transcription bubble and begin polymerizing ribonucleotides (rNTPs) at the start site
What happens during elongation in transcription?
polymerase advances 3’-5’ down template strand polymerizing one rNTP at a time onto the 3’ end of growing RNA. The 5’ end of the RNA strand is displaces from the template DNA and exits through a channel in the RNA polymerase
What happens during termination in transcription?
RNA polymerase dissociates from the template DNA at a specific termination sequence (stop site)
Initial transcript in eukaryotes is referred to as the
precursor or pre-mRNA
What is RNA processing?
when several modifications must occur to generate a mature mRNA that can be exported to the cytoplasm for translation
RNA processing produces __ __ in eukaryotes
functional mRNA
RNA polymerase starts transcription at __ , which is upstream of the codon that encodes the first amino acid
gene nucleotide +1
Where does RNA polymerase stop transcription?
downstream of the translation STOP codon
The 5’ and 3’ unsaturated regions (UTRs) are __ in the fully processed mRNA
retained
What is capping?
when specific enzymes add an atypical molecule (a guanosine methylated on its nitrogenous base (7-methylguanosine) attached in a 5’ 5o 5’ manner) to the 5’ end of transcript
When does capping occur?
shortly after transcription begins during formation of the primary transcript
What does capping do?
- facilitates nuclear export
- protects mRNA from degradation
- promotes translation
- promotes intron splicing
What is polyadenylation?
when transcription is completed enzymes cleave the 3’ end of the transcript at a specific sequence (the polyadenylation sequence AAUAAA) and adds a string of adenine nucleotides- 150-200 adenine
What does the poly(A) tail do?
- stabilizes mRNAs in the nucleus and cytoplasm
- promotes mRNA translation
Poly-A tails become shorter over time leading to
decreased translation
What does splicing do?
removes introns and joins exons
Splicing is initiated while
mRNAs are still being transcribed
Conserved sequences __ , and are essential for their removal
define the 5’ and 3’ boundaries of exons/introns
What is the donor site of RNA processing?
5’ end of intron
What is the acceptor site of RNA processing?
3’ end of intron
Many eukaryotic transcripts are
alternatively spliced
- cell-type specific splicing
- in response to external stimuli
- at different stages of development
Alternative splicing produces distinct proteins that lack/possess unique functional domains, and therefore
behave differently from one another
Alternative RNA splicing
increases the number of protein isoforms expressed from a single eukaryotic gene
What are the 3 RNAs involved in protein synthesis?
mRNA, tRNA, and rRNA
What does mRNA?
nucleotide sequence that encodes the order of amino acids a ribosome assembles into polypeptide chain
Each amino acid is encoded by a __ within the mRNA sequence
three-nucleotide codon
Each amino acid is covalently bound to a subset of tRNAs containing a specific
three-nucleotide anticodon sequence
Ribosomes are composed of numerous proteins and three (bacterial) or four (eukaryotic)
ribosomal RNA (rRNA) molecules
One of the rRNAs
catalyzes peptide bond formation between incoming aa-tRNA amino-group and the carboxyl-terminus of the growing protein chain
What happens in translation?
sequences of nucleotides in an mRNA direct the incorporation of 20 specific amino acids in a polypeptide
What is the genetic code?
the set of rules by which the translation machinery reads the info in mRNAs and translates it into amino acid sequence
What is a codon?
mRNA sequences are real as a series of three nucleotide “words”: each corresponding to a specific amino acid
__ possible combos of triplet codons can be generated by the 4 nucleotides (U,C,A,G)
64
The codons encoding one amino acid may differ in
any of their three positions (most often this difference is in the second or third position)
No codon specifies more than one
amino acid
An mRNA molecule can be read/translated in any of the three different reading frames:
-dividing the sequence of nucleotides in the mRNA into three-nucleotide codons- only 1 of the 3 reading frames specifies the correct protein
Initiating translation in the incorrect frame can
produce a non-functional protein that may have deleterious effect on the cell
T or F? Codons bind directly to their complementary amino acid
F
Translation requires adaptor molecule, __, that bind the codon on one end and deliver an amino acid, bound at the other end, to the ribosome
transfer RNAs (tRNAs)
tRNAs adopt a cloverleaf shape through
complementary intramolecular base-pairing
-this creates 4 double helical arms in each molecule
The D loop of tRNA is important for
recognizing the enzyme that attaches the amino acid to each tRNA
The T loop of tRNA is important for
recognizing the ribosome
Each tRNA contains a specific anticodon that base pairs to codons in
the mRNA
The first nucleotide of the anticodon (5’ end) pairs with the third nucleotide (3’ end) of the
codon
Some anticodons can pair with more than one codon due to a phenomenon known as
wobble base pairing
The significance of wobble base pairing effect is that
instead of 64 different tRNAs (one for each codon), organisms can have significantly fewer (min 31)
Humans have __ tRNA genes, that encode __ distinct tRNAs
500; 48
What are aminoacyl-tRNA synthetases?
specific enzymes that catalyze the covalent attachment of the appropriate amino acid to each tRNA
What is the acceptor stem of tRNA?
a conserved CCA sequence in the 3’ end of tRNA where the appropriate amino acid will be covalently attached via its C-terminus
Once an amino acid is attached, the tRNA is said to be
charged or activated
Each aminoacyl-tRNA synthetase has
- a docking site for tRNAs
- a recognition site for the anticodon
- a catalytic site for transferring the amino acid to the acceptor stem
Covalent attachment of the amino acid is
ATP dependent and produces a high energy ester bond (unstable bond)
What are ribosomes?
complexes composed of enzymatic ribosomal RNA (rRNA) and numerous accessory proteins
What do ribosomes do?
- move along a mRNA (5’ to 3’)
- read each codon
- accept the appropriate tRNA and
- catalyze the covalent attachment of the next amino acid in the growing polypeptide chain
Ribosomes share structural and functional similarities, but differ in
number of rRNAs and proteins in bacteria, archaea, and eukaryote
What is the large ribosomal subunit of ribosomes composed of?
3 distinct rRNA molecules and many accessory proteins
What is the small ribosomal subunit of ribosomes composed of?
a single rRNA molecule and many accessory proteins
What does the small ribosomal subunit of ribosomes do?
matches tRNAs to mRNA codons
What does the large ribosomal subunit of ribosomes do?
catalyzes formation of peptide bonds between new amino acid and the growing polypeptide
LSU and SSU join together on the 5’ end of an mRNA to
initiate translation
Ribosomes move in a __ direction along the mRNA synthesizing the polypeptide beginning with its __ terminus
3’ to 5’; N
An assembled ribosome contains 3 binding sites for tRNAs that coordinate the processive covalent attachment of amino acids:
A, P, and E sites
Amino acids are polymerized as they remain
attached to a tRNA
__ make up the bulk of the ribosomal subunits
rRNAs
rRNAs form the __ as well as the __ in the LSU
A, P, and E sites; catalytic transferase site
Ribosomal proteins are primarily
structural
SSU is bound by proteins collectively called __ and the __ in the P site
- translation initiation factors
- initiator tRNA
Initiator tRNAs provide the __ for the encoded peptide
first amino acid
What does AUG do?
- serves as the principle start codon
- encodes the amino acid methionine
Only an __ can deliver the first amino acid.
initiator tRNA
With the initiator tRNA in the P site and paired with the start codon,
the initiation factors disassociate, and the LSU complexes with the SSU
-Translation may now proceed
When does elongation begin?
A charged/activated tRNA with anticodon complementary to the next codon enters the A site
What is the first step of translation?
-the growing polypeptide remains covalently linked to the tRNA that just delivered the third amino acid.
-this tRNA and peptide is positioned in the P site (peptidyl) and remains base paired with the codon for that amino acid
-a charged tRNA enters the A-site and
base pairs with the codon specifying the
next amino acid.
What is the second step of translation?
- the LSU catalyzes covalent linkage of the polypeptide chain to the new amino acid
- the C-terminus of the polypeptide is covalently joined to the N-terminus of the new amino acid
- the polypeptide is transferred from the tRNA in the P site to the tRNA in the A site.
What is the third step of translation?
- the LSU translocates toward the 3’ end of the mRNA, shifting the two tRNAs from P-A to E-P in the LSU
- the E site (empty) holds the recently depleted tRNA
- the P site now holds the tRNA with the growing polypeptide
What is the fourth step of translation?
- the SSU translocates toward the 3’ end of the mRNA, bringing it back into its original position with the LSU
- this causes the empty tRNA to be ejected from the E site
- P site holds the peptide tRNA
- the A site now contains the next codon to be be processed
When is prokaryote and eukaryote translation terminated?
when a ribosome encounters one of three stop codons – UAA, UAG, UGA
What are release factors (eRF3-GTP), and what do they do?
proteins that bind stop codons in the A site – altering catalytic activity of the LSU peptide transferase
-this adds a water molecule, rather than another amino acid, to the C-terminus of the peptide – freeing the polypeptide
Circular mRNA, polysomes, and rapid ribosome recycling
increase the efficiency of translation
Association of three proteins – poly(A)-binding protein (PABP), eIF4E, and eIF4G
circularizes mRNA by forming a bridge between the 5′ (cap) and 3′ (poly A) ends of the mRNA
What is a polyribosome?
structure with multiple individual ribosomes simultaneously translating a eukaryotic mRNA
