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
