Exam 1 Flashcards
biomolecules
The molecules of living organisms
organic molecules
(carbon-containing compounds
Urey and Miller
the first cells had to arise from
the first cells had to arise from
nonliving chemicals, inorganic substances
Earth’s age
The Earth came into being about
4.54 billion years ago
4 stages of the Origin of life
- organic monomers
- Organic polymers
- Protocells or protobionts
- Protobionts acquire ability to self-replicate
explain Stage 1: Evolution of monomers
whatr the hypothesis for how monomers evolved?
Several hypothesis for how monomers evolved
1. monomers came from outer space
2. monomers came from reactions in the atmosphere
- molecules could be formed in the presence of outside energy sources using atmospheric gases
3. monomers came from reactions at hydrothermal vents
Miller and Urey Experiment
Stanley Miller and Harold Urey
conducted an experiment to test the
Oparin-Haldane hypothesis:
Showed that gases (methane,
ammonia, hydrogen, and water) can
react with one another to produce
small organic molecules (amino
acids, organic acids)
Strong energy sources
Rainfall would have washed organic
compounds from the atmosphere
into the ocean.
They would have accumulated in the
ocean, making it an organic soup.
Chemical Evolution at hydrothermal vents
Hydrothermal vents are chemical hot springs found
in seafloors.
- They might have seeded life on Earth about 4 billion
years ago. - Conditions including a 158°F (70°C) temperature
are just right for chemical reactions responsible for
the formation of amino acids and primitive
membranes.
Explain stage 2: evolution of polymers
describe how polymers form and the 3 hypotheses
In cells, monomers join to form
polymers in the presence of enzymes.
A process known as polymerization.
Iron–Sulfur World Hypothesis:
It suggests organic molecules reacted with amino
acids to form peptides in the presence of iron-nickel
sulfides.
Protein-First Hypothesis
It assumes that protein enzymes arose first.
DNA genes came afterwards.
RNA-First Hypothesis
It suggests only RNA was needed to progress
toward the formation of the first cell or cells.
Some viruses have only RNA genes.
DNA genes would have come afterward.
Stage 3 evolution of Protocells
define proteinoids
define protocells
describe strucutre of protocells
Before the first true cell arose, there
would have been a protocell or
protobiont, the hypothesized
precursor to the first true cells
A protocell would have an outer
membrane and carry on energy
metabolism
Proteinoids are small polypeptides
with catalytic properties
Define and describe proteinoid and liposomes
When proteinoids are placed in
water, they form microspheres,
structures made of proteins with
many properties of a cell
If lipids are made available to
microspheres, lipids become
associated with microspheres,
producing a lipid-protein membrane
Lipids placed into water form cell-
sized double-layered bubbles called
liposomes
They may have provided the first
membranous boundary
liposomes
Lipids placed into water form cell-
sized double-layered bubbles called
liposomes
stage 4 : evolution of a self-replication system
Describethe 2 main hypotheses
2 main hypothesis
RNA - first
The first cell would have had an RNA gene that
directed protein synthesis.
Reverse transcription could have led to DNA.
RNA was responsible for both DNA and protein
formation
RNA - DNA -RNA - Protein
Protein First
The protocell would have developed a plasma
membrane and enzymes.
Then, DNA and RNA synthesis would have been
possible.
After DNA evolved, protein synthesis would have been
carried out according to the central dogma.
After DNA formed, the genetic code had to
evolve
cell
basic unit of biology
what 3 sciences converged to make cell bio
cytology
genetics
biochem
who named cells “cells”
Robert Hooke - 1665
he observed compartments formed by cell walls of dead plant tissue
he called these compartments cells
what two factors restricted progress in early cell biology
Microscopes had limited resolution, or
resolving power (ability to see fine detail)
compound microscope
1830s
had two lenses
improved magnification and resolution
could see structures 1um clearly
Robert Brown
identified the nucleus inside plants cells using the compound microscope
Mathias Schleiden
concluded that all plant
tissues are composed of cells
thomas Schwann
concluded that all ANIMALS
tissues are composed of cells
postulated the cell theory
Cell theory
Postulated the cell theory in 1839
1. All organisms consist of one or more cells.
2. The cell is the basic unit of structure for all
organisms
Rudolf Virchow
what year?
added to the cell theory in 1855
3. all cells arise only from preexisting cells
cytology
focuses mainly on cellular structure and
emphasizes optical techniques
biochemistry
focuses on cellular structure and
function
Genetics
focuses on information flow and heredity
and includes sequencing of the entire genome (all
of the DNA) in numerous organisms
Microscopy
crucial in helping cell
biologists deal with the
problem of small size of
cells and their
components
Micrometer
(μm), also called the micron, is
one millionth of a meter (10 -6 m
Size of bacterial cells vs plants vs animal
Bacterial cells are a few μm in diameter, whereas
cells of plants and animals are 10–20 times larger
Organelles are comparable to bacterial cells in size.
nanometer
The nanometer (nm) is used for molecules and
subcellular structures too small to be seen in the
light microscope
The nanometer is one-billionth of a meter
(10-9 m)
angstrom (Å)
The angstrom (Å), which is 0.1 nm, equals about
the size of a hydrogen atom
It is used in cell biology to measure dimensions
within proteins and DNA molecules
light microscope
earliest tool of
cytologists
allowed identification of nuclei, mitochondria, and
chloroplasts within cells
light microscopy is also called
brightfield
microscopy because white light is passed directly
through a specimen
improvements in Microscopy
microtome -mid-1800s) allowed
preparation of very thin slices of
samples
dyes - A variety of dyes for staining cells
began to be used around the same
time
These improved the limit of resolution (how far apart objects
must be to appear as distinct)
the smaller the microscope’s limit of resolution, the…
greater its
resolving power (ability to see fine details)
Specialized Light Microscopy ( list the types)
Phase-contrast (PC) microscopy
Differential interference contrast (DIC) microscopy
Fluorescence microscopy
Confocal microscope
Contrast Microscopy
Phase contrast and
differential interference
contrast microscopy
make it possible to see
living cells clearly
The phase of transmitted
light changes as it passes
through a structure with a
different density from the
surrounding medium
These types of microscopy
enhance and amplify these
slight changes
Fluorescence Microscopy
allows
detection of proteins, DNA sequences, or
molecules that have been made
fluorescent by binding to antibodies
( see slides for more)
antibody
protein that binds a particular
target molecule, called an antigen
GFP
Green fluorescent protein (GFP) can be
used to study the temporal and spatial
distribution of proteins in a living cell
Confocal microscopy
uses a
laser beam to illuminate a
single plane of a fluorescently
labeled specimen
Digital video microscopy
Digital video microscopy uses
video cameras to collect digital
images Microtubules in cultured cells (M. Engelke)
limit of resolution
refers to how far apart
objects must be to appear as distinct
resolving power
ability to see fine details
The resolution for a light microscope is related to
the physical nature of light
for visible light, the limit of resolution is about
200-350 nm
Electron Microscopy
The electron microscope, which
uses a beam of electrons rather
than light, was a major
breakthrough for cell biology
limit of resolution of electron microscope
about 100 times
better than light microscopes
electron microscopy magnification is
is much higher
than light microscopes—up to
100,000×
TEM
transmission electron microscopy - electrons are transmitted through the specimen
SEM
scanning electron microscopy (SEM), the
surface of a specimen is scanned by detecting
electrons deflected from the outer surface
Friedrich Wöhler
1828
showed that a compound made
in a living organism could be synthesized in the lab
Louis Pasteur
(1860s)
showed that yeasts could
ferment sugar into alcohol
The Buchners
1897) showed that fermentation could occur with yeast
extracts
enzyme
biological catalyst
Early biochem
fermentation pathways early 1920-1940s
Glycolysis - mulitple ppl
Krebs - hans krebs
ATP - Fritz lipmann
Calvin Cycle - Melvin Calvin
Subcellular fractionation
uses centrifugation to
separate/isolate different structures and macromolecules
Ultracentrifuges
are capable of very high speeds (over
100,000 revolutions per minute; rpm
Chromatography
techniques to separate molecules
from a solution based on size, charge, or chemical affinity
Electrophoresis
uses an electrical field to move
proteins, DN A, or RN A molecules through a medium
based on size/charge
Mass spectrometry
is used to determine the size and
composition of individual proteins
Genetics
Study of inheritance of characteristics from generation to generation
19th century =
discovery of the gene
Gregor Mendel
experimentation with peas which lead to the understanding of heredity factors from parents to offspring
Heredity factors are now known as
genes
mitosis
cell division
( knaned by walther Flemming
Who formulated the chromosome theory
Morgan, Bridges, Sturtevant
chromosome theory
proposing that Mendel’s hereditary factors are located
on chromosome
Friedrich Mischer
1869
first isolated DNA which he called nuclein
components of DNA
4 different nucleotides ( 1930s)
20 different amino acids = protein
DNA as the genetic material - 1940
one gene - one enzyme concept
Beadle and Tatum formulated the one gene–one enzyme
concept (each gene is responsible for the production of a single
protein)
who proposed the Double Helix model
Watson and Crick, with assistance from Rosalind Franklin, proposed the double helix model for DNA structure (1963)
who proposed the central dogma
Crick: central dogma of molecular bio
DNA ( transcription) - RNA ( translation) - protein
What are the three kinds of RNA molecules what what do they do?
mRNAs (messenger RNAs): translated to produce protein
rRNAs (ribosomal RNAs): components of ribosomes
tRNAs (transfer RNAs): bring the appropriate amino acid for protein synthesis
what are the exceptions to the central dogma
viruses with RNA genomes
reverse transcriptase
an enzyme that uses viral RNA to synthesize complementary DNA
recombinant DNA tech
restriction enzymes cut DNA at specific places, allowing scientists to create recomb. DNA molecules w/ DNA from different sources
DNA cloning
the generation of many copies of a specific DNA sequence
DNA transformation
process of introducing DNA into cells
sequencing DNA
DNA sequencing methods are used routinely for rapidly determining the base sequences of DNA molecules. It is now possible to sequence entire genomes (entire DNA content of a cell).
Bioinformatics
Comp sci & biology merged to interpret enormous amounts of sequencing and other data
Numerous bioinformatic tools are publicly available through NCBI (National Center for Biotechnology Information)
High-throughput methods allow for dramatic increases in the speed of molecular analysis
Expression levels of hundreds or thousands of genes can be monitored simultaneously
Ex: DNA Microarray Assay
CRISPR genome editing stands for
CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats
see slide/come back to card
CRISPR is used as
a tool for genome editing
CRISPR was discovered as a
prokaryotic defense against
viral infection
Biological facts
Facts are provisional, dynamic and subject to change
a “fact” is an attempt to state our best current understanding of the world, based on observations and experiments
testing
Scientists seek to prove the null hypothesis, which is opposite to their hypothesis
The certainty of a particular hypothesis is strengthened when multiple attempts fail to confirm the null hypothesis
Experiments Test Specific Scientific Hypotheses
(idk how to make this a question)
First read peer reviewed sources, then formulate hypothesis
This may take the form of a model, which appears to be a reasonable explanation for the phenomenon
model organism
a species widely studied, well characterized, & easy to manipulate
Each has particular advantages, useful for experimental studies
Much of our knowledge is based on research using few organisms
cell cultures
Cell cultures are commonly used as model systems.
Cell cultures are used to study cancer, viruses, proteins, and cellular differentiation.
Some of what is learned from cultured cells may not reflect what happens within an intact organism
In a typical experiment, one condition is varied, called the
independent
The outcome is called the
dependent variable
in vivo
experiments involve living organisms
In vitro
experiments are done outside the living organisms
ex: in a test tube
organic Chemistry
Study of carbon-containing compounds
Biological chemistry
the study of
the chemistry of living systems
the most important atom in
biological molecules
Carbon
Carbon Atom
has a valence of 4, so it can form four
chemical bonds with other atoms
Carbon is most likely to form what type of bonds
Covalent bonds
Carbon atoms are most likely to form covalent bonds with
other carbon atoms and with oxygen (O), hydrogen (H),
nitrogen (N), and sulfur (S)
Covalent Bonds
the sharing of a pair of electrons
between two atoms
Hydrogen valence
Valence: 1
Oxygen valence
(check)
Valence: 2?
shouldit not be 6
Nitrogen valence
Valence: 3
Single Bond
Sharing one pair of electrons
between two atoms forms a
single bond
Double and Triple Bonds
Double bonds and triple
bonds involve two atoms
sharing two and three pairs of
electrons, respectively
Whether carbon atoms form
single, double, or triple bonds
with other atoms, the total
number of covalent bonds
per carbon atom is
FOUR
Stability is expressed as
Bond energy
aka the
amount of energy required to break 1 mole (~6 x
1023) of such bonds
Bond energy is expressed as
calories per mole
(cal/mol)
A calorie is the amount of energy needed to raise
the temperature of 1 g of water by 1ºC
A kcal (kilocalorie) is equal to 1000 calories
To break a covalent bond
energy is taken in
are double bonds and triple bonds easy or harder to break
Double and triple bonds
are even harder to break
solar radiation
slide page 3
Hydrocarbons
are chains or
rings composed only of carbon
and hydrogen
ex. petroleum products, including
gasoline and natural gas, are
hydrocarbon
In biology, they are of limited
importance because they are
not soluble in water, except as
a component of biological
Biological compounds normally contain…
These normally contain carbon, hydrogen, and one
or more atoms of oxygen, as well as nitrogen,
phosphorus, or sulfur
functional
groups
These (O, N, P, S) are usually part of functional
groups, common arrangements of atoms that
confer specific chemical properties on a molecule
important functional groups
Carboxyl and phosphate
groups (negatively
charged)
Amino groups (positively
charged)
Hydroxyl, sulfhydroxyl,
carbonyl, and aldehyde
groups (uncharged, but
polar
Bond Polarity
In polar bonds, electrons are not shared equally
between two atoms
Polar bonds result from a high electronegativity
(affinity for electrons) of oxygen and sulfur
compared to carbon and hydrogen
Polar bonds have high water solubility compared to
C—C or C—H bonds, in which electrons are shared
equally
WHat is carbon’s structure
tetrahedral structure
When four atoms are
bonded to the four corners
of the tetrahedron, various
special configurations are
possible, called
sterioisomers
Water has an indispensable role as
the universal solvent
About x% of a cell by weight is water
About 75–85% of a cell by weight is water
The high heat of vaporization makes water
an excellent coolant
Osmosis
the process of water moving across cellular
membranes based on the concentration of solutes present
Aquaporin (A QP)
a specialized channel protein that
allows for water to move more quickly than via osmosis
The most critical attribute of water is
its polarity,
polarity,
which accounts for water’s:
Cohesiveness
Temperature-stabilizing capacity
Solvent properties
what gives water its polarity
Unequal distribution of electrons
gives water its polarity
water molecule shape
bent
oxygen is highly….
The oxygen atom at one end of the
molecule is highly electronegative,
drawing the electrons toward it
This results in a partial negative
charge at this end of the molecule,
and a partial positive charge around
the hydrogen atoms
describe cohesion
Because of their polarity,
water molecules are attracted
to each other
The electronegative oxygen
of one molecule is associated
with the electropositive
hydrogens of nearby
molecules
Water is characterized by an extensive network of
hydrogen-bonded molecules, which make it
cohesive
Cohesion is the result of
an extensive network of
hydrogen-bonded molecules,
The combined effect of many hydrogen bonds
accounts for water’s high
Surface tension
Boiling point
Specific heat
Heat of vaporization
surface tension is the result of
s the result of the collective
strength of vast numbers of
hydrogen bonds
Allows insects to walk along
the surface of water without
breaking the surface
Allows water to move
upward through conducting
tissues of some plants
Surface tension allows _____________ in some plants
Allows water to move
upward through conducting
tissues of some plants
What gives water its its temperature-
stabilizing capacity?
High specific heat gives water its temperature-
stabilizing capacity
Specific heat—the amount of heat a substance
must absorb to raise its temperature 1ºC
The specific heat of water is 1.0 calorie per gram,
much higher than most liquids
Describe Water’s temperature stabilizing capacity
Temperature-Stabilizing Capacity
Heat that would raise the temperature of other
liquids is first used to break numerous hydrogen
bonds in water
Water therefore changes temperature relatively
slowly, protecting living systems from extreme
temperature changes
Without this characteristic of water, energy
released in cell metabolism would cause
overheating and death
Describe heat of vaporization
Heat of vaporization is the amount of energy
required to convert 1 gram of liquid into vapor
This value is high for water because of the many
hydrogen bonds that must be broken
The high heat of vaporization makes water an
excellent coolant
Why is water is able to dissolve a
large variety of substances?
Bc of its Polarity
Many of the molecules in cells are also polar and
so can form hydrogen bonds or ionic bonds with
water
hydrophilic
Solutes that have an affinity for water and dissolve
in it easily are called hydrophilic (“water-loving”)
Examples of hydrophilic molecules
Many small molecules—sugars, organic acids,
some amino acids—are hydrophilic
hydrophobic def
ex. of hydrophobic molecules
Molecules not easily soluble in water—such as
lipids and proteins in membranes—are called
hydrophobic (“water-fearing”)
NaCl in water
A salt, such as NaCl, exists as a
lattice of Na + cations (positively
charged) and Cl− anions (negatively
charged)
For a salt to dissolve in a liquid, the
attraction of anions and cations in the
salt must be overcome
In water, anions and cations take part
in electrostatic interactions with the
water molecules, causing the ions to
separate
The polar water molecules form
spheres of hydration around the ions,
decreasing their chances of re-
association
Solubility of Molecules with No Net Charge
Some molecules have no net charge at neutral pH
Some of these are still hydrophilic because they
have some regions that are positively charged and
some that are negatively charged
Water molecules will cluster around such regions
and prevent the solute molecules from interacting
with each other
Hydrophobic molecules, such as hydrocarbons,
tend to disrupt the hydrogen bonding of water and
are therefore repelled by water molecules
the importance of selectively permeable Membranes
Cells need a physical barrier between their contents
and the outside environment
Such a barrier should be
Impermeable to much of the cell contents
Not completely impermeable, allowing some
materials into and out of the cell
Insoluble in water to maintain the integrity of the
barrier
Permeable to water to allow flow of water in and
out of the cell
Membranes
whatare they and what are they composed of?
a hydrophobic
permeability barrier
Consists of phospholipids, glycolipids, and
membrane proteins
Membranes of most organisms also contain sterols
—cholesterol (animals), ergosterols (fungi), or
phytosterols (plants)
Glycolipids
sugars attached to lipids
Membranes are also
amphipathic
Amphipathic
they have both
hydrophobic and hydrophilic
regions
Amphipathic phospholipids
have a polar head; the polarity
is due to a negatively charged
phosphate group linked to a
positively charged group
They also have two nonpolar
hydrocarbon tails
Polarity of the phospholipid head is due to
negatively charged group
In water, amphipathic
molecules undergo
hydrophobic interactions
The polar heads of
membrane phospholipids
face outward toward the
aqueous environment
The hydrophobic tails are
oriented inward
The resulting structure is the
lipid bilayer
A Membrane Is a Lipid Bilayer with
Proteins
Embedded in It
Because of the hydrophobic
interior, a lipid bilayer is readily
permeable to
nonpolar molecules
However, it is quite impermeable
to most polar molecules and
highly impermeable to all ions
What is the mebrane permeable and impermeable to ?
Permeable to nonpolar molecules
However, it is quite impermeable
to most polar molecules and
highly impermeable to all ions
Cellular constituents are mostly
polar or charged and are
prevented from entering or
leaving the cell
However, very small molecules
diffuse
How do ions pass through the membrane
How does H20 and ethanol pass through the membrane
They are small uncharged polar molecules??
How does O2 and Co2 pass through the membrane
Small nonpolar molecules so they diffuse
How do cl-, and K+, Na+ pass through the membrane
Ion transport through transport proteins
How are ions transported
Even the smallest ions are unable to diffuse across
a membrane
This is due to both the charge on the ion and the
surrounding hydration shell
Ions must be transported across a membrane by
specialized transport proteins
Transport Proteins
Transport proteins act as either hydrophilic
channels or carriers
Transport proteins of either type are specific for a
particular ion or molecule or class of closely related
molecules or ions
Biological membranes are best described as
selectively permeable
Most cellular structures are made of
ordered arrays
of linear polymers called macromolecules
Important macromolecules in the cell
include
proteins, nucleic acids, and polysaccharides, and
( These three are built by polymerization)
and Lipids
what is unique about lipids
share some features of macromolecules but
are synthesized somewhat differently
Cellular Hierarchy
biological molecules and
structures are organized
into a series of levels,
each building on the
preceding one
Most cellular structures
are composed of small
water-soluble organic
molecules obtained from
other cells or synthesized
from nonbiological
molecules (CO 2 , NH 4 ,
PO 4 , etc.)
Macromolecules Are Critical for
Cellular
Form and Function
Hierarchical Assembly
The small organic
molecules then polymerize
to form biological
macromolecules
Biological macromolecules
may function on their own
or assemble into a variety
of supramolecular
structures
The supramolecular
structures are components
of organelles and other
subcellular structures that
make up the cell
biological
macromolecules
The small organic
molecules then polymerize
to form biological
macromolecules
supramolecular
structures
Biological macromolecules
may function on their own
or assemble into a variety
The supramolecular
structures are components
of organelles and other
subcellular structures that
make up the cell
Lipids do not
go through the process of Polymerization
How are macromolecules made
generated by the
polymerization of small
organic molecules
Repeating units are called
Monomers
Monomer of sugar or starch
Glucose
Monomers of Proteins
amino acids
Monomers of Nucleic acids
Nucleotides
The major macromolecular polymers in the cell are
proteins, nucleic
acids, and polysaccharides
Nucleic acids and proteins have a variety of monomers that may be
arranged in nearly limitless ways; the order and type of monomer are
critical for function
Polysaccharides, composed of one or two monomers, have relatively
few types
exons
expressed
introns
spliced out
informational
macromolecules are
Nucleic acids are called informational
macromolecules because the order of the four
kinds of nucleotide monomers in each is non-
random and carries important information
DNA and RNA serve a coding function, containing
the information needed to specify the precise amino
acid sequences of proteins
Proteins
Proteins are composed of a nonrandom series of
amino acids
Amino acid sequence determines the three-
dimensional structure, and thus the function, of a
protein
With 20 different amino acids, a nearly infinite
variety of protein sequences is possible
Proteins have a wide range of functions, including
structure, defense, transport, catalysis, and
signaling
Proteins are composed of
nonrandom series of
amino acids
Amino acid sequence determines
the three-
dimensional structure, and thus the function, of a
protein
Protein functions
Proteins have a wide range of functions, including
structure, defense, transport, catalysis, and
signaling
see table on page 14
go look at it
Polysaccharides
Polysaccharides typically consist of single
repeating subunits or two alternating subunits
The order of monomers carries no information and
is not essential for function
Most polysaccharides are structural
macromolecules (e.g., cellulose or chitin) or storage
macromolecules (e.g., starch or glycogen)
polysaccharides typically consist of
single
repeating subunits or two alternating subunits
Polysaccharides
The order of monomers…
carries no information and
is not essential for function
Most polysaccharides are
are structural
macromolecules (e.g., cellulose or chitin) or storage
macromolecules (e.g., starch or glycogen)
Macromolecules Are Synthesized by
Stepwise Polymerization of Monomers
production of most polymers follows basic
principles
- Macromolecules are always synthesized by the stepwise
polymerization of monomers - The addition of each monomer occurs by the removal of a water
molecule (condensation reaction) - The monomers must be present as activated monomers before
condensation can occur - To become activated, a monomer must be coupled to a carrier
molecule - The energy to couple a monomer to a carrier molecule is provided by
adenosine triphosphate (ATP) or a related high-energy compound - Macromolecules have directionality; the chemistry differs at each end
of the polymer
( BE ABLE TO ORDER)
primary protein strucutre
just a polypeptide no function
( 4 structures primary, secondary, tertiary, quaternary)
keratin - secondary structure
Monomer activation
Monomers with available H and OH are activated by coupling them to appropriate carrier molecule, using energy from ATP or a similar high -energy compound
Monomer Condensation
The first step in polymer synthesis involves the condensation of two activated monomers, with the release of one of the carrier molecules
Polymerization
the nth step will add the next activated monomer to a polymer that already has n monomeric units
Elongation
Carrier Molecules
A different kind of carrier molecule is used for each
kind of polymer
For protein synthesis, amino acids are linked to
carriers called transfer RNA (tRNA)
Sugars (often glucose) that form polysaccharides
are activated by linking them to ADP (adenosine
diphosphate), or UDP (uridine diphosphate)
For nucleic acids, the nucleotides themselves
are high-energy molecules (ATP, GTP)
Condensation
Activated monomers react with one another in a
condensation reaction, then release the carrier
molecule
The continued elongation of the polymer is a
sequential, stepwise process
Hydrolysis
Degradation of polymers occurs via hydrolysis,
breaking the bond between monomers through
addition of one H + and one OH− (a water molecule)
self-assembly
The principle of self-assembly states that
information needed to specify the folding of
macromolecules and their interactions to form
complex structures is inherent in the polymers
themselves
molecular chaperones
Proteins called molecular chaperones are
sometimes needed to prevent incorrect folding
Noncovalent Bonds and Interactions Are
Important in
the Folding of Macromolecules
Many cellular structures are held together by what type of bonds
noncovalent bonds and interactions
Hydrogen bonds
Ionic bonds
Van der Waals interactions
Hydrophobic interactions
Ionic Bonds
ionic bonds are strong noncovalent electrostatic
interactions between two oppositely charged ions
They form between negatively charged and
positively charged functional groups
Ionic bonds between functional groups on the same
protein play an important role in the structure of the
protein
Ionic bonds may also influence the binding
between macromolecules
Van der Waals Interactions
Van der Waals interactions (or forces) are weak attractions
between two atoms that occur only if the atoms are very
close to one another and oriented appropriately
Atoms that are too close together will repel one another
The van der Waals radius of an atom defines how close
other atoms can come to it, and it is the basis for space-
filling models of molecules
Hydrophobic Interactions
Hydrophobic interactions describe the tendency of
nonpolar groups within a macromolecule to
associate with each other and minimize their
contact with water
These interactions commonly cause nonpolar
groups to be found in the interior of a protein or
embedded in the nonpolar interior of a membran
Many Proteins ____________ Fold into
Their Biologically Functional State
Spontaneously
describe Spontaneous Folding
The immediate product of amino acid
polymerization is a polypeptide
Once the polypeptide has assumed its correct
three-dimensional structure, or conformation, it is
called a protein
The native (natural) conformation of a protein can
be altered by changing conditions, such as the pH
or temperature, or by treating with certain chemical
agents
denaturation
The unfolding of polypeptides leads
to loss of biological activity (function)
Renaturation
When denatured proteins are returned to conditions
in which the native conformation is stable, they may
undergo renaturation, a refolding into the correct
conformation
In some cases, renaturation is associated with the
return of the protein function (e.g., ribonuclease)
the spontaneity of polypeptide folding process
( Native molecule -> denatured -> renaturing -> renatured molecule)
Denaturation: First the folded polypeptide was exposed to denaturing conditions, resulting in a ribonuclease molecule with no fixed shape and no enzymatic activity
Renaturation- Then, renaturation conditions allowed the denatured polypeptide to return spontaneously to its native conformation, regaining enzymatic activity.
molecular chaperones
Some proteins require molecular chaperones,
which assist the assembly process
Molecular chaperones are not components of the
completed structures and they convey no
information
They bind to exposed regions in the early stages of
assembly to inhibit unproductive assembly
pathways that would lead to incorrect structures
self-assembly
The same principles of self-assembly that apply to
polypeptides also apply to the assembly of more
complex structures
Ribosomes and membranes are capable of self-
assembly, for example
prions
an infectious protein molecule, is a rare
example of self-assembly in proteins
virus
A virus is a complex of nucleic
acids and proteins that uses living
cells to produce more copies of
itself via self-assembly
what is a Tobacco Mosaic Virus
A good example is the tobacco
mosaic virus (TMV)
It is a rodlike particle, with a single
RNA strand and about 2130
copies of a coat protein that form
a cylindrical covering for the RNA
Self assembly of TMV
Self-Assembly of TMV Is Quite Complex
The unit of assembly is a two-layered disc of coat
protein that changes conformation (from cylinder to
helix) as it interacts with the central RNA molecule
This conformational change allows another disc to
bind and to interact with the RNA and thus to
change its conformation as well
The process repeats until the end of the RNA
molecule is reached
Spontaneity Self-Assembly of the Tobacco
Mosaic Virus (TMV)
steps
see slide 21
Limits of Self-Assembly
Some assembly systems depend additionally on
information provided by a preexisting structure
Examples
Membranes
Cell walls
Hierarchical Assembly
Hierarchical assembly is the dependence on
subassemblies that act as intermediates of the
process of assembly of increasingly complex
structures
Biological structures are almost always assembled
hierarchically
Advantages of Hierarchical Assembly
Chemical simplicity—relatively few subunits are
used for a wide variety of structures
Efficiency of assembly—a small number of kinds of
condensation reactions is needed
Quality control—defective components can be
discarded prior to incorporation into higher-level
structure, reducing the waste of energy and
materials
4 steps of CRISPR
C a s 9 protein is bound to the
targeted gene sequence with the help
of guide R N A
- The targeted gene sequence is
unwound and C a s 9 creates a
double hyphen stranded break in it. - Repair without the addition of repair
template results in gene disruption by
deletions or insertions. - Recombination with the addition of
repair template results in the
correction or replacement of defective
gene.
If a piece of DNA called a repair template is
included
the cell can repair the break using a
process called homology‐directed repair
When double stranded breaks are repaired,
the cell often introduces
erros
