Chapter 1 Cell Function And DNA RNA Organism – Biochemistry
This lesson covers Cell Function And DNA RNA Organism – Biochemistry.
What determines the lower limit of cell size
set by the minimum number of each type of biomolecule required by the cell
What is the upper limit of cell size
set by the rate of diffusion of solute molecules in aqueous systems
Who showed up first in evolution: autotrophs or heterotrophs?
autotrophs
Who showed up first in evolution: anaerobic or aerobic?
anaerobic
An organism that uses reduced inorganic compounds as its electron source
Litotrophs
obtain electrons from organic compounds
organotrophs
Are Eukaryotes more closely related to archaea or bacteria?
Archaea
which domain showed up first?
archaea. They were able to live in harsh or extreme environments
Phototrophs
trap and use sunlight
chemotrophs
derive their energy from the oxidation of chemical fuel
Autotrophs
Organisms that make their own food
Heterotroph
An organism that cannot make its own food.
Aerobic
Process that requires oxygen
Anaerobic
Process that does not require oxygen
Four major building blocks
Amino acids, Nucleic acids, lipids, sugar
secondary metabolites
pathways that lead to specialized products not found in every living cell
metabolomics
systemic characterization of the metabolome under very specific conditions
Proteomics
systematic characterization of protein complements under specific conditions
Three major functions of polysaccharides
1. energy-rich fuel stores
2. rigid structural components of cell walls
3. extracellular recognition elements that bind to proteins on other cells
Glycome
all of a cell’s carbohydrate-containing molecules
Function of lipids
serve as structural components of membranes, long term energy storage, pigments, and intracellular signals
Which is the only amino acid that occurs as its D isomer?
glycine
chiral center
carbon with four different substituents and lack a plane of symmetry
Stereoisomers
Compounds with the same structural formula but with a different arrangement of the atoms in space.
Enantiomers
isomers that are mirror images of each other
Diastereomers
stereoisomers that are not mirror images
conformation
The particular three-dimentional shape of a protein molecule
cis configuration
the configuration in which substituent groups are on the same side of a double bond
trans configuration
the configuration in which substituent groups are on the opposite sides of a double bond
Enthalpy
The heat content of a system at constant pressure
Entropy
A measure of disorder or randomness.
free energy
energy that is available to do work
how do unfavorable reactions occur?
coupling them with a favorable reaction
Reaction coupling allows for:
unfavorable reactions to happen
Is a living organism an isolated, closed or open thermodynamic system?
open system
Organisms obtain energy from their surroundings in two ways:
1. they take up chemical fuels (such as glucose) from their environment and extract energy by oxidizing them
2. They absorb energy from sunlight
What elements are essential elements for life?
P,C,O,N,S,H, Na, K, Ca, Cl
Conformation
no bond breaking between changes. This is achieved through rotating
Configuration
need to break a bond between changes
Ex. changing from cis to trans
Anyhydride
without water
chiral
a molecule that is not superimposable on its mirror image
achiral
A molecule that is superimposable on its mirror image
isomers
Two different molecules that have the same chemical formula
Are Amino acids L or D conformation?
L
Are sugars L or D conformation
D
racemic mixture
A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.
steady state
a state in which inputs equal outputs, so that the system is not changing over time
Law of Conservation of Energy
In any physical or chemical change, the total amount of energy in the universe remains constant although form of the energy may change
Law of Increasing Entropy
the total entropy of the universe is continually increasing.
Is the human body an open or closed system?
open
oxidation
loss of electrons
reduction
gain of electrons
Dehydrogenation
The removal of hydrogen from a molecule
If change in G is less than 0 what does that indicate?
-exergonic reaction
-it is favorable
-reaction is spontaneous
If change in G is more than 0 what does that indicate?
-Endergonic
-unfavorable
-not spontaneous
energy coupling
The use of an exergonic process to drive an endergonic one.
Enzymes
proteins (sometimes RNA) that increase the rate (kinetic) of a chemical reaction
Do enzymes alter free energy? (thermodynamic)
No
Do enzymes affect the kinetic or thermodynamic process of a reaction?
Kinetic. They speed up the reaction by lowering activation energy
Are enzymes consumed during a reaction?
No
Catabolism
Metabolic pathways that break down molecules, releasing energy.
Anabolism
Metabolic pathways that construct molecules, requiring energy.
Central Dogma of Biology
DNA -> RNA -> Protein
Homologs
Matching Chromosomes that are similar but not identical
Paralogs
homologous genes within a single species
orthologs
homologous genes separated by a speciation event
Autotroph
An organism that makes its own food
Phototroph
an organism that gets its energy from sunlight
Chemotrophs
Organisms that get energy from chemicals taken from the environment
Nucleus
A part of the cell containing DNA and RNA and responsible for growth and reproduction
Nucleoid
A dense region of DNA in a prokaryotic cell.
Prokaryotic
An organism whose cells do not have an enclosed nucleus, such as bacteria.
Eukaryote
organism whose cells contain a nucleus
Four major types of building blocks
Amino acids, Nucleic acids, lipids, sugar
activation energy
Energy needed to get a reaction started
ATP/NADH
The carriers for energy and high energy electrons during glycolysis
Chemoautotrophs
organism that makes organic carbon molecules from carbon dioxide using energy from chemical reactions
Photoautotrophs
Organisms that use light as a source of energy to synthesize organic substances and that use carbon dioxide as their carbon source
Chemoheterotrophs
An organism that must consume organic molecules for both energy and carbon.
Photoheterotrophs
An organism that uses light to generate ATP but that must obtain carbon in organic form.
Three types of cytoplasmic filaments
actin filaments, microtubules, and intermediate filaments
Exocytosis
Process by which a cell releases large amounts of material
Endocytosis
process by which a cell takes material into the cell by infolding of the cell membrane
how are the monomeric subunits of proteins, nucleic acids, and polysaccharides joined
by covalent bonds
How are macromolecules held together
by noncovalent interactions such as hydrogen bonds, ionic interactions, van der waal interactions, and hydrophobic effects
Most abundant elements in living organisms
carbon, hydrogen, oxygen, nitrogen
amine group
the nitrogen-containing portion of an amino acid
carbonyl group
a chemical group consisting of a carbon atom linked by a double bond to an oxygen atom
Steroisomers
molecules with the same chemical bonds and same chemical formula but different spatial arrangement of atoms
configuration
fixed spatial arrangement of atoms
How is configuration conferred?
1. double bonds around which there is little or no freedom of rotation
2. chiral centers, around which substituent groups are arranged in a specific orientation
geometric isomers
differ in the arrangement of their substituent groups with respect to the nonrotating double bond
cis-trans isomers
conformation
spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds
dynamic steady state
when the gains and losses of ecological systems are in balance
isolated system
if the system exchanges neither matter nor energy
closed system
if the system exchanges energy but not matter with its surroundings
open system
if the system exchanges both energy and matter
first law of thermodynamics
Energy cannot be created or destroyed. Amount of energy is constant, although the form of the energy may change
The free energy of formation of proteins is positive. To carry out these thermodynamically unfavorable, energy-requiring reactions, what does the cell do?
couple them to other reactions that liberate free energy
Adenosine Triphosphate (ATP)
compound used by cells to store and release energy
Keq > 1
G is large and negative
products are favored
Keq<1
G is large and positive
Why is the breakdown of ATP in cells an exergonic process
all living cells maintain a concentration of ATP far above its equilibrium concentration
Metabolism
All of the chemical reactions that occur within an organism (both catabolic and anabolic)
which came first: DNA, RNA, or protein. Why?
RNA. It can act as catalysts in their own formation meaning RNA may have been the first gene and the first catalyst
Life is characterized by: (5)
1. high degree of complexity
2. Extraction, transformation, and systematic use of energy to create and maintain structures and to do work
3. structure, function and interactions
4. Responsively interact with the surroundings
5. Replication and evolution
Is a living organism considered stable or dynamic
Dynamic
who showed up first in evolution?
Bacteria
where do prokaryotes contain their DNA
in the nucleoid
what is the cell wall of prokaryotes composed of
peptidoglycan
what is the function of the cytoskeleton (3)
-cell shape
-transport paths
-movement
Protein: monomeric, oligomeric, macromolecule, and total collection
amino acid->peptide->protein->proteome
DNA: monomeric, oligomeric, macromolecule, and total collection
Nucleic acid-> polymer or nucelotide-> DNA or RNA-> genome
Sugar: monomeric, oligomeric, macromolecule, and total collection
monosaccharide->oligo-/poly-saccharide-> Glycan-> Glycome
Lipids: monomeric, oligomeric, macromolecule, and total collection
Fatty acid-> lipid->membrane-> lipidome
conformation vs confirguation
Conformation does not require bond breaking between changes
Configuration needs to break a bond between changes
When two acids condense together and lose water (anhydride) are they stable? why or why not?
No, the negative charges will repel
What are the two possible geometric isomers?
cis and trans
The lower the potential energy the [more/less] stable the molecule
more
Which has the higher probability of forming, a conformation with high potential energy or with low potential energy?
low potential energy
Do isomers have the same chemical composition?
yes
Enantiomers have [different/identical] physical properties
identical
what is the only physical property that is not identical in enantiomers?
how they rotate in polarized light
Diasteromers have [different/identical] physical and chemical properties
different
What is the difference between chemical synthetic compounds and biosynthetic compounds
chemical synthetic compounds produce a racemic mixture but a biosynthetic compound is normally single handed
why dont cells make L and D amino acids
Macromolecules have unique binding pockets so only certain molecules fit in well and can bind. If the wrong configuration is present, they will not be able to bind. This is called stereospecificity
When an organism is dead, what is its state in accordance to the surroundings
It is equilibrium, no net energy change
How do organisms maintain homeostasis?
By keeping the concentrations of most metabolites at steady state
In steady state, the rate of synthesis of a metabolite […] the rate of breakdown of this metabolite
equals
Which is the measure of number and kinds of bonds or interaction that are made and broken
Enthalpy (H)
G<0
Exergonic, thermodynamically favorable, spontaneously move forward
G>0
Endergonic, thermodynamically unfavorable, will not move forward spontaneously (move backward)
What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= –
S= +
G= –
spontaneous
What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= +
S= –
G= +
not spontaneous
What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= +
S= +
G= +/-
Favorable at high temperature (G=-)
unfavorable at low temperature (G=+)
can entropically unfavorable reactions still be spontaneous? How? give an example
yes. Soap forms micelles, which are ordered structures due to hydrophobic interactions
A kinetic or nonspontaneous reaction is one in which the most stable state is that of the…
reactants
A thermodynamic reaction favors the [products/reactants], resulting in a spontaneous reaction that occurs without the need to constantly supply energy
products
What are the most stable states of a kinetic reaction
Those of reactants, in which an input of energy is required to move the reaction from a state of stability, to that of reacting and converting itself into products
What are the most stable states of a thermodynamic reaction
Those of products, because the reaction occurs spontaneously, without the need for energy to be added
An endergonic reaction is kinetically [stable/unstable] and thermodyncamically [favorable/unfavorable]
stable/ unfavorable
An exergonic reaction is kinetically [stable/unstable] and thermodyncamically [favorable/unfavorable]
unstable/ favorable
If all the concentrations of products and reactants are 1, what would G be? why?
0
G=-RTlnK
If all concentrations of reactants and products are 1 then k=[products]/[reactants]= 1
ln(1)=0
G=-RT*0=0
If k>1 then G is[pos/neg] and the reaction proceeds [forwards/backwards]
negative/ forward
If k<1 then G is[pos/neg] and the reaction proceeds [forwards/backwards]
positive/ backwards
Two reactions can be coupled if they share..
a common intermediate
What do DNA, RNA and Protein do?
DNA: stores information
RNA:transmits information
Proteins:; function manifests information
The 3D structure of a protein is determined by
DNa sequence (that determines the amino acid sequence)
key goal of biochemistry
understand what it means to be alive at the molecular level
2nd key goal of biochemistry
understand the effects of the molecular manipulations on the life that an organism leads
unity of biochemistry
organisms are remarkably uniform at the molecular level
Jacques Monod
“anything found to be true of the bacterium e.coli must also be true of elephants”
—————-
This uniformity reveals that all organisms on earth came from a common ancestor
a core of essential biochemical processes, common to all organisms, appeared ________ in the evolution of life.
early,
the diversity of life in the modern world has been generated by:
evolutionary processes acting on these biochemical processes common to all organisms
which three elements make up 98% of atoms in an organism?
oxygen, hydrogen, and carbon
all life requires
water
fuel molecules are made entirely of:
carbon hydrogen and oxygen
biological fuels, like the fuels that power machinery, react with __________ to produce ________________ ______________ and _________________
oxygen, carbon dioxide, water
reactions in which biological fuels reacting with oxygen to produce carbon dioxide and water are called:
combustion reactions
biological fuels that undergo combustion provide energy to power the:
cell
the four classes of biomolecules
proteins, nucleic acids, lipids, carbohydrates
proteins are constructed of _____ building blocks called:
20, amino acids
amino acids are linked by__________ ___________
peptide bonds
proteins serve as:
signal molecules, receptors for signal molecules, structural roles, allow mobility, provide defenses against environmental dangers, and are catalysts
catalysts
agents that enhance the rate of a chemical reaction without being permanently affected themselves
proteins catalysts are called
enzymes
every process that takes place in living systems depends on:
enzymes
primary function of nucleic acids:
store and transfer information
what do nucleic acids contain?
the instructions for all cellular functions and interactions
nucleic acids are constructed from only four building blocks called:
nucleotides
a nucleotide is made up of:
five carbon sugar either deoxyribose or ribose, attatched to a heterocyclic ring stucture called a base,
and at least one phosphoryl group
there are two types of nucleic acids:
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
genetic information is stored in:
DNA, the “parts list” that determines the nature of the organism
DNA is constructed from __________ deoxyribonucleotides. differing from one another only in the __________ structure of the __________
4 ,ring, bases
the four bases of DNA are:
Adenine, Guanine, Thymine, Cytosine
the information content of DNA is the sequence of nucleotides linked together by ________________ linkages.
phosphodiester
In the double helix, bases interact with one another such that:
A with T and C with G
some regions of DNA are copied as a special class of RNA molecules called______________ ________
messenger RNA
mRNA is a template for the synthesis of __________
proteins
unlike DNA, mRNA is :
frequently broken down after use
RNA is similar to DNA in composition with two exceptions:
1. the base thymine (T) is replaced with uracil (U)
2. the sugar component of the ribonucleotides contain an additional hydroxyl (-OH) group
among the key biomolecules, ___________ are much smaller than proteins or nucleic acids
lipids
lipids are not polymers made of ____________ ___________, as are proteins and nucleic acids
repeating units
a key characteristic of many biochemically important lipids is their dual chemical nature: part of the molecule is _____________ and the other part of the molecule is ___________
hydophillic, hydrophobic
hydrophillic
it can dissolve in water
hydrophobic
cannot dissolve in water
the dual nature of lipids allows:
lipids to form barriers that delineate the cell from its environment and to establish intracellular componentsl allows an “inside” and “outside” at biochemical level
lipids are also an important ___________ form of energy
storage
the hydrophobic component of lipids can undergo _____________ to provide large amounts of cellular energy.
combustion
the most common carbohydrate fuel
glucose the simple sugar
glucose is stored in animals as:
glycogen
what does glycogen consist of:
many glucose molecules linked end to end and having occasional branches
in plants, the storage form of glucose is
starch,
central dogma
proposed by Francis Crick: information flows from DNA to RNA to protein
DNA constitutes the heritable information – the __________
genome
the information of the genome is packed in discrete units called
genes
the process of copying the genome is called
replication
DNA polymerase
a group of enzymes that catalyze the replication process
Translation takes place on large macromolecular complexes called ____________, consisting of RNA and protein
ribosomes
The _______ is the basic unit of life
cell
A ____________ is a lipid bilayer: two layers of lipids organized with their hydrophobic chains interacting with one another and the hydrophilic head groups interacting with the environment
membrane
There are two basic types of cells: ___________ cells and ____________ cells
eukaryotic, prokaryotic
The main difference between the two basic cell types is the existence of membrane-enclosed compartments in ______________ and the absence of such compartments in ________________.
eukaryotes, prokaryotes
—two biochemical features minimally constitute a cell: there must be :
(1) a barrier that separates the cell from its environment and
(2) an inside that is chemically differ- ent from the environment and that accommodates the biochemistry of living.
The _____________ ______________ separates the inside of the cell from the outside, one cell from another cell.
plasma membrane
the membrane must be rendered semipermeable but in a very selective way. This ______________ ______________is the work of proteins that are embedded in the plasma membrane or associated with it
selective permeability
The plasma membrane of a plant is itself surrounded by a ______ _______
cell wall
The cell wall is constructed largely from ___________, a long, linear polymer of glucose molecules
cellulose
The inner substance of the cell, the material that is surrounded by the plasma membrane, is called the ___________.
cytoplasm
The cytoplasm is the site of a host of biochemical processes, including the:
initial stage of glucose metabolism, fatty acid synthesis, and protein synthesis.
the cytoskeleton is a network of three kinds of protein fibers—________ _____________, __________________ _____________, and ________________—that support the structure of the cell, help to localize certain biochemical activities, and even serve as “molecular highways” by which molecules can be shuttled around the cell
actin filaments, intermediate filaments, microtubules
a key difference between eukaryotic cells and prokaryotic cells is the presence of a complex array of intracellular, membrane-bounded compartments called ____________ in eukaryotes
organelles
The largest organelle is the_____________, which is a double-membrane-bounded organelle
nucleus
The ___________ is the information center of the cell, the location of an organism’s genome.
nucleus
The nuclear membrane is punctuated with ________ that allow transport into and out of the nucleus.
pores