1 - BIOCHEMISTRY AND THE ORGANIZATION OF CELLS Flashcards
Biochemistry describes the molecular nature of life processes. In living cells, many chemical reactions take place simultaneously.
Hundreds
or thousands of these smaller molecules, or monomers, can be linked to produce
macromolecules, which are also called?
macromolecules formed by the bonding of smaller units
Polymers
amino acid combine by polymerization to form?
Proteins
Nucleotides combine to form?
Nucleic acid
Polymerization of sugar monomers produces?
Polysaccharides
Proteins of the class called enzymes display
catalytic activity, which means that they increase the rates of chemical reactions compared with uncatalyzed reactions.
is the relationship between the nucleotide sequence in
nucleic acids and the amino acid sequence in proteins
Genetic code
the total DNA of a cell
Genome
Individual units of heredity, controlling individual traits by coding for a functional protein or RNA
responsible for the transmission of inherited traits, are part of the DNA found in each chromosome
Genes
most resemble the earliest cells
(karyon, “kernel, nut”) = before the nucleus
include bacteria and cyanobacteria
single-celled organism, but groups of them can exist in association
Prokaryotes
“true nucleus”
more complex organisms and can be multi-cellular and single-celled
single-celled = yeast and Paramecium
multi-celled = animals and plants
Eukaryotes
part of the cell that has a distinct function; it is surrounded by its own membrane within the cell
a membrane-enclosed portion of a cell with a specific function
Organelle
where the DNA of the cell is concentrated in one region; directs the workings of the cell
Nuclear region
particles consisting of RNA and protein; sites of protein synthesis in all living organisms, are frequently bound to the endoplasmic reticulum in eukaryotes
RIbosomes
portion of the cells outside the nucleus
Cytoplasm
aqueous portion of the cell that lies outside the membrane-bounded organelles
fluid portion of the cell outside the nuclear region
Cytosol
extensions of the plasma membrane, rather than in chloroplasts
Chromatophores
RNA + protein; sites of protein synthesis in all organisms
Ribonucleoprotein particles
an assemblage of lipid molecules and proteins
Cell membrane/plasma membrane
made up mostly of polysaccharide material
outer coating of bacterial and plant cells
Cell wall
Prokaryotes have a nuclear region, which contains DNA, and ribosomes,
the site of protein synthesis, as their main features. They have a cell membrane, but do not have an internal membrane system.
contains most of the DNA of the cell and is the site of RNA synthesis
most important eukaryotic organelle
location of the main genome
responsible for storing the cell’s DNA and for coordinating important cellular activities
Nucleus
contains enzymes that catalyze important energy-yielding reactions
respiratory organelles
Mitochondria
found in green plants and green algae; sites of photosynthesis
has its own DNA
Chloroplasts
Both mitochondria and chloroplasts contain DNA that
differs from that found in the nucleus, and both carry out transcription and
protein synthesis distinct from that directed by the nucleus.
mostly made up of the polysaccharide cellulose, giving the cell its shape and mechanical stability
have cell walls
Plant cell
have neither cell walls nor chloroplasts; same is true for some protists
Animal cell
what surrounds the nucleus?
Nuclear double membrane or nuclear envelope
part of the nucleus that is rich in RNA
Nucleolus
an aggregate of DNA and protein
a complex of DNA and protein found in eukaryotic nuclei
Chromatin
has a double membrane and is the second very important eukaryotic organelle
site of energy-yielding oxidation reactions
has its own DNA
an organelle that contains the apparatus responsible for aerobic oxidation of nutrients
Mitochondrion
the inner membrane of the mitochondrion exhibits many folds
folds in the inner mitochondrial membrane
Cristae
the space within the inner membrane
part of a mitochondrion enclosed within the inner mitochondrial membrane
Matrix
part of a continuous single-membrane throughout the cell
attached to the cell membrane and to the nuclear membrane
a continuous single-membrane system throughout the cell
Endoplasmic reticulum
studded with ribosomes bound to the membrane
site of protein synthesis
Rough endoplasmic reticulum
does not have ribosomes bound to the membrane
Smooth endoplasmic reticulum
where chloroplasts are found; specialized structures
Grana (singular granum)
separate from the endoplasmic reticulum but is frequently found close to the smooth endoplasmic reticulum
series of membranous sacs
involved in the secretion of proteins from the cell, but it also appear in cells in which the primary function is not protein synthesis
it is the site in the cell which sugars are linked to other cellular components, such as proteins
a cytoplasmic organelle that consists of flattened membranous sacs, usually involved in secretion of proteins
Golgi apparatus
membrane-enclosed sacs containing hydrolytic enzymes that could cause considerable damage to the cell if they were not physically separated from the lipids, proteins, or nucleic acid that they are able to attack
Lysosomes
contain enzymes involved in the metabolism of hydrogen peroxide (H2O2) which is toxic to the cell
Peroxisomes
found in plant cells only
contain the enzymes that catalyze the glyoxylate cycle, a pathway that converts some lipids to carbohydrate with glyoxylic acid as an intermediate
Glyoxysomes
Separates the cell contents from the outside world;
contents include organelles (held in place by the
cytoskeleton*) and the cytosol
Cell membrane
rigid exterior layer of plants
Cell wall
membrane-enclosed sac (plant cells)
Central vacuole
major components of plant material
Cellulose
sacs in the cytoplasm surrounded by a single membrane
cavities within the cytoplasm of a cell, typically enclosed by a single membrane, that may serve secretory, excretory, or storage functions
Vacuoles
What are the five kingdoms?
Monera
Protista
Fungi
Plantae
Animalia
What are the 3 domains?
Bacteria (eubacteria)
Archaea (archaebacteria)
Eukarya (eukaryotes)
consists only of prokaryotic organisms
one of the five kingdoms used to classify living organisms; includes prokaryotes
bacteria and cyanobacteria
Kingdom Monera
unicellular organisms
(Euglena, Volvox, Amoeba, and Paramecium)
one of the five kingdoms used to classify living things; includes single-celled eukaryotes
Kingdom Protista
yeasts, molds, and mushroom
Kingdom Fungi
The three kingdoms that consist mainly of
multicellular eukaryotes (with a few unicellular eukaryotes) are Fungi, Plantae, and Animalia.
true bacteria
commonly encountered prokaryotes
Eubacteria
early bacteria
lack a well-defined nucleus
found in extreme environments = Extremophiles
Archaebacteria
a relationship that benefits both species involved
Mutualism
one species gains at the other’s expense
Parasitic symbiosis
A classic example of mutualism (although it has
been questioned from time to time) is the lichen, which consists of a fungus
and an alga. The fungus provides water and protection for the alga; the alga
is photosynthetic and provides food for both partners.
The idea of endosymbiosis, in which a larger cell engulfs a smaller one, plays a large role in scenarios for the development of organelles in eukaryotic cells.
Oxidation is the loss of electrons while reduction is the gain of electrons
the most useful criterion for predicting the spontaneity of a process
requires conditions of constant temperature and pressure, which are
usual in biochemical thermodynamics
Free energy
decreases in a spontaneous (energy-releasing); exergonic
delta G is negative
delta G < 0
delta G is positive
delta G > 0
Nonspontaneous process; endergonic (energy is absorbed)
no net change in either direction; delta G = 0
Equilibrium; free energy is zero
An example of a spontaneous process is the aerobic metabolism of glucose,
in which glucose reacts with oxygen to produce carbon dioxide, water, and
energy for the organism.
An example of a nonspontaneous process is the reverse of the reaction that we
saw in Section 1.9—namely, the phosphorylation of ADP (adenosine diphosphate) to give ATP (adenosine triphosphate). This reaction takes place in living organisms because metabolic processes supply energy
What is a polar bond?
is a covalent bond between two atoms where the electrons forming the bond are unequally distributed; causes the molecule to have a slight electrical dipole moment where one end is slightly positive and the other is slightly negative.
What is electronegativity?
a chemical property that describes the tendency of an atom or a functional group to attract electrons towards itself; affected by both its atomic number and the distance that its valence electrons reside from the charged nuclei.
PERIODIC TREND:
increases as you move left to right across a period
decreases as you move down a group
What are polar molecules?
molecules that have a dipole or an uneven distribution of charge across their geometry resulting in one side being positive and the other side negative.
What are some important non-covalent bonds?
- Hydrogen bonds
- Electrostatic interactions (Coulomb force between positive and negative charges)
- Van der Waals interactions (occur when adjacent atoms come close enough that their electron clouds just barely touch)
- Hydrophobic interactions (nonpolar species tend to cluster in water in order to decrease the overall interfacial area between the hydrophobic species and water)
What is a hydrogen bond?
an attraction between two atoms that already participate in other chemical bonds; one of the atom is hydrogen while the other may be any electronegative atom
is an intermolecular force (IMF) that forms a special type of dipole-dipole attraction when a hydrogen atom bonded to a strongly electronegative atom exists in the vicinity of another electronegative atom with a lone pair of electrons.
Are all chemical bonds of the same strength?
(not sure) the bond strength between all the atoms in a molecule is not the same, so the higher the bond strength of a bond between two atoms, the higher will be the bond energy.
What are hydrophilic, hydrophobic, and amphipathic molecules?
Hydrophilic molecules - molecules that can dissolve in water; must have a charge (positive/negative) in order to interact with water, which is polar.
Hydrophobic molecules - molecules that are non-polar and do not mix with water; e.g. waxes
Amphipatic molecules - a compound comprising a hydrophilic head (polar part interacting with water) and a hydrophobic tail (nonpolar section refraining rom interactions with water)
What is an acid in contrast to a base?
Acid - any substance that increases the concentration of the H+ ion when it dissolves in water.
Base - any substance that increases the concentration of the OH- ion when it dissolves in water.
What is the acid dissociation constant or Ka?
measure of the extent to which an acid dissociates in solution and therefore its strength.
The less an acid dissociates, the smaller the value of Ka. The stronger the acid, the higher the value of Ka.
What is pH?
quantitative measure if the acidity, basicity, if aqueous or other liquid solutions.
research this again lol
How do buffered solutions differ from non-buffered ones?
A buffered solution is a solution in which a buffer is added in a small quantity. During titration, when any solution is added to the buffered solution, the pH of the solution does not change. A non-buffered solution is a solution in which a buffer is not added in the solution.
Organelles in Eukaryotes:
Nucleus
Cell membrane (plasma membrane)
Mitochondria
Endoplasmic reticulum
Ribosomes
Chloroplasts (present in green plants)
Organelles in Prokaryotes:
No definite nucleus; DNA present but not separate from the rest of the cell
Cell membrane (plasma membrane)
No mitochondria; enzymes for oxidation reactions located on plasma membrane
No endoplasmic reticulum
Ribosomes
No chloroplasts; photosynthesis (if present) is localized in chromatophores
memorize the parts of the eukaryotic cell (plant and animal), prokaryotic cell [just in case]
forces thought to exists only in living organism
Vital forces
Even so, both molecules and cells must have arisen ultimately from very simple molecules, such as water, methane, carbon dioxide, ammonia, nitrogen, and hydrogen
the study of compounds of carbon, especially of carbon and hydrogen and their derivatives
Organic chemistry
The reactions of molecules are based on the reactions of their respective functional groups.
groups of atoms that give rise to the characteristic reactions of organic compounds
Functional groups
a molecule that is the energy currency of the cell, contains
both ester and anhydride linkages involving phosphoric acid
Adenosine triphosphate (ATP)
The rest of the chemical elements are thought to have been formed in three ways:
(1) by thermonuclear reactions that normally take place in stars,
(2) in explosions of stars, and
(3) by the action of cosmic rays outside the stars since the formation of the galaxy.
Note that the most abundant isotopes of biologically important elements such as carbon, oxygen, nitrogen, phosphorus, and sulfur have particularly stable nuclei.
Many first-generation stars were destroyed by explosions called supernovas, and their stellar material was recycled to produce second-generation stars, such as our own Sun, along with our solar system.
abiotically = “absence of life”
small molecules that may bond to many others to form a polymer
Monomers
macromolecules formed by the polymerization of amino acids
Proteins
macromolecules formed by the polymerization of nucleotides
Nucleic acids
the ability to increase the rate of a chemical reaction
catalytic activity
the process of increasing the rate of chemical reactions
Catalysis
the information for the structure and function of all living organisms
Genetic code
is capable of catalyzing its own processing
is now considered by many scientists to have been the original coding material, and it still serves this function in some viruses.
RNA (ribonucleic acid)
According to the RNA-world theory, the appearance of a form of RNA capable of coding for its own replication was the pivotal point in the origin of life.
According to this hypothesis, RNA (or a system of related kinds of RNA) originally played both roles, catalyzing and encoding its own replication. Eventually, the system evolved to the point of being able to encode the synthesis of more effective catalysts, namely proteins.
According to this line of thought, the development of catalysis and the development of a coding system came about separately, and the combination of the two produced life as we know it. (double-origin theory)
A theory suggesting life began on clay particles is a variation of the double-origin theory. It proposes that coding first developed on clay surfaces, where ion patterns acted as a code, and crystal growth facilitated replication. RNA molecules were thought to have formed on these surfaces and eventually became enclosed in lipid sacs, forming protocells. These protocells existed in ponds with warm and cold sides, where double-stranded polynucleotides formed on the cold side, separated on the warm side, and then divided, repeating the cycle.
As protocells evolved into cells resembling modern bacteria, ribozymes (RNA enzymes) emerged, directing RNA duplication and catalyzing reactions. Eventually, proteins and DNA replaced ribozymes as the primary catalysts and genetic material, with RNA serving as an intermediary.
Researchers have also experimented with creating peptide nucleic acids (PNA), hybrids of proteins and nucleic acids, which could have existed in the primordial world and played a role in the origin of life. Scientists are currently trying to create artificial living cells using PNA to mimic the conditions of early Earth.
While no theory of life’s origin is conclusively proven or disproven, these ideas help explore key questions about catalysis and genetic coding.
linear structures that contain the genetic material and associated proteins
Chromosomes
a lattice of fine strands, consisting mostly of protein, that pervades the cytosol
Cytoskeleton (microtrabecular lattice)
a pathway that converts some lipids to carbohydrate with glyoxylic acid as an intermediate
Glyoxylate cycle
The enzyme catalase, which occurs in peroxisomes, catalyzes the conversion of H2O2 to H2O and O2.
In hereditary symbiosis, a larger host cell contains a genetically determined number of smaller organisms. An example is the protist Cyanophora paradoxa, a eukaryotic host that contains a genetically determined number of cyanobacteria
(blue-green algae).
a symbiotic relationship in which a smaller organism is completely contained within a larger organism
Endosymbiosis
characteristic of a reaction or process that takes place without outside intervention
Spontaneous
a thermodynamic quantity measured as the heat of reaction at constant pressure
Enthalpy
