Exam I Terminology

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DNA Replication

process by which a copy of a DNA molecule is made

transcription

process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence

Translation

process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein

Mitotic spindle

array of microtubules and associated molecules that forms between the opposite poles of a eukaryotic cell during mitosis and pulls duplicated chromosome sets apart

spindle pole

centrosome from which microtubules radiate to form the mitotic spindle

centrosome

microtubule-organizing center that sites near the nucleus in an animal cell; during the cell cycle, this structure duplicates to form the two poles of the mitotic spindle

Dynein

motor protein that uses the energy of ATP hydrolysis to move toward the minus end of a microtubule. One form of the protein is responsible for the bending of cilia

Cilium

hair-like structure made of microtubules found on the surface of many eukaryotic cells; when present in large numbers, its rhythmic beating can drive the movement of fluid over the cell surface, as in the epithelium of the lungs

flagellum

long, whiplike structure capable of propelling a cell though a fluid medium with its rhythmic beating. In Eukarya, they are longer versions of cilia; in bacteria, they are completely different, being smaller and simpler in construction

microtubule

long, stiff, cylindrical structure composed of the protein tubulin. Used by eukaryotic cells to organize their cytoplasm and guide the intracellular transport of macromolecules and organelles

Actin

protein that forms the contractile filaments of the muscle cells with myosin

intermediate filament

fibrous cytoskeletal element, about 10 nm in diameter, that forms ropelike networks in animal cells; helps cells resist tension applied from outside

keratin filament

class of intermediate filament abundant in epithelial cells, where it provides tensile strength'; main structural component of hair, feathers, and claws

Tubulin

protein from which microtubules are made

microfilament (actin filament)

thin, flexible protein filament made from a chain of globular actin molecules; a major constituent of all eukaryotic cells, this cytoskeletal element is essential for cell movement and for the contraction of muscle cells

confocal microscope

specific fluorescent microscope that captures images at a narrow depth, moving through the sample one level at a time; these images are 3D

Green fluorescent protein

protein that inhibits bright green fluorescence when exposed to light in the blue to ultraviolet range; used to monitor physiological processes, visualize protein localization, and detect transgenic expression in vivo

prokaryote

major category of living cells distinguished by the absence of a nucleus; includes the archaea and the eubacteria

eukaryote

an organism whose cells have a distinct nucleus and cytoplasm

Archaebacteria

group of microorganisms considered to be an ancient form of life that evolved separately from the bacteria and blue-green algae

eubacteria

prokaryotic microorganism consisting of a single cell lacking a nucleus and containing DNA

Cyclin

regulatory protein whose concentration rises and falls at specific times during the eukaryotic cell cycle; help control progression from one stage of the cell cycle to the next by binding to cyclin-dependent protein kinases

model organism

a living thing selected for intensive study as a representative of a large group of species

e.g. mice, flies, E. coli

Angstrom

unit of length equal to one hundred-millionth of a centimeter - used to describe wavelengths

Chloroplast

specialized organelle in algae and plants that contains chlorophyll and serves as the site of photosynthesis

Thylakoid

in a chloroplast, the flattened, disclike sac whose membranes contain the proteins and pigments that convert light energy into chemical-bond energy during photosynthesis

Stroma

in a chloroplast, the large interior space that contains the enzymes needed to incorporate CO2 into sugars during the carbon-fixation stage of photosynthesis; equivalent to the matrix of the mitochondria

Mitochondria

membrane-enclosed organelle, about the size of a bacterium, that carries out oxidative phosphorylation and produces most of the ATP in eukaryotic cells

Extracellular Matrix

complex network of polysaccharides and proteins secreted by cells. A structural component of tissues that also influences their development and physiology

Cristae

found in mitochondria; fold in the inner membrane of the mitochondria that increases the capacity of the mitochondrion to synthesize ATP

Plant Vacuole

found in plants; help maintain water balance - takes up most of interior of plant cell

some animal cells have very small ones

Endocytosis

process by which cells take in materials through an invagination of the plasma membrane, which surrounds the ingested material in a membrane-enclosed vesicle

Lysosomes

membrane-enclosed organelle that breaks down worn-out proteins and organelles and other waste materials, as well as molecules taken up by endocytosis; contains digestive enzymes that are typically most active at the acid pH found inside these organelles

Peroxisome

small membrane-enclosed organelle that contains enzymes that degrade lipids and destroy toxins

Golgi Apparatus

membrane-enclosed organelle in eukaryotic cells that modifies the proteins and lipids made in the endoplasmic reticulum and sorts them for transport to other sites

Cytosol

contents of the main compartment of the cytoplasm, excluding membrane-enclosed organelles

Endoplasmic reticulum

labyrinthine membrane-enclosed compartment in the cytoplasm of eukaryotic cells where lipids and proteins are made

Cisternae

flattened membrane vesicle found in the ER and golgi apparatus. Integral in packaging and modification processes or proteins in Golgi

Ribosome

large macromolecular complex, composed of RNAs and proteins, that translates messenger RNA into a polypeptide chain

Telomere

repetitive nucleotide sequence that caps the ends of linear chromosomes. Counteracts the tendency of the chromosome otherwise to shorten with each round of replication

Telomerase

enzyme that elongates, synthesizing the repetitive nucleotide sequences found at the ends of eukaryotic chromosomes

Centromere

specialized DNA sequence that allows duplicated chromosomes to be separated during M phase; can be seen as the constricted region of a mitotic chromosome

Nucleosome

beadlike structural unit of a eukaryotic chromosome composed of a short length of DNA wrapped around an octameric core of histone proteins; includes a nucleosomal core particle along with a segment of linker DNA that ties the core particles together

Histone

one of a small group of abundant, highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packing

30 nm Fiber

has to do with chromatin compaction; consists of helical array of nucleosomes, each comprising a core particle wrapped of DNA associated with a linker histone

Atomic number

number of protons in the nucleus

atomic mass

mass of an atom relative to the mass of a hydrogen atom; equal to number of protons plus neutrons that the atom contains

mole

amount of material containing 6.022 × 10²³ particles

molar solution

aqueous solution that contains 1 mole of a compounds dissolved in 1 liter of a solution

covalent bond

stable chemical link between two atoms produced by sharing one or more pairs of electrons

ionic bond

interaction formed when one atom donates electrons to another; this transfer of electrons causes both atoms to become electrically charged

dipole

a pair of equal and opposite electric charges or opposite signs

nonpolar

no electric charge or partial charges; hydrophobic/insoluble in water

condensation (dehydration synthesis)

chemical reaction in which a covalent bond is formed between two molecules as water is expelled; used to build polymer, such as proteins, polysaccharides, and nucleic acids

hydrolysis

chemical reaction that involves cleavage of a covalent bond with the accompanying consumption of water; the reverse of a condensation reaction

fatty acid

molecule that consists of a carboxylic acid attached to a long hydrocarbon chain. Used as a major source of energy during metabolism and as a starting point for the synthesis of phospholipids

amphipathic

having both hydrophobic and hydrophilic regions, as in a phospholipid

triglyceride (neutral fat)

consists of a glycerol backbone esterified with three fatty acids; main constituent of body’s fat stores

phospholipid

a major type of lipid molecule in many cell membranes. Generally composed of two fatty acid tails linked to one of a variety of phosphate-containing polar groups

glycerol

trihydroxy sugar alcohol with three carbon atoms and three hydroxyl groups; attracts water into the guts in the intestines, softens stools, and relieves constipation

alpha carbon of amino acid

refers to the carbon atom that is directly bonded to the amino group (-NH2), the carboxyl group (-COOH), the hydrogen atom (-H), and the side chain (R group). It is also known as the central carbon atom.

R group (side chain) of amino acid

the variable group in an amino acid that determines its unique properties and characteristics. It can be a simple hydrogen atom or a complex organic molecule; it influences its polarity, acidity or basicity, and overall chemical behavior.

peptide bond

a type of chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid. It is formed through a dehydration synthesis reaction, where a water molecule is eliminated. These are the building blocks of proteins and are responsible for linking amino acids together in a linear chain.

adenosine triphosphate (ATP)

a molecule that serves as the primary energy currency in cells. It is composed of adenosine and three phosphate groups. When one phosphate group is removed from this through hydrolysis, energy is released, and it is converted into ADP (Adenosine Diphosphate). This energy release powers various cellular processes, including muscle contraction, active transport, and chemical reactions. It is constantly synthesized and broken down in cells to provide the necessary energy for cellular activities.

ribose

type of sugar molecule that is an essential component of RNA (ribonucleic acid). It is a pentose sugar, meaning it has five carbon atoms. It plays a crucial role in the structure and function of RNA, as it forms the backbone of the RNA molecule. It is also involved in energy metabolism, as it is a key component of ATP (adenosine triphosphate), the primary energy currency of cells.

phosphate

refers to an inorganic chemical compound containing the phosphate ion (PO43-). It is an essential component of DNA, RNA, and ATP (adenosine triphosphate), which are vital for cellular energy transfer and storage.

phosphoanhydride bon

define phosphoanhydride bond

d

a high-energy bond that connects two phosphate groups in a molecule. It is formed through the condensation reaction between two phosphate groups, resulting in the release of a water molecule. This bond is found in molecules such as ATP (adenosine triphosphate) and GTP (guanosine triphosphate), which are important energy carriers in cells. The hydrolysis of this bond releases a significant amount of energy that can be used for various cellular processes.

macromolecular complex

a large assembly of molecules, typically proteins, nucleic acids, or a combination of both, that interact with each other to perform specific biological functions. These complexes are involved in DNA replication, transcription, translation, and signal transduction. Examples include ribosome, spliceosome, and DNA polymerase.

metabolic pathway

a series of chemical reactions that occur within a cell to convert one molecule into another, usually involving enzymes. These pathways are crucial for various cellular processes, such as energy production, synthesis of biomolecules, and elimination of waste products. Examples include glycolysis, the citric acid cycle, and the electron transport chain.

potential energy

stored energy that has the ability to do work due to the position or state of the object

kinetic energy

energy an object has due to its motion

catabolism

breaking things down; digestion; generate useful form of energy for the cell and some of the small molecules that the cell needs as building blocks

anabolism

building up; building blocks of food transported to cells to build molecules (pay with ATP)

thermodynamics

study of energy transformations

entropy

thermodynamic quantity that measures the degree of disorder in a system

enthalpy

the measurement of energy in a thermodynamic system

Gibbs Free Energy

a measure of the amount of usable energy (energy that can do work) in that system
negative= spontaneous
positive= nonspontaneuous

reduced carbon

carbon atoms gains bonds to less electronegative elements, most commonly hydrpgen

oxidized carbon

the carbon atoms lose electrons

substrate (reactants)

reactant in a reaction controlled by an enzyme; material that is used up

products

The elements or compounds produced by a chemical reaction.

enzyme substrate complex

A temporary complex formed when an enzyme binds to its substrate molecule(s). Lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process

endergonic

a reaction that requires energy to be driven

exergonic

a reaction that releases free energy in the process of the reaction

equilibrium constant

For a reversible chemical reaction, the ratio of substrate to product when the rates of the forward and reverse reactions are equal

Michaelis-Menten plot

-hyperbola shape
-allow us to see how rate of reaction will occur given current enzyme and substrate concentrations
-represent the relationship of saturation kinetics as a hyperbola

Lineweaver-Burke plot

inverse of rxn speed is y
inverse of substrate conc. is x

1/Vmax is y-intercept
1/Km is x-intercept

useful for testing inhibitor's effect on vmax and Km, plot two lines with and without inhibitor

slope is Km/vmax

Vmax

The maximum rate of an enzymatic reaction, reached when the active sites of the enzyme molecules in a sample are fully occupied by substrate.

Km

the concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound

Phosphorylation

Membrane-based process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons from food molecules to molecular oxygen.

dephosphorylation

the removal of a phosphate group by hydrolysis

Kinase

enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein

phosphatase

enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylation site

NADPH

Activated carrier closely related to NADH and used as an electron donor in biosynthetic pathways. In the process it is oxidized to NADP+.

Acetyl CoA

Activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic reactions, including the citric acid cycle and fatty acid biosynthesis; the acetyl group is linked to coenzyme A (CoA) by a thioester bond that releases a large amount of energy when hydrolyzed.

catalyst

a substance that accelerates the rate of a chemical reaction by lowering its activation energy; enzymes perform this role in cells

enzyme

a protein that catalyzes a specific chemical reaction

enzyme cofactor

non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst. Considered "helper molecules" that assist in biochemical transformations

enzyme coenzyme

an organic compound which binds to apoenzyme (the proteinacecous part of the enzyme) for a short time

activation energy

the energy that must be acquired by a molecule to undergo a chemical reaction