134 terms

BMB 280 Test 1

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cells
small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and then dividing in two
DNA
polymer chains made from the same set of four monomers called nucleotides, strung together in different sequences to convey information; consists of two long polynucelotide chains, each chain or strand is composed of four types of nucleotide subunits, the two strands are held together by hydrogen bonds
RNA
DNA transcribed into a chemically related set of polymers
central dogma
the flow of information from DNA to RNA to protein
genome
the entire sequence of nucleotides in an organism's DNA- provides a genetic program that instructs the cell how to behave
cytoplasm
found around the nucleus and filling the cell's interior; a transparent substance crammed with a jumble of misc. objects
plasma membrane
the membrane that separates the interior of the cell from its external environment; a protein-studded, fatty film
eukaryotes
organisms whose cells have a nucleus
prokaryotes
organisms whose cells do not have a nucleus
prokaryotes
often have a tough protective coat, or cell wall, surrounding the plasma membrane, which encloses a single compartment, containing the cytoplasm and the DNA
prokaryotes
in terms of chemistry, they are the most diverse and inventive class of cells
mitochondria
the organelles that generate energy in eukaryotic cells(contains its own DNA)
chloroplasts
evolved from photosynthetic bacteria that long ago found a home inside the cytoplasm of a plant cell ancestor(contain their own DNA)
bacteria and archaea
two domains of prokaryotes
archaea
found in environments that are too hostile for most other cells (harsh conditions of primitive Earth)
nucleus
enclosed within two concentric membranes that form the nuclear envelope and its contains the DNA
chromosomes
threadlike structures in the nucleus of eukaryotic cells that become visible as the cells begin to divide
endoplasmic reticulum
an irregular maze of interconnected spaces enclosed by a membrane; it is the site where most cell-membrane components, as well as materials destined for export from the cell, are made
golgi apparatus
modifies and packages molecules made in the ER that are destined to be either secreted from the cell or transported to another cell compartment
lysosomes
small, irregularly shaped organelles in which intracellular digestion occurs
peroxisomes
small, membrane-enclosed vesicles that provide a safe environment for a variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules
endocytosis
vesicles from inside the cell fuse with plasma membrane and release their contents into the external medium
cytosol
the part of the cytoplasm not contained within intracellular membranes; largest single compartment; the site of many chemical reactions that are fundamental to the cell's existence
cytoskeleton
composed of three major filament types: actin(muscle contraction), microtubules(thickest filament;pull apart duplicated chromosomes), intermediate(strengthen cell)
ionic bond
electrons are donated by one atom to another
covalent bond
two atoms share a pair of electrons
molecule
atoms held together by covalent bonds
double bond
sharing of 4 electrons
polar covalent bonds
bonds in which the electrons are shared unequally
covalent bonds
strongest bond type
noncovalent bonds
does not involve the sharing of electrons(used to bond marcomolecules)
hydrogen bond
electrical attraction between a positively charged region of one (Water) molecule (H atom) to a negatively charged region of a second (water) molecule; can also occur between different parts of a single large molecule, where often helps the molecule fold
hydrophillic
"water-loving": includes sugars, DNA, RNA and a majority of proteins
hydrophobic
"water-fearing"; uncharged molecules that form few or no hydrogen bonds and do not dissolve in water are called
acids
substances that release protons when they dissolve in water
base
any molecule that accepts a proton when dissolved in water
buffers
a mixture of weak acids and bases that can adjust proton concentrations
organic molecules
small and large carbon compounds are said to be
inorganic molecules
does not contain carbon: includes water
macromolecules
proteins, nucleic acids, carbohydrates, lipids
sugars
the monosaccharides; both energy sources and subunits of polysaccharides
glycosidic bonds
monosaccharides are linked by these to form larger carbohydrates
condensation reaction
a bond is formed between an -OH group on one sugar and an -OH group on another; a molecule of water is expelled as the bond is formed
hydrolysis
bonds created by condensation reactions can be broken by this reverse process in which a water molecule is consumed
glucose
has a central role as an energy source for cells(glycogen in animals and starch in plants)
cellulose
forms plant cell walls; is a polysaccharide of glucose
fatty acid
consists of a long hydrocarbon chain(hydrophobic and not very reactive) and a carboxyl group (-COOH) (behaves as an acid)
amphipathic
molecules-such as fatty acids- that possess bothy hydrophobic and hydrophillic regions are termed
saturated
a hydrocarbon tail that has no double bonds between its carbon atoms and contains the maximum number of hydrogens, is said to be___
unsaturated
a hydrocarbon tail with one or more double bonds is said to be___ because it does not contain the maximum number of hydrogen atoms that it could
lipids
molecules that are insoluble in water but soluble in fat and organic solvents such as benzene
lipid bilayer
most unique function of fatty acids is this; also the basis for all cell membranes
phospholipids
composed mainly from fatty acids and glycerol; are amphipathic in nature; most abundant lipids in cell membranes, have a phostphate containing hydrophillic head linked to a pair of hydrophobic tails
amino acids
molecules that possess a carboxylic acid group and an amino group, both linked to their α-carbon; the identity of the side chain is what distinguishes one from the other; are the SUBUNITS OF PROTEINS
peptide bond
covalent bond between two adjacent amino acids in a protein chain
proteins
polymers made up of amino acids, which are joined head-to-tail in a long chain that folds up into a 3-dimensional structure
polypeptide
combined together these polymers form proteins; have an amino group at one end and a carboxyl group at the other end(Structural polarity)
nucleotides
subunits of DNA and RNA are called___;are nucleosides that contain one or more phosphate group attached to the sugar [SUGAR+ PHOSPHATE+BASE]
nucleosides
made of a nitrogen-containing ring compound linked to a 5-carbon sugar(either ribose or deoxyribose) [SUGAR+BASE]
ribonucleotide
nucleotide containing ribose
deoxyribonucleotide
nucleotide containing deoxyribose
prymidies
nucleotide bases cytosine(C), thymine(T), uracil (U); derived from a 6-membered pyrimidine ring
purines
nucleotide bases guanine(G) and adenine(A); bear a second 5-membered ring fused to the six-membered prymidine ring
adenosine triphosphate (ATP)
a ribonucleotide which participates in the transfer of energy in hundreds of metabolic reactions(terminal phosphate group in particular is frequently split off by hydrolysis)
nucleic acid chains
___ are synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during a phosphodiester bond formation
DNA double helix
___ is composed of two polynucleotide chains that run in opposite directions and are held together by hydrogen bonds between the bases of the two chains
Lipids
Which macromolecule IS NOT A POLYMER?
van der waals attractions
a noncoavlent interaction; electrical attraction caused by fluctuating electric charges that arise whenever two atoms come within a very short distance of each other(weaker than hydrogen bonds, but play an important role in the attractions between macromolecules
enzymes
__ accelerate or catalyze just one of the many possible kinds of reactions that a particular molecule might undergo
enzyme-catalyzed reaction
a reaction usually connected in series so that the product of one reaction becomes the starting material for the next
metabolism
the sum total of all the chemical reactions a cell needs to carry out in order to survive, grow, and reproduce
catabolic pathways
one of the two streams of chemical reactions occuring in the cell, this one breaks down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that cell needs as building blocks
anabolic(biosynthetic) pathways
one of two streams of chemical reactions occurring in the cell, this one uses the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell
second law of thermodynamics
this law states that, in the universe or in any isolated system, the degree of the disorder can only increase; systems will change spontaneously toward those arrangements that have the greatest possibility
entropy
the measure of a system's disorder is called the___ of the system, and the greater the disorder the greater it is
first law of thermodynamics
this law states that energy cannot be created or destroyed-- but it can be converted from one form to another
photosynthesis
this process converts the electromagnetic energy in sunlight into chemical-bond energy in cells
enzymes
__ lower the activation energy needed to initiate reactions in the cell
spontaneous
chemical reactions proceed only in the direction that leads to a loss of free energy(energetically favorable or____ direction)
Free Energy (G)
the useful energy in a system is known as its __
energetically unfavorable
reactions that are__ ____ create order in the universe; they have a positive delta G (formation of a peptide bond)
equilibrium
at ___ the rate of the forward reaction is equal to the rate of the reverse reaction, no work can be done
proteins
__ are the main building blocks from which cells are assembled and they constitute most of the cell's dry mass(provide the cell with shape, structure and execute almost all its functions)
3-dimensional shape
this ____ shape of a protein is stabilized by noncovalent interactions between different parts of the molecule
polypeptides
another name for proteins
polypeptide backbone
each polypeptide chain consists of a _____ which is formed from a repeating sequence of the core atoms (-N-C-C) found in every amino acid
N-terminus
the amino terminus--the end of the polypeptide chain which carries the amino group(NH3+)
C-terminus
the carboxyl terminus-- the end of the polypeptide chain carrying the free carboxyl group(COOH)
side chains
projecting from the polypeptide backbone are the amino acid ______; the part of the amino acid that is not involved in forming peptide bonds--they give each amino acid its unique properties
flexible
long polypeptide chains are very___ as many of the peptide bonds that link the carbon atoms in the polypeptide backbone allow free rotation of the atoms they join
hydrogen bonds, electrostatic attractions, van der Waals attractions
these noncovalent bonds help proteins fold up and maintain their shape
hydrophobic interactions
a fourth weak force,_______, has a central role in determining the shape of a protein; nonpolar side chains of particular amino acids, tend to be forced together to minimize their disruptive effect on the hydrogen-bonded network of the surrounding water molecules
conformation
the final folded structure or________, adopted by any polypeptide chain is determined by energetic considerations: a protein generally folds into the shape in which its free energy (G) is minimized
denatured
a protein can be unfolded or ____, by treatment with solvents that disrupt the noncovalent interactions holding the folded chain together
renaturation
refolding of a protein; indicates that all the information necessary to specify the 3-D shape of a protein is contained in its amino acid sequence
chaperone proteins
protein folding in a living cell is generally assisted by special proteins called_____-
( α) alpha-helix
one of two common folding patterns(Was first discovered) found in a-keratin which is abundant in skin and its derivatives
( β) beta-sheet
one of two common folding patterns, found in the protein fibroin(silk)
alpha-helix
generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder, a hydrogen bond is made between every 4th amino acid, linking the C=O of one peptide bond to the N-H of another(short regions are common in transport proteins and receptors)
coiled-coil
two or three α helices will wrap around one another to form a particularly stable structure known as a ____
primary structure
a proteins amino acid sequence is considered its ____
secondary structure
the α helices and β sheets that form within certain segments of the polypeptide chain; these folds are elements of the protein's ____
tertiary structure
the full 3-D conformation formed by an entire polypeptide chain--including α helices, β sheets, random coils, and other loops and folds that form between the N-terminus and the C-terminus-- is referred to as the ___
quaternary structure
if the protein molecule is formed as a complex of more than one polypeptide chain, then the complete structure is designated its ____
protein domain
organizational unit _________ is defined as any segment of a polypeptide chain that can fold independently into a compact, stable structure
intrinsically disordered sequences
regions of polypeptide chains lacking any definite structure, which continually bend and flex due to thermal buffeting are abundant in cells and are called _____; are often found as short stretches linking domains in otherwise highly ordered proteins[cause FLEXIBILITY]
globular proteins
_____, proteins in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface
fibrous proteins
____, proteins that are required to span a large distance, are realtively simple, elongated 3-D structure(α-keratin, hair, nails, horns) (collagen-most abundant in animal tissues) (extracellular matrix- helps bind cells together to form tissues)
disulfide bonds
___ are formed before a protein is secreted by an enzyme in ER that links together two -SH groups from cysteine side chains that are adjacent in the folded protein(they do not change a proteins conformation but reinforce its most favored conformation)
specificity
the binding of a protein to other biological molecules always shows great ___: each protein molecule can bind to just one or a few molecules of thousands
ligand
any substance that is bound by a protein is referred to as a ___ for that protein
antibodies
immunoglobulin proteins produced by the immune system in response to foreign molecules
enzymes
a large and very important class of proteins; they are responsible for nearly all the chemical transformations that occur in cells; act as catalysts
metabolic pathways
enzymes often work in tandem with the product of one enzyme becoming the substrate for the next, creating an elaborate network of ___ that provides the cell with energy and generates the many large and small molecules that the cell needs
lysozyme
an enzyme that acts as a natural antibiotic in egg white, saliva, tears and other secretions
hemoglobin
a protein that contains a nonprotein protion essential for its function is ____; a molecule of this carries four noncovalently bound heme groups, ring-shaped molecules each with a single central iron atom(gives blood its red color and enables ___ to pick up oxygen in the lungs and release it where needed
feedback inhibition
a negative regulation: whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway
positive regulation
____, in which the enzyme's activity is stimulated by a regulatory molecule rather than being supressed
allosteric
protein molecules are ___ ; they can adopt two or more slightly different conformations and their activity can be regulated by a shift from one to another
protein phosphorylation
___ controls the activity of many types of proteins in eukaryotic cells; extensively used [involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on serine, thronin or tyrosin by a PROTEIN KINSASE]
dephosphorylation
removal of the phosphate group; ___ is catalyzed by a PROTEIN PHOSPHATASE
GTP binding proteins
_____________ act as molecular switches
motor proteins
____ generate the forces responsible for muscle contraction and most other eukaryotic cell movements, they also power the intracellular movements of organelles and macromolecules
3' end
one end of a DNA strand (hydroxyl) has a "hole"
5' end
one end of a DNA strand (phosphate) has a "knob"
A
T pairs with
G
C pairs with
cholesterol
membrane fluidity is modulated by the inclusion of ___
membrane proteins
most membrane functions are carried out by___;serve to transport particular nutrients, metabolites, and ions across the lipid bilayer; others anchor the membrane to macromolecules; others function as receptors that detect chemical signals in the cell's environment and relay them to the cell's interior
transmembrane proteins
___are amphipathic and extend through the bilayer
membrane domains
cells have ways of confining particular proteins to localized areas within the bilayer membrane, thereby creating functionally specialized regions or ____, on the cell or organelle surface
glycocalyx
sugar coating called the carbohydrate layer or____ where all the carbohydrates located on the outside of the plasma membrane form; [PROTECTS THE CELL SURFACE FROM MECHANICAL DAMAGE]
channels
___ discriminate mainly on the basis of size and electric charge, when it is open any ion or molecule that is small enough and carries the appropriate electrical charge can pass through
transporter (proteins)
___ transfers only those molecules or ions that fit into specific binding sites on the protein