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Biology 172 set 1
Terms in this set (290)
Examples of endergonic reactions
glucose+ Pi --> glucose-6-phosphate+H2O
ADP + Pi-->ATP + H2O
Cadherin is an example of:
a cell adhesion molecule
organisms that derive energy from sunlight
Integrins are proteins that form connections between the:
cytoskeleton & the extracellular matrix
building a protein by adding amino acids to the chain is an example of _________.
t/f oxidation is the gain of electrons
the entire set of chemical reactions that sustain life is called _________.
which type of cellular junction allows for the movement of proteins & transfer RNA molecules?
endergonic and anabolic
synthesis of a protein is an example of a chemical reaction that is __________ and ________
the proteins of the electron transport chain are:
embedded in the inner mitochondrial membrane
the majority of energy generated in the citric acid cycle is in the form of:
energy electrons donated to NAD+ and FADH
phosphorylating glucose during phase 1 of glycolysis:
destabilizes the glucose molecule so that is can be broken down in stage 2
For the potential energy of a proton gradient to be converted to the chemical energy of ATP, the movement of the protons down their electrochemical gradient must be coupled with ATP synthesis. This coupling is made possible by:
The inputs of glycolysis do not include:
the final acceptor of the electron transport chain is:
cellular respiration is a series of _______ reactions
Energy production during cellular respiration
a small amount of energy is produced by substrate level phosphorylation; most is produced by oxidative phosphorylation
the electron transport chain is part of:
When a single pyruvate is converted to acetyl-CoA, the other products of the reaction are:
NADH and CO2
During acetyl-CoA synthesis, pyruvate is:
organic molecules store _________ energy in their ________ bonds
during fermentation, pyruvate is:
in the absence of oxygen, fermentation
regenerates NAD+ from the reduction of pyruvate
during the citric acid cycle:
ATP is synthesized by substrate level phosphorylation
the second law of thermodynamics states that:
there is an increase in disorder in the universe over time
energy release by transferring electrons along the electron transport chain is store as potential energy in the form of:
a proton gradient
how do different sugars enter glycolysis?
sugars are converted to various forms & enter glycolysis at various stages
the citric acid cycle takes place in the:
the first law of thermodynamics states that:
energy cannot be created or destroyed
electrons farthest from the nucleus have the:
most potential energy
produce ATP; reduce CO2
many photosynthetic prokaryotes are capable of cyclic electron transport only. It is likely that such organism can ______ ___ but not ______ ___.
In plants and algae, what is a by-products of photosynthesis?
Which regulatory mechanism is activated when the overall energy availability of a cell is high?
ATP inhibits phosphofructokinase 1
the citric acid cycle is a cycle because the starting molecule, _________, is regenerated at the end
Paraquat is an herbicide that blocks the transfer of electrons from PSII. Mechanistically, paraquat is effective because it:
increases the formation of reactive oxygen species
Coenzyme Q and cytochrome C:
transfer high-energy electrons between protein complexes of the electron transport chain
during the citric acid cycle, the production of CO2 is an _________ reaction coupled to the production of ____.
The Calvin cycle & light-harvesting reactions are separated in
The Z scheme refers to
the energy inputs associated with electron transport
weaker oxidant & a stronger reductant
PSI is a ______ _______ & a _______ _________
ATP production during photosynthesis requires
light, electrons, and protons
Chemicals called un-couplers can make membranes permeable to small molecules & ions. What effect do un-couplers have on photosynthesis?
decreased ATP production because the proton-gradient would decrease
organisms with only one photosystem cannot
rubisco is characterized by:
slow catalysis & substrate confusion
CO2 reduction requires:
ATP and NADPH
in plants and algae, ___ is the source of the electrons needed for photosynthesis.
Which part of the Calvin cycle would be impacted first by the absence of light energy?
the reduction of 3-phosphoglycerate & the regeneration of RuBP
The only known "solution" to the loss of efficiency caused by rubisco-oxygenating RuBP is to raise the concentration of CO2 at the enzyme, using ATP generated by the thylakoid. What do these types of plants require?
bright, sunny habitats
most abundant protein on Earth
The reducing agent during the Calvin cycle is:
How does the metabolism occurring in chloroplasts differ from that of mitochondria?
different electron acceptors & sources
the enzyme _________ prevents chromosomes from shortening at the tips after each round of DNA replication
When a mixture of debris from killed virulent bacteria & living non-virulent bacteria are injected into mice:
the mice are killed because the non-virulent bacteria are transformed into virulent bacteria
Which strands get shortened during DNA replication
both strands get shortened at opposite ends
central dogma states that information flows from:
DNA to RNA to proteins
non-virulent bacteria can be prevented from being transformed into virulent bacteria if the debris from heat-killed virulent bacteria is first treated with:
In the experiments conducted by Avery, McCarty, and MacLeod, what hypothetical results would indicate that protein, not nucleic acid, was Griffith's transforming principle?
only the extracts from heat-killed cells treated with protease are unable to transform nonvirulent bacteria
t/f synthesis of nucleic acids always occurs in the 5'-->3' direction
What forces contribute to the stability of a DNA double helix?
hydrophobic interactions of bases in the same strand and hydrogen bonding between bases adjacent strands
In the DNA sequence 5'-TGAC-3', the phosphodiester linkage between the guanine and adenine connects:
the 3' end of the guanine to the 5' end of the adenine
enzyme that separates the 2 strands of DNA during replication
t/f the semiconservative model of DNA replication means that each DNA strand consists of some newly synthesized DNA and some parental DNA
Why are primers needed for DNA replication?
DNA polymerase can only add to an existing chain, it cannon initiate synthesis of a new strand.
the point at which DNA synthesis is initiated is called the:
origin of replication
What would happen if telomerase stopped working?
the cell would eventually die as the DNA continued to shorten.
What part of newly replicated DNA is new?
One strand is new and the other is from the original molecule
How do DNA and RNA differ?
RNA has uracil as one of its bases; DNA has thymine
RNAs are typically single-stranded; DNA is double-stranded
RNA molecules are usually much shorter than DNA molecules.
The sugar component of RNA nucleotides is ribose; the sugar component of DNA nucleotide is deoxyribose.
a _______ always forms a complementary base pair with a pyrimidine.
The strands in a double helix of DNA are:
antiparallel, complementary, held together via hydrogen bonds and wound around each other with 10 base pairs per turn
an intron is:
RNA that is removed during the processing of an RNA molecule & remains inside the nucleus
Why are single-stranded binding proteins necessary for DNA replication?
they prevent the two parental strands from coming together again
Which processes occur in the nucleus of eukaryotic cells?
DNA replication & transcription
replication bubble; replication fork
in a long DNA molecule, each origin of replication produces a __________ ______ with a ___________ ____ on each side.
What is not needed for DNA replication?
collection of cells that work together to perform a specific function
two or more tissues combined
structural protein networks in the cytoplasm
cyotosolic proteins that have assembled into structures
meshwork of proteins & polysaccharides outside the cell
outer layer of skin
layer beneath epidermis
a group of cells arranged in one or more layers
few cells & substantial amount of extracellular matrix
A hollow rod of tubulin protein in the cytoplasm of all eukaryotic cells and in cilia, flagella, and the cytoskeleton
Fine, threadlike proteins found in the cell's cytoskeleton
A component of the cytoskeleton that includes all filaments intermediate in size between microtubules and microfilaments
Globular protein that comes in alpha and beta varieties, that composes microtubules
A structure present in the cytoplasm of animal cells that functions as a microtubule-organizing center and is important during cell division. has two centrioles.
Hairlike projections that extend from the plasma membrane and are used for locomotion
A long cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules, ensheathed in an extension of plasma membrane.
structure made of spindle fibers, centrioles, and aster fibers that is involved in moving and organizing chromosomes before the cell divides
A globular protein that links into chains, two of which twist helically about each other, forming microfilaments in muscle and other contractile elements in cells.
A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.
A protein present in muscle fibers that aids in contraction and makes up the majority of muscle fiber
A special motor protien that moves along the microtubule toward its positive end; in most cells this movement is from the center to the periphery, in the axon it is anterograde transport
A special motor protein that moves along the microtubule toward the negative end; responsible for rentrograde axoplasmic transport
cell adhesion molecules
CAMs. Proteins that allow cells to hook together and form attachments to the cytoskeleton for maintaining cellular shape.
A member of an important class of cell adhesion molecules that requires extracellular calcium ions for its function.
Cell surface receptor proteins that are built into the plasma membrane. They span the membrane and bind on their cytoplasmic side to associated proteins attached to microfilaments of the cytoskeleton.
cell junctions in epithelium that reinforces tight junctions (common name)
buttonlike points of adhesion that hold the plasma membrane of adjacent cells together
Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
Points that provide cytoplasmic channels from one cell to another with special membrane proteins. Also called communicating junctions.
An open channel in the cell wall of plants through which strands of cytosol connect from adjacent cells
Fibrous protein that gives the skin form and strength
derive their energy from organic molecules such as glucose
make their own source of carbon
rely on other organisms for their organic source of carbon
breakdown of glucose to make pyruvate
citric acid cycle
acetyl-CoA is broken down & more carbon dioxide is released
carry electrons or electrons and protons
Part of the electron transport chain. A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons across the inner membrane to bind with oxygen.
electron transport chain
A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.
a chemical reaction in which electrons are transferred from one reactant to another
An oxidized molecule that can accept electrons.
The electron acceptor in a redox reaction.
The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.
the fluid filled space between the inner and outer mitochondrial membranes
Liquid in mitochondria
What takes electrons from Complex 1 and 2 and take them to Complex 3?
In the electron transport chain, what carries electrons from complex III to complex IV?
Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP
An anaerobic (without oxygen) cellular process in which organic foods are converted into simpler compounds, and chemical energy (ATP) is produced
lactic acid fermentation
Glycolysis followed by the conversion of pyruvate to lactate, with no release of carbon dioxide.
a type of fermentation that regenerates NADH and makes ethanol and carbon dioxide. done by yeast, which makes bread. CO2 makes the bread rise and alcohol is cooked off.
An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.
A storage polysaccharide in plants consisting entirely of glucose.
A metabolic sequence that breaks fatty acids down to two-carbon fragments which enter the Krebs cycle as acetyl CoA.
Any process in which electrons are added to an atom or ion (as by removing oxygen or adding hydrogen)
Loss of electrons
photosynthetic electron transport chain
Cluster of pigment molecules in the thylakoid membrane
reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars
Open-ocean zone shallow enough for sunlight to penetrate.
horizontal gene transfer
A process in which an organism incorporates genetic material from another organism without being the offspring of that organism
Stack of thylakoids
fluid-filled interior compartment enclosed by thylakoid
Fluid inside chloroplasts
CO2 absorbed from the air is added to a 5-carbon molecule
reduction part of Calvin cycle
energy and electrons are transferred to the molecules formed from carboxylation
5-carbon molecule is regenerated for carboxylation
ribulose biphosphate; a five-carbon carbohydrate that combines with CO2 to form two molecules of PGA in the first step of the Calvin Cylce
Ribulose carboxylase, the enzyme that catalyzes the first step of the Calvin cycle (the addition of CO2 to RuBP, or ribulose bisphosphate).
during the Calvin Cycle, the first stable product (intermediate) produced after CO2 is added to ribulose bisphosphate is:
An electron carrier involved in photosynthesis. Light drives electrons from chlorophyll to NADP+, forming NADPH, which provides the high-energy electrons for the reduction of carbon dioxide to sugar in the Calvin cycle.
Electromagnetic radiation that can be seen with the unaided eye
A green pigment found in the chloroplasts of plants, algae, and some bacteria
Pigment that absorbs light at different wavelengths and then pass energy onto chlorophyll
Complex of proteins associated with two special chlorophyll a molecules and a primary electron acceptor. Located centrally in a photosystem, this complex triggers the light reactions of photosynthesis. Excited by light energy, one of the chlorophylls donates an electron to the primary electron acceptor, which passes an electron to an electron transport chain.
A zigzag shaped energy curve that produces a series of energy changes in an electron during photosynthesis
A photosystem that contains a pair of P680 chlorophyll molecules and uses absorbed light energy to split water into protons and oxygen and to produce ATP.
One of two light-harvesting units of a chloroplast's thylakoid membrane; it uses the P700 reaction-center chlorophyll.
cytochrome b6f complex
part of the photosynthetic electron transport chain, through which electrons pass between photosystem II and photosystem I
cyclic electron transport
In photosynthetic light reactions, the flow of electrons that produces ATP but no NADPH or O2.
reactive oxygen species
free radicals that contain oxygen (superoxide, O2) or non-radical reactive substances that can do us harm (H2O2)
One of a class of accessory pigments in photosynthesis that reflects yellow to orange light.
A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata close and the oxygen concentration in the leaf exceeds that of carbon dioxide.
the process whereby DNA makes a copy of itself before cell division
any event that changes genetic structure
the organic process whereby the DNA sequence in a gene is copied into mRNA
The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript.
production of a functional gene product
the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm
Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases
A simple carbohydrate with a chemical composition of CH2O. Most form ring structures when in solution.
A molecule found in DNA and RNA that encodes genetic information in cells.
A molecule in the backbone of DNA and RNA that links adjoining bases
A five-carbon sugar that is a component of DNA nucleotides
A and G
purine base found in DNA and RNA
A component of nucleic acids that carries hereditary information in DNA and RNA in cells. Chemically, it is a purine base.
A class of nucleotides that includes cytosine, thymine, and uracil
A component of nucleic acid that carries hereditary information in DNA in cells. Chemically, it is a pyrimidine base.
A component of nucleic acids that carries hereditary information in DNA and RNA in cells. Chemically, it is a pyrimidine base.
A structure composed of a ribose molecule linked to one of the aromatic bases. In a deoxynucleoside, the ribose is replaced with deoxyribose.
the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide
A lack of electrical symmetry in a molecule. Charge differences on opposite ends of a structure.
This is the end that the phosphate is attached to and considered the beginning of the strand.
At which end of DNA are new bases added?
a groove that spirals around the DNA double helix; provides a location where a protein can bind to a particular sequence of bases and affect the expression of a gene
A smaller groove that spirals around the DNA double helix.
The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.
stabilizing interactions between bases in the same strand of DNA
DNA molecule that contains extra twists as a result of overwinding or underwinding
Enzymes that relieve twists and kinks in a DNA molecule by breaking and rejoining the strands.
A threadlike, gene-carrying structure found in the nucleus. Each consists of one very long DNA molecule and associated proteins.
30-nm chromatin fiber
fiber from a double-stranded DNA packaged with histones
10-nm chromatin fiber
the least compact form of chromatin; "beads-on-a-string"
Clusters of DNA, RNA, and proteins in the nucleus of a cell
A eukaryotic structural unit of chromatin that consists of DNA wound around a core of histone proteins.
Globular protein that assist in DNA packaging in eukaryotes. Histones form octamers around which DNA is wound to form a nucleosome.
The term used to describe homologous DNA sequences that are very similar or identical between different species
the newly made stand in DNA replication
Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule
Bottom strand of a DNA molecule during DNA replication; replication is continuous without Okazaki fragments.
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.
Short fragments of DNA that are a result of the synthesis of the lagging strand during DNA replication.
A molecule (a short strand of RNA or DNA) whose presence is required for formation of another molecule (a longer chain of DNA)
An enzyme that creates an RNA primer for initiation of DNA replication.
A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.
Ability of DNA polymerases to remove and replace incorrectly paired nucleotides in the course of replication.
single-stranded binding proteins
During DNA replication, molecules that line up along the unpaired DNA strands, holding them apart while the DNA strands serve as templates for the synthesis of complementary strands of DNA.
works upstream from the replication fork to relieve stress on the double helix that results from its unwinding at the replication fork
origin of replication
point at which DNA synthesis is initiated
a region of DNA, in front of the replication fork, where helicase has unwound the double helix
DNA at the tips of chromosomes
Special cells used for reproduction. Produces gametes through meiosis.
Cells divide and remain undifferentiated
Any cells in the body other than reproductive cells
a mutation in which a single base pair in DNA has been changed
Gene mutation involving changes in one or a few nucleotides
mutations that do not cause amino acid substitutions; inconsequential
amino acid replacement
a change in the identity of an amino acid at a particular site in a protein resulting from a mutation in the gene
Change resulting from amino acid substitution during translation
Condition where red blood cells assume an abnormal sickle shape
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide
Segment of DNA that can move from one site to another site on the same or different DNA molecules
A type of mutation in which one region of a chromosome is exchanged with anther region of the same chromosome
agents that increase the probability of mutations
a situation in which enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors
base excision repair
A type of DNA repair the uses a glycosylase to recognize and cleave out an erroneous base, a endonuclease to then cleave the phosphodiester backbone, a DNA polymerase to add a new nucleotide onto the intact DNA template, and a DNA ligase to join the new nucleotide to the DNA strand
nucleotide excision repair
The process of removing and then correctly replacing a damaged segment of DNA using the undamaged strand as a guide.
Cytoplasmic organelles at which proteins are synthesized.
RNA world hypothesis
describes how the Earth may have been filled with RNA-based life before it became filled with the DNA-based life we see today
A five-carbon sugar present in RNA
a nitrogen-containing base found in RNA (but not in DNA) and derived from pyrimidine
mRNA molecule formed during transcription that has a sequence of bases complementary to a gene.
Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription
the DNA strand that is complementary to the template strand; not ordinarily used as a template during transcription
Region of DNA that indicates to an enzyme where to bind to make RNA
A promoter DNA sequence crucial in forming the transcription initiation complex.
A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene
genes that are switched on all the time because they are needed for life functions vital to an organism
Protein required for the correct initiation of transcription.
general transcription factors
In eukaryotes helps to position the RNA polymerase correctly at the promoter; has a role in pulling apart the two strands of DNA to allow transcription to begin
RNA polymerase complex responsible for transcription of protein-coding genes
transcriptional activator protein
protein than enhances transcription of the viral genome from the promoter gene sequence
A segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates.
A protein complex that acts as an adapter that interacts with transcription factors bound to regulatory sites and with general initiation factors for RNA polymerase II-mediated transcription.
high-energy phosphate bond
The bond between two phosphates in an ADP or ATP molecule that readily releases its energy for cellular processes
An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene.
RNA molecule that carries copies of instructions for the assembly of amino acids into proteins from DNA to the rest of the cell. mRNA
mRNA that includes coding regions representing more than one gene
Modification of RNA before it leaves the nucleus, a process unique to eukaryotes.
The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.
addition of a short sequence or a tail of adenine (poly A-tail) nucleotides to the 3' end of an mRNA molecule. happens during RNA spilcing in eukaryotes.
The modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.
A noncoding, intervening sequence within a eukaryotic gene.
Process by which the introns are removed from RNA transcripts and the remaining exons are joined together
A coding region of a eukaryotic gene. Exons, which are expressed, are separated from each other by introns.
A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining the two adjacent exons.
An intermediate in RNA splicing in which a circular structure with a tail is created by a 5' to 2' bond
Splicing of RNA transcripts from the same gene in different ways, each of which produces a distinct protein.
Combines with proteins to form ribosomes, the structures that link amino acids to form proteins.
type of RNA molecule that transfers amino acids to ribosomes during protein synthesis
small nuclear RNA
snRNA, structural and regulatory RNAs that are components of the spliceosome often required for splicing of eukaryotic mRNAs
small single stranded RNA molecules that bind to mRNA and can degrade mRNA or block its translation
small interfering RNA
Similar to miRNA, but formed from longer, double stranded RNA molecules
holds the tRNA carrying the next amino acid to be added to the chain
one of a ribosome's three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain.
One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)
One of three different ways in which a sequence of nucleotides can be read as a series of triplets and translated into protein.
aminoacyl tRNA synthetases
An enzyme that joins each amino acid to the correct tRNA.
A set of rules that defines how the four-letter code of DNA is translated into the 20-letter code of amino acids, which are the building blocks of proteins.
1st step in translation of RNA. Two step process to establish exactly where translation will begin, ensuring that the mRNA codons are translated in the correct sequence of amino acids.
Aminoacyl tRNA brings a new amino acid to the A site. And the binding occurs due to cod an/anticodon recognition
occurs when a termination codon arrives in the A site
A class of proteins that assist ribosomes in binding to a messenger RNA molecule to begin translation.
proteins that help get charged tRNA to bind
Proteins that can trigger termination of RNA translation when a ribosome reaches a stop codon.
A segment of DNA containing adjacent genes including structural genes and an operator gene and a regulatory gene
proteins or domains grouped together because they have have similar sequences and structures; they usually have related functional mechanism
a region of protein that folds in a similar way across a protein family relatively independently of the rest of the protein
Area where the chromatids of a chromosome are attached
An aberration in chromosome structure due to fusion with a fragment from a homologous chromosome, such that a portion of a chromosome is duplicated.
Change to a chromosome in which a fragment of the chromosome is removed
duplication and divergence
the process of creating new genes by duplication followed by progressive change in sequence through evolutionary time
consists of two or more copies of paralogous genes within the genome of a single species
Model that uses DNA comparisons to estimate the length of time that two species have been evolving independently
a kind of mutation in which the order of the genes in a section of a chromosome is reversed
Fragments exchanged between two chromosomes
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