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236 Cards in this Set

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  • Back
A cell is the smallest unit which can perform all the fundamental functions of life. These include...
Reproduce, store genetic information, transfer genetic information, catalyze reactions with enzymes, respiration, use ATP as energy currency, separate/create compartment, communicate, differential gene expression
Function of cell reproduction (division)?
Pass on genetic information
How is genetic information stored in the cell?
Nucleic acids
What is respiration?
Catalysis: derive energy from simple compounds (sugars)
ATP is catalysis for...
energy release
What enables different cells to be created?
differential gene expression
How is cytoplasm separated from the environment?
phospholipid membranes
How do cells communicate?
protein receptors, ligands, signaling cascades
How is genetic information transferred?
DNA to RNA to protein
What is the cell theory?
All living things are formed by division of existing cells, thus cells are the universal building blocks of all living things.
What is a procaryotic cell?
developed first, smaller, no nucleus/nuclear membrane, no internal membrane-bound organelles (has ribosomes, DNA, thick, matrixed cell wall, vacuole, flagellum)
What is a eucaryotic cell?
developed later, larger, nucleus, membrane-bound organelles
Descendants of the ancestral procaryote evolved through gene mutations into...
...highly divergent cells that now fill every environment on Earth.
Two important endosymbiotic events occurred in the history of cell evolution. What was the first?
Anaerobic procaryote was engulfed, became mitochondria
Two important endosymbiotic events occurred in the history of cell evolution. What was the second?
Procaryotic photosynthetic bacteria was engulfed, led to chloroplast, created photosynthetic eucaryote, predecessor to plants
A procaryote first developed a nuclear membrane. What effect did this have?
Enclosed free-floating DNA into that chamber.
How did the double membrane, for example of the mitochondria, come about?
Engulfment in the two key endosymbiotic events.
Eucaryotic cell has compartments established by...
its plasma membrane
The nuclear membrane is contiguous with...
the endoplasmic reticulum
The nucleolus is located...
at the center of the nucleus
Adjacent to the ER is the...
Golgi apparatus
The endomembrane system includes these organelles:
nuclear envelope, endoplasmic reticulum, the Golgi apparatus, lysosomes, vacuoles, vesicles, peroxisomes (deal with hydrogen peroxide waste product) and cell membrane
The endomembrane system in a eucaryotic cell is...
different membranes suspended in the cytoplasm, dividing the cell into functional and structural compartments, or organelles; forming a single functional and developmental unit, either being connected together directly, or exchanging material through vesicle transport
Outside the endomembrane system are the...
Mitochondria, centrioles (organizing center for microtubials, two in every cell, function during division)
What is the sticky coat that holds different cells together called?
the extracellular matrix
What is the cytoskeleton?
Structural framework of cell; microtubials, intermediate filaments and actin all provide intracellular substrate for transport, shape, movement
How much DNA is in the nucleus?
About 2 meters! What!
Where is most ATP made?
mitochondria
What does ATP even stand for?
adenosine triphosphate
Nucleus has double-membrane structure with highly regulated pores. What form does the DNA inside take?
Chromatin and chromosomes
What does 'chromatin' refer to?
DNA wrapped around histones (proteins) and packaged into little balls called nucleosomes, as well as all the nuclear protein surrounding/involved
What happens in the nucleolis?
RRNA synthesis and packaging
What types of key support does the cytoskeleton provide for the nucleus?
Nuclear lamina=inner membrane lining; intermediate filaments and microtubials on outside
What does the ER look like?
branching tubules and flattened sacs extending throughout the cytoplasm
What does the ER do?
contributes to the formation of all plasma membranes; rough ER is the site of protein synthesis; smooth ER synthesizes lipids and houses detoxification enzymes.
What is the Golgi apparatus?
stacks of flattened membrane with polarity and a pH differential that creates different regions from beginning to end (cis-medial-trans) which facilitate reactions as a protein travels through it
How does the Golgi apparatus modify proteins from the ER?
Adds side groups such as cholesterol, methylation
Some vesicles from the ER that bud off from the Golgi form lysosomes. What do lysosomes do?
Function as the cell's stomach, the major digestive organelle. Releases nutrients from food particles and breaks them as well as other organelles down for use, recycling or excretion
Peroxisomes are almost a cell within a cell. They have a double-membrane structure. The inner membrane is very folded. They make ATP, contain their own DNA, carry out their own protein synthesis and multiply by division. What is their ultimate function?
Peroxisomes have about fifty enzymes to help them break down H2O2 (hydrogen peroxide) which is a waste product of many reactions within the cell. They break down fatty acids and other metabolic substances.
Cytosol contains...
many small molecules that play roles in numerous reactions critical to cell function
What is the path of a protein, starting from DNA?
DNA used as template to make mRNA, which travels from nucleus to cytoplasm. Ribosome clamps onto mRNA to build new protein, which might be processed for instance in the ER, then bud off in vesicles, fuse with the golgi, bud off again and travel somewhere within the cell or bind with plasma membrane and secrete contents outside the cell
Paramecium have a much higher ion concentration inside, and this would typically cause the cell to take in too much water and burst, but...
Some protists contain specialized vacuoles. Paramecium have evolved a mechanism to handle this ion difference.
Sulfatides and galactocereberosides are two types of fatty acids. Like most fatty acids, both have long hydrocarbon tails that associate with other fatty acids. This forms...
phospholipids (membranes)... lipids, fats
What is needed to both make and break macromolecules?
enzymes
How many main types of macromolecules are there?
four
What are the four main types of macromolecules?
lipids, nucleic acids, proteins, sugars
What are the primary atoms that are found in living things and the building blocks of organic compounds that further yield macromolecules?
carbon, hydrogen, oxygen, nitrogen
Keep in mind these themes of biology:
scale, form fits function
Amino acids make up...
proteins
Monomers+nucleotides=
Nucleic acids
Polysaccharides=
sugars
How do the themes of scale & form-fits-function apply to macromolecular processes?
subunits build macromolecules (with covalent bonds), macromolecules build macromolecular assemblies (with noncovalent bonds)
Sugar is the subunit. What is the macromolecule (polymer)? What type of bonds hold it together?
Polysaccharides; glycosidic bonds.
Amino acid is the subunit. What is the macromolecule (polymer)? What type of bonds hold it together?
Proteins; peptide bonds.
Nucleotide is the subunit. What is the macromolecule (polymer)? What type of bonds hold it together?
Nucleic acid; phosphodiester bonds.
Fatty acid (lipid) is the subunit. What is the macromolecule (polymer)? What type of bonds hold it together?
Hydrocarbon chain; ester linkages
What two principle reactions control the synthesis or breakdown of the four main macromolecules?
Hydrolysis and condensation
How does a condensation reaction work?
Forms covalent bonds between monomers making polymeric chains. water is released.
What is a covalent bond?
Sharing of electron pair between atoms, very stable
How does a hydrolysis reaction work?
Consumes water to break covalent bonds between monomers of a chain
All bonds are facilitated using
WATAH
A hydrogen bond is...
a sharing of hydrogen atom to establish interaction based on charge
What is the core chemical principal of the covalent bonds that make up water?
They be polar
Non-polar (uncharged) molecules do what in water?
Clump togedda
Due to its polar structure & use of hydrogen bonding, ____ is the foundational chemistry that supports the organization of all cells.
WATAH
Hydrophillic
Water-loving
Hydrophobic
Water-hating
Energy storage, structure, thermal insulation, electric insulation, & photosynthetic pigments are properties of...
lipids
What makes something a saturated fat?
long hydrocarbon tails withOUT a double bond
What makes something an unsaturated fat?
long hydrocarbon tails WITH a double bond
Lipids are amphiphatic. What does this mean?
Contain both hydrophobic & hydrophillic regions, causing unique behavior with water
Nucleotides: what is the difference between pyrimadines and purines?
Pyrimadines: one ring; purines: two rings
In RNA (single stranded), nucleotides are linked together by ______ bonds in a #' to #' Carbon orientation to form a _______.
phosphodiester, 5, 3, nucleic acids
In DNA (double stranded), the formation of the double-helix structure is enabled by...
hydrogen bonding between bases that enables rotation about the backbone
DNA: Single strands are held together by _______ bonds between the phosphate and sugar, establishing a _______.
phosphodiester, backbone
DNA: The pyrimidine bases bind to the purine bases in a specific __ to __ (__ in RNA) and ___ to ___ pairing, establishing a double helical stranded structure.
A, T (U in RNA) and G, C
Chains of amino acids held by peptide bonds are _____ and when folded correctly are ______.
polypeptides, proteins
The types and order of side chains in the peptide dicate...
how protein will fold and ultimately function.
Amino acid binding: The peptide bond between the amino and carboxyl groups of two amino acids is formed by what kind of reaction?
Condensation rxn
What is mostly responsible for the final structure of a protein?
Noncovalent interactions and some covalent bonds (disulfide) between side groups.
Protein structure: primary structure, amino acid. Secondary structure can either be?
Beta pleated sheats, alpha helix
Explain tertiary and quaternary protein structures.
Tertiary structure of protein made up of beta pleated sheats and alpha helix; Quaternary structure composed of tertiary structures
Covalent bonds such as disulfide bridges as well as noncovalent interactions such as hydrogen bonds between functional groups influence...
primary, secondary, tertiary and quaternary structures of a final protein
How are sugars linked together?
Condensation rxn forms glycosidic bond between carbons 1 and 4 of alternating sugar monomers
Cellulose, starch, and glycogen, respectively, are different structures of polysaccharides that are, respectively...
Linear (plant cell wall), branched, highly branched
Glycosidic bonds can create branches, which help liver and muscle to maintain large stores of glycogen and fats to compensate for...
long periods of fasting or increased and sustained energy demand.
What is catabolism?
enzyme catalyzed reactions that break down complex food molecules into simpler molecules
What is anabolism?
the biosynthesis of large molecules from smaller ones
Activated Carrier molecules can store and transfer energy potential toward...
the anabolic pathways.
The third phosphate bond in ATP represents an unstable high energy bond, that when broken...
releases significant free energy for work.
What is an enzyme?
A protein, on the surface of which are chemical groups so arranged as to make the enzyme a catalyst for a chemical reaction
____ possess active sites that can physically bind one or more substrates and force them to interact (in what ways?) to form a new product.
enzymes (change orientation, strain, or add charge)
The regulation of enzymes is a critical function of a cell. Enzymes can be regulated in a positive or negative way by other proteins that bind to the enzyme's active site or at some other non-active site. What are three types of these regulators?
Competetive inhibitor (binds to active site)
Allosteric inhibitor
Allosteric Activator
What is more efficient, a small release of electrons to store energy or one huge release?
Small release to avoid heat waste. Cell's strategy for making energy from food is to use small, stepwise reactions.
What are the stages of glucose metabolism in order?
Glycolysis, citric acid cycle, energy transfered to the production of ATP through differential membrane potential in the mitochondria
Where does glycolysis occur?
cytosol
Where does the citric acid cycle occur?
mitochondria
the first enzyme that glucose encounters in glycolysis is called _____. What does it do?
hexokinase. Changes conformation to sequester glucose and phosphorylate (Add phosphate group)
In step 2 of glycolysis, ___________ catalyzes the rearrangement of the chemical structure into glucose-6 phosphate. In step 3, __________ performs the limitings step.
phosphoglucose isomerase, phosphofructokinase
Kinase means the enzyme ______
phosphorylates a substrate
Isomerase means the enzyme ______
moves shit around
In steps 4 & 5 of glycolysis, what cleaves the 6-carbon in half?
Aldolase
In steps 4 & 5 of glycolysis, what rearranges the carbonyl group?
Triose phosphate isomerase
In step 6 of glycolysis, what oxidizes reduces NAD (carrier molecule) to NADH+H?
glyceraldehyde 3-phosphate DEHYDROGENASE (electron acceptor such as NAD reduced by adding a proton)
Oxidation reaction involves...
loss of electron density usually associated with addition of Oxygen
Reduction reaction involves...
addition of electron density usually associated with the addition of Hydrogen or loss of Oxygen
Glucose -> production of ATP mainly through ________ reactions.
Redox
In step 7 of glycolysis, _________ makes a high energy ATP molecule
phosphoglycerate kinase
In step 8 of glycolysis, ________ moves phosphate ester linkage from low to higher energy position
phosphoglycerate MUTASE (movement)
In step 9 of glycolysis, ______ catalyzes condensation reaction to establish high energy enol phosphate linkage
Enolase
In step 10 of glycolysis (final step), _______ turns ADP into ATP
Pyruvate kinase
How many ATP are produced during glycolysis and how many pyruvate molecules?
Four ATP and 2 pyruvate
For every one electron carrier, how many ATP are produced in the end?
3 ATP
Catalysis of glucose into ATP includes what four elements?
Glycolysis, fermentation, citric acid cycle, electron transport chain
Isomerase and mutase ____ things.
Move, rearrange
Kinase ________ things.
Phosphorylate (add PO4)
Dehydrogenase makes ______ through a _________
NADH, redox reaction
Aldolase ______ compounds
cleaves
Enolase produces _______ rxn
condensation
What is substrate level phosphorylation?
The direct synthesis of ATP in glycolysis and the citric acid cycle.
What is oxidative phosphorylation?
Any ATP created through the ETC (using oxygen)
Citric acid cycle's most important byproduct?
CO2
During the last reduction reaction in aerobic respiration, CO2 is produced and _______ is the final electron acceptor.
oxygen
If oxygen is not available during the citric acid cycle (anaerobic conditions), pyruvate undergoes ______
fermentation (converted to lactic acid)
In the citric acid cycle, the drop in pH caused by lactic acid is called ________ and enables continuous substrate phosphorylation for ATP.
lactic acidosis
Fermentation in yeast is used to convert pyruvate into...
alcohol and CO2
Some mitochondria are precisely positioned in cells to target...
ATP delivery
14/83 codes and 22 transfer RNAs of the subunits that makes up complexes of the ETC are derived from the _______
mitochondrial genome
Citric acid cycle takes _____ and turns it into ______ with ______ as a biproduct.
Pyruvate and Acetyl CoA, energy carriers, CO2
What does synthase do?
Synthesizes a new compound (merging two together)
What does aconitase do?
Removes and adds water to cause isomeration, moving of OH group to different carbon
In the citric acid cycle, ______ catalyze substrate oxidation and NAD reduction
dehydrogenases
Glycolysis produces how many ATP?
8
Pyruvate to acetyl CoA transformation produces what?
2 NADH+H
What does the citric acid cycle produce in numbers?
6 NADH+H
2 FADH2
2 GTP (s.p.)
How many ATP are produced before the ETC begins?
38 ATP
What is chemoismotic coupling and where does it begin?
coupling bond formation with ATP creation and membrane transport; begins with ETC
A system of metals in HEME compounds in the ______ function to collect four electrons and oxygen to catalyze water.
cytochrome oxidase
_______reactions shuttle electrons through the ETC ending with the reduction of Oxygen to make water
oxidative-reduction
_________ consumes 90% of oxygen we breath
cytochrome c oxidase
electron transfer enables the pumping of __________ into the intermembrane space, from which concentration and charge are used to power __________.
H+ ions; oxidative phosphorylation
A chemoismotic mechanism: H+ ion build up (low cellular pH) drives ATP synthase to catalyze ATP. This is
oxidative phosphorylation
Allosteric inhibition and activation regulate the PFK enzyme (limiting step) through _________ mechanisms.
feedback loop
Electrochemical gradient in inner membrane moves things due to
differential charge and concentration
Plants and animals use _______ which means plants break down sugar for energy and need to make their own sugar.
polysaccharides
What do plant cells have that are unique?
Cell wall (primary-strong and secondary- flexible), vacuole (mostly water), chloroplast, plasmodesmata (channels through wall for proteins and rna)
What is between plant cells?
Middle lamella, made of plectin (like glue)
Vacuoles store _______ as well as uptaking water to provide
toxins, cell waste, defensive substances; turgor pressure
Chloroplast is...
double membrane structure, stacks of internal membrane with specialized pigments
The structural organization of chloroplasts allows for the chemical rxns of _____
photosynthesis
In the middle of a chloroplast is ____
stroma
What are the important regions in the mitochondria?
intermembrane space vs matrix (inside)
What are the three main reactants in photosynthesis?
water, co2, light
What are the products of photosynthesis?
sugar and oxygen
Photosynthesis consists of both _______ and ________
the light reactions and the dark reactions (calvin cycle)
Inside chloroplast:
stroma, thlakoid membranes, granum (Stack of tm)
Photon energy is inversely proportional to....
the size of its wavelength
In photosynthesis, absorbing light energy is accomplished by...
pigments in the granum: excitation of chlorophyll sends electron to higher, less stable state
In photosynthesis, in the reaction center, electrons are __________ from splitting of water and excited by______
donated to chlorofill; photon chain
Photophosphorylation is...?
when energy of electrons is used to make ATP.
In photosynthesis, photosystem 1 and photosystem two each process specific
chlorofill pairs.
In photosynthesis, what happens in photosystem 2?
H+ pumped into thylakoid space, leading to ATP synthesis
In photosynthesis, the ETC of light reactions leads to the activation of enzymes directly involved in the?
Calvin cycle
What is the most abundant protein in the world?
rubisco
Because of the recycling capability inherent in the calvin cycle, 3 CO2 are needed to keep the cycle going and yield just one ____
g3p
___ is the blueprint for the cell. ___ selects which plans get read. ____ are the materials used to build it.
DNA, RNA, proteins
___ is regular, evenly spaced, repetitive, and spiral/helical
DNA
Chargaff's Rule states that the amount of purines in DNA equals the amount of pyrimidines. This means...
in any organism, the amount of A=T, and amount of G=C
The two strands of DNA are __ and __
antiparallel and complementary
What is semiconservative replication?
Each daughter DNA helix is composed of a CONSERVED strand and one newly synthesized strand
New nucleotide is always added onto synthesizing strand on __ end
3'
DNA: Lagging strand is oriented backwards to the fork, so small ____ help build that strand
Okazaki fragments
What is a centromere?
location on the chromosome that binds microtubules and enables movements during mitosis
What is a telomere?
specialized structure that caps the end of a DNA molecule to ensure proper replication and protection (shoelace cap)
What is a nucleosome?
DNA wound around a core of histone proteins (complex of 8)
Heterochromatin(w/ methyl groups) is _____ , while euchromatin has DNA more _____.
tightly packed, exposed
Phosphorylation and acetylation lead to an opening of chromatin, while ___ will condense it.
methylation
Highly transcribed genes are positioned...
at the periphery of chromatin territory adjacent to interchromosomal domains
What is a codon?
Combination of 3 letters (Bases) corresponding to a specific amino acid
Helicase functions to
Separate DNA strands
Primase functions to
facilitate RNA primer and begin replication
DNA polymerase does what?
synthesizes new DNA
When is info packaged in chromosomes?
When the cell is dividing. Otherwise, info in chromatin form
Basic anatomy of chromosome form:
two sister chromatids held together at centromere at different axial positions (short arm: p arm; long arm: q arm)
DNA binds to histones because
DNA has negative charge, histones positive
the fiber composed of nucleosome stacks is called
chromatin
As a cell ages, _____ becomes more prevalent
heterochromatin
A gene is expressed when it is...
made into RNA
A protein is expressed when it is...
made from RNA
DNA to RNA is called transcription. What is RNA to polypeptide called?
translation
Where do replication and transcription occur?
nucleus
Where does translation happen?
cytoplasm
Coding system that governs information flow: What letters are involved in DNA?
A,T,G,C
Coding system that governs information flow: What letters are involved in RNA?
A,U,G,C
Gene anatomy consists of...
begins with promoter region (RNA polymerase binding), initiation sequence, alternating exons and introns, splice sites, initiation and termination sequence
When DNA is transcribed to form RNA, ribonucleotides bind to the exposed strands and are added to the...
3' end of the growing strand
Each cell has the potential to become _________ in a given organism.
any type of cell
Transcription factors are proteins that bind to DNA ____, _____, or even in _______ to influence how transcription will occur.
upstream, downstream, introns
Binding (of the transcription factor to the regulatory DNA sequences) usually occurs in the _______ of the DNA helix.
major groove
H-bonds, ionic bonds, and other weaker interactions are used together to establish these two things between a TxF and a regulatory DNA sequence.
1) very strong interaction
2) extreme specificity
4 common classes of TxFs are?
helix-turn-helix, zinc finger, leucine zipper, helix-loop-helix
Helix-turn-helix motifs regulate genes involved in?
Development
Helix-loop-helix motifs regulate genes involved in?
Immune system
ZInc finger motifs regulate genes that are?
Steroid hormone receptors
Leucine zipper motifs regulate genes involved in?
Cell division
True or false: transcription factors can regulate other transcription factors.
True
Misexpression of just one regulatory gene (TxF) can cause dramatic effects because...
they can turn on and off the transcription of many different genes.
Capping the ends of mRNA serves to do what three things?
Stabilize RNA, aid in its nuclear export, allow it to register with ribosomes as completed mRNA
What is mRNA?
messenger RNA
What does alternative splicing allow?
Creating new/multiple proteins
What is a polysome?
A group of ribosomes clamped into an mRNA strand
Transfer RNA (tRNA) has a specific _______ (that is always paired with a specific anticodon) attached to the 3' end via _______.
amino acid, ATP hydrolysis
What are the four RNA binding sites on a ribosome?
e-site, p-site, a-site on the larger unit; mRNA binding site on smaller unit
Name a start codon.
AUG (away you go!)
What is the first amino acid in the initiation of translation?
Methionine
Name the three stop translation codons.
UAA, UAG, UGA
In translation, what enables just 20 amino acid choices from the 64 possible combinations?
Third base pair domain (wobble)- different ones can code for the same amino acid
What are the letters in codons?
Nucleotides
What helps bring tRNA to the A binding site?
elongation factors
What determines which tRNA can bind next in line (during elongation of translation)?
Codon to anticodon recognition
What is catalyzed by the ribosome through GTP hydrolysis during elongation of translation?
peptide bond formation
Promoter sequence is to DNA as ____ is to RNA
AUG start codon
RNA is to UAA stop codon as ____ is to DNA
terminator sequence
What is the only thing that can bind to a stop codon? (When this happens, the last amino acid is pushed out and the process of translation ends).
A special 'release factor'
The folded structure of a protein just out of a ribosome is usually _____ which means it needs the help of ________.
more open and inaccurate, chaperone molecules
What are two chaperone molecules?
Heat Shock Protein 70, HSP 60
How does HSP70 work?
It uses ATP hydrolysis to fold proteins by binding to exposed hydrophobic residues of unfolded protein.
How does HSP60 work?
Mature proteins that have been misfolded are channeled to HSP60, isolated to prevent aggregation, and corrected.
If a protein isn't correctly folded with help of a molecular chaperone, or digested in the proteasome, it will ______
aggregate
What are proteases?
Enzymes that chew up peptides
How are proteins targeted for DESTRUCTION?
Ubiquitin tags attract ubiq. transporters, which bring proteins to proteasome
Encoded, from DNA, at the 3' end of a protein is a specific __________ that directs where a protein will be transported next.
signal sequence
What are the three types of post-translational processing a protein can undergo?
proteolysis, glycosylation, phosphorylation
What is a silent mutation?
Mutation by substitution in LAST LETTER OF CODON (third base pair wobble- produces same amino acid, doesn't matter)
What is a nonsense mutation?
Mutation by substitution IN THE MIDDLE OF A CODON (UGG->UAG) producing artificial stop
What is a frame shift mutation?
Mutation by insertion or deletion of base pair, throwing off entire codon and altering entire protein