Term
| DNA polymerase is ____ correcting |
|
Definition
|
|
Term
| the enzyme ______ cleaves mismatched nucleotides by __ to ___ proofreading |
|
Definition
| the enzyme nuclease cleaves mismatched nucleotides by 3 to 5 proofreading |
|
|
Term
| a short _____ provides a ____-prime end for a DNAP to start on |
|
Definition
|
|
Term
| what enzyme synthesizes RNA primer? |
|
Definition
|
|
Term
| What is the function of Single Strand Binding Protein? |
|
Definition
| to bind to the DNA exposed by helicase, preventing it from reforming base pairs. |
|
|
Term
| what does the sliding clamp do? |
|
Definition
| keeps the polymerase attached to the template by forming a ring around the DNA |
|
|
Term
| telomerase adds a series of _____ to the ______ end |
|
Definition
|
|
Term
| the ____ system corrects nucleotide mistakes made by the _____ |
|
Definition
| DNA mismatch repair system, DNAP |
|
|
Term
| When does DNA change? (give two examples of changes) |
|
Definition
| all the time. deamination, depurination |
|
|
Term
| what fixes up the sugar-phosphate backbone? |
|
Definition
|
|
Term
| what are the cons of the most common DNA repair system? |
|
Definition
| The cons of nonhomologus end-joining are deletion of information. |
|
|
Term
| homologus recombination uses |
|
Definition
|
|
Term
| when is homologus recombination possible? |
|
Definition
| shortly after the dna is replicated |
|
|
Term
|
Definition
|
|
Term
| are all viral genomes DNA? |
|
Definition
|
|
Term
| What makes RNA less stable than DNA? |
|
Definition
|
|
Term
| why does the citric acid cycle need oxygen? |
|
Definition
|
|
Term
| what are the proteins in the ETC? |
|
Definition
| NADH hydrogenase complex, cytochrome b-c1 complex, cytochrome oxidase complex |
|
|
Term
| can large, uncharged polar molecules move across the membrane by simple diffusion? |
|
Definition
|
|
Term
| can ions pass through the membrane by diffusion? |
|
Definition
|
|
Term
| passive facilitated transport is driven by... |
|
Definition
| concentration and electrochemical gradient |
|
|
Term
| coupled transporters are an example of _____ transport |
|
Definition
|
|
Term
| net force of concentration and charge potential is called... |
|
Definition
|
|
Term
| what are the three types of active transporters? |
|
Definition
| ATP-pumps, Light-pumps, Coupled Transporters |
|
|
Term
| Transmembrane channels allow ______ solutes (mostly ions) to pass |
|
Definition
|
|
Term
HYDROPHYLIC transmembrane channels (i.e., pores lined with
____________________) |
|
Definition
| charged or polar amino acids |
|
|
Term
Five types of transmembrane channel
proteins: |
|
Definition
porins, aquaporins, gap
junctions, plasmadesmata, and ion channels |
|
|
Term
what transmembrane protein has...
large pore with low specificity
iii. nucleoporins |
|
Definition
|
|
Term
NAME ME
most small intracellular signaling molecules and ions
pass freely; propagation of signal through
tissues; cytoplasm between cells are connected;
cell to cell communication.
iii. regulation of (opening and closing) through
extracellular signals |
|
Definition
|
|
Term
i. smaller pore size than previous
channels
ii. the selectivity involves size of the
pore and distribution of charged
amino acids in pore
iii. found mostly in plasma membrane
iv. rate of transport can be very fast:
a single channel can conduct
almost one million ions per sec
vii. stimuli that regulate channels:
a. voltage-gated channels: changes in
electrical potential across a membrane
b. ligand-gated channels: controlled by
the binding of specific ligand (e.g.,
hormone, secondary messenger) |
|
Definition
|
|
Term
: open and close in response to mechanical
forces that act on membrane (e.g., stretch-activated; e.g., sound strikes
auditory hair cells, vibrations stretch ion channels, ions follow into hair
cells, electrical signal sent to brain and preserved as sound) |
|
Definition
| mechanosensitive channels |
|
|
Term
| cells obtain energy through (oxidation/reduction) |
|
Definition
|
|
Term
| glucose breakdown formula and G |
|
Definition
Glucose + o2 > CO2 + h2o
G neg |
|
|
Term
| formula for breakdown of ATP and G |
|
Definition
ATP + H20 > ADP + Pi
G neg |
|
|
Term
|
Definition
1.substrate-level phosphorylation: couple synthesis to food oxidation
2.Oxidative phosphorylation from NADH in mitochondria |
|
|
Term
| where does glycolysis happen? |
|
Definition
|
|
Term
| where does the Citric Acid Cycle happen? |
|
Definition
|
|
Term
| what is put INTO the citric acid cycle? |
|
Definition
|
|
Term
|
Definition
| partial oxidation of glucose in the absence of oxygen |
|
|
Term
| how many ATP and NADH come out of glycolysis? |
|
Definition
|
|
Term
| what is step 6 of glycolysis? |
|
Definition
| 6- glyceraldehyde-3-phosphate is oxidized by NAD and Pi, to 1,3-biphosphoglycerate, releasing NADH |
|
|
Term
| functions of the phosphate groups on sugars (3) |
|
Definition
- membrane impermeability
- binding or recognition by enzymes
- becoming the terminal group in ATP conserves energy |
|
|
Term
| is step 6 or 7 of glycolysis energetically favorable? |
|
Definition
|
|
Term
| what is step 7 of glycolysis? |
|
Definition
1,3 biphosphoglycerate + ADP > 3-phosphoglycerate + ATP
substrate-level phosphorylation |
|
|
Term
| what comes out of glycolysis (apart from energy molecules) |
|
Definition
|
|
Term
| in the absence of oxygen, pyruvate .... |
|
Definition
|
|
Term
| what's the difference between glycolysis with oxygen and without? |
|
Definition
| without, the process stops at lactate. With, it goes to CO2 and water. |
|
|
Term
| in what part of the mitochondria is CoA produced by oxidation / the Citric Cycle happening? |
|
Definition
|
|
Term
| Pyruvate produced by glycolysis moves to the mitochondrial matrix and is decarboxylated by the enzyme complex called |
|
Definition
| pyruvate dehydrogenase complex |
|
|
Term
| pyruvate to acetyl CoA is catalyzed by ... |
|
Definition
|
|
Term
| name the most important plastid |
|
Definition
|
|
Term
| why do we think chloroplasts & mitochondria are old bacteria? |
|
Definition
| cristae and thylakoid membranes, double membranes |
|
|
Term
| name the space in which the thylakoids are suspended |
|
Definition
|
|
Term
| what is the chloroplastic stroma analogous to? |
|
Definition
|
|
Term
| differences between thylakoid and cristae |
|
Definition
1. stacking patterns
2. cristae are really invaginations of membrane, thylakoid is ...?
3. chloroplast are pigmented |
|
|
Term
| what is one stack of thylakoids? |
|
Definition
|
|
Term
| immediate end-product of photosyn |
|
Definition
| glyceraldehyde 3 phosphate |
|
|
Term
| light creates ATP and _____ |
|
Definition
|
|
Term
| NADPH : high-energy electron _____ used in ______ reactions |
|
Definition
| electron donor, reductive biosynthetic |
|
|
Term
|
Definition
| a product of photosyn which is not understood |
|
|
Term
| what is the first step of the light rxns? |
|
Definition
| light excites electrons in the chlorophyll |
|
|
Term
| what happens after light excites the electrons? |
|
Definition
| they go through the electron transport chain in the thylakoid membrane |
|
|
Term
chloroplast electron flow pumps...
... in order to... |
|
Definition
| H+, in order to create electrochm proton gradiant, creates ATP in stroma |
|
|
Term
| _____ are analogous to the citric acid cycle |
|
Definition
|
|
Term
| where does the energy for CO2 carbon fixation (dark, stroma) come from? |
|
Definition
| ATP and NADPH from light rxns |
|
|
Term
| what is the final product of photosyn |
|
Definition
| glyceraldehyde 3 phosphate |
|
|
Term
| name the 2 major parts of the photosystem complex |
|
Definition
central rxn center
surrounding antenna complex |
|
|
Term
| within 10nm a molecule can .... |
|
Definition
| transfer electrons via FRETTING |
|
|
Term
| within rxn center, chlorophylls are .... |
|
Definition
|
|
Term
| on the top of PS2 is the... |
|
Definition
|
|
Term
| once chlorophyll loses its electron, the water in PS2 reduces it to |
|
Definition
|
|
Term
| how are PS1 and PS2 the same? |
|
Definition
| absorb photon, FRET, use water-split e- to reduce chloro? |
|
|
Term
| where do the dark rxns take place? |
|
Definition
|
|
Term
| where do the light rns take place? |
|
Definition
|
|
Term
| how does the citric acid cycle start? |
|
Definition
| acetyl is transferred to Oxaloacetate (making citric acid) so that it can be reduced in many small steps. |
|
|
Term
| One turn of the citric acid cycle produces: |
|
Definition
| 3 NADH + 1 FADH2 + 1GTP + 2 CO2 |
|
|
Term
| how does ATP come out of the citric acid cycle? |
|
Definition
| GTP gives its phosphate to an ADP |
|
|
Term
| Blue and red light is absorbed primarily by ..... |
|
Definition
|
|
Term
| ______ can function only as part of large ____________________ called photosystems = DEFINE |
|
Definition
Chlorophylls, multi-protein
complexes ,
antenna and photochemical
reaction center |
|
|
Term
|
Definition
a cluster of chlorophyll and accessory
(e.g., carotenoids) molecules that absorb light energy and
pass ‘virtual photons’ to the photochemical reaction center |
|
|
Term
| in PS, when is atp synthesized? |
|
Definition
| -ATP is synthesized after the first photon is absorbed by PS II |
|
|
Term
| in PS, when is NADPH synthsized? |
|
Definition
| -NADPH is synthesized after the second photon is absorbed by PS I |
|
|
Term
•An electron that is removed from a chlorophyll molecule in the reaction center of
PS II travels all the way through the electron-transport chain in the _____ until it is donated to NADPH |
|
Definition
|
|
Term
| ATP and NADPH from light reaction are used to _____ in the ____ |
|
Definition
| fix carbon (=Calvin cycle) |
|
|
Term
| what is the first reaction of the calvin cycle? |
|
Definition
| carbon dioxide combines with 5-carbon sugar and water to make two molecules of 3-phosphoglycerate |
|
|
Term
| what is the first reaction of the calvin cycle? |
|
Definition
| carbon dioxide combines with 5-carbon sugar and water to make two molecules of 3-phosphoglycerate |
|
|
Term
| what is the first reaction of the calvin cycle? |
|
Definition
| carbon dioxide combines with 5-carbon sugar and water to make two molecules of 3-phosphoglycerate |
|
|
Term
| what is the first reaction of the calvin cycle? (catalyzed by rubisco) |
|
Definition
| carbon dioxide combines with 5-carbon sugar and water to make two molecules of 3-phosphoglycerate |
|
|
Term
Rubisco is a very ____ acting enzyme, thus there is a ______ number of rubisco
complexes in stroma |
|
Definition
|
|
Term
| •Rubisco reactions are energetically favorable because of _____ |
|
Definition
| the continual source of the energy-rich ribulose 1,5-bisphosphate……how is this molecule generated? |
|
|
Term
| In the calvin cycle •For every three molecules of carbon dioxide one new molecule of _______ is produced |
|
Definition
| glyceraldehyde 3-phosphate |
|
|
Term
| Oxidative phosphorylation: |
|
Definition
| Production of ATP that is driven by electron transport in the mitochondrial inner membrane. |
|
|
Term
what is “substrate-level”
phosphorylation. |
|
Definition
| the coupling of ATP syn to food oxidation |
|
|
Term
| what is oxidative phosphorylation? |
|
Definition
| the process by which ATP is created from NADH |
|
|
Term
| where does oxidative phosphorylation take place? |
|
Definition
|
|
Term
| The transport of electrons along the inner mitochondrial membranes generates an ________ which is used for _______ |
|
Definition
| electrochemical proton gradient, the synthesis of ATP |
|
|
Term
| what is Chemiosmotic coupling ? |
|
Definition
| - the process of ATP synthesis based on the energy of proton gradient which is formed as a result of the electron transport in membranes. |
|
|
Term
| what are the two steps of chemiosmotic coupling? |
|
Definition
1. series of ECT reactions in mitochondria pumping out H+
2. H+ coming back in through ATP synthase |
|
|
Term
| what did Mitchell create? |
|
Definition
|
|
Term
| the inner mitochondrial membrane is |
|
Definition
|
|
Term
| what is cardiolipin and what does it do? |
|
Definition
Cardiolipin is a “double” phospholipid that contains four fatty acids.
It helps to make the membrane especially
impermeable to ions. |
|
|
Term
| what is the final electron acceptor? |
|
Definition
|
|
Term
| Electron transport begins when a __________ is removed from NADH and is converted into a proton and two high-energy electrons. This reaction is catalyzed by the ________ which accepts electrons. |
|
Definition
| hydride ion, NADH dehydrogenase |
|
|
Term
| Mitochondria: the pH is ______ in the matrix than in the intermembrane space. |
|
Definition
|
|
Term
| name the order of the 3 protein complexes in the ETC |
|
Definition
| NADH dehydrogenase complex, cytochrome b-c complex, cytochrome oxidase complex |
|
|
Term
|
Definition
| put a hole in the membrane, thus uncoupling ATP from ETC |
|
|
Term
|
Definition
|
|
Term
|
Definition
| insufficient breakdown of sphingolipids |
|
|
Term
Sphingolipids
are derived from ? |
|
Definition
|
|
Term
| what sort of lipid is found in neural tissues? |
|
Definition
|
|
Term
|
Definition
| lipids with a carbon headgroup, found outside the cell forming the glycocalyx. |
|
|
Term
|
Definition
| recognition and protection |
|
|
Term
| what's the difference between glycoproteins and proteoglycans? |
|
Definition
| proteoglycans have longer sugar chains. |
|
|
Term
| do choloroplasts or mitochondria have cholesterol? |
|
Definition
|
|
Term
| where do phospholipids start out, and where do they go with what enzyme? |
|
Definition
| start out from ER, get into the cytosolic layer of the bilayers, then flipase flips them around. |
|
|
Term
|
Definition
| freefloating areas of elevated levels of cholesterol, protein, and sphingolipids. Organizing centers. |
|
|
Term
| what are the 4 jobs of proteins in the bilayer? |
|
Definition
| anchors, enzymes, receptors, transporters |
|
|
Term
|
Definition
the major protein forming the cortical network supporting the
membrane through connections with specific transmembrane proteins and
associated proteins |
|
|
Term
| what proved lateral diffusion in the lipid layers? |
|
Definition
FRAT - recovery after bleaching
Hybridization of cells |
|
|
Term
| unsaturated fatty acid tails _____ fluidity in the membrane |
|
Definition
|
|
Term
| RNA can have ______ and ______ functions (whereas DNA functions solely as an information store) |
|
Definition
|
|
Term
| ______________ polymerase contains a subunit called the sigma factor that recognizes the promoter• |
|
Definition
|
|
Term
| in ____________ RNA polymerase require transcription factors, which must assemble at the promoter with the polymerase prior to transcription |
|
Definition
|
|
Term
| Two processing steps that occur only on transcripts destined to become mRNA: |
|
Definition
1.
RNA capping (= chemical modification of nucleotides)
2.
RNA polyadenylation (=addition of nucleotides) |
|
|
Term
| RNA is capped by the addition of a ____________ |
|
Definition
| guanine nucleotide with a methyl group attached |
|
|
Term
| snRNPs form the core of the ____________ |
|
Definition
|
|
Term
| Mitochondrial precursor proteins ________ into their native structures after they are synthesized on ribosomes: |
|
Definition
|
|
