exam 2 specific notes and things

2. first step in glycosis

   1. catalyzed by hexokinase

   2. hexokinase phosphorylates glucose using ATP as the source of the phosphate producing glucose 6 phosphate a more reactive form of glucose

   3. the reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophoic interior of the plasma membrane

   4. Summary of the first step in glycolysis:

      • Catalyzed by the enzyme hexokinase

      • Glucose is phosphorylated using ATP as the phosphate source

      • Produces glucose-6-phosphate, a more reactive form of glucose

      • The phosphorylation prevents glucose from leaving the cell

      • This step effectively traps glucose inside the cell for further metabolism

3. second step of glycolysis

   1. isomerase converts glucose 6 phosphate into isomer fructuose 6 phosphate

   2. isomerase

      1. ensyme that catalyzes the conversion of a molecule into one of its isomers

4. step three

   1. phosphorylation of fructose 6 phosphate catalyzed by the enzyme phosphofructokinase

   2. second ATP molecule donates a high energy phosphate to fructose 6 phosphate → fructose 1,6biophosphate

5. step four

   1. newly added high energy phosphates further destabilize fructose 1,6biophosphate

   2. emloys an exnzyme, aldolase, to transform fructose 1,6biophosphate into two three carbon isomes dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.

6. step 5

   1. isomerase transfomers dihysroxyacetone-phosphate into its isomer glyceraldehyde 3 phosphate

   2. thus the pathway will continue with two molecules of glyceraldehyde 3 phosphate

   3. at this point in the pathway there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule

second half of glycolysis (energy releasing steps)

1. produces two NADH and four ATP molecules per glucose

2. step 6

   1. oxidizes the sugar (glyceralhyde 3 phosphate) extracting high energy electrons that are picked up by the electron carrier NAD+ which then produces NADH

   2. sugar is then phosphorylated by the addition of a second phosphate group → 1,3 biosphosphoglycerate

3. step 7

   1. phosphoglycerate kinase catalyzed 1,3 biophosphoglucerate and then it donates a high energy phosphate to ADP forming one molecule of ATP.

   2. carboxyl group on the 1,3 biophosphoglucerate is oxidezed to a carboxyl group and 3 hosphoglycerate is formed

4. step 8

   1. enzyme called mutase catalyzes 3 phosphoglycerate where the remaining phosphate group moves from the third carbon to the second carbon forming 2 phosphoglycerate

5. step 9

   1. enolase catayzes in this step

      1. causes 2 phosphoglycerate to lose water from its structure

         1. dehydration reaction

      2. results in the formation of double bond that increases potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP)

6. step 10

   1. catalyzed by the enymze pyruvate kinase results in the production of a second ATP molecule

outcomes of glycolysis

1. begins with glucose and produces two pyruvate molecules, four new ATP molecules and two molecueles of NADH

3. last step in glycolysis will not occur is pyruvate kinase is not available in sufficent quantities

   1. in this case the entire glycolysis pathway will proceed but only two ATP molecules will be made in the second half

4. pyruvate kinase is a limiting enzyme for glycolysis

steps in the citric acid cyle

1. step 1

   1. prior to the first step pyruvic acid is converted to acetyl CoA

   2. condensation step that combines the two carbon acetyl group with a four carbon oxaloacetate molecule to form a six carbon molecule of citrate

   3. CoA is bound of sulfhydryl group and diffuses away to eventually combine with another acetyl group

   4. rate of reaction is controlled by negative feedback and the amount of ATP available

      1. if ATP levels increase, rate of reaction decreases

      2. if ATP short supply rate will increase

2. step 2

   1. citrate loses one water molecule and gains another as citrate is converted into its isomer isocitrate

3. step 3

   1. isocitrate is oxidzed producing α-ketoglutarate, along with a molecule of CO2 and two electrons, which reduce NAD+ to NADH

4. step 4

   1. CoA binds with succinyl group to form succinyl CoA

5. step 5

   1. high energy bond is formed and GTP or ATp is formed

6. step 6

   1. dehydration process that converts succinate into fumarate

   2. FAD become FADH2 remains attached to the enzyme and transfer the electrons to the electron transport chain directly

7. step 7

   1. water is added and malate is produced

   2. malate oxidized creating NADH and the cycle repeats

products of the citirc acid cycle

1. two carbon atoms from acetyl group (represents 4 out of the 6 carbon of one glucose molecule

2. forms 3 NADH moleucles and on FADH2 molecules and one GTP or ATP

3. cycle products then can produce nonessential amino acids

4. cycle is amphibolic

   1. both catabolic and anabolic

cellular respiration ameoba sisters

1. photosynthesis create glucose and cellular respiration breaks the glucose down to make ATP

   1. plants can do both

2. humans can’t do photosynthesis need food for the glucose to do cellular respiration

3. steps of cellular respiration

   1. glycolysis

      1. takes place in the cytoplasm and does not require oxygen (aneorbic)

      2. changes glucose into pyruvate which is a more usable form

      3. one glucose creates 2 pyrvuates, 2 atp and 2 NADH (conenzyme that transfer electrons used to make more ATP

   2. intermediate step

      1. pyrvuate transported into mitochondria

      2. transforms pyruvate into acetyl CoA where carbon dioxide is released and 2 NADH is produced

   3. kreb cycle (citric acid cycle)

      1. happens still in the mitochondria (areobic process needs oxygen for some of the processes happening in the kreb cycle)

      2. carbon dioxide is released and 2 ATP, 6 NADH and 2 FADH2 are produced

      3. FADH2 is a coenzyme that transfers electrons too

   4. electron transport chain and chemiosmosis

      1. makes the most ATP

         1. happens inside the inner mitochondrial membrane and requires oxygen for this step (aerobic)

         2. electrons are transferred from the NADH and the FADH2 to protein complexes and electron carriers

         3. electrons are used to generate a proton gradient as protons are pumped to the intermmebrane space

            1. generates an electrial and chemical gradient

            2. protons travel through the enzyme ATP synthase

               1. makes ATP by adding a phosphate to ADP

         4. in chemiosmosis protons travel down their electrochemical gradient through a portion of the ATP synthase powering it to make ATP

         5. oxygen is the final acceptor of the electrons and when oxygen combines with two hydrogens you get H2O water

fermemtation ameoba sisters

1. ATP has the ability to power many cellular processes

2. bacteria, archaea, yeast, and muscle cells, and many more

   1. handle the lack of oxygen in different ways

      1. some go through the steps of cellular respiration but instead of using oxygen for the electron transport chain they use a substitute

      2. some others use fermentation

         1. handle little to no oxygen issues, allows glycolysis to happen and for it to keep going

3. fermentation adds another step to glycolysis to regenerate nad+

   1. allows NADH to give its electrons to an electron acceptor

4. alcoholic fermentation

   1. glycolysis happens

   2. between the reactants and the prodcuts 2 acetaldehyde is produce and can act as an electron acceptor so that NADH can be oxidized to NAD+ therefore it can go through the glycolysis cycle again

   3. pyruvate creates to CO2 and 2 ethanol (ethanol is a waste)

5. lactic acid fermentation

   1. used by muscles if there is insufficent oxygen in the body

   2. also done by bacteria used in making yogurt resulting in the sour taste

   3. goes through glycolysis

      1. pyruvate is produce and then from that two lactate is produced

      2. pyruvate can act as an electron acceptor so that NADH can be oxidized into NAD+

6. cannot make as much ATP as cellular respiration

photosynthesis ameoba sister

1. plants make their own glucose in photosynthesis

2. takes in carbon dioxide and water and produces oxygen and glucose

3. pigments that plants use to capture light is chlorophyll

   1. chlorophyll abosrobs red and blue light, relfects green light hence plants mostly look green

   2. found in chloroplast

      1. two major process that occur inside the chloroplast that together make up photosynthesis

         1. light dependent reactions

            1. happen in the thylakoid

            2. takes in light and water but the water is split (electrons protons and oxygen)

            3. produces atp and nadph (used for calvin cycle)

         2. light indepedent reactions (calvin cycle)

            1. happen in the stromaa

               1. takes in carbon dioxide, atp and nadph

               2. carbon dioxide enters through the stomata

               3. atp acts as energy currency for the calvin cycle

               4. nadph is used for reducing power, add high electrons to the process

               5. produces glucose

cell cycle and cancer ameoba sisters

1. cancer happens cause cells divide too quickly, the cells are not regulated, they are non control

2. genetic links

3. uncontrolled growth that cancer cells have gives rise to more cells like them which can develop into a tumor

4. radiation and chemotherapy as solution to curing cancer

5. cell cycle

   1. interphase

      1. where cells are growing, replicating their DNA, doing cell functions

      2. where most of the cells spend their time

      3. g0

         1. cells perform cell functions but they are not preparing to divide

         2. some cells stay here temporarily some stay there permanenetly

      4. g1

         1. where the cell grows

         2. checkpoint here that checks if the cell is growing well enough, is the DNA damanged, does it have enough resources to move on

      5. synthesis

         1. replicating its DNA

      6. g2

         1. cell grows some more in preparation for mitosis (m phase)

         2. checkpoint here checks if the DNA was replicated correctly, is it growing well enough, does it have enough resources to continue?

   2. m phase

      1. where cells divide to make more cells (mitosis)

      2. checks after the metaphase stage to make sure that chromosomes are lined up in the middle correctly, that they are all lined up in the spindle correctly

   3. checkpoints

      1. check that the cell is growing correctly, replicating DNA correctly and doing everything its supposed to be doing correctly before it divides

      2. positive regulators

         1. allows cells to continue

         2. CDK (cyclin dependent kinase) and cyclin

            1. each cell cycle phase will have a different cyclin that binds with the CDK

      3. negative regulators

         1. makes things stop

         2. p53

         3. iniates apoptosis

   4. apoptosis

      1. cell self distructs if it cant pass the checkpoint and can’t be fixed to pass the checkpoints

      2. ensured that irreparable cells will not divide

mitosis ameoba sissters

1. type oc cell divison done by most of the body cells

2. produces body cells and identical cells

3. cells are not dividing all the time

4. inside each nucleus there are 46 chromosomes

5. centromere

   1. part of the chromosomes where sister chromatids are held together

   2. chromatid

      1. stand of replicated chromosomes

6. pmat

   1. prophase

      1. chromosomes are condensing (thickening and visible)

   2. metaphase

      1. middle, chromosomes line up in the middle of the cell, nucleus is disassembled

   3. anaphase

      1. away, the chromosomes move away, they are moving to the opposite sides of the cell, moving to the poles of the cell

      2. move with spindles that are fibers that help move the chromosomes away

   4. telophase (two)

      1. chromosomes are at the opposite ends of each other and new nuclei are forming on each side to make the two new cells

   5. cytokensis

      1. responsible for the final separation into two cells by splitting the cytoplasm which completes after the pmat process

meiosis

1. contibutes to genetic variety

2. makes sperm and egg cells (gametes)

   1. each have 23 chromosomes

3. reuduction division

4. interphase happens before process starts same as in mitosis

5. count chromosomes based on how many centromeres are present

6. pmat 2x

   1. put numbers after the phases to indcate if you are in the first or second diviso

   2. prophase 1

      1. before, where chormosomes condense and thicken and where the chromosomes line up with their homologous pairs

      2. homologos chromosomes

         1. chromosomes are approximately the same size and they contain the same type of genes in the same location

      3. crossing over

         1. chromosomes combine and tranfer their genetic information to each other

         2. creates recombinant chromosomes

   3. metaphase 1

      1. middle, chromsomes are in the middle of the cell in pairs

   4. anaphase one

      1. chromosomes are pulled away from each other onto opposite sides by the spindle fibers

   5. telaphase one

      1. forms nucleus over each other

      2. cytokensis happens where cytoplasm splits and then creates two new cells

   6. prophase 2

      1. no crossing over

   7. metaphase 2

      1. chromosomes line up in the middle but not in pairs anymore

   8. anaphase 2

      1. chromatids pulled away to the opposite sides of the cell

   9. telaphase 2

      1. nuclei reforming and the two cells will divide creating 4 cells

      2. cytokinesis then splits the cytoplasm

7. ending cells have 23 chromosomes therefore leading to variety

photosynthesis crash course

1. light dependent reactions

   1. photon that comes from the sun goes into chlorophyll and it gets excited

   2. photosystem 2

      1. first protein complex of the light dependent reaction

      2. in the thylakoid membrane of the chloroplast

      3. absorbs light (aka captures the photons) then uses the energy to extract electrons from the water molecules to ‘replace’ the electrons that they loss releasing oxygen in the process

      4. energized electrons from psii are picked up by electron carriers and are transported to the cytochrome complex

   3. cytochrome complex

      1. intermediate step between psii and psi

      2. uses the electron energy to pump another proton into the thylakoid

         1. used to charge the thylakoid by creating a concentration gradient

            1. protons then want to get away from each other and then push their way through ATP synthase (enzyme) which then makes ATP

   4. psi

      1. same as psii but has different products

      2. excited electrons from cytochrome complex go to psi and then the electrons get carried in an electron protein carrier and then the electron goes to another place in which NADPH is created

2. stage 2/ calvin cycle

   1. starts in the stroma (empty space of the chloroplast)

   2. called carbon fixation

      1. fix carbon onto ribulose biphosophate (RuBP) woth the help of RuBisCo

         1. becomes super unstable and then so it breaks apart into 2 molecules of 3 phosphoglycerate

         2. done to three rubp

   3. reduction

      1. atp adds phosphate group to the 3 phosphoglycerate then NADPH transfers electrons to them and then 2 molecules of glyceraldehyde 3 phosoate (g3p)

         1. used to make any carbohydrate

      2. need 5 g3p to regenerate3 rubp

   4. 3 rubp creates 6 g3p but only one makes it out of the cycle and the 5 g3p are used to remake the 3 rubp to start the cycle all over again

   5. regeneration

      1. where 5 g3p turns back into 3 rubp

cellular respiration and ATP crash course

1. glucose and 6 molecules of oxygen produces 6 water 6 carbon and energy

2. atp

   1. made up of adenin, ribose and three phosphate groups

      1. when phosphate releases energy is relasese and oh group combines and takes place of that release phosphate group

3. glycolysis, kreb cycle and electron transport chain

4. glycolysis

   1. breaking down of the glucose into 2 3 carbon molecules into pyruvate

   2. needs two ATP but makes 4 ATP and 2 pyruvate and 2 NADH

   3. occurs in the cytoplasm

5. if no oxygen the pyryvates go through fermentation which frees up some NAD+

6. kreb cycle

   1. happens in the inner membrane of the mitochondria

   2. takes the pyruvates and make 2 atp per glucose molecule and energy

   3. pyruvate is oxidized

      1. on of the carbons comes off the 3 carbon chain and bonds with an ocygen molecule and leaves the cell as co2 and then what remains is acetyl CoA

      2. happens before kreb cycle

      3. nad+ picks up an h and creates NADH

   4. FADH2 is created

   5. citric acid created, but it also breaks down to make it a cycle

7. electron transport chain

   1. NADH and FADH2 produced by the kreb cycle provides the energy that will work as a pump along a chain of channel proteins across the inner memebrane of the mitochonria

   2. the protiens will swap the electrons to send hydrogen protons from inside the center of mitochondria across the inner membrane to the outside

   3. protons that were put out are let back in through ATP synthase which then creates ATP

free energy: determines if reactions are exergonic (g<0) or endergonic (g>0)

inhibitors or changes in pH and temp affect enzyme activity

metabolic pathways: linked reactions form pathways, where products become reactants in the next step, enabling complex biochemical transformations

3 NADH molecues are produced on each turn of the citiric acid cycle, also produces 1 ARP 1 FADH2 and 2 CO2

cellular respiration stages

1. glycolysis (cytoplasm)

   1. breaks down glucose into pyruvate produces net gain of 2 ATP and 2 NADH

   2. uses glucose as input

2. pyruvate oxidation (mitochondria)

   1. converts pyruvate to acetyl Coa and prdocues NADH and CO2

3. citric acid cycle (kreb cycle)

   1. mitochondira

   2. 2 acetyl CoA molecules → 2 ATP 6 NADH 2 FADH2 and 4 CO2

4. oxidative phosphorylation (mitochondrai)

   1. incolves etc and atp synathase

   2. nadh and fadh2 and oxygen → atp and water

when oxygen is limited cell can use alternative electron acceptors for atp production or use fermentation

electron transport cahing

1. proton gradient is created when electrons move though the etc which drives atp synthesis through atp synthase

2. atp synthase convers the energy of the proton gradient into atp as protons flow back into the mitochondrial matric \

high energy state are referring to the energy electron carriers

co2 is the essential molecule that must continuously enter the calvin cycle for it to proceed

histone are proteins that help organize and package dna into structural units called nucleosomes, essential for compacting the dna to fit within the cell nucleus

centrosome is the main microtuble organizing center of the cell, its where the mitotic spindles originate during ccell division

prometaphase is where the nuclear envelope breaks down allowing spindle fibers to reach the chromosomes

proto oncogene: normal genes that code for proteins invovled in cell growth and division

mutated forms of proto oncogenes that have the potential to caues cancer causes cdk to be active without cyclin mimics the action of a normal positive regulator