Molecules and Cells Unit 2 exam

chemical reaction

a process that leads to the transformation of one set of chemical substances to another

reactants

the starting materials of a reaction

products

the resulting materials of a reaction

metabolism

sum of all the reactions occuring inside the cell of an organism

anabolic

small molecules assemble into large ones with an input of energy

catabolic 

large molecules break down into small ones with an output of energy 

energy

capacity to do work or supply heat

what are the two types of energy?

potential and kinetic

potential energy

stored energy; in biochemistry, this is essientially electrons adn their positions within molecules 

kinetic energy

energy of movement; thermal energy or heat are forms of kinetic energy

Where do electrons have the most potential energy

electrons in an outer shell have more potenital energy than do electrons in an inner shell

first law of thermodynamics 

conservation of energy; energy can not be created or destroyed  

second law of thermodynamics

the universe has a tendency to become more disordered

what are the two diffrerent energy changes

1) enthaply (internal, potential energy = delta H) 2) entropy (disorder = delta S)

Gibbs free energy equation and what it means 

delta G = delta H - T delta S; tells whether the reaction is favorable or not 

what does different delta G means

delta G < 0 = exergonic “spontaneous” reaction

delta G > 0 = endergonic reaction that requires energy

delta G = 0 = reaction is at equilibrium

transisiton state theory

during a chemical reaction, there is an intermediate molecular form in which old and new covalent bonds are partially formed; here the reaction has the highest energy than either the reactants or products

activation energy 

the required energy needed for a chemical reaction to happen 

enzymes

bind to substrates in precise orientation so that the electrons involved in the reaction interact perfectly; lowers the energy needed to arrive at the transition state, thereby speeding up the rate of the reaction

catalyst

speeds up a chemical reaction but does not change delta G and is not consumed in the reaction

active site 

the place where substrates bind to in an enzyme that is usually evolutionarily conserved; when the substrate binds to the enzyme’s active site, the enzyme changes shape slightly, called induced fit which results in tighter binding of the substrate to the active site 

energetic coupling

favorable reaction uses it to fuel an unfavorable reaction (completely anlogous to coupled transport)

competitive inhibitor

bind to active site preventing a substrate from binding

alloseteric activator 

bind at some site on a protein that changes the shape of the enzyme to allow the substrate to attach 

alloseteric inhibitor

bind at some site on a protein that changes the shape of the enzyme to prevent a substrate from attaching

pathway

used to refer to a series of chemical reactions needed to get from oen useful molecule to another

feedback regulation

occurs when the amount of a product controls the activity earlier in the pathway

oxidation

loss of electrons, loss of H atoms, or gain of bonds to O 

reduction

gain of electrons, gaining bonds with H or losing bonds to O

cellular respiration equation and define

process of extracting the energy from energy-rich food molecules to produce ATP (glucose + O2 —> CO2 + H2O + energy

what are the four parts of cellular repsiration

glycolysis, pyruvate processing, citric acid cycle, electron transport chain

glycolysis breakdown (where, inputs, outputs, etc) 

happens in the cytoplasm, starts with the ATP investment phase where glucose (6C) gets split into two 3C sugars with the input of 2 ATP and output of ADP, next is the cleavage phase where the phosphate groups are removed, then the two 3C sugars are moved to the ATP payoff phase where 2 NAD+ is reduced to NADH and 4 ADP are turned into ATP finally Pyruate is formed (this step is doubled because two 3C sugars go through the process) 

pyruvate processing breakdown (where, inputs, outputs, etc)

occurs as soon as pyruvate (3C) is transported into the mitochondrion, inputs: NAD+ and coenzyme A, outputs: CO2 (the lost C) and NADH to form a finally product of Acetyl-CoA (2C) 

citirc acid cycle breakdown (where, inputs, outputs, etc)

acetyl CoA enters the citric acid cycle, which occurs in the mitochondrial matrix; it starts with a 2C molecule (acetyl CoA) that gets added to oxaloacetate to become a 6C molecule citric acid/citrate; inputs: NAD+, ADP, FAD; outputs: 2 CO2, NADH, FADH2, ATP, creating a 4C sugar that gets regenerated again to form oxaloacetate once again (oxidizes acetyl CoA to CO2)

electron transport chain breakdown (where, inputs, outputs)

an electron moves from complex I to coenzyme Q to complex II to coenzyme Q to complex III to cytochrome C to complex IV to O2 which is the ultimate electron acceptor; complex I reduces NADH to NAD+, complex II oxidizes; the complexes pump protons creating a proton gradient that powers ATP synthesis  

chemiosmosis

using the proton gradient to make ATP

oxidative phosphorylation

cellular process that harnesses the reduction of oxygen to generate high-energy phosphate bonds in the form of adenosine triphosphate

substrate-level phosphorylation  

when a phosphate is transferred from a substrate to ADP or GDP to form ATP or GTP, coupled with the release of free energy, occurs in glycolysis and critic acid cycle 

Do carbon atoms get reduced or oxidized

During respiration, carbon atoms from food molecules are oxidized

Do oxygen atoms get reduced or oxidized

because energy-depleted electrons are ultimately given to oxygen, oxygen is reduced

why does fermentation happen and what are the two types

happens when there is no oxygen in the cell; lactic acid and alchol

lactic acid fermentation

happens in humans, glucose is turned into 2 pyruvate molecules with the input of 2 ADP that get made into ATP and 2 NAD+ that get made into NADH, then with no intermediate, pryuvate accepts electrons from NADH to form 2 lactate

alcohol fermentation 

happens in yeast, glucose is turned into two pyruvate molecules with the inputs of 2 ADP, that is changed into 2 ATP and 2 NAD+ that is changed into 2 NADH which is reduced, with the release of 2 CO2 and the creation of 2 acetylaldehyde that is reduced to 2 ethanol is created

photosynthesis equation and define

CO2 + H2O + energy —> glucose + O2; biochemical process for building carbohydrates from sunlight and carbon dioxide taken from the air

chloroplast

enclosed by a double membrane, a highly folded membrane known as the thylakoid membrane, and they are grouped into flattened sacs called grana, the area inside thylakoid membrane = thylakoid lumen

stroma 

are between thylakoid membrane and the inner membrane, location of Calvin cycle 

chlorophyll

lipid embedded in complexes called photosystems in the thylakoid membrane, reflects yellow-green light that makes it visible to human eyes 

photosystem

collection of proteins and pigments (chlorophyll) wherein electrons are energized by a photon and en e- transport chain is initiated

how is light absorbed by chlorophyll

The excited state of an electron can be passed to neighboring chlorophylls by a process called resonance

process of the light reaction 

light hits photosystem II (water is split here as well) then pass the energized electron to a lipid called plasto quinone then the elctron get passed to cytochrome complex then to a moelcule in the thylakoid lumen to photosystem I where light is hit again the electron get passed more to another complex that turns NADP+ to NADPH, this process creates a proton gradient that makes ATP synthase run to produce ATP from ADP and phosphate 

three steps of the calvin cycle or dark reaction

carboxylation, reduction, regeneration

carboxylation (calvin cycle)

CO2 dissolves from the air added to 5C molecule (ribulose-1,5-biphosphate = RuBP) by Rubisco. The 6C molecule formed is broken down into two 3C molecules of 3-phosphoglycerate

reduction (calvin cycle) 

High-energy electrons from NADPH reduce 3-phosphoglycerate to triose phosphate, and coupling ATP hydrolysis makes the reaction exergonic; rubsico must be reduced so NADPH is oxidized 

regeneration (calvin cycle)

5 of 6 triose phosphates made in the carboxylation and reduction phases are rearranged to generate 3 RuBPs

general rules of cytoskeleton assembly

size (can be huge, any size we want), dynamic(can make fibers or deconstruct fibers as needed), subunits( globular proteins or fibrous proteins), regulatory proteins (many that control the cytoskeleton)

three major types of cytoskeletal fibers 

microtubules, microfilaments, intermediate filaments

polarity

wheen microtubules and microfilaments have a positive and negative ending

motor proteins

uses ATP hydrolysis to move relative to the cytoskeletal fiber, binds to the fiber

motor protein of microfilaments 

Myosin, they move to the positive end of microfilaments 

motor proteins of microtubules

dynein moves to the minus end that faces the centrosome, and kinesin moves to the positive end that faces the plasma membrane 

actin functions

cell shape, crawling, and contraction; concentrated under the plasma membrane; allow eukaryotic cells to adopt a variety of shapes and perform a variety of functions; important in muscle contration and cytokinesis

muscle contration

each myosin head “attempts to walk” toward the positive ends of the thin filaments to which they’re attached, resulting in shortening of the sarcomere

microtubles function

cilia and flagella, which specialize in microtubules and dynein structures, distributing chromosomes during cell division, membrane transport and organelle localization, they emanate from the centrosome near cell center

intermediate filaments functions

stretch throughout the cell plasma membrane to the plasma membrane, the nuclear lamina is assembled from intermediate filaments, specifically lamins

cell division 

cell reproduction, cell doubling 

cell proliferation

population of cells actively dividing

what are the phase of cell division and what happens in each

G1 (cell grows in size and carries out normal metabolism), S (synthesis of DNA = replication), G2 (cell grows in size and prepares for mitosis) M (chromosomes condense, mitosis and cytokinesis) G0 (quiescence = non-dividing state)

cyclin-cdk complexes 

plays a major role in recognizing substrate proteins for cdk, cdk only works when cycling is bound; different cylin-cdks control different steps of the cell cycle

kinase

enzyme transfer phosphate from ATP to some substrate or protein

cell cylce checkpoints

positions in the cell cycle where it can be stopped if conditions are unfavorable

what happens at each checkpoint

G1 checkpoint or “start” (DNA damage checkpoint, can the cell proceed with the cell cycle at all, is DNA ok under social control), G2/M checkpoint (is all of my DNA replicated), spindle checkpoint (are all chromosomes attached to both poles)

apoptosis 

programmed cell death, non-recoverable damage will trigger this, which can be normal and healthy to eliminate cells that are unneeded during development or are dangerous, like immune surveillance 

alleles

different sequence versions of the same gene

homologous chromosomes

two differnt versions of a chromomes containg different alleles

sister chromatid

created from the replication of a chromosome, identical copies 

ploidy

the number of each chromosome that an organism or cell carries, one set of chromosomes is designated n

mitosis (what is it and process) 

diploid eukaryotic cell divides into two identical daughter cells; prophase(chromosomes condense), prometaphase (microtubules of the mitotic spindle attach to chromosomes), metaphase (chromosomes align in the center of the cell), anaphase (sister chromatids separate and travel to opposite poles), telophase (nuclear envelope re-froms and chromosomes decondense, cytokinesis happens) 

kinetochore

mitosis-specific protein assembly on centromeres (point of most stable attachment between sister chromatids) that connects the chromosome to microtubules of the spindle apparatus

meiosis (what is it and process)

occurs in germ cells and produces haploid gametes with half the genetic information, creating 4 haploid daughter cells; two divisions called meiosis I and meiosis II, There is a reductive division as the cell goes from diploid to haploid, during early prophase of meiosis I homologous chromoems pair to form bivalents

crossing over 

maternal and paternal alleles are mixed up during prophase I, and this occurs via a molecular process called homologous recombination, where each chromosome is joined at the exact same spot to the paired homolog 

nondisjunction

chromosome segregation errors, either homologous chromosomes or sister chromatids can fail to separate can cause chromosomal abnormalities