Properties of living organisms
1. complex structure, basic unit of organization is the cell
2. acquire, transform, store, use energy
3. sense and respond to internal and external environments
4. maintain homeostasis through internal control systems with feedback
5. store, use, and tran
energy
capacity to do work
-chemical, transport, mechanical work
transport work
enables cells to move ions, molecules, particles through cell membrane and through organelles
-used for creating concentration gradients
concentration gradients
distributions of molecules in which the concentration is higher on one side of a membrane than the other
mechanical work
used for movement
-organelles moving around in cell
-cells changing shape
-cilia and flagella beating
-mediated by motor proteins
kinetic energy
energy of motion
potential energy
stored energy
1st law of thermodynamics
law of conservation of energy
-total amount of energy in the universe is constant
-universe is a closed system (nothing enters, nothing leaves)
-energy can be converted form one type to the next
2nd law of thermodynamics
natural spontaneous processes move form a state of order (nonrandomness) to a condition of randomness/disorder (entropy)
-keeping order requires energy
-disorder loses energy to surroundings
bioenergetics
study of energy flow in biological systems
chemical reaction
substance becomes a difference substance
-breaking down or making of covalent bonds
reactants
reaction begins with 1+molecules
products
reaction ends with 1+molecules
reaction rate
speech with which reaction takes place
-disappearance rate of reactants
-appearance rate of products
free energy
the potential energy stored in the chemical bonds of a molecule
-complex molecules have more chemical bonds and higher free energies
-
activation energy
initial input of energy required to bring reactants into a position that allows them to react with one another.
exergonic reaction
when the free energy of the products is lower than the free energy of reactants----reaction releases energy
endergonic reaction
products retain part of activation energy and is greater than that of the reactants, these require a net input of energy----energy-utilizing reactions
synthesis reactions
energy-consuming reactions where complex molecules are made from smaller molecules
Coupling endergonic and exergonic reactions
simplest way for a cell to acquire activation energy
-ex. using energy released by breaking high energy bond of ATP to drive an endergonic reaction
reversible reaction
the forward reaction and its reverse reaction are both likely to take place
-net free energy plays a part in if this is possible because the net free energy change of forward reaction contributes to the activation energy of the reverse reaction
irreversible reaction
a reaction proceeds in one direction but not the other.
enzymes
proteins that speed up the rate of chemical reactions.
-biological catalysts: enzyme molecules will not change in any way
substrates
enzymatically catalyzed reactions
isozymes
enzymes that catalyze the same reaction but under different conditions or in different tissues
-important role in diagnosis of certain med. conditions
coenzymes
organic cofactors for enzymes that do not alter the enzyme's binding site, act as receptors and carriers for atoms or function groups
vitamins
precursors of coenzymes, water-soluble vitamins required for various metabolic reactions
how do enzymes increase rate of reaction?
it lowers the activation energy, making it more likely that the reaction will start, do this by binding to substrates and bringing them into the best position for reacting with each other
oxidation-reduction reactions
most important reactions in energy extraction and transfer in cells
-transfer electrons
-gains an electron= reduced (adding neg. charge reduces the electric charge on molecule)
-loses an electron= oxidized
reduced molecule
gains electron
oxidized molecule
loses electron
hydrolysis-dehydration reaction
breakdown and synthesis of large biomolecules
-dehydration-water is one of the products, losing water by having two molecules combine into one
-hydrolysis- split large molecules by adding water
dehydration synthesis
when a dehydration reaction results in the synthesis of a new molecule
hydrolysis reaction
substrate changes into one or more products through addition of water, covalent bonds of water molecule are broken.
Addition reaction
adds a functional group to one or more of the substrates
subtraction reaction
removes a functional group from one or more of the substrates
exchange reaction
functional groups are exchanged between or among substrates
kinases
transfer a phosphate group from a substrate to an ADP molecule to create ATP, or from an ATP molecule to a substrate
deamination
removal of an amino group from an amino acid or peptide
amination
addition of an amino group
transamination
transfer of an amino group from one molecule to another
ligation reaction
join two substrates using energy from ATP and enzymes known as synthetases
metabolism
all chemical reactions that take place in an organism
1. extract energy from nutrient biomolecules (ex. proteins, carbs, lipids)
2. synthesize or break down molecules
3. divided into catabolism and anabolism---take place simultaneously in cells at any giv
catabolism
reactions that release energy through breakdown of large biomolecules
anabolism
energy-utilizing reactions that result in the synthesis of large biomolecules
kilocalorie
amount of energy needed to raise the temp of 1 liter of water by 1 degree C
Intermediates
molecules of the pathway, the products of one reaction become the substrates for the next (intermediary metabolism)
key intermediates
play in more than one pathway and at as the branch points for channeling substrate in one direction or another (ex. glucose in many metabolic pathways)
How do cells regulate flow of molecules through metabolic pathways? 5 ways.
1. controlling enzyme concentrations
2. producing modulators that change reaction rates
3. using two different enzymes to catalyze reversible reactions
4. compartmentalizing enzymes within intracellular organelles
5. maintaining an optimum ration of ATP a
Enzyme modulation
frequently controlled by hormones, type of outside regulation is key element in the integrated control of body's metabolism following a meal or fasting between meals
feedback inhibition
built-in form of modulation in metabolic pathways. the end product of a pathway acts as an inhibitory modulator of the pathway, then the enzyme catalyzing the conversion is inhibited. This slows down production until cell can use it up. When levels drop,
ratio of ATP to ADP
ratio determines whether pathways that result in ATP synthesis are turned on or off
-High ATP levels, production of ATP decreases
-ATP low, cells send substrates through pathways that result in more ATP
High-energy phosphate bond
energy stored in bond between ATP with 3 phosphate groups, one of the groups is attached to ADP by a covalent bond. when bond is broken, high energy is released.
ADP + Pi + energy --><--ADP ~ P (=ATP) where Pi = inorganic phosphate group and ~ denotes a h
how much ATP does an adult human need a day?
40 kg, 88 lbs.
aerobic
ATP molecules that require oxygen, oxidative pathways
anaerobic
no oxygen, produces ATP as well but in smaller quantities
electron transport system (ETS)
in the mitochondria, transfers energy from those electrons to the high energy phosphate bond of ATP
ATP Production
catabolic pathways extract energy from biomolecules and transfer it to ATP
pg. 112
-glycolysis
-citric acid cycle
-both produce high energy electrons electrons carried by NADH and FADH2 to the electron transport system in the mitochondria
glycolysis
one molecule of glucose is converted by a series of enzymatically catalyzed reactions into 2 pyruvate molecules, producing a net release of energy PAGE 113
Pyruvate, Acetyl CoA, and Citric Acid Cycle
1.If adequate oxygen, 3-carbon pyruvate from glycolysis is moved to mitochondria
2.Pyrvate reacts with coenzyme A and produces aceytl CoA, one NADH, one CO2
3.Aceytl CoA has two parts; 2-carbon acyl unit derived from pyruvate and coenzyme A
4.coenzyme A i
Electron transport system
1. made up of mitrochondrial proteins located in the intermitochondrial membrane
-includes enzymes and iron-containing cytochromes
2. (NADH and FADH2) from citric acid cycle release high-energy electrons and H+
3. These products are moved into the electro
Oxidative phosphorylation
synthesis of ATP using electron transport system because it requires oxygen to act as the final acceptor of electrons and H+
Chemiosomotic theory
potential energy stored by concentrating H+ in the intermembrane space is used to make ATP
Aerobic metabolism of one glucose molecule
carbon dioxide, water, and 30-32 ATP
Glycolysis equation
Glucose + 2NAD + 2ADP + 2Pi = 2 pyruvate + 2ATP + 2NADH + 2H+ + H20
ANAEROBIC METABOLISM
1 glucose---> glycolysis----> 2 pyruvate and 2 lactate in form of lactic acid THIS MAKES 2 ATP
aerobic metabolism
1 glucose--->glycolysis--->2 pyruvate--->acetyl CoA--->citric acid cycle------> high energy electrons---->electron transport system----> 6H20, 30-32 ATP, 6 CO2
Branch point between aerobic and anaerobic metabolism
pyruvate is the branch point.
pyruvate to lactate = anaerobic
pyruvate to pyruvate and citric acid cycle = aerobic
proteins are the key to cell function
run a cell from day to day. protein enzymes control synthesis/breakdown of carbohydrates, lipids, structural proteins, and signal molecules
gene
region of DNA that contains the info needed to make a functional piece of RNA, which can then make a protein
transcription
DNA base sequence is used to create a piece of RNA
messenger RNA
Processed in nucleus after made (alternative splicing, RNA interference, or processed). If it is processed, it leaves nucleus and eters cytosol, tere it works with tRNA and rRNA in translation
tRNA, mRNA, rRNA
Transfer RNA, Messenger RNA, Ribosomal RNA
Post-translational modification
newly synthesized proteins may fold into complex shapes, split by enzymes, or have chemical groups added to them
constitutively active genes
continuously being read and converted to RNA messages
regulated activity genes
are first inducted or repressed, then begin to be converted to RNA messages
interference of RNA
SILENCED
Alternative splicing of RNA
Becomes processed mRNA then it is translated with rRNA and tRNA and amino acids to make a protein chain
protein chain from protein synthesis
folding and cross links, cleaved into smaller peptides, addition of groups (sugars, lipids, phosphate), assembly into polymeric proteins
transcription process
1. RNA polyamerase binds to DNA
2. The section of DNA unwinds.
3. The RNA bases bind to DNA creating single strand of mRNA
4. mRNA and the RNA polymerase detach from DNA
5. mRNA goes to cytosol after processing
during transcription bases are linked at an
RNA polymerase
required for synthesis of RNA from a double-strand of DNA
Transcription factors
bind to DNA and activate the promoter (the region that precedes the gene that is activated before transcription begins, tells the DNA where to unwind)
mRNA processing
next step in the process of protein synthesis is mRNA processing
-RNA interference: newly synthesized mRNA is inactivated/destroyed before it is translated into proteins
-alternative splicing: enzymes clip segments out of the middle/ends of mRNA strand, t
a gene contains segments called exons and introns
exons- encode proteins
introns- noncoding
mRNA is initially containing noncoding segments that must b removed before mRNA leave nucleus. Alternative splicing results in smaller pieces of mRNA that only contain coding sequence for a specific protein
mRNA translation links amino acids
Arrival in the cytosol, processed mRNA binds to ribosomes (small particles of protein/types of rRNA) to create a ribosome-mRNA complex
-then matched to the proper amino acid by help of tRNA
-tRNA contains a three-base sequence called ANTICODON that is com
dehydration synthesis
links amino acids by creating a peptide bond between the amino group of the newly arrived amino acid and the carboxyl end.
-the empty tRNA releases from mRNA
-tRNA attaches to another amino acid
ribonucleases
enzymes that break down mRNA, some forms of mRNA are broken down rapidly while others may linger in the cytosol and be translated many times
protein sorting
specific proteins go from the ribosomes directly to where they are needed in the cell
sorting signal
an address label that tells the cell where the protein should go during protein sorting
translation process
1. transcription
2. mRNA processing
3. attachment of ribosomal subunits
4. translation---> processed mRNA leaves the nucleus and associates with ribosomes. Translation matches the codons of RNA with amino acids to create a protein
5. termination
signal sequence
signal sequence tag directs the protein to the proper organelle and allows it to be transported through the organelle membrane
post-translational modification
newly made protein can form different types of covalent and noncovalent bonds after translation.`
in some common forms of post-translational modification, the amino acid chain can:
1. fold into various three-dimensional shapes---take on their tertiary structure of the protein
2. create cross-links between different regions of its amino acid chain
3. be cleaved (split) into fragments
4. add other molecules or groups
5. assemble with