Exam 2 Flashcards
eukaryotic cells
cells with a nucleus
plasma membrane
controls what goes into and out of the cell
Ribosomes
site of protein synthesis
DNA in nucleus
contains instructions for making proteins
What do only plant cells have?
cell walls
Chloroplasts covert ___ energy to ___ energy
light, chemical
Mitochondria break down molecules, generating ___
ATP
light microscope (LM)
visible light is passed through a specimen and then through glass lenses
Magnification
the ratio of an object’s image
Resolution
the measure of the clarity of the image, or the minimum distance of two distinguishable points
Contrast
visible differences in brightness between parts of the sample
organelles
the membrane-enclosed structures in eukaryotic cells
Light microscopes can magnify effectively to about ___ times the size of the actual specimen
1000
Scanning electron microscopes (SEMs)
focus a beam of electrons onto the surface of a specimen, providing images that look 3-D
Transmission electron microscopes (TEMs)
- focus a beam of electrons through a specimen
- used mainly to study the internal structure of cells
electron microscopes (EMs)
used to study subcellular structures
Cryo-electron microscopy (cryo-EM)
allows preservation of specimens at very low temperatures
- allows visualization of structures in their cellular environment, with no need for preservatives
cytology
the study of cell structure
Cell fractionation
takes cells apart and separates the major organelles from one another
- enables scientists to determine the functions of organelles
Only organisms of the domains Bacteria and Archaea consist of ___ cells
prokaryotic
Protists, fungi, animals, and plants all consist of ___ cells
eukaryotic
Basic features of all cells
–Plasma membrane
–Semifluid substance called cytosol
–Chromosomes (carry genes)
–Ribosomes (make proteins)
Prokaryotic cells are characterized by having
–No nucleus
–DNA in an unbound region called the nucleoid
–No membrane-bound organelles
–Cytoplasm bound by the plasma membrane
Eukaryotic cells are characterized by having
–DNA in a nucleus that is bounded by a double membrane
–Membrane-bound organelles
–Cytoplasm (the region between the plasma membrane and nucleus)
–larger
plasma membrane
a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell
As a cell increases in size….
its volume grows proportionately more than its surface area
A eukaryotic cell has internal membranes that divide the cell into compartments
organelles
nucleus
contains most of the cell’s genes and is usually the most conspicuous organelle
nuclear envelope
encloses the nucleus, separating it from the cytoplasm
- a double membrane; each membrane consists of a lipid bilayer
pore complex
regulate the entry and exit of molecules from the nucleus
nuclear lamina
which is composed of proteins and maintains the shape of the nucleus
nuclear matrix
a framework of protein fibers throughout the interior of the nucleus
chromosomes
In the nucleus, DNA is organized into discrete units
a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
Each chromosome contains one DNA molecule associated with proteins, called
chromatin
located within the nucleus, is the site of ribosomal RNA (rRNA) synthesis
nucleolus
Ribosomes build proteins in two locations:
–In the cytosol (free ribosomes)
–On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)
The endomembrane system consists of:
- These components are either continuous or connected via transfer by vesicles
–Nuclear envelope –Endoplasmic reticulum –Golgi apparatus –Lysosomes –Vacuoles –Plasma membrane
endoplasmic reticulum (ER)
accounts for more than half of the total membrane in many eukaryotic cells
two distinct regions of ER:
–Smooth ER, which lacks ribosomes
–Rough ER, whose surface is studded with ribosomes
Functions of Smooth ER
–Synthesizes lipids
–Detoxifies drugs and poisons
–Stores calcium ions
Functions of Rough ER
- Has bound ribosomes, which secrete glycoproteins(proteins covalently bonded to carbohydrates)
–Distributes transport vesicles, secretory proteins surrounded by membranes
–Is a membrane factory for the cell
Golgi apparatus
–Modifies products of the ER
–Manufactures certain macromolecules
–Sorts and packages materials into transport vesicles
The Golgi apparatus consists of flattened membranous sacs called
cisternae
lysosome
a membranous sac of hydrolytic enzymes that can digest macromolecules
phagocytosis
Some types of cell can engulf another cell
- forms a food vacuole
autophagy
Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules
Vacuoles
large vesicles derived from the ER and Golgi apparatus
Central vacuoles
- -found in many mature plant cells, contain a solution called sap
- -it is the plant cell’s main repository of inorganic ions, including potassium and chlorid
- -The central vacuole plays a major role in the growth of plant cells
Mitochondria
are the sites of cellular respiration, the metabolic process that uses oxygen to generate ATP
Chloroplasts
found in plants and algae, are the sites of photosynthesis
endosymbiont theory
- It suggests that an early ancestor of eukaryotes engulfed an oxygen-using nonphotosynthetic prokaryotic cell
- The engulfed cell formed a relationship with the host cell, becoming an endosymbiont
- The endosymbionts evolved into mitochondria
- At least one of these cells may have then taken up a photosynthetic prokaryote, which evolved into a chloroplast
Similarities between mitochondria and chloroplasts that support this theory:
–Enveloped by a double membrane
–Contain free ribosomes and circular DNA molecules
–Grow and reproduce somewhat independently in cells
mitochondria have a smooth outer membrane and an inner membrane folded into
cristae
The inner membrane creates two compartments:
intermembrane space and mitochondrial matrix•
are found in leaves and other green organs of plants and in algae
chloroplasts
Chloroplast structure includes
–Thylakoids, membranous sacs, stacked to form a granum
–Stroma, the internal fluid
The chloroplast is one of a group of plant organelles, called
plastids
specialized metabolic compartments bounded by a single membrane
- They contain enzymes that remove hydrogen atoms from various substances and transfer them to oxygen
Peroxisomes
Functions of peroxisomes
- Some use oxygen to break fatty acids into smaller molecules, eventually used for fuel for respiration
–In the liver, they detoxify alcohol and other harmful compounds
–Glyoxysomesin the fat-storing tissues of plant seeds, convert fatty acids to sugar to feed the emerging seedling
cytoskeleton
helps to support the cell and maintain its shape
- It interacts with motor proteinsto produce cell motility
Three main types of fibers make up the cytoskeleton:
–Microtubules are the thickest of the three components of the cytoskeleton
–Microfilaments, also called actin filaments, are the thinnest components
–Intermediate filaments are fibers with diameters in a middle range
hollow rods about 25 nm in diameter and about 200 nm to 25 microns long
Microtubules
Functions of microtubules:
-Shaping the cell
–Guiding movement of organelles
–Separating chromosomes during cell division
In animal cells, microtubules grow out from a __ near the nucleus
centrosome
In animal cells, the centrosome has a pair of ___, each with nine triplets of microtubules arranged in a ring
centrioles
flagella and cilia
microtubule-containing extensions that project from some cells
Difference between flagella and cilia
- Motile cilia are found in large numbers on a cell surface, whereas flagella are limited to one or a few per cell
- Cilia and flagella differ in their beating patterns
Cilia and flagella share a common structure
–A group of microtubules sheathed in an extension of the plasma membrane
–Nine doublets of microtubules are arranged in a ring with two single microtubules in the center
–A basal body that anchors the cilium or flagellum
–A motor protein called dynein, which drives the bending movements of a cilium or flagellum
are solid rods about 7 nm in diameter, built as a twisted double chain of actin subunits
Microfilaments
microfilaments form a
cortex just inside the plasma membrane to help support the cell’s shape
Microfilaments that function in cellular motility contain the protein __ in addition to actin
myosin
pseudopodia
- cellular extensions
- cells crawl along a surface by extending pseudopodia and moving toward them
Cytoplasmic streaming
in plant cells, is a circular flow of cytoplasm within cells, driven by actin-protein interactions
Intermediate filaments
range in diameter from 8 to 12 nanometers, larger than microfilaments but smaller than microtubules
- support cell shape and fix organelles in place
cell wall
an extracellular structure that distinguishes plant cells from animal cells
- protects the plant cell, maintains its shape, and prevents excessive uptake of water
- made of cellulose fibers embedded in other polysaccharides and protein
What organisms have a cell wall?
Prokaryotes, fungi, and some protists
Primary cell wall
Relatively thin and flexible, secreted first
Middle lamella
Thin layer between primary walls, containing polysaccharides called pectins
Secondary cell wall(in some cells)
Added between the plasma membrane and the primary cell wall
Animal cells lack cell walls but are covered by an elaborate _____
extracellular matrix (ECM)
The ECM is made up of glycoproteins such as __, ___, and ___
collagen, proteoglycans, and fibronectin
Fibronectin and other ECM proteins bind to receptor proteins in the plasma membrane called __
integrins
Extracellular matrix (ECM) function
- can regulate a cell’s behavior by communicating with a cell through integrins
- influence the activity of genes in the nucleus
- Mechanical signaling may occur through cytoskeletal changes that trigger chemical signals in the cell
cell junctions
Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact
Plasmodesmata
channels that connect plant cells
- Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell
Tight junctions
membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
Desmosomes (anchoring junctions)
fasten cells together into strong sheets
Gap junctions (communicating junctions)
provide cytoplasmic channels between adjacent cells
A cell is greater than….
the sum of its parts
Alcohol dehydrogenase
a protein that breaks down alcohol in the body
What are the structures and functions of the four important classes of biological molecules?
- carbohydrates
- proteins
- Nucleic acids
- lipids
Macromolecules are __, built from ____
polymers, monomers
Large polymers are known as ___
macromolecules
polymer
a long molecule consisting of many similar building blocks
The repeating units that serve as building blocks are called
monomers
Carbohydrates, proteins, and nucleic acids are __
polymers
Enzymes
specialized macromolecules that speed up chemical reactions such as those that make or break down polymers
A dehydration reaction occurs when…
two monomers bond together through the loss of a water molecule
Hydrolysis
- a reaction that is essentially the reverse of the dehydration reaction
- Polymers are disassembled to monomers by hydrolysis
A huge variety of polymers can be built from a small set of _____
monomers
Carbohydrates
- include sugars and polymers of sugars
- The simplest carbohydrates are monosaccharides, or simple sugars
- Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks
_____ have molecular formulas that are usually multiples of CH2O
Monosaccharides
the most common monosaccharide
Glucose (C6H12O6)
Monosaccharides are classified by
- The location of the carbonyl group (as aldose or ketose)
- The number of carbons in the carbon skeleton
disaccharide
formed when a dehydration reaction joins two monosaccharides
This covalent bond between two monosaccharides is called a
glycosidic linkage
Polysaccharides
- the polymers of sugars
- have storage and structural roles
- architecture is determined by its sugar monomers and the positions of its glycosidic linkages
Starch
- storage polysaccharides
- consists of glucose monomers
FYI The simplest form of starch is amylose
Glycogen
is a storage polysaccharide in animals
- stored mainly in liver and muscle cells
- Hydrolysis (chemical breakdown of a compound due to reaction with water) of glycogen in these cells releases glucose when the demand for sugar increases
The polysaccharide cellulose
- a major component of the tough wall of plant cells
- Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
- different ring structures alpha (α) beta (β)
alpha
Starch (α configuration) is largely helical
beta
Cellulose molecules (β configuration) are straight and unbranched
Chitin
- found in the exoskeleton of arthropods
- provides structural support for the cell walls of many fungi
Lipids
- does not include true polymers
- consist mostly of hydrocarbon regions
- important lipids are fats, phospholipids, and steroids
Fats
constructed from two types of smaller molecules: glycerol and fatty acids
Glycerol
a three-carbon alcohol with a hydroxyl group attached to each carbon
Fatty acids
consists of a carboxyl group attached to a long carbon skeleton
triacylglycerol
In a fat, three fatty acids are joined to glycerol by an ester linkage
Saturated fatty acids
have the maximum number of hydrogen atoms possible and no double bonds
-solid
Unsaturated fatty acids
have one or more double bonds
- liquid
Hydrogenation
process of converting unsaturated fats to saturated fats by adding hydrogen
TRANS FATS
major function of fats
energy storage
Humans and other mammals store their long-term food reserves in ___
adipose cells
phospholipid
- two fatty acids and a phosphate group are attached to glycerol
When phospholipids are added to water, they self-assemble into double-layered sheets called
bilayers
steroids
lipids characterized by a carbon skeleton consisting of four fused rings
Cholesterol
a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized
Enzymes are proteins that act as ___ to speed up chemical reactions
Catalysts
proteins
account for more than 50% of the dry mass of most cells
Look at the graphic for proten
presentation 5
slide 35
Polypeptides
unbranched polymers built from amino acids
protein
a biologically functional molecule that consists of one or more polypeptides
Amino acids
organic molecules with amino and carboxyl groups
Amino acids are linked by covalent bonds called
peptide bonds
Each polypeptide has a unique linear sequence of amino acids, with a ___ end (C-terminus) and an ___ (N-terminus)
carboxyl, amino end
The function of a protein usually depends on…
its ability to recognize and bind to some other molecule
The primary structure
of a protein is its unique sequence of amino acids
Secondary structure
found in most proteins, consists of coils and folds in the polypeptide chain
Tertiary structure
is determined by interactions among various side chains (R groups)
Quaternary structure
results when a protein consists of multiple polypeptide chains
Sickle-cell disease
an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
denaturation
loss of a protein’s native structure
What Determines Protein Structure?
In addition to primary structure, physical and chemical conditions can affect structure
Scientists use ___ to determine a protein’s structure
X-ray crystallography
- Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization
Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with
misfolded proteins
Chronic Wasting Disease in the deer family is also associated with misfolded proteins called
prions
The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a
gene
Genes consist of
DNA, a nucleic acidmade of monomers called nucleotides
Two types of nucleic acids
- Deoxyribonucleic acid (DNA)
–Ribonucleic acid (RNA)
gene expression
DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
- Gene expression: DNA → RNA → protein
Nucleic acids are polymers called
polynucleotides
Each polynucleotide is made of monomers called
nucleotides
Nucleotide = nucleoside + phosphate group
Each nucleotide consists of
a nitrogenous base, a pentose sugar, and one or more phosphate groups
Nucleoside
nitrogenous base + sugar•
Two families of nitrogenous bases
- Pyrimidines(cytosine, thymine, and uracil)have a single six-membered ring
–Purines(adenine and guanine) have a six-membered ring fused to a five-membered ring
In DNA, the sugar is ___ ; in RNA, the sugar is __
deoxyribose, ribose
DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a
double helix
The backbones run in opposite 5′ → 3′ directions from each other, an arrangement referred to as
(The Structures of DNA and RNA Molecules)
antiparallel
DNA pair up
complementary base pairing
adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
In RNA, thymine is replaced by
uracil
Bioinformatics
uses computer software and other computational tools to deal with the data resulting from sequencing many genomes
Analyzing large sets of genes or even comparing whole genomes of different species is called
genomics
analysis of large sets of proteins including their sequences is called
proteomics
RNA is ___ stranded
single
First law of thermodynamics
principle of conservation of energy
Energy can be transferred or transformed, but not created or destroyed
Second law of thermodynamics
Every energy transfer or transformation increases the entropy (disorder) of the universe
Metabolism
- the totality of an organism’s chemical reactions
- It is an emergent property of life that arises from orderly interactions between molecules
metabolic pathway
In a metabolic pathway, a specific molecule is altered in a series of steps to produce a product
Catabolic pathways
release energy by breaking down complex molecules into simpler compounds
- ex. Cellular respiration, the breakdown of glucose in the presence of O2
- “downhill”
Anabolic pathways
consume energy to build complex molecules from simpler ones
- “uphill”
Bioenergetics
study of how energy flows through living organisms
Energy
the capacity to cause change, can be used to do work—move matter against opposing forces, such as gravity and friction
Kinetic energy
- is energy associated with motion
- Moving objects perform work by imparting motion to other matter
Thermal energy
- the kinetic energy associated with random movement of atoms or molecules
- transfer from one object to another is called heat
Potential energy
energy that matter possesses because of its location or structure
Chemical energy
potential energy available for release in a chemical reaction
Thermodynamics
the study of energy transformations in a collection of matter
Entropy
a measure of molecular disorder, or randomness
Spontaneous processes
occur without energy input; they can happen quickly or slowly
Biological Order and Disorder
Cells create ordered structures from less organized starting materials
- Complex, ordered structures are also produced from simpler starting materials at the organismal level
Free-Energy Change, ΔG
- Gibbs free energy, G, can be simplified and referred to as free energy
- represents the difference between free energy of the final state and free energy of the initial state
Free energy
The portion of a system’s energy that can do work when temperature and pressure are uniform throughout the system, as in a living cell
ΔH
change in enthalpy (total energy)
ΔS
change in entropy
T
Temperature in Kelvin (K)
ΔG details
- ΔG is negative for all spontaneous processes
–ΔG is zero or positive for nonspontaneous processes - If a reaction has negative ΔG,the system loses free energy and becomes more stable
Stable vs unstable ΔG
unstable systems (higher G) tend to become more stable (lower G)
Equilibrium
the point at which forward and reverse reactions occur at the same rate, describes a state of maximum stability
- A process is spontaneous and can perform work only when it is moving toward equilibrium
exergonic reaction
An exergonic reaction(“energy outward”) proceeds with a net release of free energy to the surroundings
exergonic reactions occur spontaneously
endergonic reaction
An endergonic reaction(“energy inward”) absorbs free energy from the surroundings
-unspontaniously
Breaking bonds during a chemical reaction does not release energy; it ___ energy
requires
The magnitude of ΔG determines the
endergonic
quantity of energy required to drive an endergonic reaction
The magnitude of ΔG determines the
exergonic
the maximum amount of work an exergonic reaction can perform
The chemical reactions of metabolism are ___, but never reach ___ in a living cell
Reversible, equilibrium
A cell does three main kinds of work:
–Chemical work—pushing endergonic reactions
– Transport work—pumping substances across membranes against the direction of spontaneous movement
–Mechanical work—such as beating cilia or contracting muscle cells
Reactions in a closed system, such as an isolated hydroelectric system, eventually …
reach equilibrium and can then do no work
energy coupling
Cells manage energy resources to do work through energy coupling, the use of an exergonic process to drive an endergonic one
ATP (adenosine triphosphate)
is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups
- functions as one of the nucleoside triphosphates used to make RNA
Energy is released from ATP when the
terminal phosphate bond is broken by hydrolysis, the addition of a water molecule
How ATP Provides Energy That Performs Work
Cellular work (mechanical, transport, and chemical) is powered by ATP hydrolysis
•In the cell, energy from the exergonic hydrolysis of ATP is used to drive endergonic reactions
•Overall, the coupled reactions are exergonic
Phosphorylation
transfer of a phosphate group from ATP to another molecule, is typically used to power endergonic reactions
phosphorylated intermediate
The recipient molecule, a phosphorylated intermediate, is more reactive (less stable, with more free energy) that the original molecule
ATP hydrolysis
- water is used to split apart adenosine triphosphate (ATP) to create adenosine diphosphate (ADP) to get energy
Hydrolyze - break things down in the presence of a water molecule - Transport and mechanical work in the cell are also nearly always powered by ATP hydrolysis
- causes a change in protein shape and binding ability
The Regeneration of ATP
ATP is regenerated by addition of a phosphate group to adenosine diphosphate(ADP)
Enzymes speed up metabolic reactions by ___
lowering energy barriers
* Spontaneous reactions do not need added energy, but they can be slow enough to be imperceptible
catalyst
a chemical agent that speeds up a reaction without being consumed by the reaction
enzyme
a macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction
___ provides a barrier that determines the rate of spontaneous reactions
provides a barrier that determines the rate of spontaneous reactions
The initial energy needed to break the bonds of the reactants is called the
Activation energy
catalysis
the process by which a catalyst selectively speeds up a reaction without itself being consumed
The reactant that an enzyme acts on is called the enzyme’s
substrate
The enzyme binds to its substrate, forming an
enzyme-substrate complex
Most enzyme names end in
- ase
- For example, the enzyme sucrase catalyzes the hydrolysis of sucrose into glucose and fructose
active site
the region on the enzyme, often a pocket or groove, that binds to the substrate
induced fit
results from interactions between chemical groups on the substrate and the active site
- It brings the chemical groups of the active site into positions that enhance catalysis of the reaction
Catalysis in the Enzyme’s Active Site
- The substrate is typically held in the enzyme’s active site by weak bonds, such as hydrogen bonds
- The conversion of substrate to product happens rapidly, and product is released from the active site
Enzymes use a variety of mechanisms to lower EA (activation energy)
–Substrates may be oriented to facilitate the reaction–Substrates may be stretched to make the bonds easier to break
–The active site may provide a microenvironment that favors the reaction
–Amino acids in the active site may participate in the reaction
Effects of Local Conditions on Enzyme Activity
- Enzyme activity can be affected by general environmental factors, such as temperature and pH
- It can also be affected by chemicals that specifically influence the enzyme
Effects of Temperature and pH
- Each enzyme has an optimal temperature at which it catalyzes its reaction at the maximum possible rate
- Up to this point, the reaction rate increases with increasing temperature; beyond this point the rate of reaction begins to drop
Spontaneous reactions do not need __ ___, bu they can be slow enough to be ___
added energy, impossible to perceive.
Enzymes begin to denature at temperatures beyond their optimum
The optimal temperature of an enzyme is dependent on the environment in which it typically functions
Cofactors
nonprotein helpers that bind to the enzyme permanently, or reversibly with the substrate
Organic cofactors are called
coenzymes
Enzyme Inhibitors
- Certain chemicals selectively inhibit the action of specific enzymes
- if an inhibitor forms covalent bonds with the enzyme, then the inhibition is usually irreversible
- Many inhibitors bind to the enzyme by weak interactions, resulting in reversible inhibition
Competitive inhibitors
- closely resemble the substrate (the surface or material on or from), and can bind to the enzyme’s active site
- Enzyme productivity is reduced because the inhibitor blocks the substrate from entering the active site
Noncompetitive inhibitors
- Bind to another part of the enzyme, away from the active site
- Binding of the inhibitor causes the enzyme to change shape, making the active site less effective at catalyzing the reaction
__ and ___ are often irreversible enzyme inhibitors
toxins and poisons
Evolution of Enzymes
- Enzymes are proteins encoded by genes
- Changes in genes (mutations) lead to changes in the amino acid composition of the enzyme
- Altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity
If a mutation results in a new enzyme function that is beneficial to the organism, natural selection will favor the
mutated allele
Regulation of enzyme activity helps control metabolism
Cells can regulate metabolic pathways by switching on or off the genes that encode specific enzymes, or by regulating the activity of existing enzymes
Allosteric regulation
occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site
feedback inhibition
- the end product of a metabolic pathway shuts down the pathway
- Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed
How is the chemical energy stored in food used to generate ATP?
- Plant and animal cells break down organic molecules by cellular respiration in the mitochondria
- The chemical energy in food is transformed into chemical energy in ATP
- Some energy is released to the environment as heat
Energy enters ecosystems as __ and exits as ___
light, heat
The chemical elements essential to life are recycled
–Photosynthesis uses CO2and H2O to make organic molecules and O2
–Cellular respiration uses O2and organic molecules to make ATP; CO2and H2O are produced as waste
The breakdown of organic molecules is
exergonic
Fermentation
a partial degradation of sugars that occurs without oxygen
Aerobic respiration
consumes organic molecules and oxygen and yields ATP
Anaerobic respiration
similar to aerobic respiration but consumes compounds other than oxygen
Cellular respiration
a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from oxygen molecules or nutrients into adenosine triphosphate, and then release waste products.
(includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration)
Catabolic pathways release stored energy by breaking down
complex molecules
Catabolic pathways do not directly power work in the cell;
they are linked to work by ATP
True/False
Cells must constantly regenerate their supply of ATP from ADP and phosphate
True
Chemical reactions that transfer electrons between reactants are called
oxidation-reduction reactions, or redox reactions
In redox reactions, the loss of electrons from a substance is called
oxidation
The addition of electrons to a substance is called
reduction
the amount of positive charge is reduced
The electron donor is called the ___ __, it reduces the electron acceptor
reducing agent
The electron acceptor is called the __ ___, it oxidizes the electron donor
oxidizing agent
Instead of fully transferring electrons, some redox reactions change electron sharing in ___ ___
covalent bonds
The partial “gain” of electrons by O atoms and the partial “loss” of electrons by their bonding partners constitutes a redox reaction
Ex:
For example, electrons are not completely transferred in the redox reaction between methane and O2
An electron loses potential energy when it shifts from a ___ electronegative atom toward a ___ electronegative one
less, more
Redox reactions that move electrons closer to electronegative O atoms __ energy
release
Cellular respiration is a redox process because:
energy is released as hydrogen and electrons are transferred to O atoms
The oxidation of glucose transfers electrons from a __ energy state (in glucose) to a __ energy state with O atoms
higher, lower
electron transport chain
consists of a series of molecules built into the inner membrane of the mitochondria (or plasma membrane of prokaryotes)
First Stage Cellular Respiration
Glycolysis breaks down glucose into two molecules of pyruvate
in mitochondria
Second Stage Cellular Respiration
Pyruvate oxidation and the citric acid cycle complete the breakdown of glucose to CO2
Third Stage Cellular Respiration
During oxidative phosphorylation the electron transfer chain and chemiosmosis facilitate synthesis of most of the cell’s ATP
The process that generates almost 90% of the ATP is called ___ because ___
- oxidative phosphorylation
- it is powered by redox reactions
Some ATP is also formed in glycolysis and the citric acid cycle by
substrate-level phosphorylation
Substrate-level phosphorylation occurs when:
an enzyme transfers a phosphate group directly from a substrate to ADP
money as an analogy for cellular respiration:
–Glucose is like a larger-denomination bill—it is worth a lot, but it is hard to spend
–ATP is like a number of smaller-denomination bills of equivalent value—they can be spent more easily
–Cellular respiration cashes in a large denomination of energy (glucose) for the small change of many molecules of ATP
For each molecule of glucose degraded to CO2 and H2O by cellular respiration, up to ___ molecules of ATP are produced
32
Glycolysis occurs in the cytoplasm and has two major phases:
- energy investment phase
- energy payoff phase
energy investment phase
2 ATP are used to split glucose into 2 three-carbon sugar molecules
energy payoff phase
4 ATP are synthesized, 2 NAD+are reduced to NADH, the small sugars are oxidized to form 2 pyruvate and 2 H2O
Glycolysis does not release any __, and occurs whether or not __ is present
CO2, O2
Pyruvate is converted to ____before entering the citric acid cycle
acetyl coenzyme A (acetyl CoA)
Pyruvate dehydrogenase catalyzes three reactions:
- Oxidation of pyruvate’s carboxyl group, releasing the first CO2of cellular respiration
- Reduction of NAD+to NADH
- Combination of the remaining two-carbon fragment with coenzyme A to form acetyl CoA
The citric acid cycle
Krebs Cycle
- oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn
- Another 2 CO2 are produced as a waste product
- Because 2 pyruvate are produced per glucose, the cycle runs twice per glucose molecule consumed
Citric Acid Cycle steps
- First the acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate
- The next seven steps decompose the citrate back to oxaloacetate, making the process a cycle
- The NADH and FADH2 produced by the cycle carry electrons to the electron transport chain
Stepwise Energy Harvest via NAD+
- Electrons from organic molecules are transfered to NAD+
- NAD+ functions as a reducing agent in cellular respiration
- Each NADH (reduced NAD+) is used to synthesize ATP
The Pathway of Electron Transport
-Most of the components are proteins which exist
in multiprotein complexes
- Carriers alternate reduced and oxidized states
- Electrons drop in free energy as they transfer
- Finally pass to O2 and form H2O
cytochromes
(proteins with hemegroups containing an iron atom)
Reducing/Oxidizing Agent
The compound that loses and electron is call the reducing agent
The compound that gains an electron is the oxidizing agent
Location of the Stages of Cellular Respiration
Glycolysis - Cytosol of the cell
Citric Acid Cycle - Mitochondrial Matrix
Oxidative Phosphorilation - Mitochondrial Matrix
Electron Transport Chain - Intermembrane space (in mitochondria)
What is the Electron Transport Chain doing?
- It is not synthesizing ATP during the chain
- Each step causes proteins to pump H+into the
intermembrane space
-H+ then flows back out of the membrane through
ATP synthase channels
-ATP synthase uses the exergonic flow of
H+ to drive the phosphorylation of ATP
Energy flow seqeunce in cellular respiration
glucose → NADH → electron transport chain
→ proton-moative force → ATP
chemiosmosis
the use of energy in a H+gradient to drive cellular work
H+then moves down its concentration gradient back across the membrane, passing through the protein complex ___ ___
ATP synthase
The H+gradient is referred to as a ___-____ ___, emphasizing its capacity to do work
proton-motive force,
About __% of the energy in a glucose molecule is transferred to ATP, making about ___ ATP
34, 32
There are three reasons why the exact number of ATP produced is not known
- Photophosphorylation and the redox reactions are not directly coupled; the ratio of NADH to ATP molecules is not a whole number
- ATP yield varies depending on whether electrons are passed to NAD+or FAD
- The proton-motive force is also used to drive other kinds of work
Fermentation and anaerobic respiration enable cells to produce ATP without the use of ____
oxygen
Anaerobic respiration uses an electron transport chain with a final electron acceptor other than ___
oxygen
Fermentation
an extension of glycolysis that oxidizes NADH by transferring electrons to pyruvate or its derivatives
alcohol fermentation
pyruvate is converted to ethanol in two steps
–The first step releases CO2from pyruvate
–The second step produces NAD+and ethanol
•Alcohol fermentation by yeast is used in brewing, winemaking, and baking
lactic acid fermentation
pyruvate is reduced directly by NADH to form lactate and NAD+
•There is no release of CO2 in lactic acid fermentation
•Lactic acid fermentation by fungi and bacteria is used to make cheese and yogurt
What is responsible for chocolate production?
A complex series of fermentation and aerobic respiration carried out by yeasts and bacteria on cacao beans
Fermentation and anaerobic and aerobic respiration have some similarities:
–All use glycolysis (net ATP = 2) to oxidize glucose and harvest the chemical energy of food
–In all three, NAD+is the oxidizing agent that accepts electrons during glycolysis
One major difference is the mechanisms used to oxidize NADH to NAD+:
–In fermentation, an organic molecule (pyruvate or acetaldehyde) acts as a final electron acceptor
–In cellular respiration, electrons are transferred to the electron transport chain
- Another difference is the amount of ATP produced per glucose molecule
Obligate anaerobes
carry out fermentation or anaerobic respiration and cannot survive in the presence of O2
Yeast and many bacteria are ___ ____ meaning that they can survive using either fermentation or cellular respiration
facultative anaerobes
Evolutionary Significance of Glycolysis
- Early prokaryotes likely used glycolysis to produce ATP before oxygen accumulated in the atmosphere
- Used in both cellular respiration and fermentation, it is the most widespread metabolic pathway on Earth
- Glycolysis is a metabolic heirloom from early cells that continues to function in fermentation and cellular respiration
__ and the ___connect to many other metabolic pathways
Glycolysis and the citric acid cycle
Glycolysis can use many ___
carbohydrates
Proteins used for fuel must be digested to amino acids and their amino groups must be removed in a process called
deamination
Nitrogenous waste is excreted as
ammonia (NH3), urea, or other products
Fats are digested to ___ and ____
glycerol (used to produce compounds needed for glycolysis) and fatty acids
Fatty acids are broken down by ___ ___and yield acetyl CoA, NADH, and FADH2
beta oxidation
Biosynthesis (Anabolic Pathways)
- Organisms use small molecules from food to build macromolecules, such as proteins from amino acids
- These small molecules may come directly from food, from glycolysis, or from the citric acid cycle
Why is feedback inhibition the most common mechanism for metabolic control?
because it prevents wasteful production
If ATP concentration drops, respiration __; if there is plenty of ATP, respiration ___
speeds up, speeds up
Regulation of Cellular Respiration via Feedback Mechanisms
Catabolism is controlled by ___
regulating the activity of enzymes at strategic points in the pathway
