CELL BIO STUDY GUIDE 2; CHAPTERS 4,5,7,8

Fluorescent labeling is used in what?

Resolution is the process by which you can identify two points as being distinct from one another (clarity)

The difference between the two microscopes is source of illumination

∙ In light microscopes, your source of illumination is light

∙ In electron microscopes, your source of illumination is electrons Contrast conveys differences in densities

There are different types of light microscopes; some have stains, some have no  stains, some are called phase contrasts 

∙ Phase Contrasts- a type of light microscope with no stains, but inner  components of a cell are visualized

The highest resolution among light microscopes is in confocal microscopes  ∙     Fluorescent labeling is used in confocal microscopes 

Electron microscopes have much greater resolution among all microscopes and the  two different types we look at are scanning electron microscope and transmission  electron microscope

The highest resolution among electron microscopes is in what?

If you want to learn more check out Who is Aula Palatina?

∙ In both scanning and transmission electron microscopes, there are certain  prerequisites when preparing a sample

1. The specimen must be stained with heavy metal so that the electrons that are scattering from the membrane and the electrons that are passing  through the specimen will be projected onto the screen

2. In scanning electron microscopy, the scattered electrons are projected;  they scan the external topography of the cell (or sample)

3. In transmission electron microscopy, the electrons passing through the  specimen are projected

 a. The highest resolution among electron microscopes is in  transmission electron microscopes 

Cytology- study of cell structure

Biochemistry- study of chemical processes within cells

Cell fractionation- subjecting cells to a certain g force with a dense pellet in order  to separate the organelles from the cell

What are the differences in DNA location in proks and euks?

∙ Microscopes and cell fractionation go hand-in-hand in understanding the structure within cells 

Four properties of all cell; proks and euks 

∙ All cells must be made of matter 

∙ All cells must have a source of information 

∙ All cells must be organized

∙ All cells must use energy 

Common features in proks and euks

∙ Plasma membrane

∙ Cytoplasm

∙ Ribosomes- complexes where protein synthesis takes place ∙ DNA made up of nucleotides

Differences in DNA location in proks and euks

∙ Proks have circular, double-stranded DNA

∙ Euks have linear double-stranded DNA kept in a membrane-bound nucleus Let’s looks at PROKARYOTIC CELLS (yay!) If you want to learn more check out what is the laws passed by Southern states in 1865 and 1866, after the Civil War?

Two domains of prok cells are archaea and bacteria

∙ Archaea are the most primitive proks

∙ Bacteria are omnipresent- they are everywhere

The plasma membrane is not a perfect circle

∙ Bacteria have invaginated plasma membranes; increased surface area to  accommodate proteins, enzymes, complexes that allow them to do special  functions

∙ EVERYTHING is in their plasma membrane because it’s the only membrane bound structure they have

Outside the plasma membrane is the cell wall 

∙ The cell wall gives structure, offers rigidity, but is also porous (it has small  holes)

1. This allows nutrients to enter the cell

2. Based on the composition of their cell wall, we classify bacteria into Gram  + and Gram –Don't forget about the age old question of what is Standard Consolidation Theory?

Gram +

Gram -

Stain purple/violet because they absorb iodine present in gramstain

Stain pink because it cannot absorb the iodine

Composition is a thick layer of  

peptidoglycan, composed of protein  and carbohydrates. When we think of  carbohydrates, we think of starch,  which our body can easily break down

Composed of thin layer of  

peptidoglycan followed by thick layer of lipopolysaccharide

Usually, because of the thick layer of  carbohydrates, these bacteria are  nonvirulent because our antibodies can  break down these carbohydratesDon't forget about the age old question of What are the six type of Ableism?

Usually virulent- they require antibiotics to combat infection

(Virulence = infectious/harmful)

Outside the cell wall, we find the sticky and viscous glycocalyx 

∙ Composed of carbohydrates and water

∙ Most important function: Protecting the cell against dehydration ∙ It also allows the bacteria to attach to its surroundings

Capsule- modified glycocalyx of complex carbohydrates We also discuss several other topics like What is Melodrama?

∙ Gives the property of virulence to the bacteria

1. If you have a bacterium with a capsule, you must take antibiotics to fight  it

2. The capsules is a protective aspect of the cell

Flagellum- Very long, hair-like structures composed of a sheet of protein

∙ The function is flagella is movement

1. To move, bacteria coil their flagella (building pressure), and release that  pressure (propelling them forward)

2. We call this style of movement corkscrew motion 

Plasmid- holds DNA that enhances survival, plays a role in genetic recombination

∙ DNA that is essential for survival is limited in the nucleoid region ∙ Plasmid and pili make a bacteria F+ strain

1. This means the strain has the capacity to transfer some of its genes and  transform another strain of bacteria (genetic recombination)

∙ Strains that don’t have pili or plasmids are called F- strains

Ribosomes and cytoplasm are also found in bacterial cells

When bacteria are exposed to adverse conditions, they have a survival technique;  forming endospores

∙ In an endospore, bacteria protect their DNA by secreting a cell wall around  their DNA and a little bit of cytoplasm

1. The DNA is housed here until optimum conditions are reached Volume : Surface Area ratio is important in all cell response timeDon't forget about the age old question of The national security council.

∙ Dr. V’s example was Big Hero Six

1. If we only had one cell for an arm or one cell for a leg, it would be energy  inefficient because the surface area : volume ratio is poor

∙ Response time among cells is much slower between very large cells ∙ This ratio is very important in cells involved with adhesion, absorption, or  secretion 

All cells in an organism have identical sequences of nucleotides, whether it is a hair  cell or a muscle cell

∙ The reason we have different-looking cells performing different functions is  differential gene expression

1. DNA sequences will be identical in all cells, but cells looks look different  because of differential gene regulation; different concentrations and kinds  of proteins are made based on function 

ANIMAL CELLS vs PLANT CELLS

Animal Cells

Both

Plant Cells

X

Mitochondria

Cell Wall

Centrosome w/ centrioles

Nucleus

X

X

Peroxisomes

Chloroplasts

Lysosomes

Golgi and ER

X

Plasma membrane

Plasma membranes contain large concentrations of phospholipids¸ which give the membrane its property of semi-permeability 

∙ Phospholipids = semi-permeability 

∙ ALL membranes are capable of semi-permeability because ALL membranes contain phospholipids

∙ Transport protein- major component of plasma membrane, capable of selective permeability

1. Transport protein = selective permeability 

∙ Receptors- receive signals from the environment or neighboring cells 1. Receptor = cell communication 

∙ Adhesive proteins- involved in permanent adhesion (part of a tissue) and temporary adhesion (blood cells flowing, making temporary adhesions) 1. Adhesive proteins = attachment 

Cytosol- Outside the membrane-bound organelles, but inside the plasma membrane ∙ Cytosol is the central coordinating region of the cell 

Cytoplasm- Contains everything inside the cell, including cytosol and membrane bound organelles

Endomembrane System

Secretory System

Outer Nuclear Membrane (always the

Outer Nuclear Membrane

start of the endomembrane system)

Endoplasmic Reticulum (Smooth and Rough)

Endoplasmic Reticulum (Smooth and Rough)

Golgi Complex

Golgi Complex

Lysosomes (ONLY in animal cells)

Lysosomes (ONLY in animal cells)

Vacuole (ONLY in plant cells)

Vacuoles (ONLY in plant cells)

Plasma membrane

Plasma membrane

Peroxisomes

Endomembrane System- the cytoplasm is compartmentalized into membrane bound organelles, each of them performing a specific function because of their specific composition of macromolecules

Nuclear membrane- contains an outer and inner membrane

∙ Nuclear pores- small spaces where the outer nuclear membrane meets the  inner nuclear membrane

1. Nuclear pores have gatekeeper proteins which allow certain proteins to  enter the nucleus, and allow certain proteins and nucleic acids to come  out

2. They regulate the movement of compounds in and out of the nucleus

Nuclear Lamina- Layer of intermediate filaments

∙ Provides support to the inner nuclear membrane

Nuclear matrix proteins- ‘scaffold’ of proteins (irregular length)

Functions of the nucleus 

∙ Houses and protects genetic material

∙ Maintains chromosomes in their territory (they will never overlap with each  other)

∙ Gene expression (transcription- assembly of ribosomes)

1. Nucleolus- a collection of genes that are responsible for synthesizing  ribosomal RNA

a. It is the location where ribosomal assembly takes place (rRNA is  connected to the proteins that make up the large subunit and small  subunit)

b. Chromatin- complex of proteins and DNA making up chromosomes  c. It is important to recognize that ribosomes are not simply made in the  nucleus. Proteins are never made in the nucleus; they are allowed  inside by gatekeeper proteins and rRNA is attached to them at the  nucleolus; forming the large and small subunit. 

d. These two subunits then exit the nucleus separately, they only connect during protein synthesis in the cytosol

 e. The nucleus directs protein synthesis by making mRNA 

A ribosome is a complex with two parts; large subunit (large, top) and small subunit (small, bottom)

∙ Two macromolecules that make up ribosomes are nucleic acid (rRNA) and  protein

 1. rRNAprovides the bulk and structure of ribosomes 

The endomembrane system consists of organelles that usually arise by budding  from the ER

∙ The secretory system consists of organelles that get their cargo (proteins and lipids) via secretory vesicles

1. Peroxisomes do not get their proteins via secretory vesicles, they absorb  proteins from cytosol (therefore they are not a part of the secretory  system)

Outer Nuclear Membrane folds several times to form the endoplasmic reticulum- a  network of membranes that fold and extend forming spaces that collect protein and  cargo

Rough Endoplasmic Reticulum  

Functions – (first thing that comes to mind;  PROTEIN)

Smooth Endoplasmic Reticulum Functions – (first  thing that comes to mind; DETOXIFICATION)

Involved in the synthesis of proteins ∙ Ribosomes are sitting on the rough ER

Smooth ER increases in surface area as it detoxifies over  time; this is why we build tolerances to alcohol and other  toxic substances

∙ Initially, the dose is very low because it stays in the body longer. But you’ll require higher doses  

because it is metabolized more quickly (especially  true for drugs with barbiturates)

∙ Smooth ER converts alcohol and medications into  hydrophilic metabolites ready for excretion

Insertion- inserting proteins into the  membrane of the endoplasmic reticulum

Storage of calcium ions- relates to action potential  (response to stimulus)

∙ A difference in calcium ion concentration between  cytosol and smooth ER is required for muscle  contraction or enzyme release

∙ Concentration of Calcium in Smooth ER is 10-3 mM , while concentration of calcium ions in Cytosol is 10- 7 mM

1. This difference is important for nerves to pass  on information, for muscles to contract, and to  release enzymes

Sorting (glycosylation)- process by which  carbohydrates are attached to the proteins ∙ Glycosylation is initiated in the Rough  ER

∙ Glycosylation is the tagging of  

proteins by carbohydrate monomers  so that they are transported to a  

particular location

Carbohydrate catabolism 

∙ Storage carbohydrate in our body is glycogen, a  highly branched polar chain, which is present close to the smooth ER

∙ To get energy from glycogen, it must be broken  down by adding a phosphate to it (making it  

charged)

1. The glyosidic bond between a polar glucose and a charged glucose becomes very weak; it’s easy to break the glucose off from the glycogen

2. Once the glucose is broken off from the  

glycogen, it is present in the form of Glucose 6  Phosphate; a charged compound that is difficult to move out of the cell

3. To move it out of the cell, the phosphate must  be removed, and it is removed by the smooth  ER through its use of the enzyme Glucose 6  

Phosphatase. It also allows the charged glucose to be converted back to polar glucose, letting it  move around the cell to give energy

Synthesis and Modification of Lipids (specifically  phospholipids)

∙ Modifies hormones, makes oils

Golgi Complex- composed of stacks of membrane-bound sacs

∙ Golgi is the transport center of the cell 

∙ Golgi is also called the secretory and packaging center of the cell 

1. Cargo (proteins or lipids) comes out of the ER in the form of budding

a. Budding- cargo is pushed into the membrane, forming a budlike  

structure, and then is pinched off

2. Diffusion never takes place between membranes; even between Golgi  

sacs, cargo is transported only through secretory vesicles

a. This is why it is a secretory organelle; everything is packaged into  

vesicles to be passed on, nothing diffuses

3. Cis face- face of Golgi that always faces the ER and receives cargo from  

ER

4. Medial face- middle part of Golgi

5. Trans face- sacs of Golgi facing opposite to the cis, towards plasma  

membrane

∙ Medial Golgi is most important because of its following functions

1. Glycosylation is continued- more tagging takes place

2. Proteolysis- breaking; Inactive, long proteins are converted into active  

proteins

∙ Trans Golgi initiates exocytosis 

1. Very large cargo (like insulin) is packaged via vesicles to the Trans Golgi,  

where it is packaged into a vesicle that travels to the plasma membrane

a. Since the vesicle is too big to go through a transport protein, the  vesicle merges with the plasma membrane, and releases insulin to the  outside

Lysosomes are the organelles of breakdown of macromolecules, foreign substances, and autophagy in animal cells 

 ∙     Lysosomes can break down any macromolecule for reasons of detoxification,  recycling old organelles, etc. 

∙ They contain enzymes called acid hydrolases; they need a very specific  optimum pH to function (4.8)

1. They use water for breakdown (hence hydrolases)

∙ Lysosomes are usually present in the form of primary lysosomes which have a pH slightly higher than 4.8

∙ Apoptosis- programmed cell death

1. If a cell has a defective DNA, it induces its own death

∙ Autophagy- recycling of old organelles

1. Mitochondria has a life-span of 10 days, so after 10 days, a lysosome will  break it down to create a new one

Vacuoles- storage organelle of water, amino acids, ions, minerals, and waste in  plants

∙ Membrane of the vacuole is tonoplast; its capable of expanding and  contracting

∙ Water entering a plant goes through the vacuole; as it exits the vacuole it  exerts turgor pressure, giving the plant a rigid structure

∙ Protists have organelles very similar to vacuoles, so we’ll call them vacuoles  for the sake of this chapter

1. Protists are hypertonic- water will flow from the outside into the protist a. To avoid explosion, contractile vacuoles inside protists regulate flow of  water to a certain extent, maintaining cell volume 

Semi-autonomous organelles; chloroplasts and mitochondria 

Why are they called ‘semi-autonomous?’ 

∙ They have their own DNA in the nucleoid region

∙ They have their own ribosomes capable of making proteins

∙ BUT they cannot divide on their own

1. The signal of division must come from the nucleus

∙ They also can’t do all of their functions on their own

1. They must take proteins from the cell

Mitochondria is the powerhouse of the cell, but it is also known by boring people as  the respiratory center of the cell

∙ Inner Mitochondrial Membrane is invaginated; increased surface area in order to perform its functions

1. A part of the IMM is the cristae

∙ Along the cristae are complexes and proteins

2. VERY important protein found here is ATP Synthase Enzyme

∙ Mitochondrial Matrix- where ATP is made

∙ Mitochondria is involved in the modification of hormones, while also playing a role in hibernation

Mitochondria can undergo certain modifications

∙ While we have a lot of white fat cells, newborns have a lot of brown fat cells ∙ As you grow up, brown fat cells are replaced by white fat cells 1. White fat cells conserve excess energy as fat

Mitochondria and chloroplasts both divide by binary fission (like bacteria)

∙ Peroxisome also divides like the mitochondria and chloroplasts (binary fission) 1. Peroxisomes also absorb proteins from the cytosol, like mitochondria and  chloroplasts

2. HOWEVER, peroxisomes are classified under endomembrane system, not  semi-autonomous organelle because they don’t have their own DNA

Endosymbiotic Theory- explains the origins of mitochondria and chloroplasts

∙ Symbiosis- relationship between two organisms that live in the same place at  the same time

∙ When we talk about endosymbiotic theory, we use a primordial eukaryotic  cell (progressing towards becoming a eukaryotic cell)

1. Another cell, capable of oxidizing and producing ATP (like Purple Nonsulfur Bacteria) enters the primordial euk, looking for a place to live

2. The entering bacteria sheds its outer membrane, and takes the membrane of the host cell

3. The host cell considers the incoming bacteria as its own, and does not  fight it as a foreign  

4. The incoming bacteria now has a place to live and nutrition, while the host has no properties, like the ability to synthesize ATP in the presence of  oxygen

5. This is how mitochondria came to be; same for chloroplasts, but with a  photosynthetic bacteria

 6. The host cell maintains autonomy while the incoming bacteria loses its  autonomy 

Chloroplasts are plastids, which came from pro-plastids

∙ Depending on the presence of difference pigments, there are different  plastids

1. Chloroplasts contain chlorophyll and perform photosynthesis 2. Chromoplasts contain red, yellow, and orange pigments involved in  pollinations and seed dispersal

3. Leucoplasts or amyloplasts are present in tubers underground; involved in  storage of energy (starch in potatoes)

∙ Thylakoid- membrane-bound, disk-like structures

1. 1-2 dozen thylakoids are stacked into columns called grana (granum  singular)

2. Each granum is connected by structures called lamella 

 3. All the proteins and complexes involved in light reactions are in the  membrane of the thylakoid 

a. Light reactions- converting radiant energy into ATP

 b. Oxygen is released as a result in the thylakoid lumen 

∙    Carbohydrates are synthesized in the stroma

Peroxisomes- small organelles associated with breakdown, specifically detoxification

∙ Present in both plants and animals

∙ Any time it breaks down a compound, it always gives off hydrogen peroxide  

as a byproduct

1. Lysosomes use water to break down, but peroxisomes remove hydrogen  

and add oxygen to break down compounds

2. Hydrogen peroxide is a free radical- highly dangerous compounds that  

have an unpaired electron which has the capacity to rob electrons from  

completely balanced compounds, generating new families of free radicals

3. Hydrogen peroxide is not a good thing to have in the cell, so another  

enzyme (catalase) immediately breaks it down into harmless water

∙ Peroxisomes undergo binary fission, but they are not semi-autonomous  

because they originated from endoplasmic reticulum by budding

1. Small, premature peroxisomes come together to form a big, mature  

peroxisome that can divide by binary fission

2. This is why we say peroxisomes are part of the endomembrane system,  

not the secretory system

a. The way peroxisomes get their proteins is similar to  

mitochondria/chloroplasts, not like Golgi or lysosomes

∙ Peroxisomes are the venue for the process known as beta oxidation; the  

process by which fats and lipids are converted to carbohydrates

Cytoskeleton- proteins that exist throughout the lifecycle of the cell

Microtubules

Intermediate Filaments

Microfilaments (Actin)

25 nm in diameter

10-15 nm in diameter

7 nm in diameter

Made up of Alpha and Beta  tubulin, connected to form long  strands called protofilaments,  with a tube-like structure in the

Very stable; they do not undergo  dynamic instability

∙ Not polar

∙ No motor proteins

Composed of Actin Beads

∙ Two long strands of actin  beads intertwine to form  

an actin filament

middle (hence the name)

Capable of dynamic  

instability- they can polymerize and depolymerize

∙ Extend and break down

Formed by combination of three  long strands of filaments that  come together to make a rope-like protein

∙ Keratin, Vimentin, Nuclear  Lamina, and nerve cells are

all examples of  

intermediate filaments

Capable of dynamic instability, and therefore has polarity, like  microtubules

Centrosome with a centriole (in  the nucleus) is the microtubule  organizing center; they all come  from here

Gives support, structure, shape,  and rigidity 

∙ They do not degrade over  time, but if they are  

destroyed, they are gone  

forever

Actin is present as a layer below  the plasma membrane

∙ The – end of Actin is below  the plasma membrane,  

and it can polymerize  

towards the nucleus or  

away from the nucleus

Because of their dynamic  

instability, microtubules are  polar (- end towards  

nucleus/origin, + end away from nucleus/where its added)

Actin forms projections that do  not pierce the plasma  

membrane; pseudopodium

∙ As this happens, myosin  drags the cell towards  

nutrition until it is close  

enough to take it into the  

cell

Motor proteins move using  energy 

∙ They get energy by ATP  hydrolysis

∙ Motor protein dynein

moves towards the – end,  

carrying cargo towards  

the nucleus

∙ Motor protein kinesin  

moves towards the + end,

carrying cargo towards  

the plasma membrane

Cytoplasmic streaming- Actin  allows cargo to move around the  cell through the cytoplasm

∙ If you have two cells, Actin allows anchorage of the  

two cells

∙ Actin allows cells to modify cell shape when moving  

through small spaces like  

blood vessels (mobility)

Microtubules give support and  shape, but their most important  function is forming microtubule tracts, helping in the movement of cargo and organelles

Actin’s one motor protein is  myosin

Motor proteins are proteins that move using energy from ATP hydrolysis, and they  move using three different movements

∙ Head of motor protein connects to cytoskeleton protein. Head is connected by hinge to the tail, which is connected to the cargo

∙ 1st movement- Walking movement 

1. Motor protein attaches, moves forward, etc.  

2. Cytoskeletal protein is fixed

3. Motor protein moves

∙ 2nd 

 movement- Sliding movement 

1. Instead of moving the motor protein, the cytoskeleton is moved east-west  (slides)

2. Cytoskeleton moves

3. Motor protein is fixed

∙ 3rd movement- Corkscrew/Whiplash movement 

1. Used in sperm flagella and cilia

2. Cytoskeletal protein bends, energy is transferred from the head to the tail a. Think of it like a ripple effect; when you toss a stone into a body of  water, ripples form from the middle of the point of contact outwards b. In a similar fashion, energy is transferred from the head of the motor  protein to the tail, creating the whiplash movement

Composition of microtubules in flagella – Axiom (cross section of flagella and cilia)

∙ 9 microtubules present in the form of doublets (1 complete and one smaller  copy), as well as 2 single microtubules in the center

1. We call this a 9+2 arrangement 

∙ Radial spokes connect and control microtubules

∙ Nexin- protein that prevents microtubules from moving

∙ Dynein- motor protein that moves on these microtubules

∙ Remember, this composition is the same for both flagella and cilia ∙ Protein that makes up flagella in bacteria- flagellin

∙ Flagella and cilia arise from a structure below the plasma membrane called  basal body, which have triplet microtubules instead of doublets; everything  else is identical to that of flagella and cilia

CHAPTER 5 – MEMBRANE TRANSFER (yay!)

The function of a membrane is to be a formidable yet flexible barrier

∙ Formidable- a membrane will only allow substances that need to come in to  enter

∙ Flexible- A membrane cannot be rigid; proteins need to change shape ∙ All membranes are composed of phospholipids, giving the function  of semi-permeability 

∙ There are also a lot of proteins in the membrane, which give it the function of selective permeability

∙ Carbohydrates are in the membrane as well, but they are not required;  depends on the function of the membrane 

Fluid-mosaic model- arrangement of phospholipids and proteins in plasma  membrane is akin to boats on a body of water

∙ Phospholipids form the fluid on which proteins are suspended like boats 1. Phospholipids are in constant motion

∙ ‘Mosaic’ comes from the idea of ‘asymmetry’

1. There is no particular arrangement of phospholipids and proteins 2. The two layers of the phospholipids are asymmetrical; not equal a. The outside layer (called the extracellular leaflet) has a lot of  glycolipids and glycoproteins

b. The inside layer is called the protoplasmic leaflet, and has less  glycolipids and glycoproteins

Membranes are semifluid

∙ Cannot move in a 3d manner in a fluid

∙ Molecules move in a fluid medium by bilateral movement

Our membrane is flexible because phospholipids are capable of bilateral  movement and they can rotate about their axes

∙ Two factors influence the capacity to move in bilateral movement; length and  composition

1. Length of hydrocarbons influences movement

a. Polar head of phospholipid bilayer is orientated towards the outside  and inside, with the tails forming the mesh

b. Tails that are too long are incapable of movement

c. The length of the fatty acid tails is important in influencing  fluidity; shorter ones are preferable

2. Composition of fatty acid tails; they should be as unsaturated as possible a. Saturated fatty acid tails are very stiff; no possibility for movement b. Unsaturated fatty acid tails give flexibility and movement

∙ In optimum temperature, no help is required from any other compounds or  molecules to maintain fluidity 

∙ In animal cells, phospholipid flexibility must be maintained by cholesterol in  hostile environments 

1. In hot temperatures, phospholipids tend to move too fast and can break  apart; this can rupture the membrane (you don’t want that)

a. Cholesterol compactly binds to the membrane to reduce the  movement

2. In cold temperatures, phospholipids tend to move too slow and can stop;  this can completely stop the transfer of molecules in and out of the cell  (you really don’t want that)

a. Proteins rely on the membrane’s flexibility to open and close, allowing  molecular transfer

b. Cholesterol gives a cushioning effect (a warmth) to the phospholipids  in order to maintain movement

∙ Plant cells and lower eukaryotes (protists) cannot use molecules like  cholesterol in this manner

1. In hot temperatures, they instead increase the length of their fatty acid  tails, reducing movement

2. In cold temperatures, they decrease the length of their fatty acid tails,  maintaining movement

∙ When viruses invade our cells, we have masses of lipids called lipid rafts that  float around the plasma membrane

Bilateral movement is a very energy efficient process, but flipping requires energy ∙ Polar head needs to pass through polar area to reach the other side (flip)

1. This is energy inefficient and requires the presence of the enzyme flippase (good luck remembering that one)

2. Also requires ATP hydrolysis for energy

There are proteins along the membrane that are globular; they are larger than the  phospholipids

∙ Scientists created a chimera between a mouse cell and a human cell; put  them both in a culture medium, gave a spark of electricity, and a hybrid was  created

1. Mouse cells have a very well-established antigen on the plasma  membrane called the “H2 Antigen,” which humans don’t have, that can react with a fluorescently-labeled antibody

2. When the hybrid was formed, they split it into two groups of cells; one  group was frozen immediately and the other was left in the incubator 3. After a couple hours, the two groups were labeled with the  

fluorescently labeled antibody

4. In the frozen cells, the green, fluorescent antibody was present only in  one half of the cells (the mouse half)

5. In the incubated cells, the green, fluorescent antibody was present  throughout the cells; proteins (antigens) can move, even though they  are large and globular 

We’ve established that proteins can move, but not all proteins have this ability

∙ Proteins that deal with adhesion do not move (adhesive proteins that attach  to other cells do not move)

∙ Proteins involved in compartmentalizing do not move (proteins that are  involved in separating cells based on function)

Classification of proteins; integrals/intrinsic membrane proteins and  peripheral/external/extrinsic membrane proteins 

∙    Classification is based off the technique involved in isolation the protein ∙    To isolate an integral membrane protein, the membrane must be destroyed  using a detergent

1. Example: transmembrane protein- protein travels along the length of the  membrane

a. Along the length of the membrane are nonpolar, hydrophobic areas b. The transmembrane protein has alpha helical structures present  adjacent to the hydrophobic, nonpolar part of the phospholipid

c. All amino acids forming this structure are nonpolar

d. The reason we must destroy the membrane to isolate these proteins is  because they are held in position by hydrophobic exclusion 

a. Water outside and inside the cell pushes in on the protein

∙    To isolate a peripheral/extrinsic membrane protein, a solution of opposite  charge must be poured; the membrane doesn’t have to be destroyed 1. Proteins attached to polar/hydrophilic head through forces of attraction  (hydrogen/ionic bonds

∙    Proteins are really important to the membrane because most of the functions  of the membrane (besides semi-permeability) is associated with proteins ∙    Proteins present along plasma membrane; adhesive proteins, transport  proteins, and receptor proteins

 1. Adhesive proteins help a cell attach to the extracellular matrix or  neighboring cells

 2. Transport proteins help in selective permeability

 3. Receptor proteins are involved in cell communication by receiving signal  molecules from other cells

4. There are also proteins along the membrane that act as enzymes, like ATP synthase in the inner mitochondrial membrane

Glycosylation is the addition of carbohydrate chains to proteins or lipids; initiated in  the RER and continued in the Golgi

∙ In the ER, proteins are inserted into membranes, these membranes bud out  as vesicles. They are further processed in the medial Golgi, then sent out  from the trans Golgi to merge with the plasma membrane by exocytosis. As it merges, these proteins and carbohydrates will be attached to the outer and  inner surfaces of the plasma membrane 

Glycolipids are involved in tissue-specific regulation; recognizing cells of different  tissue or systems

Glycoproteins are involved in self/non-self recognition 

Glycocalyx- Dense layer of carbohydrate trees outside the cell that prevent  dehydration

∙ In animal cells, the glycocalyx protects the membrane proteins from proteases (enzymes that digest proteins) 

∙ The glycocalyx also protects the membrane from the physical and chemical aspects of the extracellular matrix 

1. Collagen is a rope-like protein that is always moving in the extracellular matrix  

2. Without the carbohydrate layer provided by the glycocalyx, the proteins are at risk of losing amino acids

∙ Finally, the glycocalyx also deals with migration of cells during embryogenesis 

1. Cells moving to form your head or nerves are guided by these carbohydrate trees in the glycocalyx  

Permeability/Transport- we have two methods by which substances are transported into the cell; energy-inefficient proesss of active transport and energy efficient process of passive transport 

∙ Active transport is the method of moving substances or solutes from an area of lower concentration to an area of high concentration; against the concentration gradient by supplying energy

1. Active transport is important because it builds a gradient, and gradients are required for all our cells because gradients maintain homeostasis 2. This is why we expend energy on active transport

∙ Passive transport (DIFFUSION = NO ENERGY) is the movement of substances or solutes from an area of high concentration to an area of low concentration towards the concentration gradient without the use of energy

1. Passive transport does not require the use of proteins; only phospholipids 2. Gases diffuse very fast through the membrane

a. Both Lamborghinis and Ferraris are fast, but the Ferrari is just slightly faster

b. Ethanol has a carboxyl group, so it is barely polar 

c. Ethane is complexly nonpolar 

d. Ethane is the Ferrari and Ethanol is the Lambo. The carboxyl group is the drag on the ethanol 

e. The more hydrocarbons added to a compound, the faster the rate of movement through the plasma membrane 

3. Some substances trickle through the membrane because of concentration, not affinity

a. There is a lot of water present on the outside and inside of the cell, so phospholipids cannot stop water from trickling through slowly

b. Urea also trickles in, even though it has no affinity to pass very fast; if nonpolar compounds are added, it can move faster, despite its larger shape

c. Non-polarity is more important than size when determining speed of passage through a membrane 

4. Glucose is a very large, polar compound; too large to move through the phospholipids (never moves through)

a. It requires transport proteins to pass through

5. Ions never never move through

6. Amino acids and ATP never never never never never pass through

There are two different types of gradients; transmembrane gradients and ion electrochemical gradients

∙ Transmembrane gradient- difference in concentrations of a solute (charges not included)

1. Can include difference in concentration of a solute or solvent ∙ Ion Electrochemical gradient- does not only include a difference in concentration of solutes, but also of charges

1. Very important in nerve-nerve/nerve-muscle transmissions, muscle contraction, movement of bacteria, movement of cells, and secretion of enzymes and hormones

Passive transport deals with passive diffusion and facilitated diffusion

∙ In passive diffusion, no energy is supplied

1. Substances travel through the phospholipid bilayer from an area of high concentration to an area of low concentration without energy

∙ In facilitated diffusion, energy is still not involved, but channels or carriers help in the diffusion from high to low concentrations

1. Both channels and carriers are very specific

2. Channels have a rate of movement from several hundred thousand particles to a million or billion per second because it is simply an unobstructed flow

3. Carriers still move from high to low, but they have a much slower rate of movement because they require a temporary physical bonding with the solute

Tonicity is in relation to the solute while Osmosis is always in relation to the solvent (always assumed as water unless specified otherwise)

∙ Tonicity deals with movement of solutes from an area of high concentration of solute to an area of low concentration of solute

∙ Red blood cells exist in isotonic mediums- concentration of solutes inside the cell and the medium are the same

1. If a red blood cell is placed in a hypertonic solution, it will shrivel (crenation)

a. This occurs because there is a low concentration of solute in the blood cell, and a high concentration of solute in the solution, so the free water from the cell moved out into the solution

b. In hypertonic solutions, the solution has more solutes than the cell

2. If a red blood cell is placed in a hypotonic solution (like de-ionized water), it will explode (osmotic lysis)

a. This is because there is a high concentration of solute in the cell and a low concentration in the solution, so water rushes into the cell (osmotic lysis)

b. In hypotonic solutions, the solution has less solutes than the cell

∙ Osmosis always relates to movement of water (unless specifically told otherwise) from an area of high concentration of free water to an area of low concentration of free water

1. Osmotic concentration is identical to tonicity

a. Osmolarity deals with solute concentration

b. Osmosis is the only term that deals with solvent (water) 

c. Hyperosmotic- hypertonic

 d. Hypo-osmotic- hypotonic

Dr. V stressed to write the following properties down directly from the powerpoint, so definitely know these

∙ Osmotic concentration- concentration of all solutes in solution 1. Hyperosmotic- solution with the higher solute concentration 

2. Hypo-osmotic- solution with the lower solute concentration 

3. Iso-osmotic- solute concentrations are equal 

Osmoregulation

Plants and freshwater organism cells are always hypertonic; they have more solutes

∙    When exposed to water, it will always try to enter the cell

 ∙     Contractile vacuoles in protists allow water to come in until it reaches  maximum density. At this point it will contract, releasing excess water to  avoid bursting

1. These special vacuoles maintain osmoregulation and cell volume in  protists

 ∙     Turgor pressure in vacuoles in plant cells

1. Plasmolysis- complete drying out of the plant (NO water or turgor  pressure)

Transport Proteins 

Channels give cells maximum rate of movement because they don’t have to  physically bind with the solute 

Gated channels are usually closed until a signal binds which tells the channel to  open; when the signal breaks off, the channel closes 

∙ There are various gated channels that depend on the signal and type of  bonding

1. Ligand-gated (NON-COVALENT BONDING) – compound (hormone, steroid,  enzyme, carboyhydrate) binds in short unit of time noncovalently very  specific to the channel

2. Intracellular regulatory protein (SIGNAL COMING FROM INSIDE)- signal is a  protein that binds to channel noncovalently

3. Phosphorylation- phosphate binds to channel covalently

4. Voltage Gated Channel- channel opens when there is a difference of  charges (no signal molecule)

5. Mechanosensitive Channels- channel opens when there is a difference of  surface tension along the membrane

a. We hear sounds thanks to our cochlear fluid along the inner ear  membrane that can distinguish minute changes in surface tension

Leaky channels- channels with a very slow rate of trickling of ions to maintain a  resting potential so that information is still passed on without active stimuli

∙ We still want housekeeper functions while we sleep

∙ Most common leaky channel is the Potassium channel

Facilitated Diffusion – Carriers (Transporters) 

Passive transport does not require energy

∙ There is a very specific transporter for whatever compound needs that  transport protein, and the compound moves from high to low concentration ∙ One problem with transporters is saturation; rate of movement does not  equal the rate of increase in concentration

1. The rate of transport does not correspond to the rate of increase in  concentration of solute

2. This problem is encountered by carriers (not channels)

Different types of transporters are based on how many solutes can be transported

∙ Uniporters- one solute can be transported 

∙ Cotransporters- more than one solute can be transported 

∙ Symporter- more than one solute in same direction 

∙ Antiporters- more than one solute in opposite direction 

Active Transport 

Active transport- the process by which solutes are moved from an area of low  concentration to an area of high concentration against the concentration gradient  using energy 

Protein involved in active transport will never be called channel/carrier/transporter;  but rather a pump

There are two different types of active transport; primary and secondary

∙ Primary Active Transport’s source of energy is ATP hydrolysis ∙ Secondary Active Transport’s source of energy is pre-existing gradient 1. The intermembrane space IMS) of the mitochondria has a high  concentration of protons and a low concentration of pyruvate. The inner  mitochondrial membrane (IMM) has a low concentration of protons and a  high concentration of pyruvate. As the protons flow from high to low  concentration down the concentration gradient into the IMM,  energy is provided to drag pyruvate up the concentration energy.

Primary Active Transport - Electrogenic Pump (pump that generates a difference of charges) (I’ll provide a picture in this unit’s study guide)

Sodium is present in large concentrations outside of the cell and potassium is  present in large concentrations inside the cell

 Na+ K+  

 ATP Pump 

Step 1. E1 Conformation- 3 Na+ ions bind on the cytosolic side 

∙ The pump has an affinity to bind with 3 Na+ ions in this conformation 

Step 2. ATP Hydrolysis- a phosphorous from ATP binds to the pump, changing its  conformation from E1 to E2

Step 3. E2 Conformation- Pump now has an affinity to bind to 2 K+ ions and release 3 Na+ ions outside the cell 

Step 4. Phosphorous is released- this changes the conformation back to E1

∙ 2 K+ ions are released inside the cell and the cell now has an affinity for 3 Na+ ions once again

In the end, 3 sodium ions were pushed outside the cell and 2 potassium ions were pushed inside the cell (difference of 1 charge generated, therefore this is an  electrogenic pump)

∙ Difference in charges creates membrane potential

∙ Electrogenic pumps are involved in nerve-nerve signal transmission,  nerve-muscle signal transmission, release of hormones and enzymes, muscle contraction, movement of flagella In prokaryotes

∙ The phosphate binding to the pump is not directly related to potassium  binding, but is directly related to sodium binding, because it triggers a  release of sodium

Exo/Endocytosis 

Cargo size decides whether a protein should be used or not

Endocytosis- cargo entering the cell

∙ Includes phagocytosis (cell eating) and pinocytosis (cell drinking) depending  on cargo

∙ When cargo is coming in, plasma membrane is invaginated and engulfs the  cargo, forming a vesicle  

1. Coat protein- helps in budding process

a. As soon as the vesicle buds off, the coat protein breaks off the vesicle Exocytosis- cargo leaving the cell (begins in the trans Golgi)

∙ Transmembrane proteins called V snares are inserted into the vesicle that  direct the vesicle to its desired location, whether it be an organelle or outside  the cell

∙ Coat proteins help in budding process of trans Golgi

∙ Transmembrane proteins called T snares along plasma or organelle  membranes

∙ Vesicle docks, V and T snares bind, cargo leaves the cell

Cholesterol Receptor-Mediated Endocytosis (very specific, I’ll add a picture in the  study guide) 

Pitted membrane (slight invagination of membrane) present in receptor-mediated  endocytosis

∙ Below the pitted membrane is a layer of a specific type of protein clathrin, so  we call this a clathrin-coated pit

∙ Tails of LDL receptors embedded into clathrin pit

∙ Cholesterol with LDL binds to LDL receptors

∙ When the receptors are saturated with LDL, the receptors send a signal to the clathrin to close and form a vesicle

∙ The vesicle contains two recyclable items; clathrin and receptors ∙ First, clathrin surrounding the vesicle breaks off and is recycled back into the  membrane

∙ Now we are left with an endosome; no clathrin is present, but receptors are  cargo are

∙ To recycle the receptors, the endosome buds into two; one part contains the  receptors and the other contains the LDL cargo

∙ Lysosome then comes in contact with LDL vesicle and breaks it down

CHAPTER 7 WE MADE IT

Our cells are factories of energy, with energy constantly being made and used

∙ Metabolism- sum of all reactions that take place in the body (anabolism +  catabolism)

∙ Cellular metabolism- all the metabolic activities and reactions that take place  within a cell

Two factors dictate the fate of any reaction; direction and rate

∙ Optimum reactants and energy determine direction of any reaction 1. Enzymes and catalysts speed up rate of reaction

∙ Reversible reactions reach equilibrium when the rate of the forward reaction  equals the rate of the reverse reaction

∙ Forward reactions reach equilibrium when all the reactants are converted to  products

Metabolic pathways- series of reactions that occur to give one product in which the  products of the initial reactions become the reactants of the following reaction

∙ Multi-enzyme complex allows reactions to be time efficient, energy  efficient, and have each reaction occur in a completely synchronized  manner

∙ Anabolic pathways are involved in synthesizing large compounds from small  compounds with the use of energy (alpha ketoglutarate + ammonia + NADH  = glutamine)

Energy is the capacity to do work or cause change

∙ Potential energy is energy of position

∙ Kinetic energy is energy of motion (heart in body)

∙ Thermal energy- kinetic energy in reference to random movement (heat) 1. Transferring thermal energy from one system to another allows travels  from an area of high heat to an area of low heat

∙ Chemical energy (the most important type of energy for biologists)-  potential energy released when bonds between molecules are broken

One common factor between all different types of energy; they all release and can  be converted to heat energy 

∙ Heat is not a source of energy for us because heat flows from high to low concentration, and we are warm-blooded thanks to our  maintenance of homeostasis 

Unit of energy is a calorie- the amount of energy required to increase the  temperature of 1 gram of water 1 degree Centigrade

∙ Whenever we measure energy content in a living cell or energy being taken  up by a living cell, we always use kilocalories (1000cal = 1kcal) 

 Thermodynamics- the study of changes in heat/thermal energy 

First Law of Thermodynamics- energy can neither be created nor destroyed, but  can be transferred from one form or level to another

∙ Flow of energy- Sun -> plants -> duck -> people -> lion -> decomposers ->  plants -> etc.

1. Only 1% of the sun’s energy is captured by photoautotrophs, and it is  stored as chemical energy in the different bonds of the producers

Second Law of Thermodynamics (Entropy and HEAT)- In every  transfer/conversion, part of the energy is always converted into heat; we call this  process entropy

∙ Entropy is a system of disorder, and disorder is said to be stable 1. When standing on a diving board, you have a lot of potential energy. This  orderly situation is unstable because you tend to fall and do work. When  falling off the board, you do work and release that stored energy,  achieving a state of less energy, and therefore more stable because you  are not required to do more work 

2. Once energy is released to a low state, a system becomes disorderly, and  thus, stable

We are considered open systems because we are always exchanging energy within  our body and with the environment

∙ Our cell will never be in a state of equilibrium because there are constant  interactions taking place

How do we know if a reaction is spontaneous or not?

Enthalpy- total energy (uses variable H)  

∙ H = G + TS

1. G is usable, free energy that is available to do work

2. T is temperature and S is entropy, or unusable energy (there is a direct  relationship between temperature and heat)

∙ ∆G = ∆H - T∆S

1. Changes in free energy is given by changes in total energy minus  temperature times changes in entropy

2. ∆G is positive if you have a high enthalpy (H)

3. We can use this equation to tell us whether a reaction is spontaneous or  not

a. Spontaneous reactions occur with very little input of energy

b. Instantaneous reactions occur very quickly

c. All spontaneous reactions are not instantaneous; if you have a  fire in one corner of the room and a match in the other, the match will  not light right away

∆G is positive (+)

∆G is negative (-)

Based off the equation, we need a high  enthalpy to achieve a positive ∆G ∙ This means that the products  have more energy than the  

reactants

1. CO2 and H2O have no energy,  

but they can synthesize a  

carbohydrate, which has a lot of

energy

Based off the equation, we need a low  enthalpy to achieve a negative ∆G ∙ This means that the reactants  have more energy than the  

products

1. Carbohydrate burning with O2

will yield a lot of energy

For the reaction to take place, a lot of  activation energy is required, and  therefore is not spontaneous

For the reaction to take place, not much  activation energy is required, and  therefore it is spontaneous

Anabolic, Endergonic reactions yield a  +∆G

Catabolic, exergonic reactions yield a  -∆G

CO2 + H2O -> Glucose; ∆G = +686 kcal

Glucose + O2 -> CO2 + H2O; ∆G = -686  kcal

∆G+ = instability

∆G- = stability

 Energy is stored in ATP through electrostatic repulsion 

∙ Very little activation energy pushes the phosphates out

1. ∆G for ATP hydrolysis is -7.3 kcals (exergonic reaction) 

2. ∆G for ATP synthesis is +7.3 kcals (endergonic reaction) 

a. Energy is required to attach a negatively charged phosphate to ADP,  which already has two negatively charged phosphates

How does the cell use ATP? 

The cell uses ATP for chemical means, not mechanical or transport

 ∙      The cell uses ATP to convert endergonic reactions into net exergonic  reactions 

1. Glucose + Phosphate -> Glu. P; ∆G= +3.3kcal

a. The first thing the cell does is hydrolyze ATP into ADP and Phosphate  with a ∆G of -7.3kcals

b. -7.3 + 3.3 = -4.0 kcal

c. The endergonic reaction was converted to net exergonic thanks to ATP  hydrolysis

∙ ATP can be used for chemical, transport, mechanical means, but the cell uses  it for converting net endergonic into net exergonic

How do we reduce activation energy? 

Activation energy- energy required to initiate a reaction

We can reduce activation energy to speed up a reaction with catalysts and enzymes

∙ Activation energy is necessary to bring reactants close together by stressing  the bonds of the reactants until they reach transition level, which is when the  bonds change from their stable states to their breaking points

Enzymes are large, globular proteins with an important domain called the active  site, where reactants combine; this forms an enzyme-reactant complex 

∙ The attachment of a substrate to the active site of an enzyme is very specific, following the lock and key model

∙ Domain is related to tertiary structure of a protein

∙ Induced fit- when a reactant comes into the active site, it does not fit  compactly, but as time goes on, the different amino acids of the active site fit precisely into the different bonds of the reactants, stressing the bonds until  they break

Prosthetic group- Permanently attached to enzymes

Temporarily attached compounds help the enzyme function

∙ Cofactors- inorganic compounds that temporarily bind to the enzyme  enhancing enzyme activity

∙ Coenzymes- organic, non-proteinaceous compounds

What are the conditions necessary for optimum enzyme activity? Temperature (98.6 degrees F or 37 degrees C for us)

∙ Amino acids are very sensitive to changes in temperature because of  denaturation 

pH (2 in our stomach and in Dr. Pepper, 7.362-7.42 in blood)

∙ Amino acids can be polar/charged, so they are sensitive to changes in Ph (H+  concentration)

How can an enzyme get saturated? 

If we have 10 molecules of enzymes and 2 molecules of reactants, not all of the  enzymes have been saturated

∙ Rate of reaction increases when all enzymes are saturated with reactants ∙ Rate of reaction increases with lots of enzymes and little reactants ∙ To become saturated, the reactant must be in the active site of the enzyme

How do we regulate enzyme activity? 

Biochemical regulation’s main goal is conserving energy

There are two major types of enzyme inhibitors; competitive and noncompetitive

∙ Competitive inhibitors compete for the active site

1. Inhibitor has same 3d structure as substrate

2. It binds to the active site, preventing any substrates from binding, and  therefore preventing future reactions

3. Most inhibitors are reversible

∙ Noncompetitive inhibitors are allosteric- they bind to another part of the  enzyme, not the active site; this changes the 3d structure of the enzyme so  that the active site loses its 3d shape

1. Allosteric inhibition is rate limiting

a. A + B –-(2 minutes)--> C + D –(4 minutes)--> E + F –(2 minutes)--> G  + H

b. The purple highlighted step takes the longest time, and therefore it is  the rate-limiting step

c. Allosteric inhibitors attack the enzyme at the rate-limiting step; the  step that takes the longest

d. This slows the reaction down to a standstill

∙ Competitors deal with cooperativity

1. They bind to the enzyme, stabilizing its structure

2. Enzymes can be active or inactive, so substances like allosteric inhibitors  prevent the enzyme from reaching its active form

3. Cooperativity- when a substrate binds to the enzyme, the enzyme is  capable of retaining its active form for extended periods of time ∙ Feedback inhibition- form of allosteric inhibition by which a product of the  reaction binds to a site other than the active site, changing the 3d structure  of the enzyme so that it cannot function

∙    Enzymes evolved through mutation

Glycolysis takes place in the cytosol catalyzed by free-floating enzymes, but a lot of  ATP is produced by the enzymes and complexes along the mitochondrial inner  membrane

The plasma membrane of bacteria is involved in ATP synthesis

Chapter 8 – Here we go

Life is nothing but a flow of energy

Aerobic respiration is breakdown in the presence of oxygen

Anaerobic respiration vs fermentation

∙ Anaerobic respiration is breakdown in the absence of oxygen

∙ Fermentation is breakdown in the absence of oxygen using organic molecules

Aerobic

Anaerobic

Fermentation

O2 receives the de

energized electron

Inorganic compound  

receives the de-energized electron

Organic compound  

receives the electron

In aerobic respiration, O2 absorbs a de-energized electron and water is made

In anaerobic respiration, an inorganic compound (like CO2) absorbs the de-energized electron and methane is made

Reducing potential: The way in which we conserve energy by transferring  energized electrons from one compound to the other

∙ Oxidized compounds lose electrons

∙ Reduced compounds gain electrons (charge is reduced)

∙ Compounds that lose the electron lose the negative potential energy of the  electron, while compounds that receive the electron gain the negative  potential energy of the electron

ATP is an energy currency 

NADH, FADH2, and NADPH are all energy intermediates (checks)

When we think of coenzymes we think organic and non-proteinaceous

∙ NAD+ (a type of coenzyme) is the oxidized form of NAD (Nicotinamide Adenine Dinucleotide)

∙ NAD+ coenzyme receives 2 electrons, but the medium tries to  neutralize the charge by offering two protons

1. NAD+ + e- + e- + H+ + H+ 

2. 1 electron neutralizes the charge on NAD, and the other electron  binds to a proton to make a hydrogen atom, so we are left with…. 3. NADH + H+ 

 4. Remember: NADH is the energy intermediate and NAD+ is the  coenzyme

∙ NAD+ can receive electrons and therefore is a reducing agent, but NADH can  only carry electrons (CANNOT receive them)

1. NADH is an electron carrier, NOT AN ELECTRON RECEIVER

2. NAD+ can be reduced and NADH can be oxidized 

∙ Anytime there is a transferring of two electrons and a proton, the enzyme  involved will contain the term dehydrogenase 

∙ Anything there is a transferring of a phosphate, the enzyme involved will  contain the term kinase 

∙ Anything there is a removal of a phosphate, the enzyme involved will contain  the term phosphatase 

Direct ATP Synthesis

Indirect ATP Synthesis

Direct Substrate Level  

Phosphorylation

∙ A high energy substrate can  phosphorylate ADP to form ATP

∙ Forming ATP is endergonic

Chemiosmotic Oxidative  

Phosphorylation in the mitochondria ∙ Along the inner mitochondrial  membrane is the electron  

transport chain

∙ NADH and FADH2 (energy  

intermediates) are oxidized,  

supplying the energy to create a  proton gradient

Maximum ATP by Direct Substrate  Level Phosphorylation is provided  by Glycolysis

Once the proton gradient is created, the protons flow from high -> low through  the ATP synthase enzyme, providing the energy to synthesize ATP in the  mitochondrial matrix

There are four pathways for carbohydrate catabolism

∙ Glycolysis takes places in the cytosol

∙ Pyruvate oxidation takes place in the mitochondrial matrix ∙ Kreb’s Cycle takes place in the mitochondrial matrix

Oxidative Phosphorylation takes place in the inner mitochondrial membrane Glycolysis 

Glycolysis is said to be an evolutionary memory because the energy output via  glycolysis is very low, yet we maintain it through evolution because it is the only  pathway that can proceed in the presence and absence of oxygen

First step- Glucose (with 6 carbons) becomes glucose 6 phosphate 

∙ The ∆G will be positive because we are making a bigger molecule ∙ ATP is broken down into ADP and P, and the P attaches to the glucose, as  shown in green on the diagram

∙ The enzyme involved is hexokinase (6 carbons and kinase)

Second step- Glucose 6 phosphate becomes its structural isomer fructose 6  phosphate 

∙ The enzyme involved is phosphoglucoisomerase

∙ Nothing was added, but the carbon chains were altered

Third step- Fructose 6 phosphate becomes Fructose 1,6 biphosphate 

∙ In this step we try to make a compound that can break down in equal  numbers

∙ To make two 3-carbon compounds with equal molecules, a second P must be  added, as shown in green in the diagram

∙ Enzyme involved is phosphofructokinase

These first three steps make up the energy investment phase or priming phase, now we move on to cleavage phase

Step 4- Fructose 1,6 biphosphate splits into dihydroxi acetone phosphate and  glyceraldehyde 3 phosphate, two 3 carbon compounds

∙ These are two different compounds

∙ Enzyme involved is aldolase

Step 5- Dihydroxi acetone phosphate becomes glyceraldehyde 3 phosphate, so now  we have 2 molecules of glyceraldehyde 3 phosphate

∙ Only one molecule changes in this step, while the other stays the same ∙ Enzyme involved is triosphosphateisomerase

Now we are in the energy liberation phase

Step 6- Both molecules of glyceraldehyde 3 phosphate become 1,3  biphosphoglycerate 

∙ Inorganic phosphate comes into glyceraldehyde 3 phosphate from the cytosol 1. Now we have a phosphate attached to the 1st and 3rd carbon, making the  compound unstable because of their repulsion

∙ Hydronium ion is removed (H+) and transferred to coenzyme NAD+ 1. First energy compound is made in this step in the form of NADH ∙ Enzyme involved is glyceraldehyde 3 phosphate dehydrogenase

Step 7- Both molecules of 1,3 biphosphoglycerate become 3 phosphoglycerate 

∙ One unstable phosphate (P) is broken off and ATP is synthesized (direct  substrate level phospholyration)

∙ Enzyme involved is phospoglycerokinase

Step 8- Both molecules of 3 phosphoglycerate become 2 phosphoglycerate 

∙ Phosphate (P) moves from 3rd carbon to 2nd carbon

∙ Enzyme involved is phosphoglycomutase

Step 9- Both molecules of 2 phosphoglycerate become phosphoenol pyruvate 

∙ H2O is removed from the compound at this step to destabilize the molecule,  and allow the P to easily be removed

∙ Enzyme involved is enolase

Step 10- Both molecules of phosphoenol pyruvate become pyruvate ∙ The P is removed and ATP is synthesized

At the end of glycolysis, net ATP is 2, because we used 2 ATP in the priming phase,  but created 4 ATP in the energy liberation phase