exam 2 bio

Ch. 6 – Cells: Size & Surface Area-to-Volume Ratio

- The unaided human eye can see objects down to about XX (0.1 mm), around the size of a XX XX

- Most plant and animal cells are smaller than XX, so we usually need a XX XX to see them.

- A typical bacterial cell is about XX XX in size.

- Mitochondria are also around XX XX.

- Viruses, ribosomes, proteins, lipids, and atoms are much XX and usually require XX XX to be seen clearly.

- Light microscopes can generally resolve objects down to about XX nm (0.2 µm).

- Electron microscopes have much greater XX and can show structures much smaller than cells.

Ch. 6 – Cells: Size & Surface Area-to-Volume Ratio

- The unaided human eye can see objects down to about 100 µm (0.1 mm), around the size of a human egg.

- Most plant and animal cells are smaller than 100 µm, so we usually need a light microscope to see them.

- A typical bacterial cell is about 1 µm in size.

- Mitochondria are also around 1 µm.

- Viruses, ribosomes, proteins, lipids, and atoms are much smaller and usually require electron microscopy to be seen clearly.

- Light microscopes can generally resolve objects down to about 200 nm (0.2 µm).

- Electron microscopes have much greater resolution and can show structures much smaller than cells.

Why are cells so small?

Cells stay XX because of the XX XX-to-XX ratio.

- Surface area = amount of XX XX available for exchanging materials.

- Volume = amount of XX inside the XX that needs nutrients and produces waste.

- As a cell gets larger, its volume XX faster than its XX XX.

- Therefore, a large cell has a XX surface area-to-volume ratio, making it harder to XX enough nutrients, oxygen, and wastes across the membrane.

- Smaller cells have a XX surface area-to-volume ratio, which makes exchange with the environment more XX.

Main idea: Cells are generally XX Because being small allows them to exchange materials XX enough to survive.

Why are cells so small?

Cells stay small because of the surface area-to-volume ratio.

- Surface area = amount of cell membrane available for exchanging materials.

- Volume = amount of cytoplasm inside the cell that needs nutrients and produces waste.

- As a cell gets larger, its volume increases faster than its surface area.

- Therefore, a large cell has a smaller surface area-to-volume ratio, making it harder to move enough nutrients, oxygen, and wastes across the membrane.

- Smaller cells have a higher surface area-to-volume ratio, which makes exchange with the environment more efficient.

Main idea: Cells are generally small because being small allows them to exchange materials efficiently enough to survive.

Why are cells so small? — Surface Area : Volume Ratio

Cells are microscopic because small cells have a much better XX XX-to-XX ratio.

The key idea is that cells constantly need to move materials across their XX:

- XX and XX move in

- XX XX and XX move out

The more XX XX a cell has compared with its volume, the easier it is to exchange these materials.

Lung alveoli example

Your lungs contain millions of tiny air sacs called XX. They are arranged in clusters that look like XX.

Compare:

- 8 small spheres, radius = 1

- 1 large sphere, radius = 2

They have the same total volume, but the 8 smaller spheres have more than twice the total surface area.

That means there is much more membrane available for:

- O₂ to diffuse from the alveoli into the blood

- CO₂ to diffuse from the blood into the alveoli

So having many XX structures is more efficient than having one XX structure.

Why not have one giant cell?

As a cell gets larger:

- Its XX increases faster than its XX XX

- The amount of membrane available per unit of cytoplasm XX

- XX and XX cannot enter fast enough

- XX cannot leave fast enough

So cells stay small to maintain a high XX XX -to-XX ratio.

Brush border epithelium

Some cells increase their surface area even more by having folds or projections called XX.

The brush border epithelium contains many XX, which creates a tremendous amount of surface area for XX.

Main idea:

More surface area = XX XX = faster and more efficient movement of substances in and out.

Why are cells so small? — Surface Area : Volume Ratio

Cells are microscopic because small cells have a much better surface area-to-volume ratio.

The key idea is that cells constantly need to move materials across their membrane:

- Oxygen and nutrients move in

- Carbon dioxide and wastes move out

The more surface area a cell has compared with its volume, the easier it is to exchange these materials.

Lung alveoli example

Your lungs contain millions of tiny air sacs called alveoli. They are arranged in clusters that look like grapes.

Compare:

- 8 small spheres, radius = 1

- 1 large sphere, radius = 2

They have the same total volume, but the 8 smaller spheres have more than twice the total surface area.

That means there is much more membrane available for:

- O₂ to diffuse from the alveoli into the blood

- CO₂ to diffuse from the blood into the alveoli

So having many small structures is more efficient than having one large structure.

Why not have one giant cell?

As a cell gets larger:

- Its volume increases faster than its surface area

- The amount of membrane available per unit of cytoplasm decreases

- Nutrients and oxygen cannot enter fast enough

- Waste cannot leave fast enough

So cells stay small to maintain a high surface area-to-volume ratio.

Brush border epithelium

Some cells increase their surface area even more by having folds or projections called microvilli.

The brush border epithelium contains many microvilli, which creates a tremendous amount of surface area for absorption.

Main idea:

More surface area = more membrane = faster and more efficient movement of substances in and out.

FIGURE 6.7 GEOMETRIC RELATIONSHIPS BETWEEN SURFACE AREA AND VOLUME

Large cell: XX XX XX:volume ratio

Small cell: XX XX XX:volume ratio

Surface area XX while total volume remains XX.

Total surface area = XX × XX × number of XX × number of XX

Total volume = XX × XX × XX × number of XX

Surface area-to-volume ratio = XX ÷ XX

You want a XX surface area-to-volume ratio. The XX the ratio, the better the cell is at XX things across the XX.

One small cell: 1 × 1 × 1

Surface area = 1 × 1 × 6 × 1 = 6

Volume = 1 × 1 × 1 × 1 = 1

Surface area-to-volume ratio = 6 ÷ 1 = 6

One large cell: 5 × 5 × 5

Surface area = 5 × 5 × 6 × 1 = 150

Volume = 5 × 5 × 5 × 1 = 125

Surface area-to-volume ratio = 150 ÷ 125 = 1.2

If the cell becomes 5 times bigger on every side, the volume increases much faster than the surface area. Bigger is not always better because the cell becomes much less efficient at transporting substances across the membrane.

125 small cells: 1 × 1 × 1

5 × 5 × 5 = 125 total cells

Surface area = 1 × 1 × 6 × 125 = 750

Volume = 1 × 1 × 1 × 125 = 125

Surface area-to-volume ratio = 750 ÷ 125 = 6

The one large cell and the 125 small cells have the same total volume, 125, but the 125 small cells have much more total surface area.

Large cell surface area = 150

125 small cells surface area = 750

The small cells have 5 times more surface area.

Cells deal with the problem of getting too large by breaking the same amount of space into many, many XX XX. This gives many more opportunities to transport oxygen, nutrients, carbon dioxide, and wastes across the cell membrane.

Main idea: You want a XX surface area-to-volume ratio. Bigger number = better. XX cells are more efficient than large cells.

FIGURE 6.7 GEOMETRIC RELATIONSHIPS BETWEEN SURFACE AREA AND VOLUME

Large cell: Low surface area:volume ratio

Small cell: High surface area:volume ratio

Surface area increases while total volume remains constant.

Total surface area = height × width × number of sides × number of boxes

Total volume = height × width × length × number of boxes

Surface area-to-volume ratio = surface area ÷ volume

You want a high surface area-to-volume ratio. The bigger the ratio, the better the cell is at transporting things across the membrane.

One small cell: 1 × 1 × 1

Surface area = 1 × 1 × 6 × 1 = 6

Volume = 1 × 1 × 1 × 1 = 1

Surface area-to-volume ratio = 6 ÷ 1 = 6

One large cell: 5 × 5 × 5

Surface area = 5 × 5 × 6 × 1 = 150

Volume = 5 × 5 × 5 × 1 = 125

Surface area-to-volume ratio = 150 ÷ 125 = 1.2

If the cell becomes 5 times bigger on every side, the volume increases much faster than the surface area. Bigger is not always better because the cell becomes much less efficient at transporting substances across the membrane.

125 small cells: 1 × 1 × 1

5 × 5 × 5 = 125 total cells

Surface area = 1 × 1 × 6 × 125 = 750

Volume = 1 × 1 × 1 × 125 = 125

Surface area-to-volume ratio = 750 ÷ 125 = 6

The one large cell and the 125 small cells have the same total volume, 125, but the 125 small cells have much more total surface area.

Large cell surface area = 150

125 small cells surface area = 750

The small cells have 5 times more surface area.

Cells deal with the problem of getting too large by breaking the same amount of space into many, many small cells. This gives many more opportunities to transport oxygen, nutrients, carbon dioxide, and wastes across the cell membrane.

Main idea: You want a HIGH surface area-to-volume ratio. Bigger number = better. Small cells are more efficient than large cells.

The Cell Theory

1662: Invention of the microscope; Robert Hooke; cork appeared as "a great

many little boxes" (or "celles”)

1673: Anton van Leewenhook; pond water:

"Little eels, or worms, lying all huddled up together and

wriggily, and the whole water seemed to be alive with

these animalcules and cells fill'd with juices.”

1839 Matthias Schleiden and Theodor Schwann,

brought 200 years of scattered observations

together into a simple, testable Cell Theory:

1. The XX is the fundamental unit of life.This is why we do not consider XX to be alive, they are not based on the XX.

2. All organisms are composed of XX or more XX.

3. All cells come from XX XX.

(Pasteur 1859 - Death of Spontaneous Generation

What defines a cell? A cell

1. Is the l XX level of structure capable of performing all Xactivities of life

2. Is bounded by a XX XXX “XX”

3. Contains XX, XX XX, XX

The Cell Theory

1662: Invention of the microscope; Robert Hooke; cork appeared as "a great

many little boxes" (or "celles”)

1673: Anton van Leewenhook; pond water:

"Little eels, or worms, lying all huddled up together and

wriggily, and the whole water seemed to be alive with

these animalcules and cells fill'd with juices.”

1839 Matthias Schleiden and Theodor Schwann,

brought 200 years of scattered observations

together into a simple, testable Cell Theory:

1. The cell is the fundamental unit of life.This is why we do not consider viruses to be alive, they are not based on the cell. 

2. All organisms are composed of one or more cells.

3. All cells come from preexisting cells.

(Pasteur 1859 - Death of Spontaneous Generation

What defines a cell? A cell

1. Is the lowest level of structure capable of performing all 5 activities of life

2. Is bounded by a plasma membrane “envelope”

3. Contains cytoplasm, DNA enzymes, organelles

Cell Fractionation & Centrifugation

If you have tissue cells in a test tube or flask and you want to study what is inside the cells, you can separate the different components of the cell using cell fractionation.

First, the tissue cells are homogenized. Homogenization means breaking the xx xx, such as by blending them, without completely destroying all of the xx structures and organelles.

XX XX → XX → XX

The homogenate is the XX that contains all of the broken XX XX and organelles.

Next, the homogenate is placed into a XX

Centrifugation spins the sample very quickly. This separates the different cell components based mainly on their XX and XX

Larger and heavier cell components settle toward the XX of the tube first, while smaller and lighter components remain in the XX.

Main idea: Cell fractionation and centrifugation allow scientists to break cells XX and separate their XX so the different parts of the cell can be studied XX

Cell Fractionation & Centrifugation

If you have tissue cells in a test tube or flask and you want to study what is inside the cells, you can separate the different components of the cell using cell fractionation.

First, the tissue cells are homogenized. Homogenization means breaking the cells open, such as by blending them, without completely destroying all of the cell structures and organelles.

Tissue cells → Homogenization → Homogenate

The homogenate is the mixture that contains all of the broken cell pieces and organelles.

Next, the homogenate is placed into a centrifuge.

Centrifugation spins the sample very quickly. This separates the different cell components based mainly on their size and density.

Larger and heavier cell components settle toward the bottom of the tube first, while smaller and lighter components remain in the liquid.

Main idea: Cell fractionation and centrifugation allow scientists to break cells open and separate their organelles so the different parts of the cell can be studied individually.

Differential Centrifugation

Differential centrifugation separates cell components based mainly on their xx and xx by spinning the sample at progressively xx xx

If you spin the homogenate at a relatively low speed, such as 1,000 g, the biggest and heaviest components settle to the bottom first.

1,000 g for 10 min

Pellet contains:

Nuclei and large cellular debris

The pellet is the material that collects at the bottom of the tube.

The liquid above the pellet is called the supernatant.

You pour the supernatant into a new tube and spin it faster.

20,000 g for 20 min

Pellet contains:

xx and xx

These are smaller than xx, so they require a higher centrifugation speed to pellet.

Then the supernatant is transferred again and spun even faster.

80,000 g for 60 min

Pellet contains:

xx

xx are small membrane fragments or vesicles produced when cell membranes, especially the endoplasmic reticulum, break apart during homogenization.

Finally, the remaining supernatant is spun at a very high speed.

150,000 g for 3 hr

Pellet contains:

xx'

xx are extremely small, so a very high centrifugal force is needed to pull them down into a pellet.

If you wanted to isolate ribosomes, you would first remove the larger structures step-by-step:

xx → xx/xx → xx→ xx

Main idea: The larger and heavier cell components pellet at lower speeds, while smaller components require higher speeds and longer centrifugation times.

Differential centrifugation = repeatedly spinning the supernatant at higher and higher speeds to separate different cell components.

Differential Centrifugation

Differential centrifugation separates cell components based mainly on their size and density by spinning the sample at progressively higher speeds.

If you spin the homogenate at a relatively low speed, such as 1,000 g, the biggest and heaviest components settle to the bottom first.

1,000 g for 10 min

Pellet contains:

Nuclei and large cellular debris

The pellet is the material that collects at the bottom of the tube.

The liquid above the pellet is called the supernatant.

You pour the supernatant into a new tube and spin it faster.

20,000 g for 20 min

Pellet contains:

Mitochondria and chloroplasts

These are smaller than nuclei, so they require a higher centrifugation speed to pellet.

Then the supernatant is transferred again and spun even faster.

80,000 g for 60 min

Pellet contains:

Microsomes

Microsomes are small membrane fragments or vesicles produced when cell membranes, especially the endoplasmic reticulum, break apart during homogenization.

Finally, the remaining supernatant is spun at a very high speed.

150,000 g for 3 hr

Pellet contains:

Ribosomes

Ribosomes are extremely small, so a very high centrifugal force is needed to pull them down into a pellet.

If you wanted to isolate ribosomes, you would first remove the larger structures step-by-step:

Nuclei/debris → mitochondria/chloroplasts → microsomes → ribosomes

Main idea: The larger and heavier cell components pellet at lower speeds, while smaller components require higher speeds and longer centrifugation times.

Differential centrifugation = repeatedly spinning the supernatant at higher and higher speeds to separate different cell components.

The Fundamental Units of Life: A Cell is a Living Unit Greater Than the Sum of Its Parts

A cell has XX XX, meaning the different parts of the cell work together to produce a functioning living unit.

Prokaryotic cells are very old. Fossil evidence suggests they have existed for about 3.6–3.8 billion years.

Bacteria are XX XX.

A typical rod-shaped bacterium may contain the following structures:

Pili

Pili are short XX XX structures found on the surface of some XX

They can help bacteria:

- XX to XX

- Attach to things such as XX

- Connect with other XX XX

- XX or XX material with other cells

Nucleoid

Bacteria do not have a XX

Instead, their DNA is located in a region called theXX

The nucleoid is the area where the bacterial DNA is XX

Ribosomes

XX contain ribosomes because they need to make XX.

Ribosomes carry out XX XX and produce the proteins the bacterium needs to survive and function.

Plasma Membrane

The XX is surrounded by the plasma membrane.

The plasma membrane is a XX XX

Its job is to control what XX and XX the cell.

It helps keep the XX of the cell separate from the XX environment.

Cell Wall

Outside the XX XX is the cell wall.

The cell wall is rigid and provides:

- XX

- XX

- XX

- A XX shape for the XX

Capsule

Not all bacteria have a capsule.

The capsule is an XX, often XX-rich covering around the XX.

It can provide additional XX

Some pathogenic bacteria have capsules that can help them survive in the body and make it more difficult for the host immune system to recognize or eliminate them.

Flagella

Some bacteria have one or more flagella, while others do not.

Flagella are XX structures used for XX

They allow bacteria to swim through their XX

Example: Bacillus coagulans

Bacillus coagulans is a rod-shaped bacterium.

The image on the slide shows a thin section of Bacillus coagulans viewed using a transmission electron microscope, or TEM.

Main Idea

Bacteria have been extremely successful forms of life for billions of years.

Most bacteria are beneficial or harmless, while some bacteria can cause disease.

Even though bacteria are simpler than eukaryotic cells, all of their structures work together to make a complete living cell

The Fundamental Units of Life: A Cell is a Living Unit Greater Than the Sum of Its Parts

A cell has emergent properties, meaning the different parts of the cell work together to produce a functioning living unit.

Prokaryotic cells are very old. Fossil evidence suggests they have existed for about 3.6–3.8 billion years.

Bacteria are prokaryotic cells.

A typical rod-shaped bacterium may contain the following structures:

Pili

Pili are short hair-like structures found on the surface of some bacteria.

They can help bacteria:

- Attach to surfaces

- Attach to things such as catheters

- Connect with other bacterial cells

- Communicate or exchange material with other cells

Nucleoid

Bacteria do not have a nucleus.

Instead, their DNA is located in a region called the nucleoid.

The nucleoid is the area where the bacterial DNA is concentrated.

Ribosomes

Bacteria contain ribosomes because they need to make proteins.

Ribosomes carry out protein synthesis and produce the proteins the bacterium needs to survive and function.

Plasma Membrane

The cytoplasm is surrounded by the plasma membrane.

The plasma membrane is a phospholipid bilayer.

Its job is to control what enters and leaves the cell.

It helps keep the inside of the cell separate from the outside environment.

Cell Wall

Outside the plasma membrane is the cell wall.

The cell wall is rigid and provides:

- Structure

- Support

- Protection

- A sturdy shape for the cell

Capsule

Not all bacteria have a capsule.

The capsule is an outer, often water-rich covering around the bacterium.

It can provide additional protection.

Some pathogenic bacteria have capsules that can help them survive in the body and make it more difficult for the host immune system to recognize or eliminate them.

Flagella

Some bacteria have one or more flagella, while others do not.

Flagella are long structures used for movement.

They allow bacteria to swim through their environment.

Example: Bacillus coagulans

Bacillus coagulans is a rod-shaped bacterium.

The image on the slide shows a thin section of Bacillus coagulans viewed using a transmission electron microscope, or TEM.

Main Idea

Bacteria have been extremely successful forms of life for billions of years.

Most bacteria are beneficial or harmless, while some bacteria can cause disease.

Even though bacteria are simpler than eukaryotic cells, all of their structures work together to make a complete living cell

Appearing on the scene a mere ~1.5 Billion years ago…

 Eukaryotic cells are generally much XX than prokaryotic

cells

 Eukaryotic cells are characterized by:

XX

XX in a XX that is bounded by a membranous

nuclear envelope

XX-XX organelles

 XX in the region between the plasma membrane,

nucleus, and organelles

Appearing on the scene a mere ~1.5 Billion years ago…

 Eukaryotic cells are generally much larger than prokaryotic

cells

 Eukaryotic cells are characterized by:

 Compartmentalization

 DNA in a nucleus that is bounded by a membranous

nuclear envelope

 Membrane-bound organelles

 Cytoplasm in the region between the plasma membrane,

nucleus, and organelles

Typical Eukaryotic Cells

Hallmark: Compartmentalization and Organelles

A typical animal cell is around 30–50 micrometers. The XX is usually one of the first structures you recognize. Animal cells also have an XX system, including the XX XXX, XX XX, and XX. Proteins move through this system and can eventually be exported from the cell.

XX are the site of aerobic respiration and ATP production. XX are double-membrane bound.

Plant cells are very similar to animal cells, but they have a few major differences. A large central XX can take up about 90% of the cell volume. The XX stores many substances, especially water, and helps the plant maintain support. The membrane around the XX is called the tonoplast.

Plant cells also contain XX. XX are the site of photosynthesis and sugar production, and photosynthesis also releases oxygen. XX are double-membrane bound.

Plant cells also contain XX because they still need to make ATP.

Plant cells have a rigid, box-like cell wall made of cellulose. The cell wall helps support and protect the cell.

Plant cells also have XX, which are channels between neighboring plant cells that allow communication and movement of materials.

Animal cells do not have a XX XX. They have a plasma membrane, and outside the plasma membrane many animal cells have an extracellular matrix.

Main differences:

Animal cell: XX XX XX, no XX, no large central XX

Plant cell: XX XX, XX, large central XX

Typical Eukaryotic Cells

Hallmark: Compartmentalization and Organelles

A typical animal cell is around 30–50 micrometers. The nucleus is usually one of the first structures you recognize. Animal cells also have an endomembrane system, including the endoplasmic reticulum, Golgi apparatus, and vesicles. Proteins move through this system and can eventually be exported from the cell.

Mitochondria are the site of aerobic respiration and ATP production. Mitochondria are double-membrane bound.

Plant cells are very similar to animal cells, but they have a few major differences. A large central vacuole can take up about 90% of the cell volume. The vacuole stores many substances, especially water, and helps the plant maintain support. The membrane around the vacuole is called the tonoplast.

Plant cells also contain chloroplasts. Chloroplasts are the site of photosynthesis and sugar production, and photosynthesis also releases oxygen. Chloroplasts are double-membrane bound.

Plant cells also contain mitochondria because they still need to make ATP.

Plant cells have a rigid, box-like cell wall made of cellulose. The cell wall helps support and protect the cell.

Plant cells also have plasmodesmata, which are channels between neighboring plant cells that allow communication and movement of materials.

Animal cells do not have a cell wall. They have a plasma membrane, and outside the plasma membrane many animal cells have an extracellular matrix.

Main differences:

Animal cell: no cell wall, no chloroplasts, no large central vacuole

Plant cell: cell wall, chloroplasts, large central vacuole

The Evolutionary Origins of Mitochondria and Chloroplasts: Lynn Margulis

Endosymbiotic theory: a long-term relationship where one cell XX another cell. Over evolutionary time, the two became so dependent on each other that they could no longer live XX.

Lynn Margulis proposed that XX and XXX originated from free-living bacteria that were engulfed by larger ancestral cells about 1.5 billion years ago.

As oxygen became more common in the atmosphere because of photosynthesis, it created a challenge for many early cells because oxygen can be XX and XX.

One way early cells increased their surface area-to-volume ratio was by folding their plasma membrane inward. These folds likely contributed to the development of internal membranes, including the endomembrane system and eventually the nuclear envelope.

An early eukaryotic ancestor engulfed an aerobic, oxygen-using bacterium. Instead of digesting it, the bacterium survived inside the host cell. The bacterium helped the host use oxygen efficiently and produce energy. Over time, many bacterial genes were transferred to the host nucleus, and the bacterium eventually became the mitochondrion.

Early eukaryote + aerobic bacterium → mitochondrion

Later, some cells containing mitochondria engulfed a photosynthetic bacterium. Instead of digesting it, the photosynthetic bacterium remained inside the cell and provided the ability to perform photosynthesis. Over time, it became the chloroplast.

Eukaryotic cell + photosynthetic bacterium → chloroplast

This helps explain why animal cells have mitochondria but not chloroplasts, while plant cells have both mitochondria and chloroplasts.

Evidence for endosymbiotic theory:

Mitochondria and chloroplasts are similar in XX to XX .

Both have XX XX

Both contain their own XX.

Both contain their own XX.

Both reproduce by a process similar to bacterial binary fission.

Mitochondria and chloroplasts still contain remnants of their original bacterial genomes.

Main idea: Mitochondria evolved from aerobic bacteria, while chloroplasts evolved from photosynthetic bacteria that were engulfed by ancestral eukaryotic cells and formed permanent symbiotic relationships

The Evolutionary Origins of Mitochondria and Chloroplasts: Lynn Margulis

Endosymbiotic theory: a long-term relationship where one cell lives inside another cell. Over evolutionary time, the two became so dependent on each other that they could no longer live independently.

Lynn Margulis proposed that mitochondria and chloroplasts originated from free-living bacteria that were engulfed by larger ancestral cells about 1.5 billion years ago.

As oxygen became more common in the atmosphere because of photosynthesis, it created a challenge for many early cells because oxygen can be chemically reactive and damaging.

One way early cells increased their surface area-to-volume ratio was by folding their plasma membrane inward. These folds likely contributed to the development of internal membranes, including the endomembrane system and eventually the nuclear envelope.

An early eukaryotic ancestor engulfed an aerobic, oxygen-using bacterium. Instead of digesting it, the bacterium survived inside the host cell. The bacterium helped the host use oxygen efficiently and produce energy. Over time, many bacterial genes were transferred to the host nucleus, and the bacterium eventually became the mitochondrion.

Early eukaryote + aerobic bacterium → mitochondrion

Later, some cells containing mitochondria engulfed a photosynthetic bacterium. Instead of digesting it, the photosynthetic bacterium remained inside the cell and provided the ability to perform photosynthesis. Over time, it became the chloroplast.

Eukaryotic cell + photosynthetic bacterium → chloroplast

This helps explain why animal cells have mitochondria but not chloroplasts, while plant cells have both mitochondria and chloroplasts.

Evidence for endosymbiotic theory:

Mitochondria and chloroplasts are similar in size to bacteria.

Both have double membranes.

Both contain their own DNA.

Both contain their own ribosomes.

Both reproduce by a process similar to bacterial binary fission.

Mitochondria and chloroplasts still contain remnants of their original bacterial genomes.

Main idea: Mitochondria evolved from aerobic bacteria, while chloroplasts evolved from photosynthetic bacteria that were engulfed by ancestral eukaryotic cells and formed permanent symbiotic relationships

X-linked ALD

Affected organelle: XX

Cause: Very-long-chain XX XX cannot be broken down properly and build up.

Treatment: XX replacement, stem-cell transplant, or gene therapy in some cases.

Progeria

Affected organelle: XX / XX XX

Cause: LMNA mutation causes abnormal progerin protein and damages the nucleus.

Treatment: Lonafarnib and supportive care.

Tay-Sachs

Affected organelle:XX

Cause: HEXA mutation causes GM2 ganglioside to build up in nerve cells.

Treatment: No cure; mainly supportive care.

X-linked ALD

Affected organelle: Peroxisome

Cause: Very-long-chain fatty acids cannot be broken down properly and build up.

Treatment: Hormone replacement, stem-cell transplant, or gene therapy in some cases.

Progeria

Affected organelle: Nucleus / nuclear lamina

Cause: LMNA mutation causes abnormal progerin protein and damages the nucleus.

Treatment: Lonafarnib and supportive care.

Tay-Sachs

Affected organelle: Lysosome

Cause: HEXA mutation causes GM2 ganglioside to build up in nerve cells.

Treatment: No cure; mainly supportive care.

The Nucleus and Its Envelope – Most of the Cell’s Genes

The nucleus contains most of the cell’s XX. Most of your DNA is found inside the XX.

DNA usually exists in a loose, relaxed form called XX

Nucleolus: makes the components that will become XX

The DNA stays inside the XX, but many materials have to move in and out through XX XX.

XX XX control movement between the nucleus and cytoplasm.

Things that move into the nucleus:

XX needed for DNA synthesis

Other molecules needed for XX XX and XX XX

Things that move out of the nucleus:

XX made from DNA

Ribosomal components

Nuclear pore complexes are the structures that allow this XX

Nuclear envelope: a XX XX surrounding the XX

Nuclear lamina: a supportive protein “XX” just underneath the nuclear envelope that helps maintain the XX and structure of the nucleus.

Main idea: The nucleus storesXX, while nuclear pores control what enters and leaves.

The Nucleus and Its Envelope – Most of the Cell’s Genes

The nucleus contains most of the cell’s genome. Most of your DNA is found inside the nucleus.

DNA usually exists in a loose, relaxed form called chromatin.

Nucleolus: makes the components that will become ribosomes.

The DNA stays inside the nucleus, but many materials have to move in and out through nuclear pores.

Nuclear pores control movement between the nucleus and cytoplasm.

Things that move into the nucleus:

Nucleotides needed for DNA synthesis

Other molecules needed for DNA replication and gene expression

Things that move out of the nucleus:

mRNA made from DNA

Ribosomal components

Nuclear pore complexes are the structures that allow this transport.

Nuclear envelope: a double membrane surrounding the nucleus.

Nuclear lamina: a supportive protein “cage” just underneath the nuclear envelope that helps maintain the shape and structure of the nucleus.

Main idea: The nucleus stores DNA, while nuclear pores control what enters and leaves.

The Endomembrane System

The endomembrane system is a system of membranes inside a eukaryotic cell.

It includes:

XX X

XX XX reticulum

XX XX reticulum

XX XX

XX

XX

XX

XX XX

The nuclear envelope is continuous with the XX XX, so these membranes are physically connected.

As materials move through the endomembrane system, small membrane sacs called XX bud off from one membrane and move to another.

Vesicles can fuse with the XX XX because both the vesicle and Golgi are made of membranes.

The Golgi apparatus receives proteins and other materials, modifies them, sorts them, and gives them their XX XX information.

Vesicles are very common in XX XX. They transport groups of XX and other materials to where they need to go next.

General pathway:

Nuclear envelope → ER → vesicles → Golgi apparatus → vesicles → lysosomes/vacuoles or plasma membrane

Materials can also move back through the system.

Main idea: The endomembrane system moves and processes materials through the cell using connected membranes and transport vesicles

The endomembrane system regulates protein

traffic and performs metabolic functions in the

cell

The Endomembrane System

The endomembrane system is a system of membranes inside a eukaryotic cell.

It includes:

Nuclear envelope

Smooth endoplasmic reticulum

Rough endoplasmic reticulum

Golgi apparatus

Lysosomes

Vacuoles

Vesicles

Plasma membrane

The nuclear envelope is continuous with the endoplasmic reticulum, so these membranes are physically connected.

As materials move through the endomembrane system, small membrane sacs called vesicles bud off from one membrane and move to another.

Vesicles can fuse with the Golgi apparatus because both the vesicle and Golgi are made of membranes.

The Golgi apparatus receives proteins and other materials, modifies them, sorts them, and gives them their final destination information.

Vesicles are very common in eukaryotic cells. They transport groups of proteins and other materials to where they need to go next.

General pathway:

Nuclear envelope → ER → vesicles → Golgi apparatus → vesicles → lysosomes/vacuoles or plasma membrane

Materials can also move back through the system.

Main idea: The endomembrane system moves and processes materials through the cell using connected membranes and transport vesicles

The endomembrane system regulates protein

traffic and performs metabolic functions in the

cell

The endomembrane system regulates XX

traffic and performs XX XX in the

cell

Rough ER • Has bound XX, which secrete XX (proteins

covalently bonded to carbohydrates)

• Distributes XX XX, secretory proteins surrounded by

membranes

• Is a membrane factory for the cell

Smooth

SMOOTH ER

• Synthesizes XX

• Metabolizes XX

• Detoxifies xx and XX

• Stores XX XX

Golgi

Apparatus

The Golgi apparatus consists of flattened membranous sacs called

XX. Functions of the Golgi apparatus:

• Modifies products of the XX

• Manufactures certain XX

• Sorts and packages materials into XX XX

Endoplasmic reticulum (ER)

rER: Synthesis of secreted

xx, XX,

membrane proteins.

‘Rough’ appearance due

XX s in the process

of threading new proteins

Into the ER lumen.

sER: Synthesis of

lipids, fatty acids,

plasma membrane

The endomembrane system regulates protein

traffic and performs metabolic functions in the

cell

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

Smooth

ER

• Synthesizes lipids

• Metabolizes carbohydrates

• Detoxifies drugs and poisons

• Stores calcium ions

Golgi

Apparatus

The Golgi apparatus consists of flattened membranous sacs called

cisternae. Functions of the Golgi apparatus:

• Modifies products of the ER

• Manufactures certain macromolecules

• Sorts and packages materials into transport vesicles

Endoplasmic reticulum (ER)

rER: Synthesis of secreted

proteins, glycoproteins,

membrane proteins.

‘Rough’ appearance due

ribosomes in the process

of threading new proteins

Into the ER lumen.

sER: Synthesis of

lipids, fatty acids,

plasma membrane

Ribosomes: XX XX

Ribosomes are complexes made of ribosomal XX (XX) and XX.

Free ribosomes = found in the =XXX

Bound ribosomes = attached to the XX XX or XX XX

Ribosomes are found in XX, XX and XX

A ribosome has two parts:

-XX XX

- XX XX

During protein synthesis, the ribosome reads the information on XX.

tRNA brings amino acids to the XX.

The ribosome links the amino acids together in the correct order to build a protein.

Main idea: Ribosomes are responsible for XX XX and make theXX XX, or amino acid sequence, of a protein

Ribosomes: Protein Synthesis

Ribosomes are complexes made of ribosomal RNA (rRNA) and proteins.

Free ribosomes = found in the cytosol

Bound ribosomes = attached to the rough ER or nuclear envelope

Ribosomes are found in bacteria, archaea, and eukaryotes.

A ribosome has two parts:

- Large subunit

- Small subunit

During protein synthesis, the ribosome reads the information on mRNA.

tRNA brings amino acids to the ribosome.

The ribosome links the amino acids together in the correct order to build a protein.

Main idea: Ribosomes are responsible for protein synthesis and make the primary structure, or amino acid sequence, of a protein

The Golgi: Sorting and Shipping

Functions of the Golgi:

Further modifies XX and XX, such as adding sugar tags or phosphate groups.

Sorts and packages materials that will be sent to XX XX or exported from the cell.

Camillo Golgi discovered the Golgi apparatus in 1898 and later received the Nobel Prize in 1906 for work on the nervous system.

How materials move through the Golgi:

XX move from the ER to the Golgi.

Vesicles XX XX and enter the Golgi.

They enter on the XX face, which is the side XXto the ER.

Proteins move through flattened membrane sacs called XX.

During cisternal maturation, proteins move from th XX side toward the XX side and are modified as they go.

At the trans face, new XX bud off and carry proteins to their final destination.

Some vesicles can also transport certain proteins back to the ER.

Possible destinations:

XX XX

XX

Other parts of the cell

Outside the cell

Main idea: The Golgi receives proteins from the XX, XX them, sorts them, XX them, and ships them to the correct locatioN

The Golgi: Sorting and Shipping

Functions of the Golgi:

Further modifies proteins and lipids, such as adding sugar tags or phosphate groups.

Sorts and packages materials that will be sent to different locations or exported from the cell.

Camillo Golgi discovered the Golgi apparatus in 1898 and later received the Nobel Prize in 1906 for work on the nervous system.

How materials move through the Golgi:

Vesicles move from the ER to the Golgi.

Vesicles fuse together and enter the Golgi.

They enter on the cis face, which is the side closest to the ER.

Proteins move through flattened membrane sacs called cisternae.

During cisternal maturation, proteins move from the cis side toward the trans side and are modified as they go.

At the trans face, new vesicles bud off and carry proteins to their final destination.

Some vesicles can also transport certain proteins back to the ER.

Possible destinations:

Plasma membrane

Lysosomes

Other parts of the cell

Outside the cell

Main idea: The Golgi receives proteins from the ER, modifies them, sorts them, packages them, and ships them to the correct locatio

Lysosomes contain XX enzymes and have an acidic pH of about 4.8.

Hydrolytic enzymes include:

XX → break down proteins

XX → break down lipids

XX→ break down nucleic acids

Other enzymes can break down carbohydrates

Functions of lysosomes:

Digest XX and XX

Digest XX XX or XX organelles

Recycle damaged XX XX

Help with programmed cell death (XX)

When a lysosome fuses with a food vacuole, its enzymes enter the compartment and the pH becomes XX. The acidic environment helps the enzymes digest the food particles by breaking XX XX

Phagocytosis = bringing XX/XX into the cell and digesting it with XX.

Autophagy = “XX XX”; lysosomes digest and recycle damaged structures that are already inside the cell, such as damaged XX

Tay-Sachs: lysosomal storage disease caused by missing HexA enzyme → toxic lipids build up in brain cells.

Main idea: Lysosomes are the cell’s XX and XX compartments.

and ships them to the correct location.

Lysosomes

Lysosomes contain hydrolytic enzymes and have an acidic pH of about 4.8.

Hydrolytic enzymes include:

Proteases → break down proteins

Lipases → break down lipids

Nucleases → break down nucleic acids

Other enzymes can break down carbohydrates

Functions of lysosomes:

Digest bacteria and macromolecules

Digest worn-out or damaged organelles

Recycle damaged plasma membranes

Help with programmed cell death (apoptosis)

When a lysosome fuses with a food vacuole, its enzymes enter the compartment and the pH becomes acidic. The acidic environment helps the enzymes digest the food particles by breaking chemical bonds.

Phagocytosis = bringing material/food into the cell and digesting it with lysosomes.

Autophagy = “cell eating”; lysosomes digest and recycle damaged structures that are already inside the cell, such as damaged mitochondria.

Tay-Sachs: lysosomal storage disease caused by missing HexA enzyme → toxic lipids build up in brain cells.

Main idea: Lysosomes are the cell’s digestive and recycling compartments.

Peroxisomes: Oxidation

Peroxisomes are organelles in the cell and are not part of the XX system. They XX XX and XX fatty acids so the cell can get energy from fats.

Breaking down fatty acids produces XX XX (H₂O₂), which is toxic. Peroxisomes contain enzymes that convert it into harmless products.

Peroxidase: involved in XX XX

Catalase: breaks down XX XX.

2H₂O₂ → 2H₂O + O₂

Adrenoleukodystrophy (ALD): peroxisomal enzyme disorder that affects fatty acid breakdown. Related to “Lorenzo’s Oil.”

Zellweger syndrome: peroxisomal biogenesis disorder, meaning peroxisomes do not form or function properly.

Main idea: Peroxisomes break down fatty acids and detoxify hydrogen peroxide.

Peroxisomes: Oxidation

Peroxisomes are organelles in the cell and are not part of the endomembrane system. They break down and oxidize fatty acids so the cell can get energy from fats.

Breaking down fatty acids produces hydrogen peroxide (H₂O₂), which is toxic. Peroxisomes contain enzymes that convert it into harmless products.

Peroxidase: involved in oxidation reactions.

Catalase: breaks down hydrogen peroxide.

2H₂O₂ → 2H₂O + O₂

Adrenoleukodystrophy (ALD): peroxisomal enzyme disorder that affects fatty acid breakdown. Related to “Lorenzo’s Oil.”

Zellweger syndrome: peroxisomal biogenesis disorder, meaning peroxisomes do not form or function properly.

Main idea: Peroxisomes break down fatty acids and detoxify hydrogen peroxide.

Cytoskeleton: Network of Fibers for Cell Shape and Movement

The cytoskeleton has 3 main types of fibers. The easiest way to tell them apart is by their size, what protein they are made of, what they look like, and what they mainly do.

Microtubules

XX of the three: about 25 nm.

XX XX.

Made of XX.

Tubulin is a dimer made of alpha-tubulin + beta-tubulin.

The tubulin dimers join together to form long hollow tubes called microtubules.

Main functions: maintain XX XX , move organelles, move chromosomes during cell division, and form cilia and flagella.

Think: big hollow support tubes.

Microfilaments

Smallest of the three: about 7 nm.

Made of actin.

Actin forms two intertwined strands.

Main functions: maintain cell shape, allow changes in cell shape, help with cell movement, animal cell division, and muscle contraction.

Very important in muscle contraction.

Think: very thin twisted actin strands used for movement and contraction.

Intermediate Filaments

Middle-sized: about 8–12 nm.

Made of many different types of fibrous proteins.

Examples: keratin and lamin A.

Fibrous proteins are coiled together into cable-like structures.

Main functions: maintain cell shape, provide strength, anchor the nucleus and other organelles, and form the nuclear lamina.

Lamin A is part of the nuclear lamina.

Keratin is another type of intermediate filament.

Think: strong protein cables used for support and anchoring.

Big differences:

Microtubules = biggest, hollow, tubulin, transport/support, cilia/flagella

Microfilaments = smallest, actin, movement and muscle contraction

Intermediate filaments = middle-sized, many proteins, strong cables, structural support

Cytoskeleton: Network of Fibers for Cell Shape and Movement

The cytoskeleton has 3 main types of fibers. The easiest way to tell them apart is by their size, what protein they are made of, what they look like, and what they mainly do.

Microtubules

Largest of the three: about 25 nm.

Hollow tubes.

Made of tubulin.

Tubulin is a dimer made of alpha-tubulin + beta-tubulin.

The tubulin dimers join together to form long hollow tubes called microtubules.

Main functions: maintain cell shape, move organelles, move chromosomes during cell division, and form cilia and flagella.

Think: big hollow support tubes.

Microfilaments

Smallest of the three: about 7 nm.

Made of actin.

Actin forms two intertwined strands.

Main functions: maintain cell shape, allow changes in cell shape, help with cell movement, animal cell division, and muscle contraction.

Very important in muscle contraction.

Think: very thin twisted actin strands used for movement and contraction.

Intermediate Filaments

Middle-sized: about 8–12 nm.

Made of many different types of fibrous proteins.

Examples: keratin and lamin A.

Fibrous proteins are coiled together into cable-like structures.

Main functions: maintain cell shape, provide strength, anchor the nucleus and other organelles, and form the nuclear lamina.

Lamin A is part of the nuclear lamina.

Keratin is another type of intermediate filament.

Think: strong protein cables used for support and anchoring.

Big differences:

Microtubules = biggest, hollow, tubulin, transport/support, cilia/flagella

Microfilaments = smallest, actin, movement and muscle contraction

Intermediate filaments = middle-sized, many proteins, strong cables, structural support

Structure of a Flagellum or Cilium

Cilia and flagella are structures used for XX and are built from XX. They have the XX basic internal structure.

9 + 2 arrangement:

9 XX microtubule doublets arranged in a XX

2 single microtubules in the XX

This is called the 9 + 2 arrangement.

Dynein proteins:

Motor proteins that form XX XX between neighboring outer microtubule doublets.

Dynein causes the microtubules to XX against each other.

This sliding produces the XX/XX of cilia and flagella.

Radial spokes and cross-linking proteins:

XX and XX the microtubules.

Help convert microtubule sliding into XX.

Plasma membrane:

The entire cilium or flagellum is covered by an extension of the cell’s XX XX.

Basal body:

Located at the XX where the cilium/flagellum attaches to the XX.

XX the structure.

Has 9 groups of microtubule triplets rather than the 9 + 2 arrangement.

Structure of a Flagellum or Cilium

Cilia and flagella are structures used for movement and are built from microtubules. They have the same basic internal structure.

9 + 2 arrangement:

9 outer microtubule doublets arranged in a circle

2 single microtubules in the center

This is called the 9 + 2 arrangement.

Dynein proteins:

Motor proteins that form cross-bridges between neighboring outer microtubule doublets.

Dynein causes the microtubules to slide against each other.

This sliding produces the bending/movement of cilia and flagella.

Radial spokes and cross-linking proteins:

Connect and stabilize the microtubules.

Help convert microtubule sliding into bending.

Plasma membrane:

The entire cilium or flagellum is covered by an extension of the cell’s plasma membrane.

Basal body:

Located at the base where the cilium/flagellum attaches to the cell.

Anchors the structure.

Has 9 groups of microtubule triplets rather than the 9 + 2 arrangement.

Compare: Cilia vs. Flagella?

Microtubules control the beating of flagella and

cilia, microtubule-containing extensions that

project from some cells

Cilia and flagella

differ in their

XX XX

and many other

features

Centrioles vs. Cilia and Flagella

Centrioles:X microtubule triplets; help XX microtubules during XX XX.

Cilia/flagella: X + X arrangement; used for XX.

Basal bodies: X microtubule XX and anchor cilia/flagella.

Compare: Cilia vs. Flagella?

Microtubules control the beating of flagella and

cilia, microtubule-containing extensions that

project from some cells

Cilia and flagella

differ in their

beating patterns

and many other

features

Centrioles vs. Cilia and Flagella

Centrioles: 9 microtubule triplets; help organize microtubules during cell division.

Cilia/flagella: 9 + 2 arrangement; used for movement.

Basal bodies: 9 microtubule triplets and anchor cilia/flagella.

Mitochondria and chloroplasts change energy

from one form to another

Mitochondria =

XX XX

(Chapter 9)

Chloroplasts =

XX

(Chapter 10)

Both are XX XX bound

organelles

Mitochondria vs. Chloroplasts

Both are XX XX organelles with their own XX and XX

Mitochondria: XX XX and XX production; inner folds = XX, inside = XX

Chloroplasts: XX; thylakoids/grana inside, surrounding fluid = stroma.

Mitochondria and chloroplasts change energy

from one form to another

Mitochondria =

cellular respiration

(Chapter 9)

Chloroplasts =

photosynthesis

(Chapter 10)

Both are double

membrane bound

organelles

Mitochondria vs. Chloroplasts

Both are double-membrane organelles with their own DNA and ribosomes.

Mitochondria: cellular respiration and ATP production; inner folds = cristae, inside = matrix.

Chloroplasts: photosynthesis; thylakoids/grana inside, surrounding fluid = stroma.

Chapter 7 Concepts – Why Life Needs a

Membrane Compartment

7.1 Cellular membranes are fluid mosaics of lipids and proteins

that are selectively permeable and act as a selective barrier to

separate the living cell from its surroundings

7.2 Membrane proteins give a plasma membrane a unique identity

7.3 The plasma membrane has a ‘sidedness’, with an E-face

(external to cell) and a P-face (internal to cell)

7.4 The Cell wall and the extracellular matrix (Ch 6)

7.5 Passive transport is diffusion of a substance across a

membrane with no energy investment

7.6 Active transport uses energy to move solutes against their

gradients

7.7 Bulk transport across the plasma membrane occurs by

exocytosis and endocytosis

Chapter 7 Concepts – Why Life Needs a

Membrane Compartment

7.1 Cellular membranes are fluid mosaics of lipids and proteins

that are selectively permeable and act as a selective barrier to

separate the living cell from its surroundings

7.2 Membrane proteins give a plasma membrane a unique identity

7.3 The plasma membrane has a ‘sidedness’, with an E-face

(external to cell) and a P-face (internal to cell)

7.4 The Cell wall and the extracellular matrix (Ch 6)

7.5 Passive transport is diffusion of a substance across a

membrane with no energy investment

7.6 Active transport uses energy to move solutes against their

gradients

7.7 Bulk transport across the plasma membrane occurs by

exocytosis and endocytosis

Plasma Membrane: Fluid Mosaic Model

The plasma membrane is made mainly of a XX XX. Phospholipids are amphipathic, meaning they have both a XX and a XX region.

Hydrophilic XX: XX, interact with XX, and face the watery environments XX and XX the cell.

Hydrophobic XX: XX, avoid XX, and point toward the XX of the membrane.

If phospholipids are placed in water, they spontaneously form a XX. No enzyme is needed. The hydrophobic tails move XX from water while the hydrophilic heads remain in XX with water.

Fluid mosaic model: “fluid” means the phospholipids and many proteins can move XX the XX. “Mosaic” refers to the XX XX scattered throughout the membrane.

Integral membrane proteins: proteins that are embedded in the XX and may span the entire phospholipid bilayer.

Peripheral proteins: proteins attached to the XX of the membrane. They do not extend into the XX interior and often interact with XX XX.

Integral proteins have mostly XX amino acids where they contact the hydrophobic lipid tails. Parts exposed to the watery cytoplasm or extracellular fluid tend to contain more XX amino acids.

The membrane is semipermeable/selectively permeable, meaning some substances cross more XX than others.

Small nonpolar molecules: can pass directly through the XX XX.

Polar molecules and ions: do not easily XX through the hydrophobic interior and generally need membrane proteins to cross.

Main idea: The membrane is a fluid phospholipid bilayer with proteins embedded in or attached to it, and its hydrophobic center controls what can easily cross.

Plasma Membrane: Fluid Mosaic Model

The plasma membrane is made mainly of a phospholipid bilayer. Phospholipids are amphipathic, meaning they have both a hydrophilic and a hydrophobic region.

Hydrophilic heads: polar, interact with water, and face the watery environments inside and outside the cell.

Hydrophobic tails: nonpolar, avoid water, and point toward the inside of the membrane.

If phospholipids are placed in water, they spontaneously form a bilayer. No enzyme is needed. The hydrophobic tails move away from water while the hydrophilic heads remain in contact with water.

Fluid mosaic model: “fluid” means the phospholipids and many proteins can move within the membrane. “Mosaic” refers to the different proteins scattered throughout the membrane.

Integral membrane proteins: proteins that are embedded in the membrane and may span the entire phospholipid bilayer.

Peripheral proteins: proteins attached to the surface of the membrane. They do not extend into the hydrophobic interior and often interact with integral proteins.

Integral proteins have mostly hydrophobic amino acids where they contact the hydrophobic lipid tails. Parts exposed to the watery cytoplasm or extracellular fluid tend to contain more hydrophilic amino acids.

The membrane is semipermeable/selectively permeable, meaning some substances cross more easily than others.

Small nonpolar molecules: can pass directly through the phospholipid bilayer.

Polar molecules and ions: do not easily pass through the hydrophobic interior and generally need membrane proteins to cross.

Main idea: The membrane is a fluid phospholipid bilayer with proteins embedded in or attached to it, and its hydrophobic center controls what can easily cross.

1 and 2 are membrane proteins 1 is an example of an integral membrane protein, 2 is a peripheral membrane protein. 3 and 4, 3 is a glycoprotein, glycoproteins are made through a proteins journey through the endoplasmic reticulum and the golgi. 4 is glycolipids. 5 and 6, 5 is showing cholesterol in the membrane. 6 is jus the phospholipid itself two tails and the phospholipid itself. 7 and 8, 7 is part of the cytoskeleton of the cell. Its inside the cell and its a number of different proteins that give the cell inside it its shape and vesicles. 7 is showing actin microfilaments, 8 is a series fo proteins that are outside the plasma membrane and this is called the extracellular matrix. 9 and 10, 9 is the E face, 10 is p face.

1 and 2 are membrane proteins 1 is an example of an integral membrane protein, 2 is a peripheral membrane protein. 3 and 4, 3 is a glycoprotein, glycoproteins are made through a proteins journey through the endoplasmic reticulum and the golgi. 4 is glycolipids. 5 and 6, 5 is showing cholesterol in the membrane. 6 is jus the phospholipid itself two tails and the phospholipid itself. 7 and 8, 7 is part of the cytoskeleton of the cell. Its inside the cell and its a number of different proteins that give the cell inside it its shape and vesicles. 7 is showing actin microfilaments, 8 is a series fo proteins that are outside the plasma membrane and this is called the extracellular matrix. 9 and 10, 9 is the E face, 10 is p face.

Synthesis and Sidedness of Membranes

Membranes have two distinct sides:

P-face = XX/XXface

E-face = XX/XX face

The two sides of the membrane are not identical. This asymmetry is established while membrane proteins and lipids are made and processed in the XX and XX XX.

Every protein has a specific XX XX, meaning a specific order of XX XX. That sequence helps determine its XX XX, such as alpha helices, and eventually its overall 3D shape.

For membrane proteins, that 3D shape and orientation are very important. A protein has to stay positioned XX in the membrane to function properly.

Main idea: Membranes are XX. The inside and outside faces are XX, and proteins must maintain the correct XXX and orientation in the membrane.

Synthesis and Sidedness of Membranes

Membranes have two distinct sides:

P-face = inside/cytoplasmic face

E-face = outside/extracellular face

The two sides of the membrane are not identical. This asymmetry is established while membrane proteins and lipids are made and processed in the ER and Golgi apparatus.

Every protein has a specific primary sequence, meaning a specific order of amino acids. That sequence helps determine its secondary structure, such as alpha helices, and eventually its overall 3D shape.

For membrane proteins, that 3D shape and orientation are very important. A protein has to stay positioned correctly in the membrane to function properly.

Main idea: Membranes are asymmetric. The inside and outside faces are different, and proteins must maintain the correct shape and orientation in the membrane.

Fig 7-9: Sidedness of Integral

Membrane Proteins:

How does an Integral Membrane

Glycoprotein get delivered to the

E-face (external to cell) with the

sugars facing out

Sidedness of Integral Membrane Proteins

If a protein is going to become a glycoprotein, meaning a protein with sugars attached, those sugar groups eventually need to face the XX of the cell.

As the protein is synthesized in the rough ER, it becomes inserted into the XX XX. It is woven through the membrane as an XX XX protein.

As it moves from the ER to the cis face of the Golgi, additional sugar tags are XX and XX.

As the protein continues through the Golgi, the carbohydrate branches become more XX.

When a transport vesicle buds off from the XX, the sugar portion of the glycoprotein is facing the XX of the vesicle.

When that vesicle fuses with the plasma membrane, the inside of the vesicle becomes continuous with the outside of the cell.

So:

Inside of vesicle → becomes XX XX /XX side

Outside of vesicle → becomes XX XX / XX side

This is why the sugar ends up facing XX the cell.

The integral membrane protein stays embedded in the XX XX because it is already woven through the vesicle membrane.

P-face = side facing the XX

E-face = side facing XX the cell

Secreted proteins are different.

A secreted protein, such as insulin, also moves through the ER and Golgi, but it does not become XX in the membrane. It stays XX inside the vesicle.

When the vesicle fuses with the plasma membrane, the secreted protein is released XX the cell because nothing is holding it in the membrane.

Important difference:

Integral membrane protein → remains in XXX

Secreted protein → released XX XX

Main idea: Membrane sidedness is preserved during ER → Golgi → vesicle → plasma membrane transport. The side facing the inside of the ER/Golgi/vesicle eventually becomes the E-face outside the cell.

Fig 7-9: Sidedness of Integral

Membrane Proteins:

How does an Integral Membrane

Glycoprotein get delivered to the

E-face (external to cell) with the

sugars facing out

Sidedness of Integral Membrane Proteins

If a protein is going to become a glycoprotein, meaning a protein with sugars attached, those sugar groups eventually need to face the outside of the cell.

As the protein is synthesized in the rough ER, it becomes inserted into the ER membrane. It is woven through the membrane as an integral membrane protein.

As it moves from the ER to the cis face of the Golgi, additional sugar tags are added and modified.

As the protein continues through the Golgi, the carbohydrate branches become more developed.

When a transport vesicle buds off from the Golgi, the sugar portion of the glycoprotein is facing the inside of the vesicle.

When that vesicle fuses with the plasma membrane, the inside of the vesicle becomes continuous with the outside of the cell.

So:

Inside of vesicle → becomes E-face / extracellular side

Outside of vesicle → becomes P-face / cytoplasmic side

This is why the sugar ends up facing outside the cell.

The integral membrane protein stays embedded in the plasma membrane because it is already woven through the vesicle membrane.

P-face = side facing the cytoplasm

E-face = side facing outside the cell

Secreted proteins are different.

A secreted protein, such as insulin, also moves through the ER and Golgi, but it does not become embedded in the membrane. It stays loose inside the vesicle.

When the vesicle fuses with the plasma membrane, the secreted protein is released outside the cell because nothing is holding it in the membrane.

Important difference:

Integral membrane protein → remains in membrane

Secreted protein → released outside cell

Main idea: Membrane sidedness is preserved during ER → Golgi → vesicle → plasma membrane transport. The side facing the inside of the ER/Golgi/vesicle eventually becomes the E-face outside the cell.

Six Major functions of membrane proteins

1. cell-cell XX and

Cell-cell XX.

Ex: Glycophorins on RBCs,

organ

2. XX junctions

and cell-cell adhesion.

Ex: Gap Junctions, Tight

junctions, desmosomes)

3. Attachment to the

XX and XX

Ex: Integrins

4. Transporters:

Hydrophilic channels/carriers:

XX XX

Ex: Glucose transporters, CFTR

Pumps: XX XX(ATP)

Ex: Na-K pump

5. XX

Ex: ATP synthase (Ch 9 and 10)

6. XX: Signal transduction

Ex: G-protein linked receptors

(GPLRs) (Ch 11).

Six Major functions of membrane proteins

1. Cell-cell recognition and

Cell-cell adhesion.

Ex: Glycophorins on RBCs,

organ

2. Intercellular junctions

and cell-cell adhesion.

Ex: Gap Junctions, Tight

junctions, desmosomes)

3. Attachment to the

cytoskeleton and ECM.

Ex: Integrins

4. Transporters:

Hydrophilic channels/carriers:

Facilitated diffusion

Ex: Glucose transporters, CFTR

Pumps: Active Transport (ATP)

Ex: Na-K pump

5. Enzymes.

Ex: ATP synthase (Ch 9 and 10)

6. Receptors: Signal transduction

Ex: G-protein linked receptors

(GPLRs) (Ch 11).

What is the Genetic Basis for HIV Resistance?

a) HIV must bind to immune cell-

surface protein XX and “co-

receptor” XX to infect a cell.

(CCR5 is a GPCR)

b) People who are genetically resistant

to HIV-resistant have non-functional

XX; HIV cannot infect their cells.

What are the implications for HIV

drug development / prevention?

HIV Resistance / CCR5

- HIV uses XX and XX to enter certain immune cells.

- A nonfunctional XX can make a person resistant to CCR5-dependent HIV infection.

- XX inhibitor drugs block XX and reduce HIV entry.

CFTR, Cystic Fibrosis, and Trikafta

- XX is a chloride ion channel.

- CFTR mutations cause abnormal Cl⁻ and water movement → thick, sticky mucus.

- Trikafta helps certain defective CFTR proteins reach the membrane and/or work better.

What is the Genetic Basis for HIV Resistance?

a) HIV must bind to immune cell-

surface protein CD4 and “co-

receptor” CCR5 to infect a cell.

(CCR5 is a GPCR)

b) People who are genetically resistant

to HIV-resistant have non-functional

CCR5; HIV cannot infect their cells.

What are the implications for HIV

drug development / prevention?

HIV Resistance / CCR5

- HIV uses CD4 and CCR5 to enter certain immune cells.

- A nonfunctional CCR5 can make a person resistant to CCR5-dependent HIV infection.

- CCR5 inhibitor drugs block CCR5 and reduce HIV entry.

CFTR, Cystic Fibrosis, and Trikafta

- CFTR is a chloride ion channel.

- CFTR mutations cause abnormal Cl⁻ and water movement → thick, sticky mucus.

- Trikafta helps certain defective CFTR proteins reach the membrane and/or work better.

Concept 6.7: How do Extracellular components

and connections between cells help coordinate

cellular activities?

Most cells synthesize and secrete materials that

are XX to the plasma membrane

1. XX XX XX

(XX)

2. The XX XX (XX) of

animal cells

3. XX XX

Extracellular Components and Connections Between Cells

Most cells make and secrete materials that end up XX the plasma membrane. These extracellular structures help XX cells and allow XX to communicate with each other.

Plant cells have a XX XX lining the inside of the cell.

Outside the plasma membrane is the XX XX, which is made mainly of XX.

Plant cells also have small channels called XX that connect neighboring cells.

Plasmodesmata = XX between plant cells.

They allow materials and signals to move from one plant cell to another, allowing rapid XX-to-XX communication.

Other extracellular structures include:

1. Plant cell walls → XX, XX and XX

2. Extracellular matrix (ECM) → found XX animal cells

3. Intercellular junctions → XX neighboring cells

Main idea: Structures XX the plasma membrane help support cells and connect them so they can communicate and coordinate their activities

Concept 6.7: How do Extracellular components

and connections between cells help coordinate

cellular activities?

Most cells synthesize and secrete materials that

are external to the plasma membrane

1. Plant Cell Walls

(cellulose)

2. The extracellular

matrix (ECM) of

animal cells

3. Intercellular junctions

Extracellular Components and Connections Between Cells

Most cells make and secrete materials that end up outside the plasma membrane. These extracellular structures help support cells and allow cells to communicate with each other.

Plant cells have a plasma membrane lining the inside of the cell.

Outside the plasma membrane is the cell wall, which is made mainly of cellulose.

Plant cells also have small channels called plasmodesmata that connect neighboring cells.

Plasmodesmata = junctions between plant cells.

They allow materials and signals to move from one plant cell to another, allowing rapid cell-to-cell communication.

Other extracellular structures include:

1. Plant cell walls → cellulose, support and protection

2. Extracellular matrix (ECM) → found outside animal cells

3. Intercellular junctions → connect neighboring cells

Main idea: Structures outside the plasma membrane help support cells and connect them so they can communicate and coordinate their activities

The E side: XX XX (ECM)

A complex mixture of XX and XX (collagen, proteoglycans,

and fibronectin) surrounding each animal cell.

1. Integrins: transmembrane

XX; cell surface

XX and XX proteins

Extracellular Matrix (ECM)

The extracellular matrix is the material XX animal cells. It is a complex, sticky mixture of XX and XX that surrounds cells and helps with support, elasticity, attachment, communication, and cell recognition.

The 4 major components are:

Integrins: transmembrane XX that span the XX XX. They connect the actin XX of the cytoskeleton inside the cell to the XX XX outside the cell. They also act as cell-surface XX and XX XX.

Fibronectin: attaches the XX XX to XX. It helps form the connection between the XX of the cell and the cytoskeleton XX.

Collagen: a major structural XX of the XX. It provides XX and XX to tissues such as skin and connective tissue. Collagen contains a lot of helical structure and makes up a large portion of the XX XX.

Proteoglycans: heavily “XX” proteins that form a XX-rich layer or “sugary blanket” around cells. There are many different proteoglycans, not just one type.

Overall connection:

Actin cytoskeleton → integrin → fibronectin → collagen/proteoglycan ECM

The ECM also helps cells recognize and interact with their surroundings, including XX vs. XX XX recognition and cell signaling.

Diseases related to abnormal ECM:

Marfan syndrome → XX

Osteogenesis imperfecta → XX

Epidermolysis bullosa → XX XX defects

Metastatic cancer → XX/altered ECM

Exam disease associations:

Marfan syndrome → XX

Osteogenesis imperfecta → XX

Epidermolysis bullosa → laminin β3 (LAMB3)

Main idea: The ECM is a network outside XX XX that provides XX and connects to the XX through XX and XX

The E side: Extracellular matrix (ECM)

A complex mixture of carbohydrates and proteins (collagen, proteoglycans,

and fibronectin) surrounding each animal cell.

1. Integrins: transmembrane

glycoproteins; cell surface

receptors and signalling proteins

Extracellular Matrix (ECM)

The extracellular matrix is the material outside animal cells. It is a complex, sticky mixture of carbohydrates and proteins that surrounds cells and helps with support, elasticity, attachment, communication, and cell recognition.

The 4 major components are:

Integrins: transmembrane glycoproteins that span the plasma membrane. They connect the actin microfilaments of the cytoskeleton inside the cell to the extracellular matrix outside the cell. They also act as cell-surface receptors and signaling proteins.

Fibronectin: attaches the extracellular matrix to integrins. It helps form the connection between the outside of the cell and the cytoskeleton inside.

Collagen: a major structural protein of the ECM. It provides strength and elasticity to tissues such as skin and connective tissue. Collagen contains a lot of helical structure and makes up a large portion of the extracellular matrix.

Proteoglycans: heavily “sugared” proteins that form a carbohydrate-rich layer or “sugary blanket” around cells. There are many different proteoglycans, not just one type.

Overall connection:

Actin cytoskeleton → integrin → fibronectin → collagen/proteoglycan ECM

The ECM also helps cells recognize and interact with their surroundings, including self vs. non-self recognition and cell signaling.

Diseases related to abnormal ECM:

Marfan syndrome → fibrillin

Osteogenesis imperfecta → collagen

Epidermolysis bullosa → collagen-related defects

Metastatic cancer → disturbed/altered ECM

Exam disease associations:

Marfan syndrome → fibrillin

Osteogenesis imperfecta → collagen

Epidermolysis bullosa → laminin β3 (LAMB3)

Main idea: The ECM is a network outside animal cells that provides support and connects to the cytoskeleton through integrins and fibronectin.

Intercellular Junctions – Binding Membranes Together

Tight junctions: form a continuous seal between XX XX. They prevent materials from XX between cells. A major example is intestinal epithelial cells, where tight junctions keep food particles and digestive contents from passing between the cells into the body. Celiac disease can be associated with “leaky” tight junctions.

Desmosomes: strong XX junctions that XX cells together like rivets or snaps. They are attached to XX XX such as keratin. A major example is the XX XX, where desmosomes help keep sheets of cells tightly connected.

Gap junctions: XX XX that form hollow channels between neighboring cells. These channels allow XX XX and molecules to move directly from one cell to another, allowing rapid cell-to-cell communication. Heart cells use gap junctions so they can communicate and contract together.

Quick differences:

Tight junctions = XX cells together, prevent XX

Desmosomes = XX cells XX, provide XX

Gap junctions = channels for XX between cells

Main idea: Tight junctions seal, desmosomes hold, and gap junctions communicate.

Disease associations:

Celiac disease → tight junctions

Epidermolysis bullosa → desmosomes

Epilepsy and Charcot-Marie-Tooth → gap junction

Intercellular Junctions – Binding Membranes Together

Tight junctions: form a continuous seal between neighboring cells. They prevent materials from leaking between cells. A major example is intestinal epithelial cells, where tight junctions keep food particles and digestive contents from passing between the cells into the body. Celiac disease can be associated with “leaky” tight junctions.

Desmosomes: strong adhesion junctions that hold cells together like rivets or snaps. They are attached to intermediate filaments such as keratin. A major example is the skin epidermis, where desmosomes help keep sheets of cells tightly connected.

Gap junctions: communicating junctions that form hollow channels between neighboring cells. These channels allow small ions and molecules to move directly from one cell to another, allowing rapid cell-to-cell communication. Heart cells use gap junctions so they can communicate and contract together.

Quick differences:

Tight junctions = seal cells together, prevent leakage

Desmosomes = anchor cells together, provide strength

Gap junctions = channels for communication between cells

Main idea: Tight junctions seal, desmosomes hold, and gap junctions communicate.

Disease associations:

Celiac disease → tight junctions

Epidermolysis bullosa → desmosomes

Epilepsy and Charcot-Marie-Tooth → gap junction

Chapter 7: The Plasma Membrane

Osmosis: How does water move in living cells?

Osmosis = movement of water across a XX XX. It depends on the relationship between the XX concentration on XX sides of the membrane.

Water moves XX its concentration gradient:

XX free H₂O / XX solutes / XX → XX free H₂O / XX solutes / XX

Isotonic solution: XX solute concentration XX and XX the cell. There is also the XX amount of free water on both sides. Water is constantly moving XX and XX, but there is no net movement.

Animal cell in isotonic solution → XX

Plant cell in isotonic solution → XX because water enters and leaves equally so the vacuole is not maximally full.

Hypotonic solution: XX solutes and more free water XX the cell. Water moves into the XX.

Animal cell in hypotonic solution → XX rushes in → cell XX → may XX/lyse. A red blood cell placed in pure water can eventually pop because it has no cell wall.

Plant cell in hypotonic solution → water XX and fills the large XX XX→ vacuole pushes against the cellulose XX XX → cell becomes XX. Turgid is the normal/healthy condition for many plant cells because the cell wall prevents bursting.

Hypertonic solution: more XX and less free water outside the XX. Water moves XX of the XX.

Animal cell in hypertonic solution → XX water → XX.

Plant cell in hypertonic solution → XX water → the cell membrane/protoplast XX XX from the cell wall → plasmolyzed.

Quick way to remember:

Hypotonic = water XX cell

Isotonic = water XX and XX equally

Hypertonic = water XX of cell

Animal cells:

Hypotonic → lysed

Isotonic → normal

Hypertonic → shriveled

Plant cells:

Hypotonic → turgid

Isotonic → flaccid

Hypertonic → plasmolyzed

Main idea: Water always moves from an area of XX free-water concentration to an area of XX free-water concentration, or from hypotonic toward hypertonic

Chapter 7: The Plasma Membrane

Osmosis: How does water move in living cells?

Osmosis = movement of water across a semipermeable membrane. It depends on the relationship between the solute concentration on both sides of the membrane.

Water moves down its concentration gradient:

High free H₂O / fewer solutes / hypotonic → Low free H₂O / more solutes / hypertonic

Isotonic solution: same solute concentration inside and outside the cell. There is also the same amount of free water on both sides. Water is constantly moving in and out, but there is no net movement.

Animal cell in isotonic solution → normal

Plant cell in isotonic solution → flaccid, because water enters and leaves equally so the vacuole is not maximally full.

Hypotonic solution: fewer solutes and more free water outside the cell. Water moves into the cell.

Animal cell in hypotonic solution → water rushes in → cell swells → may burst/lyse. A red blood cell placed in pure water can eventually pop because it has no cell wall.

Plant cell in hypotonic solution → water enters and fills the large central vacuole → vacuole pushes against the cellulose cell wall → cell becomes turgid. Turgid is the normal/healthy condition for many plant cells because the cell wall prevents bursting.

Hypertonic solution: more solutes and less free water outside the cell. Water moves out of the cell.

Animal cell in hypertonic solution → loses water → shrivels.

Plant cell in hypertonic solution → loses water → the cell membrane/protoplast pulls away from the cell wall → plasmolyzed.

Quick way to remember:

Hypotonic = water INTO cell

Isotonic = water IN and OUT equally

Hypertonic = water OUT of cell

Animal cells:

Hypotonic → lysed

Isotonic → normal

Hypertonic → shriveled

Plant cells:

Hypotonic → turgid

Isotonic → flaccid

Hypertonic → plasmolyzed

Main idea: Water always moves from an area of high free-water concentration to an area of low free-water concentration, or from hypotonic toward hypertonic

Passive vs Active Transport

Passive transport: molecules move XX their concentration gradient, from XX concentration → XX concentration. No XX or energy is required.

Simple diffusion: small XX molecules like O₂ and CO₂ can move directly through the phospholipid bilayer because they are small and nonpolar.

Facilitated diffusion: XX molecules, XX molecules, and ions cannot easily pass through the hydrophobic bilayer, so they need XX XX to help them cross. They still move down their concentration gradient, so no XX is required.

Channel proteins: act like tunnels through the membrane. Their interiors are often XX/XX, which allows ions or polar molecules to pass through.

Carrier proteins: bind a XX, change XX, and move it across the membrane. They act more like gates than open tunnels.

Active transport: moves substances XX their concentration gradient, from XX Concentration → XX concentration. This requires XX, usually XX

Na⁺/K⁺ ATPase: classic example of XX XX. It hydrolyzes XX and uses that energy to pump:

3 XX out of the cell

2 XX into the cell

Cells spend energy doing this because maintaining different concentrations of Na⁺, K⁺, and other ions is extremely important for many cells, including muscle and nervous system cells.

Quick difference:

Simple diffusion =d gradient, no XX, no XX

Facilitated diffusion = XX gradient, needs XX, no ATP

Active transport = against XX, needs XX, uses ATP

Main idea: Passive transport never requires XX. Facilitated diffusion is still passive transport because the molecule moves down its concentration gradient. Active transport requires XX because it moves substances against their concentration gradient

Passive vs Active Transport

Passive transport: molecules move down their concentration gradient, from high concentration → low concentration. No ATP or energy is required.

Simple diffusion: small nonpolar molecules like O₂ and CO₂ can move directly through the phospholipid bilayer because they are small and nonpolar.

Facilitated diffusion: polar molecules, charged molecules, and ions cannot easily pass through the hydrophobic bilayer, so they need membrane proteins to help them cross. They still move down their concentration gradient, so no ATP is required.

Channel proteins: act like tunnels through the membrane. Their interiors are often hydrophilic/polar, which allows ions or polar molecules to pass through.

Carrier proteins: bind a molecule, change shape, and move it across the membrane. They act more like gates than open tunnels.

Active transport: moves substances against their concentration gradient, from low concentration → high concentration. This requires energy, usually ATP.

Na⁺/K⁺ ATPase: classic example of active transport. It hydrolyzes ATP and uses that energy to pump:

3 Na⁺ out of the cell

2 K⁺ into the cell

Cells spend energy doing this because maintaining different concentrations of Na⁺, K⁺, and other ions is extremely important for many cells, including muscle and nervous system cells.

Quick difference:

Simple diffusion = down gradient, no protein, no ATP

Facilitated diffusion = down gradient, needs protein, no ATP

Active transport = against gradient, needs protein, uses ATP

Main idea: Passive transport never requires ATP. Facilitated diffusion is still passive transport because the molecule moves down its concentration gradient. Active transport requires ATP because it moves substances against their concentration gradient

How does water cross the plasma membrane?

XX are transmembrane channel proteins that allow water to move rapidly across the plasma membrane.

Water is XX, so it does not move efficiently through the hydrophobic center of the phospholipid bilayer. Aquaporins provide a hydrophilic channel that water can pass through.

This is facilitated diffusion, so:

- Water moves down its XX XX

- No XX is required

XX increase the rate of water movement

Main idea: Aquaporins are water channels that allow rapid XX across the plasma membrane

How does water cross the plasma membrane?

Aquaporins are transmembrane channel proteins that allow water to move rapidly across the plasma membrane.

Water is polar, so it does not move efficiently through the hydrophobic center of the phospholipid bilayer. Aquaporins provide a hydrophilic channel that water can pass through.

This is facilitated diffusion, so:

- Water moves down its concentration gradient

- No ATP is required

- Aquaporins increase the rate of water movement

Main idea: Aquaporins are water channels that allow rapid osmosis across the plasma membrane

Endocytosis — bringing things XX via the XX XX

Endo = XX the cell

Brings things XX the cell through the XX XX

Plasma membrane is dynamic — it grows and shrinks as materials move in and out.

Phagocytosis

XX XX

Brings in a large particle, such as food or an undigested macromolecule.

Membrane acts like an XX membrane

Pseudopods/pseudopodia extend around the particle and XX it

Brings the particle into the cell in a food vacuole

The material can then be digested in a XX

Pinocytosis

XX XX

Brings in XX/extracellular fluid

Cells have regulated ways to bring liquid and dissolved molecules into the cell.

Materials are concentrated in areas called XX XX

Coated pits bring materials XX the XX as coated vesicles

This is not just a random process

Receptor-mediated endocytosis:

A very specific/regulated form of XX

A molecule called a XX is located on the surface of the cell.

The receptor acts like an antenna that picks up a XX of interest.

XX molecules bind to the receptor.

The receptors gather the XX around XX XX

The coated pit then brings them into the cell in a XX.

The molecules are delivered to wherever their next destination is.

LDL receptor

Classic example of XXX XX endocytosis

LDL receptor is a receptor for XX

Cells need XX.

XX needs to be pulled from the bloodstream into cells in a regulated way.

XX can be used by cells to make steroid hormones.

Familial Hypercholesterolemia (FH)

Defective LDL receptors → less receptor-mediated LDL uptake → high LDL in the blood.

Exocytosis

The reverse of XX

XX things XX of the cell.

Vesicles leave from the XX XX.

Can release:

XX

XX

XX

XX XX

These materials can be released into the bloodstream.

Main comparison

Phagocytosis → cellular eating → large particles

Pinocytosis → cellular drinking → liquid

Receptor-mediated endocytosis → specific molecules

Exocytosis → moves materials OUT of the cell

Endocytosis — bringing things IN via the cell membrane

Endo = within the cell

Brings things into the cell through the plasma membrane

Plasma membrane is dynamic — it grows and shrinks as materials move in and out.

Phagocytosis

Cellular eating

Brings in a large particle, such as food or an undigested macromolecule.

Membrane acts like an amoeboid membrane

Pseudopods/pseudopodia extend around the particle and encircle it

Brings the particle into the cell in a food vacuole

The material can then be digested in a lysosome

Pinocytosis

Cellular drinking

Brings in liquid/extracellular fluid

Cells have regulated ways to bring liquid and dissolved molecules into the cell.

Materials are concentrated in areas called coated pits

Coated pits bring materials into the cell as coated vesicles

This is not just a random process

Receptor-mediated endocytosis

A very specific/regulated form of endocytosis

A molecule called a receptor is located on the surface of the cell.

The receptor acts like an antenna that picks up a molecule of interest.

Specific molecules bind to the receptor.

The receptors gather the molecules around coated pits

The coated pit then brings them into the cell in a vesicle.

The molecules are delivered to wherever their next destination is.

LDL receptor

Classic example of receptor-mediated endocytosis

LDL receptor is a receptor for cholesterol

Cells need cholesterol.

Cholesterol needs to be pulled from the bloodstream into cells in a regulated way.

Cholesterol can be used by cells to make steroid hormones.

Familial Hypercholesterolemia (FH)

Defective LDL receptors → less receptor-mediated LDL uptake → high LDL in the blood.

Exocytosis

The reverse of endocytosis

Exports things OUT of the cell.

Vesicles leave from the Golgi apparatus.

Can release:

Hormones

Enzymes

Neurotransmitters

Waste products

These materials can be released into the bloodstream.

Main comparison

Phagocytosis → cellular eating → large particles

Pinocytosis → cellular drinking → liquid

Receptor-mediated endocytosis → specific molecules

Exocytosis → moves materials OUT of the cell

 An electrogenic pump:

Stores energy by generating

XX (X charge separation)

across membranes.

Sodium-Potassium Pump,

XX XX

Some popular drugs are

XX XX XX (PPIs):

Co-transport: XX XX

driven by XX concentration

gradient

XX indirectly transports other

solutes against their

concentration gradient.

Electrogenic Pumps and Co-transport

Electrogenic pumps are XX XX that move charged particles across a XX and create a XX XX across that membrane.

A common example is a XX XX. A proton is an XX ion.

Proton pump:

Uses XX.

Pumps XX ions across the XX.

Builds up many XX charges on one side of the membrane.

Creates an XX XX, kind of like charging a battery.

This stored electrical energy can later be used by the cell.

Electrogenic pumps are important for processes such as nerve signaling and maintaining ion gradients.

Examples:

Sodium-potassium pump

Proton pump

Proton pump inhibitors (PPIs) are drugs that block certain proton pumps.

Co-transport:

Sometimes cells use the H⁺ gradient to move another substance across the membrane.

In the example on the slide, the cell uses ATP to pump H⁺ across the membrane first.

This creates a high concentration of H⁺ on one side.

H⁺ then moves back down its concentration gradient through a sucrose-H⁺ cotransporter.

Sucrose moves through the same transporter at the same time.

So:

ATP → proton pump → H⁺ gradient → H⁺ moves back → sucrose is transported

The ATP is not directly powering the sucrose transporter. It is indirectly providing the energy by first creating the H⁺ gradient.

This is called secondary active transport or co-transport.

Main idea: Electrogenic pumps use XX to create an XX gradient and XX XX. Cells can then use th

 An electrogenic pump:

Stores energy by generating

voltage (H+ charge separation)

across membranes.

Sodium-Potassium Pump,

Proton Pump

Some popular drugs are

Proton Pump Inhibitors (PPIs):

Co-transport: active transport

driven by H+ concentration

gradient

ATP indirectly transports other

solutes against their

concentration gradient.

Electrogenic Pumps and Co-transport

Electrogenic pumps are membrane proteins that move charged particles across a membrane and create a voltage difference across that membrane.

A common example is a proton pump. A proton is an H⁺ ion.

Proton pump:

Uses ATP.

Pumps H⁺ ions across the membrane.

Builds up many positive charges on one side of the membrane.

Creates an electrical gradient, kind of like charging a battery.

This stored electrical energy can later be used by the cell.

Electrogenic pumps are important for processes such as nerve signaling and maintaining ion gradients.

Examples:

Sodium-potassium pump

Proton pump

Proton pump inhibitors (PPIs) are drugs that block certain proton pumps.

Co-transport:

Sometimes cells use the H⁺ gradient to move another substance across the membrane.

In the example on the slide, the cell uses ATP to pump H⁺ across the membrane first.

This creates a high concentration of H⁺ on one side.

H⁺ then moves back down its concentration gradient through a sucrose-H⁺ cotransporter.

Sucrose moves through the same transporter at the same time.

So:

ATP → proton pump → H⁺ gradient → H⁺ moves back → sucrose is transported

The ATP is not directly powering the sucrose transporter. It is indirectly providing the energy by first creating the H⁺ gradient.

This is called secondary active transport or co-transport.

Main idea: Electrogenic pumps use ATP to create an ion gradient and electrical charge. Cells can then use that stored gradient to move other molecules, such as sucrose, across the membrane

Medicines related

to Membrane Pumps

PPIs: Temporarily XX the

XX gastric proton pump

in stomach parietal cells

The most widely prescribed

medications worldwide:

$13 billion in global sales.

Proton pump inhibitors are drugs just over the counter and they temporarily block the XX XX in potassium proton pumps that are in the stomach, less acid pumped into the stomach means you don’t have acid reflux and heartburn. These are prescribed and used readily.

Medicines related

to Membrane Pumps

PPIs: Temporarily block the

H+/K+ gastric proton pump

in stomach parietal cells

The most widely prescribed

medications worldwide:

$13 billion in global sales.

Proton pump inhibitors are drugs just over the counter and they temporarily block the hydrogen ion in potassium proton pumps that are in the stomach, less acid pumped into the stomach means you don’t have acid reflux and heartburn. These are prescribed and used readily.

Concept 8.1: How does an organism transform

matter and energy into work?

Metabolism is the totality of an organism’s

XX XX

Metabolism is an XX XX of life that

arises from orderly interactions between

Molecules

Concept 8.1: How does an organism transform

matter and energy into work?

Metabolism is the totality of an organism’s

chemical reactions

Metabolism is an emergent property of life that

arises from orderly interactions between

Molecules

Organization of the Chemistry of Life into

Metabolic Pathways

A metabolic pathway begins with a specific

XX and ends with a XX

Each step is catalyzed by a XX XX

Some starting molecule A will undergo three biochemical transformations by three different XX. So reaction 1 2 and 3 and it’ll make some product. Every step has a specific XX that is going to be involved in picking up whats the starting molecule for it. 

Organization of the Chemistry of Life into

Metabolic Pathways

A metabolic pathway begins with a specific

molecule and ends with a product

Each step is catalyzed by a specific enzyme

Some starting molecule A will undergo three biochemical transformations by three different enzymes. So reaction 1 2 and 3 and it’ll make some product. Every step has a specific enzyme that is going to be involved in picking up whats the starting molecule for it. 

How is Energy related to Cellular Work?

Energy is the capacity to do XX (to change the state or motion of mass)

Terms to Know: What are the forms of Energy?

Kinetic energy is energy associated with XX

Thermal energy is XX XX associated with

movement of XX or XX

Potential energy is energy that matter possesses because

of its XX orXX

Chemical energy is XX XX available

for release in a XX XX

Thermodynamics is the study of XX XX

How is Energy related to Cellular Work?

Energy is the capacity to do work (to change the state or motion of mass)

Terms to Know: What are the forms of Energy?

Energy is the capacity to do work (to change the state or

motion of mass).

Kinetic energy is energy associated with motion

Thermal energy is kinetic energy associated with

movement of atoms or molecules

Potential energy is energy that matter possesses because

of its location or structure

Chemical energy is potential energy available

for release in a chemical reaction

Thermodynamics is the study of energy transformations

The First Law of Thermodynamics:

Conservation of energy: the energy of the universe

is XX

Energy can be XX and XX,

but it cannot be XX or XX

The Second Law of Thermodynamics:

During every energy transfer or transformation,

some energy is XX, and is often lost

as XX

Every energy transfer or transformation increases

the entropy (disorder) of the universe

The First Law of Thermodynamics:

Conservation of energy: the energy of the universe

is constant

Energy can be transferred and transformed,

but it cannot be created or destroyed

The Second Law of Thermodynamics:

During every energy transfer or transformation,

some energy is unusable, and is often lost

as heat

Every energy transfer or transformation increases

the entropy (disorder) of the universe

Exergonic vs. Endergonic

Free energy = XX available to do XX

ΔG = XX in XX XX

Exergonic reactions:

XX energy.

ΔG < X

Spontaneous

Usually XX pathways = XX molecules down

Start with XX-energy reactants and produce XX-energy products

Give up XX and order

Example: glucose → CO₂ + H₂O

Breaking down glucose releases about 686 kcal/mol of energy that can be used for cellular work.

Glucose contains lots of stored potential energy in C-H and C-C bonds. During cellular respiration, glucose is broken down step-by-step so the cell can capture as much energy as possible.

CO₂ and H₂O are low-energy products because they have very little usable chemical energy left.

Catabolic pathway = XX XX → releases XX→ XX → XX ΔG.

Endergonic reactions:

Require an XX of energy.

ΔG > X

Nonspontaneous

Usually XX pathways = XX molecules up

Start with XX-energy reactants and produce XX energy products

Require XX and gain XX

Example: CO₂ + H₂O + energy → glucose

Building glucose requires about 686 kcal/mol of energy.

Photosynthetic organisms use energy from sunlight to build glucose from CO₂ and H₂O. Glucose has more free energy than CO₂ and H₂O, so energy has to be added.

Anabolic pathway = building up → requires energy → endergonic → positive ΔG.

Important:

Spontaneous does not mean fast. It means the reaction is XX XX.

A nonspontaneous reaction will not proceed on its own and needs an XX XX or coupling to another favorable reaction.

Enzymes XX reactions up, but they do not change XX or turn a positive ΔG reaction into a spontaneous one by themselves.

Quick difference:

Exergonic = XX XX = XX = ΔG < X = XX

Endergonic = XX XX = XX = ΔG > X = XX

Main idea: Catabolic pathways break XX XX molecules down and release XX energy, while anabolic pathways require XX to build higher-energy, more ordered molecules.

Exergonic vs. Endergonic

Free energy = energy available to do work.

ΔG = change in free energy.

Exergonic reactions:

Release energy.

ΔG < 0

Spontaneous

Usually catabolic pathways = breaking molecules down

Start with high-energy reactants and produce lower-energy products

Give up energy and order

Example: glucose → CO₂ + H₂O

Breaking down glucose releases about 686 kcal/mol of energy that can be used for cellular work.

Glucose contains lots of stored potential energy in C-H and C-C bonds. During cellular respiration, glucose is broken down step-by-step so the cell can capture as much energy as possible.

CO₂ and H₂O are low-energy products because they have very little usable chemical energy left.

Catabolic pathway = breaking down → releases energy → exergonic → negative ΔG.

Endergonic reactions:

Require an input of energy.

ΔG > 0

Nonspontaneous

Usually anabolic pathways = building molecules up

Start with low-energy reactants and produce higher-energy products

Require energy and gain order

Example: CO₂ + H₂O + energy → glucose

Building glucose requires about 686 kcal/mol of energy.

Photosynthetic organisms use energy from sunlight to build glucose from CO₂ and H₂O. Glucose has more free energy than CO₂ and H₂O, so energy has to be added.

Anabolic pathway = building up → requires energy → endergonic → positive ΔG.

Important:

Spontaneous does not mean fast. It means the reaction is energetically favorable.

A nonspontaneous reaction will not proceed on its own and needs an energy input or coupling to another favorable reaction.

Enzymes speed reactions up, but they do not change ΔG or turn a positive ΔG reaction into a spontaneous one by themselves.

Quick difference:

Exergonic = releases energy = catabolic = ΔG < 0 = spontaneous

Endergonic = requires energy = anabolic = ΔG > 0 = nonspontaneous

Main idea: Catabolic pathways break high-energy molecules down and release usable energy, while anabolic pathways require energy to build higher-energy, more ordered molecules.

Concept 8.3: How does ATP powers cellular

work? …By coupling exergonic reactions to

endergonic reactions

A cell does three main kinds of work

XX

XX

XX

Cells do work by XX XX, the use of an exergonic

process to drive an endergonic one, mediated by XX

The hydrolysis of XX to XX is exergonic; The release

of energy comes from the chemical change to a state of

lower free energy, not from the phosphate bonds themselves

ATP and Energy Coupling

Cells need an input of XX to perform XX XX.

ATP hydrolysis is an XX reaction, meaning it releases XX XX that can be coupled to an endergonic reaction that needs energy.

ATP + H₂O → ADP + Pi + energy

During hydrolysis, the terminal phosphate group is removed from XX.

The released energy can then be used to drive XX XX and other reactions that would not occur spontaneously on their own.

Important: Energy is not released simply because the phosphate bond is “high-energy.” Breaking a bond requires XX. ATP hydrolysis releases XX overall because the products, ADP + Pi, have much lower XX XX and are more stable than ATP.

Main idea: ATP hydrolysis lowers free energy and releases usable energy, allowing cells to couple an exergonic reaction to an endergonic process.

Concept 8.3: How does ATP powers cellular

work? …By coupling exergonic reactions to

endergonic reactions

A cell does three main kinds of work

Chemical

Transport

Mechanical

Cells do work by energy coupling, the use of an exergonic

process to drive an endergonic one, mediated by ATP

The hydrolysis of ATP to ADP is exergonic; The release

of energy comes from the chemical change to a state of

lower free energy, not from the phosphate bonds themselves

ATP and Energy Coupling

Cells need an input of energy to perform cellular work.

ATP hydrolysis is an exergonic reaction, meaning it releases free energy that can be coupled to an endergonic reaction that needs energy.

ATP + H₂O → ADP + Pi + energy

During hydrolysis, the terminal phosphate group is removed from ATP.

The released energy can then be used to drive cellular work and other reactions that would not occur spontaneously on their own.

Important: Energy is not released simply because the phosphate bond is “high-energy.” Breaking a bond requires energy. ATP hydrolysis releases energy overall because the products, ADP + Pi, have much lower free energy and are more stable than ATP.

Main idea: ATP hydrolysis lowers free energy and releases usable energy, allowing cells to couple an exergonic reaction to an endergonic process.

ATP Hydrolysis & the ATP Cycle

ATP structure:

XX base

XX sugar

3 XX XX

ATP hydrolysis:

A XX molecule is used to break off the terminal XX

ATP → ADP + Pi

Pi = XX XX

This reaction releases XX

About 7.3 kcal/mol is released under standard conditions.

ATP hydrolysis is XX and has a XX XX

Cells use the energy released from XX XX to drive endergonic reactions that require energy.

Energy coupling:

Exergonic XX XX → provides XX → XX cellular work

The released phosphate can also be transferred to another molecule, giving that molecule extra energy and making it more reactive.

ATP cycle:

ATP is constantly broken down into XX + XX to do cellular work.

Because cells use ATP constantly, ATP has to be regenerated almost immediately.

ADP + Pi + energy → ATP

Most ATP regeneration in eukaryotic cells happens in the XX during cellular respiration.

The mitochondria use energy from nutrients to join XX and XX back together and regenerate XX

So the cycle is:

XX → XX +XX + XX XX

ADP + Pi + energy input → XX

Main idea: Cells constantly cycle between ATP and ADP. ATP hydrolysis releases energy for cellular work, and mitochondria continuously regenerate ATP so the cell can stay alive.

ATP Hydrolysis & the ATP Cycle

ATP structure:

Adenine base

Ribose sugar

3 phosphate groups

ATP hydrolysis:

A water molecule is used to break off the terminal phosphate.

ATP → ADP + Pi

Pi = inorganic phosphate

This reaction releases energy.

About 7.3 kcal/mol is released under standard conditions.

ATP hydrolysis is exergonic and has a negative ΔG.

Cells use the energy released from ATP hydrolysis to drive endergonic reactions that require energy.

Energy coupling:

Exergonic ATP hydrolysis → provides energy → endergonic cellular work

The released phosphate can also be transferred to another molecule, giving that molecule extra energy and making it more reactive.

ATP cycle:

ATP is constantly broken down into ADP + Pi to do cellular work.

Because cells use ATP constantly, ATP has to be regenerated almost immediately.

ADP + Pi + energy → ATP

Most ATP regeneration in eukaryotic cells happens in the mitochondria during cellular respiration.

The mitochondria use energy from nutrients to join ADP and Pi back together and regenerate ATP.

So the cycle is:

ATP → ADP + Pi + energy released

ADP + Pi + energy input → ATP

Main idea: Cells constantly cycle between ATP and ADP. ATP hydrolysis releases energy for cellular work, and mitochondria continuously regenerate ATP so the cell can stay alive.

How does ATP

perform work in cells? (A: By energy coupling)

Energy coupling using XX XX & formation of a

XX XX

1. Glutamic acid + ATP interact.

ATP is XX, releasing XX

kcal of energy and creating a

XX XX

2. The phosphorylated

intermediate is more XX).

NH3 displaces the phosphate,

formingXX

The overall process is now

XX = spontaneous!

How ATP Performs Work: Energy Coupling

Cells do work by XX XX. This means an energy-releasing reaction is coupled to an energy-requiring reaction.

Amino acids have to be XX in cells. Building amino acids is an aXX process, so it requires energy and is generally XX

Example: making glutamine from glutamic acid.

Glutamic acid is the starting material for glutamine. To make glutamine, ammonia (NH₃) is added to glutamic acid.

Glutamic acid + NH₃ → glutamine

ΔG = +3.4 kcal/mol

Because ΔG is positive, this reaction by itself is XX and XX.

Step 1:

XX XX and XX are brought together inside an enzyme.

XX is hydrolyzed to XX

The terminal phosphate from XX is transferred toXX XX

This creates a XX XX

A phosphorylated intermediate is a molecule with a XX temporarily attached to it.

Adding the phosphate makes glutamic acid more XX XX

ATP hydrolysis releases about 7.3 kcal/mol of free energy under standard conditions.

ATP → ADP + Pi

ΔG = XX kcal/mol

Step 2:

XX enters and reacts with the phosphorylated XX XX

NH₃ displaces the XX XX.

XX is formed.

The phosphate is released as XX XX, Pi.

Energy coupling:

Glutamic acid + NH₃ → XX

ΔG = +XX kcal/mol

ATP → ADP + Pi

ΔG = −7.3 kcal/mol

Net ΔG:

+3.4 + (−7.3) = −3.9 kcal/mol

Because the overall ΔG is now negative, the coupled reaction is XX and thermodynamically favorable.

ATP provides more than enough free energy to drive the +3.4 kcal/mol glutamine-forming reaction.

The purpose of phosphorylation is to make the intermediate more reactive so the next step can occur more easily.

After ATP has been used, ADP and Pi can later be regenerated back into ATP, mainly through cellular respiration in mitochondria.

Main idea: ATP hydrolysis drives endergonic reactions by coupling them to an exergonic reaction. In this example, ATP phosphorylates glutamic acid, making it more reactive so ammonia can react with it to form glutamine.

Important correction: the original reaction is endergonic, but after coupling it with ATP hydrolysis, the overall process becomes exergonic, not endergonic

How does ATP

perform work in cells? (A: By energy coupling)

Energy coupling using ATP

hydrolysis & formation of a

Phosphorylated Intermediate

1. Glutamic acid + ATP interact.

ATP is hydrolyzed, releasing -7.3

kcal of energy and creating a

phosphorylated intermediate

2. The phosphorylated

intermediate is more reactive).

NH3 displaces the phosphate,

forming glutamate.

The overall process is now

exergonic = spontaneous!

How ATP Performs Work: Energy Coupling

Cells do work by energy coupling. This means an energy-releasing reaction is coupled to an energy-requiring reaction.

Amino acids have to be synthesized in cells. Building amino acids is an anabolic process, so it requires energy and is generally endergonic.

Example: making glutamine from glutamic acid.

Glutamic acid is the starting material for glutamine. To make glutamine, ammonia (NH₃) is added to glutamic acid.

Glutamic acid + NH₃ → glutamine

ΔG = +3.4 kcal/mol

Because ΔG is positive, this reaction by itself is endergonic and nonspontaneous.

Step 1:

Glutamic acid and ATP are brought together inside an enzyme.

ATP is hydrolyzed to ADP.

The terminal phosphate from ATP is transferred to glutamic acid.

This creates a phosphorylated intermediate.

A phosphorylated intermediate is a molecule with a phosphate temporarily attached to it.

Adding the phosphate makes glutamic acid more chemically reactive.

ATP hydrolysis releases about 7.3 kcal/mol of free energy under standard conditions.

ATP → ADP + Pi

ΔG = −7.3 kcal/mol

Step 2:

Ammonia enters and reacts with the phosphorylated glutamic acid.

NH₃ displaces the phosphate group.

Glutamine is formed.

The phosphate is released as inorganic phosphate, Pi.

Energy coupling:

Glutamic acid + NH₃ → glutamine

ΔG = +3.4 kcal/mol

ATP → ADP + Pi

ΔG = −7.3 kcal/mol

Net ΔG:

+3.4 + (−7.3) = −3.9 kcal/mol

Because the overall ΔG is now negative, the coupled reaction is exergonic and thermodynamically favorable.

ATP provides more than enough free energy to drive the +3.4 kcal/mol glutamine-forming reaction.

The purpose of phosphorylation is to make the intermediate more reactive so the next step can occur more easily.

After ATP has been used, ADP and Pi can later be regenerated back into ATP, mainly through cellular respiration in mitochondria.

Main idea: ATP hydrolysis drives endergonic reactions by coupling them to an exergonic reaction. In this example, ATP phosphorylates glutamic acid, making it more reactive so ammonia can react with it to form glutamine.

Important correction: the original reaction is endergonic, but after coupling it with ATP hydrolysis, the overall process becomes exergonic, not endergonic

How Enzymes Speed Up Metabolic Reactions

A XX is a chemical agent that speeds up a reaction without being consumed by the reaction.

An enzyme is a XX XX

Example: sucrase catalyzes the hydrolysis of sucrose.

Sucrose + H₂O → glucose + fructose

Sucrase has an active site that binds sucrose. Water is also involved in the reaction.

When sucrose binds to sucrase, the enzyme changes shape slightly and helps position the molecules correctly.

Sucrase helps break the glycosidic bond in sucrose. Water is split and its H and OH are added to the two products.

This produces two monosaccharides:

Glucose

Fructose

The enzyme itself is not used up, so sucrase can be used again.

Main idea: Enzymes speed up reactions by binding specific substrates and helping break or form bonds more easily without being consumed.

How Enzymes Speed Up Metabolic Reactions

A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction.

An enzyme is a catalytic protein.

Example: sucrase catalyzes the hydrolysis of sucrose.

Sucrose + H₂O → glucose + fructose

Sucrase has an active site that binds sucrose. Water is also involved in the reaction.

When sucrose binds to sucrase, the enzyme changes shape slightly and helps position the molecules correctly.

Sucrase helps break the glycosidic bond in sucrose. Water is split and its H and OH are added to the two products.

This produces two monosaccharides:

Glucose

Fructose

The enzyme itself is not used up, so sucrase can be used again.

Main idea: Enzymes speed up reactions by binding specific substrates and helping break or form bonds more easily without being consumed.

Classes of Enzymes

Oxidoreductases: move XX and/or XX between molecules. One molecule becomes XX and the other becomes XX

Oxidation = XX electrons

Reduction = XX electrons

Transferases: transfer a XX XX from one molecule to another.

Hydrolases: use XX to break a bond.

A-B + H₂O → A-H + B-OH

Sucrase is an example of a hydrolase.

Lyases: remove groups from molecules in a way that often creates a XX XX, or add groups across a double bond.

Isomerases: rearrange XX within a molecule to form an XX

Same atoms, different XX

Ligases: XX two molecules together.

Ligate = join

Usually require energy, often from XX

Three important special cases for Ch. 9 & 10:

Dehydrogenase = XX hydrogen atoms, usually transferring electrons and H⁺ to another molecule.

Kinase = transfers a XX XX, often from XX, onto another molecule.

Decarboxylase = removes a XX XX, usually releasing CO₂.

Quick way to remember:

Oxidoreductase = electron transfer

Transferase = moves a functional group

Hydrolase = breaks using water

Lyase = makes/breaks double bonds

Isomerase = rearranges

Ligase = joins

Main idea: enzyme classes are named based on the type of chemical reaction they catalyze.

Classes of Enzymes

Oxidoreductases: move electrons and/or protons between molecules. One molecule becomes oxidized and the other becomes reduced.

Oxidation = loses electrons

Reduction = gains electrons

Transferases: transfer a functional group from one molecule to another.

Hydrolases: use water to break a bond.

A-B + H₂O → A-H + B-OH

Sucrase is an example of a hydrolase.

Lyases: remove groups from molecules in a way that often creates a double bond, or add groups across a double bond.

Isomerases: rearrange atoms within a molecule to form an isomer.

Same atoms, different arrangement

Ligases: join two molecules together.

Ligate = join

Usually require energy, often from ATP

Three important special cases for Ch. 9 & 10:

Dehydrogenase = removes hydrogen atoms, usually transferring electrons and H⁺ to another molecule.

Kinase = transfers a phosphate group, often from ATP, onto another molecule.

Decarboxylase = removes a carboxyl group, usually releasing CO₂.

Quick way to remember:

Oxidoreductase = electron transfer

Transferase = moves a functional group

Hydrolase = breaks using water

Lyase = makes/breaks double bonds

Isomerase = rearranges

Ligase = joins

Main idea: enzyme classes are named based on the type of chemical reaction they catalyze.

Induced Fit in Enzyme Action

Enzymes are large XX XX with a specific region called the XX XX, where XX XX.

When an enzyme interacts with its substrates, both the substrate and the enzyme can change shape slightly. This is called XX XX.

Induced fit is similar to a handshake: when two hands meet, they adjust their shape to fit together better. In the same way, when the substrate enters the active site, the enzyme XXXaround it.

E + S → ES complex → E + P

E = enzyme

S = substrate

ES = enzyme-substrate complex

P = product

The enzyme-substrate complex forms when the XX bind to the enzyme’sXX XX

While the substrates are in the active site, the enzyme can squeeze, bend, and properly position them. This stresses certain chemical bonds and makes the reaction easier to occur.

The enzyme changes shape temporarily during the reaction, but after the products are released, the enzyme returns to its original form and can be used again.

Example: Hexokinase

Hexokinase is the first enzyme in glycolysis. Glycolysis contains 10 enzyme-controlled steps.

Hexokinase binds:

Glucose

ATP

The enzyme undergoes induced fit and transfers a phosphate group from ATP to glucose.

Glucose + ATP → Glucose-6-phosphate + ADP

Glucose-6-phosphate is a phosphorylated form of glucose.

Main idea: Induced fit means the enzyme changes shape when its substrates bind, allowing the active site to hold and position the substrates properly so bonds can be changed more easily. The enzyme is unchanged after the overall reaction and can be reused.

Induced Fit in Enzyme Action

Enzymes are large protein molecules with a specific region called the active site, where substrates bind.

When an enzyme interacts with its substrates, both the substrate and the enzyme can change shape slightly. This is called induced fit.

Induced fit is similar to a handshake: when two hands meet, they adjust their shape to fit together better. In the same way, when the substrate enters the active site, the enzyme bends around it.

E + S → ES complex → E + P

E = enzyme

S = substrate

ES = enzyme-substrate complex

P = product

The enzyme-substrate complex forms when the substrates bind to the enzyme’s active site.

While the substrates are in the active site, the enzyme can squeeze, bend, and properly position them. This stresses certain chemical bonds and makes the reaction easier to occur.

The enzyme changes shape temporarily during the reaction, but after the products are released, the enzyme returns to its original form and can be used again.

Example: Hexokinase

Hexokinase is the first enzyme in glycolysis. Glycolysis contains 10 enzyme-controlled steps.

Hexokinase binds:

Glucose

ATP

The enzyme undergoes induced fit and transfers a phosphate group from ATP to glucose.

Glucose + ATP → Glucose-6-phosphate + ADP

Glucose-6-phosphate is a phosphorylated form of glucose.

Main idea: Induced fit means the enzyme changes shape when its substrates bind, allowing the active site to hold and position the substrates properly so bonds can be changed more easily. The enzyme is unchanged after the overall reaction and can be reused.

The Active Site and Catalytic Cycle of an Enzyme

An enzyme has a specific XX XX that only certain substrates can fit into. The enzyme does not bind just any molecule; it is specific for its XX

Substrates enter the active site

The correct substrates bind to the XX at the same time if both are needed for the reaction.

Enzyme-substrate complex forms: induced fit

Once the substrates bind, the enzyme changes shape and “scrunches” around them. This is XX XX

X XX in the active site help the reaction

The amino acid R groups in the active site can:

XX the substrates correctly

Stretch or strain XX XX

Interact with the XX

Create a good XX for the reaction

That microenvironment might be acidic, charged, hydrophobic, or otherwise favorable for the reaction.

Substrate is converted to product

Covalent bonds can break and new bonds can form.

S → P

Products are released

Once the reaction is complete, the products leave the active site.

Enzyme is ready to be used again

The enzyme itself is not consumed and can catalyze another reaction.

Main idea: Enzymes speed reactions by specifically binding substrates, changing shape through induced fit, and using active-site R groups to position and stress the substrates so bonds can break and new products can form.

The Active Site and Catalytic Cycle of an Enzyme

An enzyme has a specific active site that only certain substrates can fit into. The enzyme does not bind just any molecule; it is specific for its substrates.

Substrates enter the active site

The correct substrates bind to the enzyme at the same time if both are needed for the reaction.

Enzyme-substrate complex forms: induced fit

Once the substrates bind, the enzyme changes shape and “scrunches” around them. This is induced fit.

R groups in the active site help the reaction

The amino acid R groups in the active site can:

Position the substrates correctly

Stretch or strain covalent bonds

Interact with the substrates

Create a good microenvironment for the reaction

That microenvironment might be acidic, charged, hydrophobic, or otherwise favorable for the reaction.

Substrate is converted to product

Covalent bonds can break and new bonds can form.

S → P

Products are released

Once the reaction is complete, the products leave the active site.

Enzyme is ready to be used again

The enzyme itself is not consumed and can catalyze another reaction.

Main idea: Enzymes speed reactions by specifically binding substrates, changing shape through induced fit, and using active-site R groups to position and stress the substrates so bonds can break and new products can form.

Enzymes Lower the Activation Energy (EA)

Activation energy (EA) = the XX amount of XX that must be added to a reaction before bonds can begin to XX and the reaction can move forward.

Any time a covalent bond is broken, XX has to be put into the system first.

Example:

A-B + C-D → A-C + B-D

In this reaction:

Bonds between A-B and C-D have to break

New bonds A-C and B-D have to form

Without an enzyme:

The activation energy barrier is very XX

The molecules may not have enough XX to reach the point where bonds can break.

You could sometimes force the reaction by adding a lot of heat or strong acid, but cells usually cannot tolerate those conditions.

Because the energy barrier is so high, the reaction happens very slowly.

With an enzyme:

The enzyme binds the XX at the XX XX

The enzyme undergoes XX XX.

The active site positions the substrates correctly.

R groups in the active site can pull, bend, twist, or strain certain bonds.

This makes it easier for those bonds toXX.

The enzyme helps bring the substrates to the transition state using less energy.

Transition state:

The unstable, XX XX point in the reaction.

Bonds are partially breaking and new bonds are beginning to form.

Once the reaction reaches the transition state, it can continue toward the products.

So the enzyme XX the amount of energy needed to reach the transition state.

Without enzyme → XX activation energy hill

With enzyme → XX activation energy hill

The enzyme therefore makes the chemical reaction happen XX XX.

Very important: enzymes do NOT change ΔG.

ΔG = the difference in free energy between the reactants and products.

The amount of free energy stored in the chemical bonds of the reactants is already determined by those molecules. The enzyme does not change how much energy the reactants or products contain.

So:

Enzyme lowers EA

Enzyme increases reaction rate

Enzyme does NOT change ΔG

Enzyme does NOT change how much energy is ultimately released or required

Enzyme does NOT change whether a reaction is exergonic or endergonic

If the reaction is exergonic before adding the enzyme, it is still exergonic after adding the enzyme.

If the reaction is endergonic before adding the enzyme, the enzyme does not magically make it exergonic. Energy still has to be supplied or the reaction has to be coupled to another reaction.

In the graph:

Y-axis = free energy

X-axis = progress of the reaction

Black curve = reaction without enzyme

Red curve = reaction with enzyme

Black peak is higher because more activation energy is needed without the enzyme

Red peak is lower because the enzyme lowers activation energy

Both pathways start at the same reactant energy

Both pathways end at the same product energy

Therefore, ΔG is exactly the same with or without the enzyme

Main idea: Enzymes speed up reactions by lowering the activation energy needed to reach the transition state. They make bond breaking and bond formation easier, but they do not change the overall free-energy change, ΔG, of the reaction

Enzymes Lower the Activation Energy (EA)

Activation energy (EA) = the minimum amount of energy that must be added to a reaction before bonds can begin to break and the reaction can move forward.

Any time a covalent bond is broken, energy has to be put into the system first.

Example:

A-B + C-D → A-C + B-D

In this reaction:

Bonds between A-B and C-D have to break

New bonds A-C and B-D have to form

Without an enzyme:

The activation energy barrier is very high.

The molecules may not have enough energy to reach the point where bonds can break.

You could sometimes force the reaction by adding a lot of heat or strong acid, but cells usually cannot tolerate those conditions.

Because the energy barrier is so high, the reaction happens very slowly.

With an enzyme:

The enzyme binds the substrates at the active site.

The enzyme undergoes induced fit.

The active site positions the substrates correctly.

R groups in the active site can pull, bend, twist, or strain certain bonds.

This makes it easier for those bonds to break.

The enzyme helps bring the substrates to the transition state using less energy.

Transition state:

The unstable, high-energy point in the reaction.

Bonds are partially breaking and new bonds are beginning to form.

Once the reaction reaches the transition state, it can continue toward the products.

So the enzyme lowers the amount of energy needed to reach the transition state.

Without enzyme → large activation energy hill

With enzyme → smaller activation energy hill

The enzyme therefore makes the chemical reaction happen much faster.

Very important: enzymes do NOT change ΔG.

ΔG = the difference in free energy between the reactants and products.

The amount of free energy stored in the chemical bonds of the reactants is already determined by those molecules. The enzyme does not change how much energy the reactants or products contain.

So:

Enzyme lowers EA

Enzyme increases reaction rate

Enzyme does NOT change ΔG

Enzyme does NOT change how much energy is ultimately released or required

Enzyme does NOT change whether a reaction is exergonic or endergonic

If the reaction is exergonic before adding the enzyme, it is still exergonic after adding the enzyme.

If the reaction is endergonic before adding the enzyme, the enzyme does not magically make it exergonic. Energy still has to be supplied or the reaction has to be coupled to another reaction.

In the graph:

Y-axis = free energy

X-axis = progress of the reaction

Black curve = reaction without enzyme

Red curve = reaction with enzyme

Black peak is higher because more activation energy is needed without the enzyme

Red peak is lower because the enzyme lowers activation energy

Both pathways start at the same reactant energy

Both pathways end at the same product energy

Therefore, ΔG is exactly the same with or without the enzyme

Main idea: Enzymes speed up reactions by lowering the activation energy needed to reach the transition state. They make bond breaking and bond formation easier, but they do not change the overall free-energy change, ΔG, of the reaction

Environmental Factors Affecting Enzyme Activity

Every enzyme has an XX XX of conditions where it works best. Two major factors are temperature and pH.

Temperature:

Human enzymes usually work best around normal body temperature, about XX

There is usually a small range around the optimum where the enzyme still works well.

If body temperature gets too high, enzymes can begin to XX

Denaturation changes the enzyme’s XX XX, including the active site, so the enzyme can no longer work properly.

At very high temperatures, enzyme activity can drop XX

If temperature is too low, enzymes usually do not XX, but molecular movement slows down, so enzyme activity also slows.

High fever:

Around 104°F and above, some human proteins and enzymes can begin losing normal function.

As temperature rises too far, enzyme activity decreases because the enzyme structure becomes unstable.

Thermophilic bacteria:

Thermophiles live in very hot environments, such as hot springs.

Their enzymes are adapted to high temperatures.

The example on the graph has an optimum around 77°C.

Some thermophiles can have enzymes that function near 100°C.

pH:

Enzymes also have an optimal pH.

If pH changes too far from the optimum, the charges and interactions between amino acid R groups can change.

This can alter the active site and reduce enzyme activity.

Examples:

Pepsin → stomach enzyme → works best around pH 2

Trypsin → intestinal enzyme → works best around pH 8

Main idea: Enzymes work best at specific temperatures and pH values. Conditions that are too hot, too cold, too acidic, or too basic can reduce enzyme activity, and extreme conditions can denature the enzyme

Environmental Factors Affecting Enzyme Activity

Every enzyme has an optimal range of conditions where it works best. Two major factors are temperature and pH.

Temperature:

Human enzymes usually work best around normal body temperature, about 37°C.

There is usually a small range around the optimum where the enzyme still works well.

If body temperature gets too high, enzymes can begin to denature.

Denaturation changes the enzyme’s 3D shape, including the active site, so the enzyme can no longer work properly.

At very high temperatures, enzyme activity can drop sharply.

If temperature is too low, enzymes usually do not denature, but molecular movement slows down, so enzyme activity also slows.

High fever:

Around 104°F and above, some human proteins and enzymes can begin losing normal function.

As temperature rises too far, enzyme activity decreases because the enzyme structure becomes unstable.

Thermophilic bacteria:

Thermophiles live in very hot environments, such as hot springs.

Their enzymes are adapted to high temperatures.

The example on the graph has an optimum around 77°C.

Some thermophiles can have enzymes that function near 100°C.

pH:

Enzymes also have an optimal pH.

If pH changes too far from the optimum, the charges and interactions between amino acid R groups can change.

This can alter the active site and reduce enzyme activity.

Examples:

Pepsin → stomach enzyme → works best around pH 2

Trypsin → intestinal enzyme → works best around pH 8

Main idea: Enzymes work best at specific temperatures and pH values. Conditions that are too hot, too cold, too acidic, or too basic can reduce enzyme activity, and extreme conditions can denature the enzyme

How do Cells Regulate Enzyme Activity?

And how can medicines be designed to regulate enzyme activity?

1. What is a Competitive Inhibitor (C)? A molecule that

binds to and inhibits the XX XX to block XX

Example: XX (binds Pancreatic lipase),

XX (binds transpeptidase)

2. What is a Non-Competitive Inhibitor (N)? Molecule that

binds to an XX XX (“other site”) changes XX

of XX XX to block XX (see also next slide)

Example: XX (RTI)

How Cells Regulate Enzyme Activity

Cells need enzymes to turn on and off depending on when a reaction is needed. One way they regulate enzymes is with inhibitors.

Competitive inhibitor:

Binds directly to the XX XX

Competes with the normal substrate for the same binding site.

Only one can occupy the active site at a time.

If inhibitor concentration is high, enzyme activity drops a lot.

If substrate concentration is high, the substrate has a better chance of binding, so the inhibition is reduced.

Competitive inhibitor = binds active site.

Examples:

Alli (orlistat) inhibits pancreatic lipase.

Pancreatic lipase normally breaks down dietary fats in the small intestine.

Alli occupies the active site, so fewer lipids can bind and be digested.

Undigested fats pass through the digestive tract, so fewer calories from those fats are absorbed.

Penicillin inhibits bacterial transpeptidase.

Transpeptidase is needed for bacterial cell-wall formation.

Blocking it prevents bacteria from properly building their cell walls.

Noncompetitive inhibitor:

Does not bind the active site.

Binds to an allosteric site, meaning an “other site” on the enzyme.

Binding changes the enzyme’s shape.

The active site changes shape enough that the substrate can no longer bind or react properly.

Increasing substrate concentration does not overcome this type of inhibition in the same way as competitive inhibition.

Noncompetitive inhibitor = binds allosteric site → changes active site shape.

Example:

Nevirapine inhibits HIV reverse transcriptase.

Reverse transcriptase is an enzyme HIV needs for replication.

Nevirapine binds away from the active site and changes enzyme activity.

It has been used as part of HIV treatment and in prevention of mother-to-child transmission.

Quick difference:

Competitive inhibitor = active site = directly competes with substrate

Noncompetitive inhibitor = allosteric site = changes enzyme shape

Main idea: Cells and medicines can regulate enzymes by blocking the active site directly or by binding somewhere else and changing the shape of the enzyme.

How do Cells Regulate Enzyme Activity?

And how can medicines be designed to regulate enzyme activity?

1. What is a Competitive Inhibitor (C)? A molecule that

binds to and inhibits the Active Site to block reaction

Example: Alli (binds Pancreatic lipase),

Penicillin (binds transpeptidase)

2. What is a Non-Competitive Inhibitor (N)? Molecule that

binds to an Allosteric site (“other site”) changes shape

of active site to block reaction (see also next slide)

Example: Nevirapine (RTI)

How Cells Regulate Enzyme Activity

Cells need enzymes to turn on and off depending on when a reaction is needed. One way they regulate enzymes is with inhibitors.

Competitive inhibitor:

Binds directly to the active site.

Competes with the normal substrate for the same binding site.

Only one can occupy the active site at a time.

If inhibitor concentration is high, enzyme activity drops a lot.

If substrate concentration is high, the substrate has a better chance of binding, so the inhibition is reduced.

Competitive inhibitor = binds active site.

Examples:

Alli (orlistat) inhibits pancreatic lipase.

Pancreatic lipase normally breaks down dietary fats in the small intestine.

Alli occupies the active site, so fewer lipids can bind and be digested.

Undigested fats pass through the digestive tract, so fewer calories from those fats are absorbed.

Penicillin inhibits bacterial transpeptidase.

Transpeptidase is needed for bacterial cell-wall formation.

Blocking it prevents bacteria from properly building their cell walls.

Noncompetitive inhibitor:

Does not bind the active site.

Binds to an allosteric site, meaning an “other site” on the enzyme.

Binding changes the enzyme’s shape.

The active site changes shape enough that the substrate can no longer bind or react properly.

Increasing substrate concentration does not overcome this type of inhibition in the same way as competitive inhibition.

Noncompetitive inhibitor = binds allosteric site → changes active site shape.

Example:

Nevirapine inhibits HIV reverse transcriptase.

Reverse transcriptase is an enzyme HIV needs for replication.

Nevirapine binds away from the active site and changes enzyme activity.

It has been used as part of HIV treatment and in prevention of mother-to-child transmission.

Quick difference:

Competitive inhibitor = active site = directly competes with substrate

Noncompetitive inhibitor = allosteric site = changes enzyme shape

Main idea: Cells and medicines can regulate enzymes by blocking the active site directly or by binding somewhere else and changing the shape of the enzyme.

8.21 Feedback Inhibition of Enzyme Activity

Feedback inhibition is a form of negative feedback. Negative feedback means the end product of a pathway XX or shuts down the process that makes it.

Example: Threonine → Isoleucine

Pathway:

Threonine → Intermediate A → Intermediate B → Intermediate C → Intermediate D → Isoleucine

When isoleucine levels are low:

Enzyme 1 is active.

Threonine binds to the active site.

The pathway continues.

More isoleucine is produced.

When enough isoleucine is present:

Isoleucine binds to an allosteric site on Enzyme 1.

This changes the shape of the active site.

Threonine cannot bind properly.

The pathway is switched off.

Isoleucine production slows or stops.

When isoleucine gets used up:

Less isoleucine binds to the allosteric site.

Enzyme 1 becomes active again.

Threonine can bind.

The pathway turns back on.

So:

More isoleucine → pathway OFF

Less isoleucine → pathway ON

This is negative feedback because the final produc XX its own production.

Equilibrium: forward and reverse reactions occur at the same rate, so there is no XX XX in reactants and products.

Metabolic disequilibrium:

Cells are constantly carrying out XX

Products usually do not XX

Products are often immediately used asXX in the next step.

Cells are therefore usually not at equilibrium.

Main idea: Feedback inhibition is negative feedback where the end product, isoleucine, binds allosterically to the first enzyme and shuts down the pathway when enough product has been made.

8.21 Feedback Inhibition of Enzyme Activity

Feedback inhibition is a form of negative feedback. Negative feedback means the end product of a pathway reduces or shuts down the process that makes it.

Example: Threonine → Isoleucine

Pathway:

Threonine → Intermediate A → Intermediate B → Intermediate C → Intermediate D → Isoleucine

When isoleucine levels are low:

Enzyme 1 is active.

Threonine binds to the active site.

The pathway continues.

More isoleucine is produced.

When enough isoleucine is present:

Isoleucine binds to an allosteric site on Enzyme 1.

This changes the shape of the active site.

Threonine cannot bind properly.

The pathway is switched off.

Isoleucine production slows or stops.

When isoleucine gets used up:

Less isoleucine binds to the allosteric site.

Enzyme 1 becomes active again.

Threonine can bind.

The pathway turns back on.

So:

More isoleucine → pathway OFF

Less isoleucine → pathway ON

This is negative feedback because the final product inhibits its own production.

Equilibrium: forward and reverse reactions occur at the same rate, so there is no net change in reactants and products.

Metabolic disequilibrium:

Cells are constantly carrying out reactions.

Products usually do not accumulate.

Products are often immediately used as reactants in the next step.

Cells are therefore usually not at equilibrium.

Main idea: Feedback inhibition is negative feedback where the end product, isoleucine, binds allosterically to the first enzyme and shuts down the pathway when enough product has been made.