Intro to Cell and Molecular Biology Chapter 4

What was believed to be in the atmosphere in the Reducing Atmosphere Hypothesis?

water vapor, hydrogen gas, methane, and ammonia, and a lack of oxygen

How did methane and ammonia contribute to redox reactions?

They readily gave up electrons, which oxidized them but reduced other molecules in the atmosphere.

Which experiment focuses on the Reducing Atmosphere Hypothesis?

Miller-Urey Experiment

What does the Extraterrestrial Hypothesis theorize?

Organic carbon, including amino acids and nucleic acids bases, came to earth via meteorites

What gas is mainly invovled in the Deep-Sea Vent Hypothesis?

hydrogen sulfide

How were important biological molecules formed according to the Deep-Sea Vent Hypothesis?

When hot, gaseous substances are expelled from the vents, organic compounds could form in the temperature gradient between the hot vent and cold, surrounding water

How were polymers of organic molecules thought to have synthesized?

On the surface of clay. Clay contains plate-like layers where monomers could have come together to form polymers.

What is a protobiont?

Prebiotic polymers that formed a boundary to separate itelf from its surroundings

What may have protobionts existed as?

liposomes (vesicles surrounded by a phospholipid bilayer)

What two RNA mutations may have occured that caused chemical evolution among early RNA

1.) Mutation that caused RNA to be able to self-replicate.

2.) Mutation that caused RNA to be able to syntehsize its own building blocks.

What is a possible reason why DNA took over the function of storing genetic information?

Because RNA had to store genetic info and catalyze important reactions

How and why did proteins come to evolve from RNA?

RNA synthesized the first polypeptide. Proteins are more stable in different environments. Protein has 20 different amino acids so it can fold into many different shapes and is more versatile.

Resolution

Clarity of an image

Contrast

Relative differences in light, color between adjacent regions of a sample

Magnification

ratio between the image prodouced by a microscope and it’s actual size

Light microscopy

uses light for illumination

Electron microscopy

Uses an electron beam for illumination, has better resolution than light microscopes

plasma membrane

bilayer of phospholipids and embedded proteins that separates the cell from its surroundings

cytoplasm

entire inner region of cell (*not to be confused with cytosol)

nucleoid

where genetic material is located in prokaryotes

ribosomes

synthesize polypeptides

Where are ribosomes found in prokaryotes?

free-floating in the cytoplasm

Where are ribosomes found in eukaryotic cells?

free-floating in the cytoplasm or attached to the outside of the rough ER

cell wall

rigid structure outside cell membrane

What is the function of the glycocalyx?

To prevent the cell from drying out and to prevent cellular material from leaking out the cell.

How is the glycocalyx formed?

It is made of hydrophilic oligosaccharides that are embedded in the plasma membrane.

What is the difference between a glycocalyx and a capsule?

A capsule is used as protection from degradation by some bacterial cells when in an animal’s immune system

Pili

allow prokaryotes to attach other prokaryotes

anchoring pili

holds cell in place

contractile pili

build a pilus to extend and retract it for motility

conjugate pili

pilus is formed to connect with another bacterium, and DNA is injected into the other side, a form of mating

How is flagellum powered?

a transmembrane rotor powered by the electrochemical gradient within the plasma membrane

What’s different about the archaeal flagellum compared to the prokaryotic flagellum?

The archaeal flagellum is powered by hydrolyzing ATP into ADP and phosphorus

Did eukaryotes descend from Bacteria or Archaea?

BOTH

catabolism

the breakdown of polypeptides into smaller molecules

anabolism

the synthesis of polypeptides from smaller monomers

What is the order of the sizes of cytoskeletal protein filaments from largest to smallest?

Microtubules, intermediate filaments, microfilaments (actin filaments)

What are microtubules made from?

alpha and beta-tubulin

Where do microtubules grow and shrink from?

can grow from the + end only

can shrink from the + or - end

What is it called when microtubules grow and shrink to fit the needs of the cytoskeleton?

dynamic instability

Where is the Microtubule-Organizing Center in eukaryotes?

The centrosome

How do microtubules grow from the centrosome?

The (-) is anchoring onto the centrosome and it grows from the (+) end.

What does the rope-like structure of intermediate filaments help with?

tension which increases rigidity

What is the key difference between intermediate filaments compared to microtubules, and microfilaments?

intermediate filaments tend to have a permenent length

Where are microfilaments concentrated?

Near the plasma membrane

What is pseudopodia?

temporary arm-like projection used for engulfing particles and cell movement

movement of cargo

the tail of kinesin holds cargo while the head moves along the microtubule

movement of filament

myosin is fixed in place and causes the motor protein to move

bending of filament

When linking proteins are bound to filaments, dynein moves toward the negative end and causes the filaments to bend

nuclear envelope

double membrane that encloses the nucleus

nuclear pores

where the inner and outer nuclear envelope make contact with each other

nucleolus

assembly of ribosomal subunits

nuclear lamina

where intermediate filaments are

nuclear matrix

when chromosomes are organized into chromosome territories

chromatin

DNA + proteins inside the nuclear matrix

What makes the rough ER rough?

there are ribosomes studded on the surface of the rough ER

What are some functions of the rough ER?

sorting of proteins destined for other places within the endomembrane system, insertion of proteins into the ER membrane, attachment of carbohydrates to lipids and proteins (glycosylation)

What are some functions of the smooth ER?

lipid synthesis (*think phospholipids), calcium storage, metabolism for detoxing

What are the three parts of the Golgi apparatus?

cis, medial, trans

Vesicular transport model

components travel through the Golgi cisternae via vesicles (example: cis to medial)

Cisternal maturation model

Many vesicles fuse at the cis end of the Golgi and become a cisternae. The existing cisternae become medial and a cisternae is lost at the trans end.

What is proteolysis?

Proteases and polypeptides are packaged into one vesicle where proteases cut the polypeptide into smaller pieces and transport it out of the cell by fusing to the plasma membrane (Example: proinsulin and insulin)

Describe the entire secretory pathway.

Proteins for secretions are synthesized in the ER, travel through the Golgi, and are sent to the plasma membrane via a vesicle

Describe the process of glycosylation.

Carbohydrates are linked together in the ER and then sent to the Golgi. Proteins/lipids are sent to the Golid where they are joined with the carbohydrates, mainly in the medial Golgi

Lysosomes

contain acid hydrolases that aid in the breakdown of molecules via hydrolysis

How does the cell protect itself from potential damage from lysosomes?

acid hydrolase operates at an acidic pH but the cytosolic pH is a neutral buffer meanign acid hydrolase don’t have much effect if released into the cytosol

Peroxisomes

catalyze detoxifying reactions

catalase

found within peroxisomes and breaks down hydrogen peroxide

intermembrane space

the region between the inner and outer membrane of the mitochondria

mitochondrial matrix

the part enclosed by the inner mitochondrial membrane

What is the name of the bacteria chloroplasts evolved from?

cyanobacteria

What is the name of the bacteria mitochondria evolved from?

proteobacteria

sorting signals

a short sequence of amino acid that directs a protein to the correct cell

cotranslational sorting

when proteins destined for the ER, Golgi, lysosomes, vacuoles, or secretory vesicles begin synthesis in the cytosol and then halts temporarily until the ribosome binds to the ER

post-translational sorting

the uptake of proteins into the nucleus, mitochondria, chloroplasts, or peroxisomes after the protein is completely made in the cytosol

What are the two functions of a signal reception particle (SRP)?

1. To recognize the ER signal sequence and pause translation

2. To bind to the SRP receptor in the ER membrane to continue translation

True or False: Animal cells have a cell wall.

False

transmembrane protein

protein made of nonpolar amino acids embedded within the nonpolar region of the phospholipid bilayer

What level of protein folding do transmembrane proteins utilize?

secondary level, alpha helix

lipid-anchored protein

one of the lipids within the bilayer is covalently attached to an amino acid side chain within the anchored protein

integral membrane proteins

proteins that cannot be removed without disrupting the integrity of the plasma membrane

peripheral membrane proteins

proteins noncovalently bound to integral membrane proteins OR to polar heads of the phospholipids

Which noncovalent bonds do peripheral membrane proteins utilize?

hydrogen and ionic