Cell Bio exam 3

How many nucleotides in length are tRNA?

75-85

What is the job of tRNA?

take individual amino acids to its approximate location where it can be incorporated into a growing peptide

How are amino acids attached to tRNAs?

by specific aminoacyl synthetases

How many tRNA exist for the different amino acid families?

50 tRNA molecules that fit into 20 amino acid families

What is the structure of tRNA?

cloverleaf structure with 5’ and 3’ ends close to each other with 3 ladders

What are the 3 loops of the tRNA?

D loop, TψC loop, variable loop

What is the function of the D loop and TψC loop?

have modified Uracil nucleotides

What is the function of the variable loop?

contains the anticodon which is complementary to the codon in the messenger RNA

What is the mechanism that ensures the right amino acid is put on the right tRNA?

The amino acid synthetase takes an amino acid and energizes it. In the 1st active site of the enzyme an amino acid is attached to an ATP which gives you an energized amino acid bound to AMP and two phosphates. The second active site takes the energized amino acid and binds it to tRNA and releases AMP

Does protein synthesis cost energy?

yes, ATP

What are the major players of protein synthesis?

mRNA, tRNA, ribosomal subunits

What are the minor players of initiation?

IF1, IF2, IF3

What is the first step of protein synthesis initiation?

40s ribosomal subunit binds to mRNA at a precise location with the help of IF3

What is the first codon no matter the protein?

AUG which codes for methionine

What is the first anticodon of the tRNA no matter the protein?

UAC

How does the tRNA know where to bind to the start codon?

IF1 and IF2 bind to the appropriate tRNA that contains the methionine amino acid and the appropriate UAC anticodon and bring it to the mRNA

What happens after the tRNA is in place?

the 60s ribosomal subunit will bind

What happens after the 60s ribosomal subunit binds?

the IFs will disappear and the 60s and 40s ribosomal subunits will combine to form an 80s ribosome signaling the end of initiation

How many amino acids can be hidden between the subunits and how does this hiding happen?

20 and the subunits are hollow

Where is the best place to regulate protein synthesis?

initiation

How do you regulate protein synthesis?

Phosphorylate IF2 (add a phosphate to it) which will inactivate it

What happens when you phosphorylate IF2?

it will inactivate and tRNA will not bind and neither will the 60s ribosomal subunit

What are the different ‘rooms’ of protein synthesis?

P site (peptidyl or donor site) and A site (acceptor site)

What are the minor players of elongation?

Tu, Ts, Peptidyl transferase, and g-translocase

What are Tu and Ts?

temperature unstable and temperature stable

What does peptidyl transferase do?

break the bond between the carboxyl carbon of the amino acid and the 3’ end of the tRNA to set the amino acid free and then takes the amino acid and transfers it to the A site to form a peptide bond

What does G-translocase do?

takes the mRNA and shifts it one codon through the tunnel and releases the tRNA from the P site that no longer has an amino acid

What do Tu and Ts do?

bring the tRNA into the appropriate site

How is tRNA locked into place in the A site?

GTP is hydrolyzed to force it into appropriate place and lock it in

What happens to Tu and Ts after the lock in of tRNA?

they disappear

How are proteins able to fold into tertiary structure during protein synthesis?

ribosomes have pores that allow the protein to stick out and fold

What are the stop codons?

UAG, UAA, UGA

What are the termination factors?

R1 and R2

Which stop codons does R1 recognize?

UAA and UAG

Which stop codons does R2 recognize?

UAA or UGA

How do the release factors work?

they act as a bowling ball and break the protein off the tRNA sending the tRNA in one direction and the protein in another

What happens to the initiation complex during termination?

IF3 acts a second bowling ball and breaks apart the ribosomal subunits and mRNA

What do antibitotics do?

block protein synthesis of bacteria

Why do we have to have a long course of antibiotics?

it takes time to stop protein synthesis and kill the bacteria

Why can’t we take more pills in a shorter amount of time?

at high concentrations antibiotics start blocking our natural protein synthesis

What are the 7 major compartments of the cell?

ER, nucleus, mitochondria, Golgi apparatus, lysosomes, peroxisomes, cytoplasm

How much of the membrane of the cell does the plasma membrane make up?

2-5%

What kind of barrier is the plasma membrane?

semipermeable membrane

What does it mean by dynamic membrane?

many different molecules make up the plasma membrane that move around each other

What is the lipid bilayer?

hydrophobic tails and hydrophilic heads arranged in a bilayer

What is the base of cholesterol?

sterol which has 4 rings and hydroxyls coming off it

What happens if cholesterol is present in the bilayer?

it acts as a barrier that decreases fluidity

What are glycolipids?

some type of lipid (usually phospholipid) that has a sugar attached to it

Where are the sugars attached on the glycolipids and how do they function?

only on the polar head of the outer monolayer and function as an antenna to help identify the cell

What are the 4 primary phospholipids?

Phosphatidyl choline, ethanolamine, serine, and inositol

How do phospholipids move?

they spin and move laterally within their monolayer plane

Why does fluidity have to be regulated in the lipid bilayer?

too much spinning and fluidity makes it nonselective and too much rigidity makes it so that materials that need to get in cannot

How do animals who cannot regulate temperature decrease fluidity?

increase the tail length of the phospholipid which will cause steric interaction

How do animals who cannot regulate temperature increase fluidity?

increase the unsaturation of the phospholipids which will create kinks that make them unable to pack as close together

What is the phospholipid present in the outer monolayer?

Phosphatidyl-choline

What are the phospholipids present on the cytoplasmic mono layer?

Phosphatidyl- Ethanolamine, Serine, Inositol

What charge do the different phospholipids have?

Choline has a positive charge while Ethanolamine, Serine, Inositol have a negative charge

How thick is the plasma mebrane?

4-5 nm

How much of the membrane is lipids and proteins?

50% lipids and 50% proteins

What are transmembrane proteins called?

integral proteins

What do transmembrane proteins do?

go completely through the membrane; domain that interact with outside, center, and cytoplasmic parts of the cell

How do peripheral proteins work?

they anchor to one monolayer but do not go all the way through

How are peripheral proteins anchored?

have a cytoplasmic domain that is hydrophilic and membrane domain that is hydrophobic, lipoprotein (protein with lipid attached), and bonding through weak bonds with another protein

What is membrane transport?

movement of molecules into and out of the cell

What is osmotic homeostais?

the series of transport mechanisms taken to keep water at equilibrium

How can water move in and out of the cell?

diffusion or with ions

What is ionic homeostasis?

the balance of ions in the cell

What is diffusion?

the movement of molecules from a high concentration to a low concentration that is not very fast

What is usually transported by diffusion?

water, small molecules, ions, amino acids, simple sugars

What are membrane transport proteins?

specific proteins that bind to molecules and take them across the cell

What are the advantages of membrane transport proteins?

move at a much faster rate than diffusion and can move against a gradient

What are uniport carriers?

membrane transporters that will bind to one type of molecule and move it in one direction

What are symport carriers?

membrane transporters that will transport 2 molecules at the same time in one direction (Glucose-sodium transporter)

What are antiport carriers?

membrane transporter that will transport 2 different molecules 2 different directions (Sodium potassium ATPase pump)

How do channels work?

they are gated to a certain extent and are very specific to certain ions that functions as a transmembrane protein

How do you open a gate via a ligand?

The ligand binds to the domain acting as a gate opening it and allowing the specific molecules for that channel to move through rapidly. When the ligand disappears, the gate closes

How do you open a gate via voltage?

An action potential will move through the membrane and depolarize it causing the charges to switch sides. The voltage change will open the gate and rapid redistribution of molecules will occur. Repolarization will occur and the gate will close

What is the process of endocytosis?

when a group of molecules comes into contact with the membrane which begins to fold in and become deeper to form a vesicle which will move inside where it can be processed

How do vesicles move in the cell?

They are drawn and pulled by actin filaments that will move it to a specific location

Where does endocytosis occur?

anywhere on the surface of the cell

When does endocytosis occur?

24/7

What is pinocytosis?

small vesicles carrying liquid or small organic molecules in bulk

What is phagocytosis?

larger vesicles holding organic matter being brought in

What is exocytosis?

The mechanism we use to take more membrane out so we can replace it and make the membrane uniform, the exact reverse of endocytosis

When does exocytosis occur?

on demand in response to signaling

Where does exocytosis occur?

normally binds to a region that has a lot of calcium released

What is clathrin?

a homotrimer protein that accumulate on the cytoplasmic surface and coat a specific vesicle so that it goes to its specific location in a process called receptor mediated endocytosis

What is cytoplasm made of?

70% water, 25% proteins, and 5% small organic molecules

What is matrix cytoplasm?

cytoplasm inside the organelles

What is ground cytoplasm?

cytoplasm outside of the organelles

What is the advantage of a contiguous ER membrane?

anything within the membrane of the ER can move around, go inside nucleus, and come back out

What are the 3 types of ER?

rough, smooth, and transitional

What are the characteristics of rough ER?

studded with 80s ribosomes linked together by 2 glycoproteins that anchor it to the ER membrane

What is the lumen?

the center of the ER

How are 80s ribosomes drawn to the ER?

during standard initiation in the cytoplasm, a leader sequence will be translated and it will direct the unit to bind to the ER

What is the leader sequence?

20 codon sequence that translates 20 amino acids that are hydrophobic

What happens to leader sequence after the ribosome is bound?

it gets clipped away as it is not part of the final protein

What are different fates of proteins synthesized in the ER?

matrix cytoplasm, peripheral and face either the matrix or ground cytoplasm, transmembrane and threaded through the membrane on both sides

What is glycosylation?

the creation of a custom sugar

What is a dolichol?

a transmembrane lipid that is the site of glycosylation