BIOL 3000 - Exam 3 - Translation

Where does translation occur?

Cytoplasm

When does translation occur?

Either G1 or G2

What is the main component of translation?

80s

In eukaryotes, translation is dependent on the ______ ribosome

80S

The 80S ribosome is made of what two ribosomes?

1. 60S ribosome

2. 40S ribosome

60S ribosome

Joins amino acids together to form peptide chains (3 rRNA molecules and 46 proteins)

80s ribosome

Responsible for reading the mRNA

Ribosome

Highly complex cellualr machine responsible for the synthesis of proteins from mRNA

List the 3 different sites of the ribosome.

1. E site (exit)

2. P site (tRNA first binds here to start translation)

3. A site (new tRNA enters through here)

What are the 4 arms of a tRNA?

Psi arm, D arm, variable arm, and anticodon arm

The ribosome reads the mRNA strand in the _____' to ____' direction

5' to 3'

tRNA

RNA molecule that serves as the physical link between mRNA and amino acids.

Has an anticodon arm, a variable arm, a psi(T) arm, and a D arm.

Carries amino acids that form a chain when translated.

What 3 nucleotides does each tRNA end in?

3' CCA

What is the function of the anticodon arm in tRNA?

It has base pairs that are complimentary to the codons of mRNA and allows the correct amino-acid to match with the mRNA codons.

What is the function of the variable arm in tRNA?

It is an enzyme that attaches the specific amino acid to the tRNA, matching it with the correct anticodon on the anticodon arm.

What is the function of the Psi (T) arm and D arm in tRNA?

Provides structure and stability to the tRNA during translation/when interacting with the ribosome.

An _______ bond on the 3' end allows amino acids to bind and form a chain when translated.

ester

Why is tRNA NOT double-stranded if it looks double stranded from base pairs matching with themselves?

The whole structure only has one backbone

Codon

3 nucleotides read at a time from 5' to 3'

____ nucleotides = 1 codon.

_____ codon = 1 amino acid.

3, 1

What is THE start codon in initiation?

AUG (Auburn Is Great)

What are the 3 stop codons in initiation?

UAA (University of Alabama Awful)

UGA (University of Georgia Awful)

UAG (University of Alabama Gross)

Reading frame

One of three possible ways of reading a nucleotide sequence

Open reading frame

A sequence of DNA triplets (between start and stop codons) that can be transcribed into mRNA and later translated into proteins

How many reading frames does each codon have?

3

What are the "rules" of mRNA?

Written in linear form, comma-less, coded in triplets, unambiguous, degenerate, specific start and stop codons, non-overlapping, and universal

List the 4 stages of translation.

1. activation

2. initiation

3. elongation

4. termination

Activation

tRNAs bring the correct amino acid to the ribosome to build polypeptide chains

Where are free amino acids covalentely attached to in tRNA?

3'

How does Aminoacyl-tRNA synthetase catalyzes activation reactions?

ATP

T/F: Without a charged aminoacyl-tRNA, tRNA cannot be read

True.

What is the end product of activation?

Aminoacyl tRNA, aka "activated" amino acid

There is not a unique tRNA for every single codon. To account for this, what occurs?

"Wobble". This means that the third nucleotide within a codon can code for multiple amino acids

Initiation

Ribosome assembles and binds to mRNA molecule.

Go through the initiation stage of translation step-by-step

1. 40S ribosome (small subunit) searches for 5' guanine cap to associate with mRNA molecule

2. 40S ribosome binds to mRNA and searches for start codon. It will read mRNA to find a suitable start codon, since not every AUG is a suitable start codon.

3. 40S ribosome binds to an aminoacyl-tRNA containing MET and UAC anticodon (matches AUG)

4. THEN, 40S ribosome recruits the 60S ribosome to form the 80S ribosome

5. MET-tRNA occupies the P site of the 80S ribosome

Kozak sequence

helps guide the ribosome to the correct start codon on the mRNA. The ribosome scans along the mRNA from the 5' end and uses this sequence to identify the AUG start codon within a favorable context for initiating translation.

Variations in the Kozak sequence can affect how efficiently a specific mRNA is translated. A ________ Kozak sequence may lead to reduced protein production, while a ________ Kozak sequence may increase protein expression.

weaker, stronger

Elongation

Ribosome moves down the mRNA strand in a process known as translocation. tRNA comes into the A site and grows an amino acid chain.

These two factors allow specific entry of an incoming tRNA molecule at the A site in the ribosomal subunit.

elongation factors and GTP

This protein catalyzes the addition of the correct AA-tRNA at the A

G protein

These prevent the wrong charged tRNA from entering the A site

Initiation factors

Go through the elongation stage of translation step-by-step

1. tRNA that was in the P site moves to the E site to be released into the cytoplasm.

2. tRNA with a growing peptide chain moves to the P site.

3. A site is vacant and ready for the next charged tRNA to enter.

4. Process is repeated until complete peptide chain is formed.

After charged tRNA was placed in the A site, what was released from GTP and provided energy?

phosphate

The cleavage of GTP to EDP when tRNA enters the A site releases?

Elongation factors

A _______ bond forms between amino acids in the P and A sites.

peptide bond; made by peptidyl-transferase center

What is the energy cost for protein synthesis?

2 ATPS and 2 GTP

____ high energy ___ bond for each peptide bond formed

4; phosphate

Termination

A release factor (protein) finds to a stop codon and binds to the A site of the ribosome.

The amino acid chain is released and the mRNA and ribosome dissociate.

Are there any tRNAs for a stop codon?

No

Proteins called ___ bind to the A site of the ribosome

Release factors

Proteins

Large biological molecules (macromolecules) consisting of one or more polypeptide chains that perform a wide variety of functions in living organisms. There are 20 unique versions of these.

List the 3 things that the functional diversity and versatility of a protein derives from

1. chemical diversity of the amino acid side chains

2. flexibility of polypeptide chains

3. large number of ways in which polypeptide chains interact with different amino acids and fold

This identifies and differentiates amino acids from each other.

Side chain

All amino acids have this group.

Carboxylic group

The backbone of a polypeptide is made from:

alpha carbon linked to an amino group and carboxyl group.

the R groups are not part of the backbone

A peptide bond is a COVALENT bond between the _______ _______ and _________ ________ of two adjacent amino acid residues

carboxyl carbon, amide nitrogen

Everytime a peptide bond is formed, ______ is released

water

The peptide bond is in the ______ _____ of the amino acids coming together.

peptide plane

peptide plane

Plane formed by carboxyl carbon, the carboxyl oxygen and the amide nitrogen. Oxygen will always be sticking out and they will all have the same bonding and distance from each other.

True or false: any bond to the alpha carbon has 360 degree rotation

True

What bond is between the amino acid backbone?

Amide bond

___ bond in some excreted or exterior surface proteins between the side chains of cysteine

Disulfide

What is the alpha carbon bound to?

R-group

Why is the peptide plane said to be coplanar?

It can turn in any direction and not change the functionality of the polypeptide chain.

_____ groups can turn the amino acid groups any direction it wants (unless it hits something)

R-groups

Non-polar (hydrophobic) amino acids

These types of amino acids tend to repel water by facing inward and pack closely in together

Polar (hydrophilic) amino acids

These types of amino acids tend to form hydrogen bonds with one another, to the peptide backbone, to other molecules and to water

Charged amino acids

These amino acids tend to reside on the outside of a globular protein and interact with other side chains or macromolecules to give structure

Positive charged amino acid

Lysine, arginine, and histidine

Negative charged amino acid

Aspartic acid and glutamic acid

List the 2 types of chemical interactions that stabilize proteins

1. covalent bonds

2. electrostatic bonds

covalent bonds

Bond created by the sharing of electron pairs creating a very stable reaction. They are stronger (and harder to break) than electrostatic bonds bc they are sharing electrons across.

They make up the amino bonds of the amino acid backbone and disulfide bonds are between the side chains.

electrostatic bonds

Bond from interaction of amino acids based on their charge. Proteins are flexible because of these interactions! They are weaker (and easier to break) than covalent bonds bc they are not sharing electrons across.

Make up the hydrogen bonds and Van der Walls interactions in amino acids.

True or false: the backbone is the same for all amino acids

True

What are the three parts of an amino acid?

Amino group, side chain, and carboxylic group

What type of reaction forms a peptide bond?

Hydrolysis reaction

A peptide bond is a ___ bond between the ___ carbon and ___ nitrogen of two adjacent amino acid residues

Covalent; carboxyl; amide

The functional diversity and versatility of a protein derives from?

CHemical diversity, flexibility of the polypeptide, and interaction diversity (combination lead to higher order protein structure)

List the 4 different levels of protein structure

1. primary

2. secondary

3. tertiary

4. quaternary

For most proteins, what is the final functional form?

Tertiary

How many polypeptide chains are in a tertiary structure?

One

How many polypeptide chains are in a quaternary structure?

Two or more

primary structure

Linear sequence of amino acids; held together by covalent bonds

What are the two ends of the primary structure called?

Amino terminus/NH2 (N-terminus) and Carboxyl terminus/COOH (C-terminus)

secondary structure

highly regular local substructures of protein. LOCALIZED 3D shape.

List 3 types of secondary structures. Which is the simplest one we have? Which is the most common?

1. Beta turn - simplest

2. Beta sheets

3. Alpha helix - most common

Beta turn

Simplest secondary structure. Usually only involves 3 or 4 residues. Will almost always find a glycine residue here, bc it has a small R-group and allows a 180º turn.

This helps reverse the direction of the polypeptide chain and makes compact folding of the chain possible

Beta sheets

Secondary structure. Two or more strands widely separated in a 1º sequence and running side-by-side. Hydrogen bonds run between strands

Beta sheets going in a circle.

Porin

Alpha helix

Most common secondary structure. Highly regular local substructures of a protein. Has a twisted ribbon shape.

Tertiary structure

Made from folding the secondary structural elements into a compact and nearly solid object stabilized by chemical bonding interactions

True or false: All proteins have tertiary structure?

True

Tertiary structure bond interactions are mostly?

electrostatic

How are tertiary structures maintained?

Covalent bonds and elctrostatic interactions

Quaternary structure

3D structure of multi-subunit proteins and how they stick together.

True or false: all proteins have quaternary structure?

False

Which structure is maintained by the sum of covalent and electrostatic interactions?

Tertiary

List 3 types of post-translational modifications that improve protein stability of secondary structures when they are vulnerable outside the cell

1. disulfide bridge

2. metal binding

3. binding of effector molecules

Disulfide bridge

Protein stability method where covalent bonds form between sistine residues to provide tighter structure to the protein. They make the protein bond last as long as possible outside of the cell; reversible and not commonly found in intracellular proteins due to the reducing nature of the cytoplasmic but common in secreted proteins

The disulfide bridge is highly sensitive to the environment and (reversibe/irreversible?)

reversible