Foundation of Biology --> Chapter 5

Freshman year Bio 1

Proteins are?

• Diverse

• Everywhere in the cell (Ubiquitous)

• Versatile

Proteins Help?

Mediate many of the reaction and cellular processes that contribute to cellular functions

Proteins are made up of what?

Amino acid monomers

Amino acid Structure is made up of what?

Amino group and a Carboxyl group

What does the R group of each amino acid affect?

• Chemical properties of amino acids

• Folding and the three-dimensional shape of the protein

• Function of the protein

What are the R group Chemical properties?

• Hydrophilic or Hydrophobic

• Basic or Acidic

• Polar or Nonpolar

What is the First Level of Protein Structure?

Primary

What happens during the Primary Stage?

The sequence (order) of amino acids

What is the Second Level of Protein Structure?

Secondary 

What happens during the Secondary Stage?

The Interaction of nearby amino acids (influenced by R groups)

What is the Third Level of Protein Structure?

Tertiary

What happens during the Tertiary Stage?

Proteins Structures become three Dimensional Shapes (Influenced by R groups)

What is the Fourth Level of Protein Structure?

Quaternary

What happens during the Quaternary Stage?

Different proteins subunits may come together

• This does not happen for all Proteins

What Stages always happen in Proteins?

Primary, Secondary, and Tertiary

A Protein Shape..?

Determines its Function

A Protein Structure Can be Changed Through?

Denaturation

What is Denaturation?

Protein has the same amino acid sequence but NOT the same three-dimensional shape

A Denaturation protein loses what?

Its Function

What protects proteins from Denaturation?

Protein chaperones

What an Example of Denaturation?

• Cooking Eggs

• Starts from Water Soluble to Insoluble

What does DNA get transcribed into?

mRNA

What is the process that makes mRNA from DNA?

Transcription

What is the process that makes proteins from mRNA?

Translation

What do proteins provide and carry out in a cell?

Structure and many essential activities.

What structure carries out translation?

Ribosome!!

In prokaryotes, where does transcription occur?

In the cytoplasm

What enzyme synthesizes RNA from DNA in both cell types?

RNA polymerase

In prokaryotes, what structure makes polypeptides?

Ribosome

In eukaryotes, where does transcription occur?

In the nucleus

What is formed in eukaryotes before mRNA leaves the nucleus?

Pre-mRNA

What processing steps occur for eukaryotic pre-mRNA?

5′ cap addition, 3′ poly(A) tail, and intron removal.

Where does mRNA go after processing in eukaryotes?

To the cytoplasm

What happens to mRNA in the cytoplasm of eukaryotes?

It is translated by ribosomes into polypeptides.

Where does translation occur in prokaryotes compared to eukaryotes?

• Prokaryotes: Translation occurs in the cytoplasm at the same time as transcription (no nucleus).

• Eukaryotes: Translation occurs in the cytoplasm, but after transcription and RNA processing in the nucleus.

How is mRNA different in prokaryotic and eukaryotic translation?

• Prokaryotic mRNA: Used directly for translation, no processing (no cap, tail, or intron removal).

• Eukaryotic mRNA: Made as pre-mRNA, then processed with a 5′ cap, 3′ poly(A) tail, and intron removal before translation.

What does translation require according to the central dogma?

Translation requires several cellular components to make protein from RNA.

What are the main cellular components required for translation?

• Messenger RNA (mRNA)

• Ribosome

• Transfer RNAs (tRNAs)

• Initiation factors

• Release factors

What does the mRNA indicate?

The amino acid sequence of the protein

What are RNA nucleotides group into?

3- Nucleotide codon that correspond to amino acids

mRNA bases read from what to what?

It reads from 5’ to 3’

What codons are required?

A Start and Stop codon.

What is the Start Codon?

AUG

What is the Stop Condons?

UAA, UAG, or UGA

Translate this: GCAUGACUCUUGACUGAC

MET- Thr - Leu - Asp

• Write Start codon

• DO NOT WRITE STOP

What does each transfer RNA (tRNA) carry to the mRNA codon?

An amino acid corresponding to the mRNA codon.

What are the two representations of tRNA shown on the slide?

• Clover-leaf configuration with sequence

• 3D ribbon model

What are the two main labeled regions on a tRNA molecule?

• Amino acid attachment site (3′ end)

• Anticodon (in the anticodon loop)

What do ribosomes do?

Ribosomes translate mRNA into protein.

What are ribosomes made of?

Proteins and ribosomal RNAs (rRNAs).

How many subunits do ribosomes have?

Two subunits — one small and one large.

In what direction does the ribosome read mRNA?

From 5′ to 3′, incorporating the appropriate amino acids.

How many tRNA binding sites are in the ribosome?

Three — A site, P site, and E site.

What happens at the A site of a ribosome?

It accepts the incoming amino acid carried by a tRNA.

What happens at the P site of a ribosome?

It is where the growing protein (polypeptide) may be found.

What happens at the E site of a ribosome?

It is where the tRNA exits the ribosome.

What does each transfer RNA (tRNA) do?

Carries an amino acid to its corresponding mRNA codon.

What is the relationship between a tRNA anticodon and an mRNA codon?

The tRNA anticodon is antiparallel and complementary to the mRNA codon.

What type of pairing occurs between a codon and anticodon?

Specific codon–anticodon pairing.

How do codon and anticodon bases align?

The first base of the codon (5′ end) pairs with the last base of the anticodon (3′ end).

What are Translation Three Steps?

• Initiation

• Elongation

• Termination

What is the first step in the initiation of translation?

Initiation factors (proteins) bind to mRNA.

What happens after initiation factors bind to mRNA?

The small ribosomal subunit binds.

What tRNA enters during initiation of translation?

tRNA met

What do initiation factors and tRNA met scan for?

A start codon.

What happens when the large ribosomal subunit binds?

Initiation factors are released.

Where is tRNA met​ positioned after initiation is complete?

In the P site of the ribosome.

At what site does the correct charged tRNA bind during elongation?

At the A site.

What determines which tRNA binds at the A site?

The next codon on the mRNA.

Where is a peptide bond formed during elongation?

Between amino acids on tRNAs in the P site and A site.

What happens to the amino acid chain during elongation?

The amino acid sequence is transferred from the P site to the A site, adding the new amino acid to the chain.

What moves during elongation, the ribosome or the mRNA?

The mRNA translocates one codon (the ribosome does not move).

Where is the growing protein located after translocation?

In the P site.

What happens to the A site after mRNA translocates?

It becomes open for the next charged tRNA.

What happens when a stop codon enters the A site during translation?

A release factor enters the A site.

What does the release factor do during termination?

It releases the polypeptide (amino acid sequence) from the tRNA in the P site.

What happens to the ribosome after the polypeptide is released?

The ribosome dissociates (falls apart).

What happens after a peptide bond forms and elongation continues?

The next amino acid addition begins.

Where does all protein synthesis begin?

On “free” ribosomes.

Are free ribosomes attached to the endoplasmic reticulum (ER)?

No, free ribosomes are not attached to the ER.

What happens to a protein with no signal sequence?

It remains in the cytosol.

Where does a protein go if it has an amino-terminal signal sequence?

To the chloroplast or mitochondrion.

Where does a protein go if it has an internal signal sequence?

To the nucleus!

What is the main purpose of protein sorting?

To send a newly made protein to the correct location where it is needed.

What may the first few amino acids of a protein have?

A signal sequence.

What happens if a protein has no signal sequence?

The ribosome stays “free” and the protein stays in the cytoplasm.

What happens if a protein has a signal sequence?

The ribosome attaches to the endoplasmic reticulum (ER).

Where can proteins go if they have an amino-terminal signal sequence?

To the chloroplast or mitochondrion (plural word for mitochondria)

Where can proteins go if they have an internal signal sequence?

To the nucleus.

Ribosomes that attach to the ER make proteins that end up where?

• Within the lumen of the endomembrane system

• Secreted out of the cell

• Embedded in the cell membrane

What does protein sorting ensure?

That proteins go to the correct location where they are needed.

Are all genes expressed all the time in a cell?

No, not all genes are expressed all the time.

Why is gene expression regulated?

It saves the cell energy by making proteins only when needed.

What are the main levels where protein synthesis can be controlled?

• Block DNA accessibility

• Block transcription

• Block RNA processing

• Other regulatory methods

Into how many protein families can proteins be grouped?

About 25,000 protein families.

What are protein families?

Groups of proteins that are structurally and functionally similar due to a common evolutionary origin.

How can proteins evolve?

Through mutations in the coding sequences of DNA.

What effects can mutations have on proteins?

They can cause positive, negative, or neutral changes in protein structure or function.

What happens to beneficial protein mutations?

Proteins with beneficial mutations can be retained in a population through natural selection.