Protein Synthesis Part 1 Outline

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AP Biology

Protein Synthesis – Part 1

(Associated Learning Objectives: 1.14, 1.15, 1.16, 2.22, 2.31, 2.33, 2.36, 2.37, 3.4, 3.6, 3.18, 3.24, 3.25, 4.1, 4.2, 4.3, 4.4)

Important

concepts from previous units:

1)

2)

3)

Proteins are constructed from the macromolecules called amino acids.

Amino Acids are linked by a covalent peptide bond by a hydrolysis reaction.

DNA is more stable than RNA; but RNA evolved before DNA did.

I.

George Beadle and Edward Tatum (1934)

A.

They develop the one gene-one enzyme hypothesis. This proposes that a single gene has the genetic information for making one enzyme. This is later changed to become the

one gene - one polypeptide

(protein) hypothesis; as enzymes are a

type

of polypeptide (protein).

II.

III.

Transcription

(means “ the process of making a

working copy

of an original”)

A.

This process is the making of a

disposable copy

of DNA but in the form of RNA

.

The

disposable

copy will become known as mRNA – messenger RNA. It is a

disposable copy

of the “Million Dollar DNA Blueprint”.

1.

2.

The

message

(mRNA) will be sent to the

RNA nucleotides use Ribose

instead construction site

(ribosomes)

for building

the protein.

of Deoxyribose as the five carbon sugar. This makes the

RNA

less stable

than DNA; that is good since the cell only needs it to send a

temporary

message on how to construct the protein.

B.

C.

3.

In RNA, Uracil replaces Thymine. Thymine can’t exit nuclear pores. Remember, ribosomes are out in the cytoplasm, so Thymine needs to be substituted by Uracil.

DNA serves as a

template

(guide) for making the mRNA. A = U and C = G (Still can use

Chargaff’s Rule

.)

In Eukaryotic cells, the mRNA must first be “modified” before translation can occur. The modification occurs in the nucleus. (Prokaryotes

DO NOT

modify the mRNA. They sent it to the ribosome “as is”.)

1.

Primary Transcript

(before modification) is modified to produce the

secondary transcript

( after modification has occurred). The

secondary transcript

is what will be sent out of the nucleus to the ribosome.

D.

This is considered the

first part

of

Protein Synthesi

s

.

Translation

(means “The process of taking from one language and

changing

to another language”)

A.

In this process, the cell is

turning

nucleotide language (DNA/RNA) into amino acid language to make

B.

C.

proteins. Remember, amino acids are the building blocks of proteins.

This process occurs at the Ribosome. The ribosome has a nickname… “the Translator”. It is also considered a “construction site” since the cell is

building

a protein.

This is considered the

second part

of

Protein Synthesis.

IV.

Codon

“A.K.A Triplet Code” (This is the amino acid language.)

A.

Codons are

determined

by the template strand of DNA (Important Blueprint Information) but are READ ON

THE RNA! (The mRNA is what is being translated; not the DNA.)

1.

The codons MUST be read 5’

3’on the mRNA!

(Because this is how the mRNA was made.

You do not write a sentence and then read it backwards do you. It would make no sense.)

B.

RNA Codon Chart

for Amino Acids (Contains the 20 known amino acids for living organisms.)

1.

The chart was started by Marshall Nirenberg (early 1960’s) (He won a Noble Prize for this.) a.

UUU- Phenylalanine was the first one recorded.

2.

61of the 64 possible codons ( 4³) codes for an Amino Acid. a.

4 refers to the four nucleotides possible (A, C, U, G); 3 refers to the number of pieces in a

UNIT (codon).

3.

4.

5.

AUG

is the

start codon

or Methionine. It depends on the

position

in the mRNA. If it is the first codon on the 5’ end, it will be the start codon. If it is not the first, it will be regular methionine.

UAA, UAG

, and

UGA

are the

stop codons.

These codons stop the process of transcription.

Redundancy is

wasteful

, so enter Inosine. This nucleotide can act as a “Wild Card”. When put in

6.

the

third

position of an

anticodon

, it can represent

any

nucleotide. (This is useful for such amino acid sequences such as Serine or Arginine.)

This chart is

universal

for

all

living organisms and vituses.

(

Viruses are

not

living.) This hits on the theme of

Unity

and

Diversity

. Unity in that it indicates Common Ancestry among all

C.

organisms and viruses. Diversity is in the differences of the

sequences

of amino acids strung together to make a protein.) a.

Remember, RNA evolved first (but it is unstable) then mutated to DNA (which is more stable). This is why ALL living organisms and most viruses are DNA based.

Reading Frame

- This term refers to a set of

3 consecutive nucleotides

read in

5’

3’

direction.

V.

RNA Synthesis

and

Modification

-The

making

of mRNA. This process occurs at the

nucleolus

. (Remember, the nucleolus is “like” a copy machine because we are making a

cheap

disposable copy of the DNA sequence.)

A.

Three Phases of production to

a transcription unit

- piece of mRNA.

1.

Initiation

a.

- This is building our

A protein called a

factory

to make mRNA basically.

Transcription Factor

attaches to the

TATA box

to

determine

the b.

c.

direction

the “factory” will proceed. The

TATA box

is part of the

promoter

sequence.

(Look at the TATA sequence, can you see it running in

different

directions. This orients the

“factory” to the direction it will transcribe.)

Then additional transcription factors (proteins and enzymes) are added to the “factory”.

Finally

, RNA Polymerase II

joins to

complete

the factory. The whole “factory” is called a

Transcription Initiation Complex

. (Can you see the definition in the term? Transcription is the process being done. Initiation refers to the beginning process. Complex indicates we

2.

3.

d.

have many parts involved in making the structure.)

This is a

step by step controlled process

. (The cell “controls” each step to help make sure c.

nothing goes wrong.)

Elongation

- This refers to the

actual making

of the mRNA molecule. a.

This

must

be made in the

5’

3’

direction! b.

RNA Polymerase II

separates

the DNA Double Helix to

make room to work

.

RNA Polymerase II

also

adds nucleosides

to the growing molecule. i. Nucleosides come from the cytoplasm.

Lysosomes

recycle and provide them. d.

After helix.

RNA Polymerase II

has past the DNA transcription point, the DNA reforms the e.

Cells can make

multiple copies

of RNA because the DNA is

left intact and protected

nucleus.

Termination

(Just like it sounds… stop the transcription.) a.

A

stop codon

is made (for the ribosome) and the “factory” molecule slows down.

in the b.

RNA Polymerase II

slows down

until

it stops transcription by forming an AAUAAA sequence and is then released from the DNA.

B.

Modification

of the Primary Transcript for EUKARYOTIC Cells (This also occurs in the nucleus.)

1.

Front end (5’) modification

of the mRNA molecule. a.

A 5’

protective cap

is added. (This would be like you putting on a hard hat to protect your head when you go outside into a “construction site”.)

2.

b.

This cap acts as a

signal

to the ribosome particles, telling it where to attach.

Back end (3’) modification

of the mRNA molecule. a.

A Poly A Tail is added. (“poly” means “many”; 50-250 Adenines will be added onto the tail.) b.

This acts as protection against

digestive enzymes

in the cytoplasm. (Remember, it is a construction site and things are being broken down as well as being built.)

3.

Middle modification

of the mRNA molecule. (This modification is referred to as

RNA

Alternative Splicing

.) a.

During this step

, remove

the non-coding

introns

(These act as spacers) using

Spliceosomes

. (A

spliceosome

is a

collection

of snRNPs.) i.

snRNP’s

(

s

mall

n

uclear

r

ibo

n

ucleic

p

roteins act as scissors.) Remember,

Ribozymes are RNA molecules that

act as enzymes

. b.

c.

Then

rearrange

the

separated

coding

exons

(

important blueprint pieces

.) to the

needed

configuration. This is why it is called

alternative

; pieces (exons) can be

rearranged

in

different orders

. (This is REALLY important in the making of antibodies by our immune system. Remember the

variable

portion of the antibody structure.)

“Stitch” the pieces together to make the

finalized secondary mRNA transcript that is know

ready

for transport to the ribosomes for translation into proteins.

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