Protein Synthesis

The Genetic Code (extra notes)

• Bases are read in triplets (groups of 3) called codons

• There are 64 codons (4³) but only 20 amino acids, so multiple codons can code for the same amino acid

  • Example: CCA, CCC, CCG, CCT all → proline

Important Features of Genetic Code

• Linear: read in one direction (5' → 3' on mRNA)

• Non-overlapping: each base belongs to only one codon

• Universal: almost all organisms use the same code

• Start codon: AUG (methionine)

• Stop codons: UAA, UAG, UGA (don’t code for an amino acid)

When a certain protein of the body is in high demand…

numerous RNA transcripts of its gene will be produced

ex: when we eat sugar → our body needs insultin protein

DNA is stored and protected in the…

nucleus

Protein Synthesis (chain of events)

DNA →RNA → Endoplasmic Reticulum → Ribosomes →Amino Acids →Protein

ONE GENE =

ONE POLYPEPTIDE

When multiple amino acids join together they form a

they form a polypeptide chain, which can then fold into a specific three-dimensional shape to become a functional protein. 

Genes (at a molecular level) are…

a sequence of nucleotides from DNA

**DISCLAIMER → this is just for clarification and not to confuse genes for pure DNA. nucleotides also differ from

What do proteins do?

They:

• Run cellular processes (like metabolism)

• Control physical traits

• Can cause genetic disorders if missing or changed

Archibald Garrod

• studied a disease called alkaptonuria — people’s urine turned black because it had a chemical called alkapton.

• He thought people with alkaptonuria had a defective enzyme that couldn’t break down alkapton.

• This defect was inherited.

🧩 Conclusion: A problem in a gene → defective enzyme → disease

Beadle and Tatum

→Discovery with Arginine/Mold

• Some mutant molds only grew when given arginine (an amino acid).

• This showed that one or more enzymes that make arginine were defective.

🧩 Conclusion: Each gene controls one enzyme in a chemical pathway.

Identify the roles of mRNA, tRNA, and rRNA

1. mRNA (messenger RNA)

• Acts as a template of the gene.(only one)

• Carries the instructions from DNA in the nucleus to the ribosome.

• Has codons (triplets) that tell the cell which amino acids to put in order.

➡ Role: Brings the genetic message to the ribosome.

2. rRNA (ribosomal RNA)

• Forms the ribosome, along with proteins.

• The ribosome is the place where the protein is built.

• rRNA helps:

  • hold the mRNA in place

  • connect amino acids together

➡ Role: Makes up the ribosome and helps build the protein.

3. tRNA (transfer RNA)

• Brings the correct amino acids to the ribosome.

• Each tRNA has an anticodon that matches with an mRNA codon.

➡ Role: Delivers the amino acids and matches them to mRNA codons.

When something goes wrong in protein synthesis it can lead to:

• No protein being made

OR

• Protein being made incorrectly → wrong shape and function

**5 key differences between DNA and RNA

1. Sugar

2. Bases

3. Strands

4. Length

5. Location

Genes don’t just code for proteins they also code for:

(probably not important)

• antibodies

• hormones

• structural proteins

→ these all affect an organism’s physical traits

4 scientists :

• Mendel

• Garrod Archibald

• Beadle & Tatum

• Vernon Ingram

Vernon Ingram’s Experiment

Vernon Ingram studied hemoglobin

In normal hemoglobin, the β chain has this sequence:

Valine – Histidine – Leucine – Threonine – Proline – Glutamic acid – Glutamic acid

• In sickle cell anemia, one glutamic acid is replaced by valine:
  Valine – Histidine – Leucine – Threonine – Proline – Valine – Glutamic acid

• This tiny change causes red blood cells to become sickle-shaped → blocking blood flow → serious disease.

🧩 Conclusion: A single amino acid change → major health effect.

mRNA

• carries the DNA “message” to the ribosome

• “consists of nucleotides that can be read as codons and translated into proteins”

• transcribed in nucleus and translated outside

• single stranded

• only contains the code for ONE GENE

• has a short life →destroyed when no longer needed

t-RNA

• 1st comes due to signal triggered by the mRNA and ribosome match/link up

• brings amino acid to the ribosome

• they come based on whatever codon needs its anti codon and they bring the corresponding amino acid

r-RNA

• binds to mRNA

• used to help build/make ribosomes cuz for some reason they need help being made

• act as a base for building the proteins

• varies in length?

DEFINE Transcription

Transcription is the process where a cell makes an mRNA copy of a gene.

• happens purely in the nucleus

STEPS of Transcription 

1. Initiation

2. Elongation

3. Termination

4. Capping and Tailing

5. Splicing

Translation

• happens in RIBOSOME

Initiation

1. ribosome clamps onto the mRNA

2. reads the code in codons (3 nucleotides at a time)

Elongation

1. t-RNA brings the correct amino acid

2. The amino acids join together form a polypeptide chain

Termination

1. Ribosome reaches a  stop codon

2. The completed protein is released

The genetic code///RNA polymerase both move in one direction

5’ →3’

Transcription Voice Note in detail

True or False: Introns are recycled

True. The diff nucleotides are recycled for more mRNA

Alternative Splicing

can join different combinations allowing one gene to make many different proteins

tRNA structure

At the tip of each tRNA, is an anticodon a 3 base sequence

• it is complementary to the mRNA codon

• Basically da same as the DNA triplet but ofc U replaces T

Wobble Hypothesis

There are 61 possible codons (combinations of 3) but we do NOT have 61 different tRNAs….

• Some tRNAs can match for more than one codon

  • EX: UAU and UAC both code for tyrosine. So if a tRNA anticodon is AUA it can still bind to UAC even though it shouldddd bind to UAU

• This flexibility is called the Wobble Hypothesis

Termination of Trancsription

When RNA polymerase reaches the terminator sequence it stops copying.

**The exact terminator varies by the gene

• As transcription ends RNA polymerase releases the newly born mRNA transcript.

**although RNA polymerase job ends here it can still be reused for more jobs

Capping and Tailing

The newly transcribed mRNA is scared and needs protection and signals

• A 5’ end cap (of methylguanosine) is added to the start of the mRNA during translation

  • These protect mRNA from the enzymes that will fight it in the nucleus.

  • It also helps the ribosome recognize mRNA during translation!

• A “poly-A-tail” of 50-250 adenfines are added to the 3’ end by poly-A polymerase

  • also protects the mRNA from fights and degration

Splicing

The mRNA contains introns and exons.

• Introns are cutout and recycled in the spliceosome

  • splicing happens inside a spliceosome (made up of the small ribonucleoprotein)

• Alternative splicing → can join exons in diff combinations allowing one gene to make many diff proteins.

After Transcription is complete

the MATURE mRNA leaves the nucleus through nucleus pore → to the cytoplasm to be translated

Initiation of Transcription

• Transcription begins when RNA polymerase binds to the promoter region of DNA.

  • The promoter tells the enzyme where to start and which DNA strand to copy.

• Most promoters contain a TATA box, a sequence high in A’s and T’s which is easier to open bc A and T pairs only have 2 hydrogen bonds

**RNA polymerase binds at the promoter (BEFORE UTR) and does not transcribe the promoter itself

Elongation for Transcription

• RNA polymerase builds the mRNA strand in the 5’ → 3’ direction.

  • Coding strand →Identical, Template strand → being synthesized on

• mRNA is complementary to the template DNA strand (…Thymine →Uracil)

• RNA polymerase moves along the gene, adding nucleotides to grow the mRNA chain

Aminoacyl-tRNA

• basically the thing circled in the picture

  • The amino acid is attached to the 3’ end and is called/named “Aminoacyl-tRNA”

aminoacyl-tRNA synthase

The enzyme responsible for adding the appropriate A.A to each tRNA (aminoacyl-tRNA synthase)

• The are about 20 of these enzymes (one for each amino acid)

The Ribosome(s)

When mRNA reaches the cytoplasm, the ribosome recognizes its 5’ cap

• The ribosome has 2 subunits (large + small/the flat one) both made up of rRNA and proteins

• The big subunit clamp onto the mRNA (+ short rRNA) and moves from 5’ → 3’

• It reads the codons one (3 bases) at a time AND

  links new amino acids to the growing chain - this is the “reading frame”

Three Binding Sites (The Reading Frame)

Inside the ribosome:

1. A site

• Where the aminoacyl tRNA enters

2. P site (Peptidyl?)

• Holds the tRNA with the growing chain of amino acids (polypeptide)

3. E site (Exit)

• Where empty tRNA leaves the ribosome

Stages of TRANSLATION**

1. Initiation

2. Elongation

3. Termination

4. Extra Polysomes?????

5. Post Translational Modifications??

Initiation of Translation

• Begins at AUG the start codon (AUG = Methionine)

• The Met tRNA binds near the 5’ cap

• The ribosome moves along the mRNA in a process called scanning

Elongation of Translation

Met tRNA lies in the P site.

• A second tRNA enters the A site

• The enzyme peptidyl transferase forms a bond between Met and the next amino acid (basically links Met and next A.A)

  

• The Met is released from its tRNA and that empty tRNA moves to the E site.

• The ribosome keeps moving forwards repeating this process

Termination of Translation

The ribosome eventually reaches a STOP codon

• Stop codons have no amino acids

• A release factor binds and helps free the completed polypeptide protein from the ribosome

Polysomes

Many ribosomes can translate the same mRNA at once…

• This group of ribosomes is called polysomes

********“Post-Translational Modifications”

After translation, proteins often need changes to become functional

These changes may include:

• Cutting the chain

• Adding phosphatase or methyl groups…

• Adding sugar →becomes glycoproteins

• Adding lipids → becomes lipoproteins

housekeeping genes

Some genes are always active because the cell needs them all the time.
These are called housekeeping genes.

Cells can turn genes on or off depending on what they need.

There are 4 levels of control:

1. Transcriptional Control

Controls which genes get copied from DNA → mRNA.

2. Post-transcriptional Control

Controls which introns and exons are kept or removed when mRNA is edited (splicing).

3. Translational Control

Controls how often or how fast mRNA is translated into a protein.

4. Post-translational Control

Some proteins must be modified or sent through membranes before they work.
This affects how quickly they become active.

Two main categories of Mutations:

Single-gene mutations

• Affect one gene’s nucleotide sequence

Chromosome mutations

• Affect big sections of chromosomes (many genes)

Somatic vs Gamete Mutations

• Somatic cells (body cells): mutations usually go unnoticed; not passed to children

• Gametes (egg/sperm): more serious because they can be inherited

The following are point mutations (affect 1 base pair):

🎯 Silent Mutation

• A change in DNA that does NOT change the amino acid

• No change in phenotype

• Sometimes it happens in introns (which are cut out). Wrong thingy is transcribed but its cut out anyway

Example:
UUU → UUC
Both code for Phe, so the protein stays the same.

🎯 Missense Mutation

• A DNA change that replaces one amino acid with another

• Can cause diseases like:

  • Sickle cell anemia

  • Some cases of Cystic Fibrosis

Can also be helpful when your body makes new antibodies.

🎯 Nonsense Mutation

• A mutation that changes a codon into a STOP codon

• Translation stops too early → incomplete protein

• Often lethal to the cell

Both missense & nonsense come from substitution mutations.

Deletion Mutation

• Removes one or more nucleotides

• Changes the reading frame → changes amino acids → defective protein

Example:
AUG GGA UUC AAC
→ remove one base → AUG GAU UCA AC (shifted)

Insertion Mutation

• Adds an extra nucleotide

• Also causes a frameshift mutation

• (Similar effect to deletion)

Translocation

• A piece of a chromosome breaks off and is moved to a non-homologous chromosome

• Can create fusion genes with completely altered function

🔁 Inversion

• A piece of a chromosome flips its direction

• No DNA lost or gained

• But the gene wont be read/ read wrong

Deletion & Duplication (Chromosomal)

• A part of the chromosome is lost (deleted)

• Or copied twice (duplicated)

Causes of Mutations

✔ Spontaneous mutations

• Natural mistakes by the cell’s machinery

✔ Induced mutations

Caused by mutagens like:

• UV light

• Benzene

• Radiation (nuclear energy)

• Other chemicals

Cancer

Cancer = diseases with uncontrolled cell division.

Two main gene problems:

❌ Tumor suppressor genes (like p53)

• Normally stop bad cells from dividing

• In cancer, they are turned off or broken

❌ Proto-oncogenes

• Normally control cell growth

• In cancer, they are stuck ON

This leads to:

• Fast, uncontrolled division

• Tumor (mass of abnormal cells)

Transcription Factors

proteins that turn genes on.
They do this by binding to DNA and helping RNA polymerase start transcription.

Galinda would be the Transcription Factors

Types of Point Mutation

• Silent Mutation

• Missense Mutation

• Nonsense Mutation