Learning Outline

Making Proteins

BIO 095

Each cell can be thought of as a "protein factory" making the many proteins that build and run the cell (and build other kinds of molecules like carbohydrates and lipids)

We begin with a review of DNA, then move on to the process of DNA synthesis itself.

Structure of DNA

Nucleotides

Nucleotide is the subunit, made of three components:

• Sugar (ribose in RNA; deoxyribose in DNA)
  
  
• Phosphate
  
  
• Nitrogen base
  
  
  • Different types of nitrogen base: cytosine, guanine, adenine, thymine (DNA only), uracil (RNA only)
    
    
  • First letters are used as abbreviations: C, G, A, T, U
    
    
  • Bases may link C-G or G-C and T-A or A-T (in RNA, U-A or A-U)
    
    
    • This rule is complementary or obligatory "base-pairing"
      

Nucleotides combine to form a double helix structure

• Sugar and phosphate groups link together to form the "backbones" of the double helix
  
  
• The nitrogen bases link in pairs to connect the two backbones

Nucleotides link to form DNA. Sugars and phosphates link to form the backbones and bases link in pairs to hold both helices together. (Click image to enlarge it and view source)

DNA double helix model. (click image for larger view)

Genetish—language of genetics

Genetish is a made-up word introduced by author Matt Ridley to describe the coding used by cells in DNA/RNA

Codon

• Every three bases make up one "word" or codon in genetish
  
  
• Each different codon represents a different amino acid
  
  
  • Amino acids combine to form polypeptides or proteins
    

Gene

• A sequence of codons containing the information needed to make one polypeptide/protein is called a gene (gene = "recipe" for one protein)
  
  
• Genes are found at various locations along a DNA molecule (chromatin/chromosome)
  
  
• All genes on all chromosomes is a set of information called the genome

Codon table. This table is a type of "phrasebook" for the language of "genetish" --showing the meaning of different possible codons.

Function of DNA

The information molecule

Master code for proteins made by the cell

• Proteins perform functions that regulate the cell, make up parts of the cell, and regulate the synthesis (and breakdown) of other types of molecules (lipids, carbohydrates, so on)
  

In humans, temporary "working copies" of specific genes from DNA are in the form of RNA (review Cell Structure & Function)

Information "between the genes" formerly called "junk DNA" may also have functions in regulating gene expression, etc.

Acronym Table
rRNA ribosomal RNA	Forms ribosomes
mRNA messenger RNA	Unfolded strand contains gene (code for one polypeptide)
tRNA transfer RNA	Brings specific amino acids to ribosome and places them according to code on mRNA
nuclear DNA	"Master" genetic code in the nucleus
mDNA or mtDNA mitochondrial DNA	Additional "master" genetic code in the mitochondrion

 

Survival Guide for Anatomy & Physiology includes an analogy for learning protein synthesis more easily.

 

Transcription of RNA

Transcription

mRNA is a "transcribed" copy of one gene in DNA

DNA unzips at one gene, and other side "fills in" with RNA nucleotides with bases that complement the exposed bases of the DNA strand

• Promoter - sequence of bases that tells the cell where to start transcribing the gene
  
  
• RNA polymerase - enzyme that facilitates formation of mRNA strand

Transcription
(click image to enlarge)

Editing

mRNA transcript is edited before leaving nucleus

• Introns - parts of sequence that are deleted ("nonsense")
  
  
• Exons - parts of sequence the remain in the final mRNA molecule
  
  
• A structure called the spliceosome forms on the mRNA, facilitating the splicing of transcript (removal of introns, gluing together of exons)

DNA editing (simplified)
(click image for larger view)

Other forms of RNA (tRNA, mRNA) produced in a similar manner

• The edited transcript then usually folds into a complex shape, unlike the simple strand of mRNA

mRNA leaves nucleus via nuclear pores

Translation of RNA (protein synthesis)

Location

• Translation occurs in the cytoplasm outside the nucleus

Process

• Initiation - mRNA associates with rRNA of ribosome
  
  
• Elongation - tRNA brings amino acids into place (anticodons on tRNA complement codons on mRNA) elongating string of amino acids
  
  
• Termination - protein is released

Translation.
EAch tRNA (blue) brings a specific amino acid to ribosome (green) and links to the complementary codon on mRNA strand. As amino acids link together with peptide bonds, a polypeptide grows in length.

Mutations

Definition

• Chromosomal mutations - additions, deletions to chromosome
  
  
• Point mutations - change in one or few nucleotides in a gene sequence

Cause

• Mutations can be spontaneous (no known cause)
  
  
• Can be caused by radiation (x-ray, UV, etc.), chemicals, mechanical damage, extreme temperature, and other factors

Regulation of gene expression

Chromosome level

• Packing - DNA wraps around histone proteins, forming "beads" called nucleosomes
  
  
• Packing can prevent certain genes from being activated (transcribed)
  

Transcription level

• Master genes turn on a group of other genes
  
  
• Enhancer genes change the rate of transcription of other genes
  
  
• Regulatory chemicals, such as steroid hormones, may activate certain genes
  
  
• mRNA can be edited in different ways (exons can be linked in different ways)
  
  
• mRNA can be "made ahead of time" and then "masked" until needed later

Translation level

• Translation can be halted by regulatory mechanisms in the cell
  
  
• Interferon released by nearby virus-infected cells can trigger the activation of genes that produce translation-inhibiting proteins
  
  
  • This causes the cell to be more careful in checking mRNA and will halt translation of viral RNA that has infected the cell
    
    
• RNA interference (RNAi)
  
  
  • Mechanism by which translation of mRNA can be disrupted (interference)
    
    
  • May help regulate gene expression
    
    
  • May help defend against mutations and viral RNA infection
    
    
  • Also called gene silencing

Location of DNA

Nucleus

• 46 chromosomes (diploid number) within nucleus (except during cell division)

DNA location and structure.

Mitochondrion

• Single, ringlike strand of DNA comprising one chromosome

Mitochondrial DNA (mtDNA). This ringlike strand of DNA, similar to that seen in bacteria, contains genes that code for enzymes needed in mitochondrial function. Click on image to see larger source image, which is labeled with gene locations.