genetics - Do apes and humans share 99% of DNA or 99% of genes? What is the difference?

I made an answer on the Scifi.SE that can be read here. It is about how the characters in the story Jurassic Park might have gotten DNA for all the species shown.

In my answer, I said this:

Apes and Humans, for example, share over 99% of their genes. That means the difference between our species is less than 1% of our genes. In fact, all life on Earth shares about 50% of it's genes.

but in the original posting (before someone edited it) I chose to use the word DNA instead of genes.

He left this comment in the section to explain the edit:

Sorry, I'm a biologist, I can't help it. Humans and apes share 99% similarity in the coding sequences of their DNA, the ~5% that codes for genes, not on all the DNA. I simplified this to genes for the answer.

I have a basic high school understanding of DNA and genes, so I'm afraid I fail to see the difference between using "DNA" or using "genes" in my statement. I understand that genes are specific sequences of DNA that are used by the cell in some way. I understand that DNA is more generic, including all of the strands, whether they are used or not, whether they seem to code for something or not.

So is it wrong then to say that apes and humans share 99% of their DNA or is it equally correct to say "genes"?

Answer

So, a quick molecular biology lesson.

• Proteins are the things that make up a good percentage of our cells (which make up a good percentage of us), and are the things that do the work of the cells - many are catalysts and are known as "enzymes".


• 
  

  Proteins are encoded by genes - while the statement that one gene codes for one protein is not quite correct (one gene can code for different variations of the same basic protein), it's a good way to think about things in this context.

  
  
  


• 
  

  Genes are made up of DNA, a polymeric molecule that constitutes our chromosomes, the informational portion of which resides four “letters” (chemical bases).

  
  


• 
  

  However, now we get to the key part — although all genes are made of DNA, not all the DNA of chromosomes makes up genes. In fact, as @terdon mentioned in a comment, only about 5% (or less) of the 4 billion letters in the total DNA — the genome — constitute genes - those sequences that
  directly code for protein.

  
  


• 
  

  The function of the rest of the genome is not entirely clear. Some is regulatory, some may be structural, and may be “junk DNA”. However it’s stuck around for millions of years, so it we assume it must have some purpose. This non-coding DNA differs between species to a greater extent than the genes themselves do, so perhaps it somehow contributes to the differences between organisms.

  
  
  

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From AndroidPenguin

Here are the links to a paper about the function of "junk" DNA from 2013.

1. 
   

   Summary in NY Times

   
   


2. 
   
   

   Abstract in Nature

   
   


3. 
   

   ENCODE threads on nature.com