DNA & the Human Genome: Quick Review

A Quick Primer or Easy Review Of the Human Genome

The Human Genome is the total set of information in a human being — including the DNA of both the cell nuclei and the cells’ mitochondria (MtDNA).

Chromosomes

Humans normally have 46 chromosomes, arranged in 23 pairs of DNA strands. There are 22 pairs of homologous strands (similar looking), called autosomes, and a sex determinant that is either a pair of X chromosomes in females or an X and a Y males.

Genes

A gene is a segment of the DNA strand that contains information, and is considered both functional and inherited. The Human Genome contains approximately 20,000 to 25,000 genes. They contain sequences of DNA that can be replicated, and most of the encoding produces proteins, but not all do. Some code for ribonucelic acids (RNA).

DNA

Deoxyribonucleic Acids (DNA) are mostly long string-like sequences of nucleotides. The bonds form a double-helix shape that looks like a spiraling ladder. These strands combine with histone proteins to form a complex, called chromatin.

Nucleotides

There are two nucleic acids — single-stranded RNA, and double-stranded DNA. Each of these are composed of 4 nucleotides — they are the same in both, with the exception of cytosine (DNA) and uracil (RNA).

Nucleotides are made of a combination of molecular blocks — a nitrogenous base, a 5-carbon sugar and a phosphate group. These can be divided into two types — purine and pyrimidine. Purines contain 4 nitrogens and have 2 fused rings of atoms; and pyrimidines have 2 nitrogens in a single ring of atoms. In DNA, purines pair with pyrimidines and they share weak hydrogen bonds that run through the center of the double helix:

• adenine >-< thymine (or) uracil
• guanine >-< cytosine

The 5 Nucleotides of DNA and RNA (ATGC and AUGC)

• adenine (purine) — pairs with thymine or uracil
• thymine (pyrimidine) — [DNA only] pairs with adenine
• guanine (purine) — pairs with cytosine
• cytosine (pyrimidine) — pairs with guanine
• uracil (pyrimidine) — [RNA only] pairs with adenine

Sugar-Phosphate Backbone of DNA and RNA

On the outer edge of each strand of DNA or RNA is a “backbone” that consists of a phosphate group (PO), and a 5-carbon sugar. The phosphates links to the next sugar group (deoxyribose or ribose) to form a phosphodiester bond, and the sugar group connects to both the next phosphate group, and to the nitrogenous base (ATGC or AUGC).

In 5-carbon rings, each carbon is numbered from 1′ to 5′ (pronounced “1 prime” to “5 prime”).

Ribose and Deoxyribose are nearly the same structure, except for the 2′ carbon position is attached to a hydroxyl in ribose, and only a hydrogen in deoxyribose (meaning one less oxygen atom).

• ribose — [RNA only] a 5-carbon ring that includes two hydroxides (C₅H₁₀O₅)
• deoxyribose — [DNA only] a 5-carbon ring that has only one hydroxide (C₅H₁₀O₄)
• phosphate — a phosphorous atom with 4 oxygen atoms attached PO₄^-3.

With nucelotides, the phosphate group is completed by adding two hydrogens and an R group, so like R-H₂PO₄. So there are 2 hydroxyls, a double-bonded oxygen and the attached R group. In the case of nucleotides, the R group is the sugar deoxyribose or ribose. And ribose ends up with each carbon being attached to an oxygen molecule; but with deoxyribose, only 4 of the carbons attach to an oxygen. The 5′ carbon attaches to an oxygen on the phosphate group.

An ester is a bond between an alcohol group and an acidic group. An alcohol is a compound that has at least one hydroxyl group (HO^– or ^–OH). The bond is considered dehydrating, meaning that a water molecule is released (H₂O). So, with the phosphodiester backbone, I’m pretty sure the phosphate is the acid, and the sugars are the alcohols. So, 2 linkages are created with the 2 hydroxyls of the phosphate — one bonds with the 3′ carbon and one with the 5′ carbon. (“di” meaning 2, and “ester” referring to the 2 bonds that form from the phosphate’s hydroxyl groups). 

The strands of DNA and RNA are therefore constructed with a 5′ on one end of the strand and a 3′ on the other end. (DNA strands are written by convention with this 5′-to-3′ directionality.) In DNA, the paired strand will have an backbone that is constructed in the opposite direction, with a 3′ and 5′. The 5′ end has an attached phosphate group, and the 3′ end has the sugar’s hydroxyl group.

Summary Questions

What is the human genome?
The set of all the information in a person’s cell nucleus and in the separate mitochondria. This is in the form of DNA.

How many chromosomes does a human have?
46 chromosomes, organized as 23 pairs.

What is an autosome?
Any of the pairs of chromosomes that are homologous (look similar) and are not sex chromosomes.

What are the sex chromosomes — and which are female vs. male?
The sex chromosomes are referred to X and Y, and females are considered XX and males XY. The X and Y chromosomes look very different.

What is a gene?
A functional section of DNA that is acquired through heredity.

What do genes do?
Genes code for the making of small molecules — mostly proteins but also RNA.

How many genes does a person have?
There are approximately 20,000 to 25,000 human genes. (The human genome has reportedly not been fully completed.)
In mitochondria DNA, which is considered separate, there are 37 genes.

What is DNA?
Deoxyribose nucleic acid is a long molecule of genetic code that includes all of the instructions for making molecules that control our metabolic functions. It is comprised of linked, base-pairs of nucleotides.

What is the difference between DNA and RNA?
RNA is single-stranded chain of nucleotides, and DNA is a double-stranded chain of base-pairs that forms a double helix. DNA contains the nitrogenous base thymine and RNA contains uracil instead.

What are nucleotides? And what holds the nucleotides together?
On the inside of the helix, weak hydrogen bonds link the nitrogenous base-pairs. On the outside, there is a phosphodiester chain — comprised of alternating phosphate and sugar groups. The sugars are each bonded to a nitrogenous base.

What are the 4 nucleotides of DNA? Which pairs with which?
Adenine and guanine are purines (two rings and 4 nitrogens).
Thymine and cytosine are pyrimidines (1 ring and 2 nitrogens).
Adenine pairs with thymine.
Guanine pairs with cytosine.

How many base pairs does human DNA have? In DNA there are approximately 3 billion base pairs of nucleotides.
And in mtDNA about 16,500 base pairs.

Explain what a phosphodiester backbone is:
The phosphodiester backbone is a linkage that arranges nitrogenous bases in a sequence. There is a phosphate group that links to a sugar group. The nucleic acid will begin with a phosphate bonding to the 5′ carbon of the sugar group, and the 3′ of the sugar will bond with the next phosphate group. The bond between the sugar and phosphate create an ester bond — a dehydrating chemical reaction which releases a water molecule at each bond. The convention of writing out nucleic acids is to start at the 5′ and end at the 3′, and with DNA the paired strand would do the opposite — 3′ on the starting end and 5′ at the end. A phosphate groups is on the 5′ end.

How many base pairs does each human gene have?

According the Human Genome Assembly, v. GRCh37 each gene has the following maximum number of base-pairs:

Note: The Human Genome Assembly also lists the “total lengths” separately and says that some “scaffolds” have been “unplaced.” These total lengths are somewhat higher figures for some genes.

Why I Made This Page

I have been developing a program that uses Shared DNA Relatives data from 23AndMe. And I ran into a small problem. I knew the basics of chromosomes, but how long is each chromosome in base pairs?

The data I was getting was different for each customer’s download. I could tell that, for 23AndMe, the chromosomes all seemed to start at 1. But the endings were not consistent on the higher end. I compared the maximum numbers I was coming up with to the Chromosome page on Wikipedia. And while my numbers were in the general count as those on Wikipedia, they all seemed to be 2 million smaller than what I was getting from 23AndMe. So, I asked on the service’s support board for an answer, and I was referred to the Human Genome Assembly GRCh37.

I’ll just be honest and say that I have very little idea of what that is, exactly. But they do seem to have comparable information that likely is the answer to my original question. The fella that sent me there said this was the latest information being used by scientists. News to me that sequencing is still taking place.

I have already taken Biology, Anatomy/Physiology and Chemistry courses, and just needed a reminder page.