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Class notes PHGY 170 (PHGY170)
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Comprehensive notes for PHGY 170
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The Nucleus:Structure and Function:
The nucleus is the leader of the cell. It gives orders to each organelle, telling them what to do. In other
words, it makes “laws” for eukaryopolis. These “laws” are stored in the nucleus as DNA. Since the
nucleus has such an important role in the cell, it is essential that it is protected from other cell
processes. Here are some ways it isolates itself from the rest of the cell:
- A special double layered membrane
- Very selective nuclear pores
- A unique cytoplasm
These are all functions that help protect the nucleus and it’s package – DNA. To accomplish this, The
nucleus needs to perform 3 tasks:
1. Regulate what molecules can access DNA
2. Separate the DNA from the other cell compartments
3. Keep the DNA organized – DNA is fragile and easily damaged, so any problems with DNA will
lead to major problems in the cell and body.
There are 4 key components of the nucleus that work together to fulfill these tasks:
1. The Nuclear envelope
The nuclear envelope controls what molecules have access to the nucleus, end separates the DNA from
other cell compartments. It is a double membrane structure that encloses the nuclear material. The
outer membrane of the nuclear envelope is connected to the Endoplasmic Reticulum (ER) which is
important for making proteins. The nuclear envelope contains pores which regulate traffic in and out of
the nucleus. Small molecules (O, H2O) pass through the membrane freely. Nuclear pore complexes
(NPC’s) in the nuclear membrane regulate the movement of large molecules (eg. Proteins) into and out
of the nucleus.
2. The Nucleolus
The Nucleolus creates ribosomal RNA’s and assembles them into the ribosomal subunits used by the cell
to translate proteins. The nucleolus is the site of high amounts of rRNA gene transcription, and the DNA
that encodes these genes is organized here.
3. The Nucleoplasm and Nuclear Matrix
The nucleoplasm is viscous, water-based fluid that is enclosed in the nuclear membrane. It contains
dissolved molecules and ions that are essential for the functions of the nucleus. The main functions of
the nucleoplasm are to maintain shape and structure of the nucleus and serve as a suspension
substance for the nuclear contents.
,The nuclear matrix is a network of filaments within the nucleoplasm that helps to organize the DNA in
chromosomes into compartments.
4. The Chromosomes and Chromatin
Strands of DNA are organized and stored in chromatin that make up chromosomes within the nucleus.
Chromatin:
- Complex of DNA and proteins forming highly organized fibers
Chromosomes:
- Highly condensed chromatin found in the nucleus only during cell division.
DNA and RNA Structure
DNA is a linear molecule made up of a sequence of smaller molecules called nucleotides. Referred to as
C,T,G, and A. Segments of this DNA sequence contain genetic information. Genes are inherited from a
combination of parental genes. Genes define physical traits (phenotypes). Genes are stored in long
strands of DNA that complex with proteins to form highly organized fibers call chromatin. Chromatin
condenses into chromosomes.
Genes:
Every cell in the body contains the complete genome including every gene. However, specific cells have
different genes turned on and off to function properly. For example, a muscle cell will have the genes
necessary to make bone turned off.
DNA Structure:
The basic building blocks of DNA are nucleotides. Each nucleotide is made up of 3 components:
1. A nitrogenous base
There are 2 types of base in DNA
- Purines: these have 2 rings in its structure. The 2 purines in DNA are adenine and guanine (A&G)
- Pyrimidines: these only have 1 ring in their structure the 2 pyrimidines in DNA are cytosine and
thymine (C & T).
*Thymine exists only in DNA and uracil exists only in RNA
, 2. A five-carbon sugar (ribose)
In chemistry, the carbons of a hydrocarbon are numbered. Both 2-deoxyribose and ribose are 5-carbon
sugars (monosaccharides) and hence their carbons are named 1-5. Because of this numbering system,
each sugar will have a 5’ end of the sugar and a 3’ end. The 5’ end is where the phosphate is attached in
a single nucleotide. This becomes important later during replication.
3. A phosphate group
Phosphates are a part of what is called the DNA “sugar-phosphate backbone”. Phosphates are attached
to the 5’ carbon of one sugar and the 3’ carbon of another by a phosphodiester bond. In DNA a
phosphodiester is a covalent bond formed by a phosphate group to the 5’ carbon of one sugar and the
3’ carbon or another sugar.
How DNA forms a single strand:
The sugar-phosphate backbone of DNA is held together by phosphodiester bonds
1. The oncoming nucleotide is added to the 3’ sugar of the existing chain of DNA. The phosphate of
the incoming nucleotide binds to the oxygen on the 3’ sugar.
2. A diphosphate (2 phosphate groups together) is formed as a by-product
3. A phosphodiester bond is formed between the new nucleotide and the existing strand of DNA.
DNA Base pairs:
The purines of one strand will always base pair with the pyrimidines of the opposing DNA strand. This
means that hydrogen bonds between opposite bases on each strand form cross-linkages.
- Adenine pairs with Thymine (A+T)
- Guanine pairs with Cytosine (G+C)
This bonding leads to the formation of a double-stranded DNA molecule. Each strand of the DNA is
called antiparallel to the other because they run in opposite directions. (Remember, Nucleotides are
added in a 5’-to-3’ direction).
The Double-Stranded Helix
The nitrogenous bases of each nucleotide are hydrophobic, while the sugar-phosphate backbone is
hydrophilic. As a result, when placed in an environment with lots of water (i.e. a cell), the bases stack
themselves in the center while the sugar-phosphate backbone remains outside. In order for the bases to
come into contact with as little water as possible, this “ladder” of double-stranded DNA twists itself into
a spiral staircase – a double-stranded helix.
, DNA sequence and genetic code:
Different types of codes use a different combination of several finite representative components to
create a more complicated language.
Codes:
Morse Code: 2 components – short and long
Computer binary: 2 components – 0&1
Genome: 4 components – A, C, T, and G
Written English: 26 components – the English alphabet
DNA organization:
We have discussed that genes are small pieces of DNA that contain specific genetic material. Typically
genes contain information to make a protein, and this is referred to as encoding DNA. In eukaryotes
these genes are located on chromosomes and are separated by large spaces of DNA called non encoding
DNA. These do not correspond to protein production.
DNA coding:
Exons are the sections of a gene that contain the information that is used to make a protein, called the
coding sequences, or coding DNA. Introns are sections of DNA that are not used to make protein, called
noncoding sequences, or non-coding DNA. There are also sections termed regulatory sequences which
take control when a gene is turned on or used. The important thing to take away is that most of a gene
is not actually used to make a protein – only a small portion is (exons).
RNA structure:
The functions of Dna and Rna differ substantially, therefore, there are a few major differences between
the structural components of these molecules.
- RNA uses the pyrimidine uracil instead of thymine
- The nucleotides in RNA contain ribose rather than deoxyribose. This gives them an extra OH
group.
- RNA is less stable than DNA as it forms in single strands rather than double helixes.
The main purpose of DNA is to carry genetic information, whereas the fundamental purpose of RNA is to
transport small copies of genes around the cell for a variety of uses.
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