Genetics

State the 3 primary functions of genetic material

Genetic information is a mechanism of regulation; it provides the tools necessary for the moment to moment cellular processes that help cells survive in fluctuating environments. In addition, it allows these processes and adaptations to be passed on to future generations.

State two reasons why genes are necessary

Genetic information exhibits a remarkable amount of _______ among living organisms. Variation of the ______ sequence among humans is small; human DNA differs between individuals at approximately 1 nucleotide out of every 1200, or about 0.08%

Humans share about 98% of their nucleotide sequence with chimpanzees, about 60% with a fruit fly, and about 50% with a banana! Why do these similarities exist?
The amount of uniformity found in genomes of living organisms also demonstrates that small changes in the ____ ______ can make a significant difference.

Additionally, differences between organisms are caused not just by variation in their nucleotide sequences, but also differences in the regulation of how those sequences are expressed. Explain

The versatility of the genetic code is best understood by first distinguishing between genetics and epigenitcs. The raw material of genetics, the _______, is the complete sequence of nucleotides of the genetic material. The genome is usually ____ but can be ____ in some viruses. (See the Biological Molecules and Enzymes Lecture for a review of DNA and RNA structure).

These sequences of nucleotides comprise a huge repository of information. By reading the _______, the cellular machinery is able to make all of the proteins and products that sustain life. However, this process is not like reading a book cover to cover. The cell can create ________ products and _______ amounts of those products from the same single genetic code in response to the cellular environment.

Changes in the kind or amount of gene products are not due to changes in the genome; instead, what do they depend on?

The importance of being able to alter the expression of the genes in a genome is illustrated by considering how many different types of cells there are in a human body. Each cell contains the same complete ______, yet some cells become bone while others become muscle liver, etc. Regulation affects which ______ from the genome are expressed, and the products of that gene expression affect the cell's _______ and _______

The concept of epigentics explains how some of these changes in gene expression take place. Define epigentics 
These changes instruct the cellular machinery how to read the _______, thereby _______ gene expression

Epigenetic changes do not change the _______ itself. State 3 types of epigenetics changes

What is the purpose of epigenetic control 
Epigenetic control of gene expression changes continually, allowing gene expression to adapt to changes in the organism's ______ and ______ environment

In addition to changing gene expression throughout the lifetime of an individual, _______ _______ ________ and _______ ________ can be passed down from one generation to the next.

Epigenetic changes influence how the cellular machinery reads the _______. 
*You may encounter the term epigenome, which encompasses all of the epigenetic changes that affect gene expression. However, keep in mind that the epigenome is not a physical structure, but rather an ongoing process of _______

The genetic sequence is often thought of as a set of functional units called ______ (2 definitions)

Within a cell's lifetime, the function of the genome is to code for the products, usually _______, that are necessary for cellular processes. State The Central Dogma of gene expression 
All ______ organisms use this method to express their genes

Retroviruses (which are not living organisms) store their information as _____ and must first their _____ to _____ in order to express their genes. State the 3 major functions of the genetic code

All living organisms have ______-______ DNA as their genetic material

In eukaryotic cells, double-stranded DNA sequences are arranged into ________. This compact organization is necessary because of the ______ ______ of eukaryotic genomes. If a double strand of all the DNA in a single human cell were stretched out straight, it would measure around ___ _____ in length.

A chromosome consists of compactly wrapped _____ and ______ in a hierarchy of organizational levels. The sections of DNA that are not in use are wrapped tightly around globular proteins called _______. Histones have basic functional groups that give these proteins a net _______ charge at the normal pH of the cell (see the discussion of the isoelectric point in the Acids and Bases Lecture of the Chemistry Manual).
The net positive charge attracts the negatively charged ______ _______ and assists in the _______ process

_______ histones wrapped in DNA form a nucleosome. Nucleosomes, in turn, wrap into coils called _______, which wrap into _______. The entire DNA/ protein complex (including a very small amount of RNA) is called _______.

By mass, chromatin is about one third ____, two thirds _____, and a small amount of _____. How did chromatin receive its name?

Not all chromatin is equally compact. The cellular machinery that "reads" the genetic code can only act on chromatin that is _______. Thus the structure of chromatin influences ______ ______ and is influenced by ________ regulation.

Chromatin that is tightly condensed in the manner described above is called _________. Some chromatin, called _______ _______, is permanently coiled.

To manufacture the products encoded in a nucleotide sequence, the chromatin containing that section of the genome must be _______. When chromatin is uncoiled and able to be transcribed (a process that will be further described later in this lecture), it is called ________

Euchromatin is only coiled during ______ _______. Nucleotide sequences that code for protein products often contain _____ _____ _____ (define).

In contrast, non-coding regions of DNA (found only in eukaryotes) often contain _______ _______ (define)
In animals, DNA is found only in the ______ and the ________

Because the structure of chromatin is important in determining which sequences of DNA are transcribed, the coiling and uncoiling of chromatin is highly regulated by _______ controls according to the needs of the cell.

Chemical changes to histone proteins help control which sections of DNA are tightly wound and which are accessible to cellular machinery. Chemical epigenetic changes can also control which coding sequences are ______ and _______

The most common example of epigenetic regulation through chemical change is _____ ________, which involves the addition of an extra methyl group to particular _______ nucleotides.

Methylation causes DNA to be wound more _______. Methylated sections are ________to cellular machinery and cannot be ________, so the expression of genes in these sections is _______. Sections of RNA that do not code for protein products, called ____-_____ _____, contribute to the regulation of the chemical changes that affect chromatin structure.

Inside the nucleus of a human somatic cell, there are ____ double- stranded DNA molecules. T he chromatin associated with each one is wound into a _______. In human cells, each chromosome possesses a partner that codes for the same traits as itself. Two such chromosomes are called _______.

Humans possess ____ homologous pairs of chromosomes. Although the traits are the same (e .g. eye color), the actual genes may code for different versions of the trait (e.g. blue vs. brown). Different forms of the same gene are called ______, as will be discussed in greater detail later in this lecture. Any cell that contains homologous pairs of chromosomes is said to be _______. Any cell that does not contain homologues is said to be ______.

2.4 Transcribing DNA to RNA 
A major function of the genome is to code for the products (usually proteins) that are necessary for cell to carry out the processes of life. Most cell spend the majority of their lives in the ___-_____ phase of G₀.

G₀ is far from being a period of rest as the name implies, explain what happens in this phase (2 story). 
Although cells manufacture protein products throughout the cell cycle, most production takes place during  when the cell is not exerting energy in _____ ______.

Genes undergo _______ and _______ in order to make products. ________ is the process by which RNA is manufactured from a DNA template. During transcription, an ____ ______, which essentially copies the information in DNA, is created.

Different genes can code for different types of RNA, state 4 types.

Some of these RNAs, such as rRNA, tRNA, and snRNA, are functional _____ ______ that serve important purposes in the cell. However, a large portion of the RNA transcribed is mRNA, which serves as the "message" that is ________ for protein production.

To produce proteins, transcribed mRNA must undergo the process of ________. Translation takes the nucleotide sequence of the RNA transcript and translates it into the language of ______ ______, which are then strung together to form a functional _______. 
In eukaryotes, nuclear DNA cannot leave the _______ and mitochondrial DNA cannot leave the _______ ______. Eukaryotic transcription takes place only in these two
places.

The purpose of transcription is to create an RNA copy of a DNA template. Transcription is itself a form of regulation of gene expression. If transcription did not exist, and instead the whole genome was translated directly into proteins, every cell in an organism would be the same. Instead, only DNA which has first been transcribed into RNA has the opportunity to be translated into a protein.

Transcription includes three main stages: _______, ________, and _______. The beginning of transcription is called _______ Explain the steps (6-story).

Define Promoter
_______ sequences help regulate where on the genome transcription can take place and how often certain sequences are transcribed. Promoter regions of DNA have some sequence variability, which serves a _______ function. The most commonly found promoter nucleotide sequence recognized by a given species of RNA polymerase is called the ________ sequence. Variation from the consensus sequence causes RNA polymerase to bond _____ tightly and _____ often to a given promoter, which leads to the associated genes being transcribed _____ frequently.

There is no proof-reading mechanism that corrects for errors in the _______ process. (Errors in RNA are not called ______, unlike errors in DNA.) Errors created in RNA are not ______ to progeny. Most genes are transcribed many times in a cell's lifetime, so errors in individual instances of transcription are not generally _______.

________ is the main level of activation or deactivation of genes. In both prokaryotic and eukaryotic cells, regulation of gene expression occurs at the level of ________ via proteins called ________ and ________. Activators and repressors bind to DNA close to the _______ and either activate or repress the activity of ____ ________.

Activators and repressors are often _________ regulated by small molecules such as ______. Gene regulation in eukaryotes adds complexity by involving the interaction of many genes and other proteins called _______. Because of this, more room is required than is available near the _______. Define enhancer

Regulation of Transcription in Prokaryotes 
Although regulation of gene expression occurs in both prokaryotes and eukaryotes, it serves different purposes. The primary function of gene regulation in prokaryotes is to respond to changes in the _______, such as changes in the concentration of specific nutrients in and around the cell. In contrast, the maintenance of ______ (define), is the hallmark of multicellular organisms. What is the primary function of gene regulation in multicellular organisms?

Prokaryotic mRNA typically includes several genes in a single transcript (_______), whereas eukaryotic mRNA includes only one gene per transcript (_________).

In the Jacob-Monod model of prokaryotic genetic regulation, the genetic unit consisting of the operator, promoter, and genes that contribute to a single prokaryotic mRNA is called the _______. A well-studied and commonly used example of an operon is the _____ _______ in the species E. coli.

E. coli generally prefer to use _______ as a fuel source when it is present in the environment. The lac operon codes for enzymes that allow E. coli to import and metabolize _______ when glucose is not present in sufficient quantities.

The lac operon is activated only if both of two conditions are met. Name those conditions and explain how they are met.

In an example of positive control, CAP activates the promotor, allowing the formation of an _______ _______ and the subsequent transcription and translation of three proteins.

A second regulatory site on the lac operon, called the ______, is located adjacent and downstream to the promoter. When lactose is not present in the cell, a ____ ______ protein binds to the operator site and prevents transcription of the lac genes, thereby preventing gene expression. This process is called ______ _______.

When lactose is available, it will bind to the lac repressor protein, making that protein ______ to bind to the operator site. Without inhibition from the repressor protein, transcription of the lac genes can proceed. The presence of lactose can therefore _______ the transcription of the lac operon only when glucose is not present. The promoter and gene for the lac repressor are located ______ and _______ to the CAP binding site.

Most genetic regulation occurs at the level of transcription. In other words, the amount of a given type of protein within a cell is likely to be related to how much of its mRNA is transcribed. One reason for this is that mRNA has a _____ half life in the cytosol, so soon after transcription is completed, the mRNA is _______ and its protein is no longer ________. Also, many proteins can be transcribed from a single mRNA, creating an _______ effect.

2.5 Modification of RNA
When transcription is complete, the RNA products of transcription are modified by the cell. In addition to _______ modifications, the post-transcriptional modification of RNA is one of the major means through which gene expression is regulated. Post-transcriptional processing of RNA occurs in both _______ and _______ cells.

In eukaryotes, each type of RNA undergoes post-transcriptional processing. Modifications to RNA transcripts, particularly to mRNA strands prior to translation, allow the cell to employ additional methods of _____ _______, which will be further described below. In prokaryotes, rRNA and tRNA go through _____-________ processing, but almost all mRNA is translated directly to _______.

Post-transcriptional Processing of mRNA in Eukaryotes
In eukaryotes, the initial mRNA nucleotide sequence arrived at through transcription is not ready to be translated into proteins until it has first been ______ by the cell. The initial RNA nucleotide sequence arrived at through  transcription is called the ______ _______ (also called ______ or _______ ______ ______).

The modifications that change a primary transcript into a final, processed mRNA serve several purposes. List 4 such purposes