Three primary functions of genetic material
- 1. coding for products necessary within the lifetime of an organism
- 2. passing information between cells
- 3. passing information from one generation to the next.
While the genome contains a vast wealth of information, the way a cell uses this information to make products is flexible, varying with the ______ and _____ of the cell. When considering the processes that lead to gene expression, location can be used as orienting tool. In eukaryotes, but not prokaryotes, the nuclear membrane separates the processes of transcription and translation in both space and time, which allows step-by-step ______ of gene expression.
- environment and needs
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. Thus, what are two roles genes are crucial for?
- 1)both the passing of hereditary traits and
- 2)the cellular activities of an organism's lifetime.
Genetic information exhibits a remarkable amount of ______ among living organisms. Variation of the nucleotide 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 ___% of their nucleotide sequence with chimpanzees, about ___% with a fruit fly, and about ___% with a banana! Why do these similarities exist?
- because the genetic language necessary to carry out the basic processes of life is universal.
The amount of uniformity found in _____ of living organisms also demonstrates that small changes in the DNA sequence 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).
In other words, the sequence of nucleotides alone does not determine what an organism is like; how and when a sequence is read is also important.
The versatility of the genetic code is best understood by first distinguishing between genetics and epigenetics. 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. [True or False]-The cell can create different products and different 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?
They depend on how the genome is read by the cellular machinery.
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 ______.
- function and identity
The concept of epigenetics explains how some of these changes in gene expression take place. Define Epigenetics
Epigenetics (Greek: epi ~around): is a term used to describe changes that are made around the genome that do not alter the actual nucleotide sequence. These changes instruct the cellular machinery how to read the genome, thereby altering gene expression.
Epigenetic changes do not change the _____ itself. Name 3 types of Epigenetics changes
- 1)the attachment of chemical markers to the genome
- 2)histone protein modification
- 3)use of non-coding RNAs to influence gene expression.
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.
- The purpose of epigenetic control is to provide a system of regulation that allows gene expression to adapt to the needs of the organism.
- internal and external
In addition to changing gene expression throughout the lifetime of an individual, ______ ______ _____ and ____ ____ can be passed down from one generation to the next
epigenetic chemical markers and histone modifications
The genetic sequence is often thought of as a set of functional units called genes. For the MCAT® it is best to consider the definition of a gene in terms of its functions. Define/describe a gene
- Gene: a nucleotide sequence that can code for a certain product or set of products depending on factors such as alternative splicing and protein modification.
- A gene is also a unit of heredity - a sequence of nucleotides that codes for a trait, meaning a genetically influenced characteristic.
Within a cell's lifetime, the function of the genome is to code for the products, usually _____, that are necessary for cellular processes. Quickly describe the Central Dogma of gene expression, how does this differ in retroviruses? All _____ organisms use this method to express their genes.
- DNA is transcribed to RNA, which is translated to amino acids to form a protein.
- Retroviruses (which are not living organisms) store their information as RNA and must first convert their RNA to DNA in order to express their genes.
What are the genetic code's three major functions:
- 1. coding for necessary products during the lifetime of a cell
- 2. copying genetic information for the creation of new cells within an organism, and
- 3. passing on genetic information to the next generation.
All living organisms have _____-stranded DNA as their genetic material In eukaryotic cells, double-stranded DNA sequences are arranged into ______ (Greek: chroma ~ color, soma ~ body). This compact organization is necessary because of the _____ size of eukaryotic genomes. If a double strand of all the DNA in a single human cell were stretched out straight, it would measure around ___ feet in length. **Of course, the nucleus of the cell is much smaller than this! Chromosomes allow the genome to be compressed and organized.
- 5 feet
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 ______. They 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).
- DNA and protein
The net ______ charge of the histone function group attracts the ______ charged DNA strands 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 ______ (Greek: chroma: color).
By mass, chromatin is about one third ____, two thirds ______, and a small amount of ____. How did chromatin received its name?
- because the large amount of basic amino acid content in histones allows chromatin to absorb basic dyes.
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.
- gene expression
Chromatin that is tightly condensed in the manner described above is called _______. Some chromatin, called _______ ________, is permanently coiled.
- heterochromatin (Greek: heteros ~ other)
- constitutive heterochromatin
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 (Greek: eu ~ well or properly)
Euchromatin is only coiled during _____ ______. Nuclceotide sequences code for protein products often contain single copy DNA (define)
- nuclear division
- single copy DNA: nucleotide sequences represented by only one copy of a nucleotide sequence, and are associated with regions of euchromatin that are being actively transcribed.
In contrast, non-coding regions of DNA (found only in eukaryotes) often contain repetitive DNA (define)
Repetitive DNA: has multiple consecutive copies of the same nucleotide sequence and remains tightly coiled in regions of heterochromatin
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 _______.
unwound and transcribed
The most common example of epigenetic regulation through chemical change is _____ _______, which involves the addition of an extra ______ group to particular ______ nucleotides.
- DNA methylation
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.
- non-coding RNA (ncRNA)
Inside the nucleus of a human somatic cell, there are ___ double- stranded DNA molecules. The 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 _______.
- homologues (Greek: homologein ~ to agree with, homo ~ same, logia ~ collection)
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 _____.
- diploid (Greek: di- ~ twice)
- haploid (Greek: haploos ~ sin gle or simple)
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.
Far from being a period of rest as the name implies, during G0 , cells are busy serving their various functions within the body and producing ______ for this purpose. Although cells manufacture protein products throughout the cell cycle, most production takes place during ____ when the cell is not exerting energy in ____ _____.
- self replication
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.
- transcription and translation
- RNA transcript
Different genes can code for different types of RNA name 4:
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.
- 1)ribosomal RNA (rRNA), 2)transfer RNA (tRNA), 3)small nuclear RNA (snRNA), and 4)messenger RNA (mRNA).
- end products
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 _____. **Recall from the Biological Molecules and Enzymes Lecture that proteins form the basis of many cell structures and regulate practically all cellular processes. Creating proteins through transcription and translation is essential to the processes of life.
- amino acids
The purpose of transcription is to create an RNA copy of a DNA template. Transcription is itself a form of ______ of gene expression. What 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 ______. Explain each step (6-story)
- initiation, elongation, and termination
- 1)In initiation, a group of DNA binding proteins called transcription factors identiftes a promoter on the DNA strand.
- 2)At the promoter, the transcnpt10n factors assemble into a transcription initiation complex, which includes the major enzyme of transcription, RNA polymerase.
- 3)After binding to the promoter, RNA polymerase unzips the DNA double helix, creating a transcription bubble. Next the complex switches to elongation mode.
- 4)In elongation, RNA polymerase transcribes only one strand of the DNA nucleotide sequence into a complementary RNA nucleotide sequence. *The transcribed strand is called the template strand or (-) antisense strand. The other strand, called the coding strand or (+) sense strand, protects its partner against degradation.
- 5)RNA polymerase moves along the DNA strand in the 3' ~ 5' direction, building the new RNA strand in the 5' ~ 3' direction.
- 6)The end of transcription is called termination, which occurs when a specific sequence of nucleotides known as the termination sequence is reached. It can also involve special proteins, known as Rho proteins, that help to dissociate RNA polymerase from the DNA template.
promoter: a sequence of DNA nucleotides that designates a beginning point for transcription
______ 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 _______ sequence causes RNA polymerase to bond _____ tightly and _____ often to a given promoter, which leads to the associated genes being transcribed _____ frequently.
- consensus sequence
- consensus sequence
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 ______ or ______. Activators and repressors bind to DNA close to the ______ and either activate or repress the activity of _____ _______.
- activators and repressors
- RNA polymerase
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
- Enhancers: short, non-coding regions of DNA found in eukaryotes. They function similarly to activators but act at a much greater distance from the promoter.
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)
- Homeostasis: a stable and unchanging state of the intracellular and extracellular compartments, is the hallmark of multicellular organisms. The primary function of gene regulation in multicellular organisms is to control the intra- and extracellular environments of the cell.
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 the two conditions and the three step process of how it works:
1.glucose is scarce and 2. lactose is present.
- 1)Low glucose levels lead to high cAMP levels.
- 2)cAMP binds to and activates a catabolite activator protein (CAP).
- 3)The activated CAP protein binds to a CAP site located adjacent and upstream to the promoter on the lac operon.
- **In an example of positive control, CAP ac tivates the promotor, allowing the formation of an initiation complex 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 _____ ______.
- lac repressor
- gene repression
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
- adjacent and upstream
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.
- eukaryotic and prokaryotic cells
In eukaryotes, each type ofRNA 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 _____.
- gene regulation
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 ______ _____ RNA [hnRNA]).
- primary transcript
- pre-mRNA, or heterogeneous nuclear
The modifications that change a primary transcript into a final, processed mRNA serve several purposes. Name 4:
- 1) helping the molecules that initiate translation recognize the mRNA
- 2)protecting the mRNA from degradation
- 3)eliminating extraneous sequences of nucleotides from the transcript before translation
- 4)providing a mechanism for variability in protein products produced from a single transcript.
Post-transcriptional processing includes modification of both ends of an mRNA sequence. Even before the eukaryotic mRNA is completely transcribed, its ___' end is capped in a process using GTP. The two roles of the 5' cap
- 1)Serves as an attachment site in protein synthesis during translation
- 2)Serve as a protection against degradation by enzymes that cleave nucleotides, called exonucleases.
The 3' end of the transcript is similarly protected from exonucleases by the addition of a long series of ______ nucleotides. When this _____ ____ has been added, the 3' end is said to be polyadenylated.
The primary transcript is much _____ than the mRNA that will be translated into a protein. Before leaving the nucleus, portions of the primary transcript are excised and discarded through the process of _____. The portions of transcript that are removed are called _____, while the portions that become part of the mature mRNA and will code for proteins are called _____. Introns are generally much _____ than exons. They do not code for ______ and are ______ within the nucleus.
The process of splicing removes _____ from the primary transcript and joins the ends of the _____ together to form one, uninterrupted coding sequence of _____.
The mechanism of splicing involves several _____ ______ _______. Each snRNP contains both an assortment of _____ and _____. During the splicing process, snRNA acts as a _____ (define)
- small nuclear ribonucleoproteins (snRNPs, "snurps")
- proteins and snRNA
- ribozyme: an RNA molecule capable of catalyzing specific chemical reactions. (Note that this is one of the few enzymes that is not a protein.)
Splicing occurs when ______ recognize nucleotide sequences at the ends of the _____. The snRNPs pull the ends of the introns together, forming an _____ _____ or _____.
- intron loop or lariat