BTEC 1322 Chapter 2 Lecture Outline S25 PDF

**Chapter 2- An Introduction to Genes and Genomes\*** \*Lecture outlines are to be used as a study guide only and *do not* represent the comprehensive information you will need to know for the exams. Understanding DNA is the foundation of biotechnology. DNA is replicated, then the processes of tra...

**Chapter 2- An Introduction to Genes and Genomes\*** \*Lecture outlines are to be used as a study guide only and *do not* represent the comprehensive information you will need to know for the exams. Understanding DNA is the foundation of biotechnology. DNA is replicated, then the processes of transcription and translation produce protein products. **[2.1 A Review of Cell Structure ]** Cells are the smallest unit of life. Cells vary in their shape, size and function. The genetic information found in all cells is **deoxyribonucleic acid (DNA)**. **Genes** control the activities of cells, and the genes determine physical traits of the organism. **Prokaryotic Cells** Every cell has a **plasma (cell) membrane** that contains **cytoplasm**. Some cells also have **organelles**. Bacteria are **prokaryotic cells**, that *do not* have a **nucleus** (Table 2.1). Bacterial cells have a relatively simple cell structure compared to eukaryotic cells (Fig. 2.1). **Eukaryotic Cells** Plant and animal cells are **eukaryotic cells**, they have a true nucleus. Eukaryotic cells are: fungi, protists, plants and animals (Fig. 2.2). Eukaryotic cells have **mitochondria**, an organelle that is responsible for producing much of the **adenosine triphosphate (ATP)** for the cell. The cytoplasm consists of the **cytosol**, a semi-fluid liquid that contains the organelles. Organelles carry out specific functions for the cell (Table 2.2). The largest organelle in the cell is the nucleus, which contains most of the DNA in the cell, and it is surrounded by the **nuclear envelope**. **[2.2 The Molecule of Life ]** Scientists discovered the structure and function of DNA. **DNA Structure** The two major types of **nucleic acids** in the cell are DNA and **ribonucleic acid (RNA).** A number of experiments were done that gave supporting evidence that DNA is the genetic material in cells. The individual building blocks of DNA are called **nucleotides**. Each nucleotide consists of a **pentose sugar** called deoxyribose, a phosphate and a **nitrogenous base**. The nitrogenous bases that identify each nucleotide are: **adenine (A)**, **thymine (T)**, **guanine (G)**, and **cytosine (C)** (Fig. 2.3). Early scientists, such as, E. Chargaff, R. Franklin, J. Watson and F. Crick, helped to determine the structure of DNA. Watson and Crick determined the structure of DNA (Fig. 2.4). A strand of DNA is connected along the 'backbone' through **phosphodiester bonds**. Each strand of DNA has a **polarity**: a 3' end and a 5' end. Watson and Crick determined that the two strands of DNA form a right-handed double helix. The two strands are held together through the hydrogen bonding of the **complementary base pairs**. Based on Chargaff's rule, the complementary base pairing is: A/T and G/C. The direction of the two strands are *antiparallel*. **What Is a Gene?** A **gene** is a unit of inheritance, that is determined by the nucleotide sequence. A modern definition of a gene is that it is used to produce RNA. Genes influence how cells appear in what we call **traits**. Traits can be linked to a single gene or multiple genes that produce proteins that interact. **[2.3 Chromosome Structure, DNA Replication, and Genomes ]** Understand how DNA is organized into chromosomes and how DNA is replicated in cells. **Chromosome Structure** DNA is packaged into **chromosomes**. In the (nucleus) DNA is in a loose state when the cell is not dividing. The DNA is wrapped around proteins called **histones** to form **chromatin**. When the cell is ready to divide, the chromatin compacts to chromosomes (Fig. 2.5). Bacteria have a single circular chromosome. Eukaryotes can have one or more sets of chromosomes, which are linear. Humans inherit 23 chromosomes from your mother **(maternal chromosomes)** and 23 chromosomes from your father **(paternal chromosomes)**. These chromosome pairs are called **homologous pairs**, or **homologues**. Chromosome sets 1 -- 22 are the **autosomes**, and the 23^rd^ set are the **sex chromosomes**, X and/or Y. The human **gametes** (sperm and egg cells) have a **haploid (n) number** of chromosomes. All cells of the body are **somatic cells**. Somatic cells have a **diploid (2n)** number of chromosomes. Somatic cells have 46 chromosomes. Sex chromosomes have genes that determine sex traits. Before DNA replication, the chromosome is copied and produces two **sister chromatids**. The two sister chromatids are joined together at the **centromere**. During cell division, the sister chromatids are pulled apart by the **microtubules** attaching at the centromere. The centromere divides the chromosome into two parts -- the **p arm** (short) and the **q arm** (long). The end of the linear chromosome is called the **telomere**. There is intense research of the telomere, which has been implicated in cellular aging and certain cancers, called **senescence**. **[Karyotype analysis for studying chromosomes ]** **Cytogenetics** is the science of analyzing chromosomes. One method to study chromosomes is a **karyotype** (Fig. 2.6). In humans, chromosome 1 is the largest, and chromosome 21 is the smallest. A new method for karyotype analysis is called **spectral karyotype**, that uses specific probes to colorize the chromosome, which provides a more detailed analysis of chromosomes. **FISH**, **fluorescence in situ hybridization**, is a way to analyze chromosomes for altered structure. **[DNA replication]** Somatic cells divide by **mitosis**. Gametes (sperm and egg cells) are formed from **meiosis**. When the sperm and egg cells combine, they form a **zygote**. Before both mitosis and meiosis, the DNA is replicated by a process called **semiconservative replication** (Fig. 2.7). Both parental strands are separated and a complementary strand is made. DNA replication is accomplished by a number of enzymes and proteins (Fig. 2.8). **DNA helicase** separates the two parental strands; DNA replication begins at the **origin of replication**; **RNA primers** are added to the template DNA by the enzyme **RNA primase**; **DNA polymerases**, like **DNA polymerase III**, is used to add the complementary nucleotides to build the daughter strands. The semiconservative replication produces a **leading strand** and a **lagging strand**. The sugar-phosphate backbone is connected by using **DNA ligase**. **[What is a genome?]** The **genome** is all of the DNA in a cell. The study of the genome is called **genomics**. The **Human Genome Project**, was an effort to sequence the entire sets of human chromosomes. This was done, in part, to identify the locations of genes to aid in improving human health. **DNA sequencing** is a method to identify the order of the nucleotides that comprise a gene. **[2.4 RNA and Protein Synthesis]** Genes direct the synthesis of proteins. Proteins have a variety of functions in the cell: cell structure, enzymes, hormones and cell signals, receptor and transport, and antibodies. Genes are transcribed into **messenger RNA (mRNA)** by a process called **transcription**. Then proteins are made from mRNA by a process called **translation** (Fig. 2.9). RNA is single stranded, and not double stranded like DNA. The nitrogenous bases of RNA are similar, but not the same as DNA. There is uracil (U) in RNA. Also, the sugar in RNA is a ribose sugar. The process of DNA to mRNA to protein is called the Flow of Genetic Information. **Copying the Code: Transcription** DNA is used as a template to make RNA. The enzyme responsible for this is **RNA polymerase**, which carries out transcription (Fig. 2.10). Genes are transcribed. There is a unique section on DNA called a **promoter**. RNA polymerase binds at the promoter, which is at the beginning of the gene. Proteins called **transcription factors** and DNA sequences called **enhancers** direct RNA polymerase where to bind on DNA. The DNA **template strand** is used to make the mRNA. The opposite DNA strand is the *coding strand*. RNA polymerase moves down the DNA template strand and add bases in the 5' to 3' direction. The progress of RNA polymerase is stopped at a location on DNA called a terminator. Transcription of genes happen when the cell needs the gene product (protein). **[Transcription produces different types of RNA]** Other types of RNA are: - **transfer RNA (tRNA)**: carries the amino acids to the ribosome. - **ribosomal RNA (rRNA)**: a physical part of the ribosome. - **noncoding RNA (ncRNA)**: diverse functions in the cells. **[mRNA processing]** In eukaryotic cells, the mRNA is processed in the nucleus before it is used for translation. The initial transcript that is made is called the **primary transcript (pre-mRNA)**. Part of processing the pre-mRNA is **RNA splicing**, where the **introns** are removed, and the **exons** are linked together to make the final transcript (Fig. 2.11). Splicing allows for flexibility in the types of proteins that can be made from a single gene. In the process called **alternative splicing,** different exons of the same gene can be used to make different proteins. For example, different antibodies are made by alternative splicing. Many human genes can be spliced in different ways. Understanding alternative splicing has lead to gene therapies for certain genetic diseases. Two other steps are done in mRNA processing to make the final transcript: - a unique guanine base (with a methyl group) is added at the 5'-end of the mRNA, called a 5' cap. - At the 3' end of the mRNA, a process called **polyadenylation** will add a series of adenine nucleotides, called a "poly-A tail". Once these three steps are complete (i. splicing, ii. 5' cap, iii. 3' poly A tail), the final transcript exits the nucleus and enters the cytoplasm to get translated by a ribosome. **Translating the Code: Protein Synthesis** Translation happens in the cytosol of the cell. Three (3) different types of RNA are involved: - mRNA: a copy of the gene, has the genetic message from DNA - rRNA: part of the structure of the **ribosome**, which performs translation - tRNA: carries the amino acids to the ribosome **[The genetic code]** Ribosomes "read" the nucleotides in mRNA and codes for the corresponding **amino acid**. The ribosome forms a chemical bond (peptide bond) between the amino acids to make a **polypeptide**. The code is read in 3-nucleotide unit called a **codon**. Each codon codes for an amino acid (Table 2.3). Important codons in the genetic code are the start codon (AUG) and the stop codons. These codons direct the progress of the ribosome. There is universality of the **genetic code**. Because of this universality, biologists can use techniques called **recombinant DNA technology** to clone human genes into bacteria, for example. Overall, the universality makes it easy to clone different genes into different organisms. **[Ribosomes and tRNA molecules ]** Ribosomes are made from ribosomal proteins and rRNAs. The ribosome has two parts, a large subunit and a small subunit. When both subunits come together, there are pockets, or grooves, that allows translation to happen. One groove is called the **A (aminoacyl) site**, where the 'charged' tRNA will enter, the **P (peptidyl) site**, where the peptide bond is formed, and the **E site**, where the 'empty' tRNA exits the ribosome (Fig. 2.12). The tRNA is a small molecule that folds back on itself. At the 3' end of the tRNA, an enzyme called the aminoacyl tRNA synthetase will attach the amino acid, creating an **aminoacyl transfer RNA (tRNA)**, that is 'charged' with its corresponding amino acid. A charged tRNA will carry the amino acid to the ribosome, and enter the ribosome at the A site. The anticodon loop of the tRNA binds to its corresponding codon in the mRNA. **[Stages of translation]** There are fundamental differences in where the stages of translation happen in a prokaryote versus a eukaryote. The focus here will be the three stages of translation in a eukaryote. The three stages are: *initiation*, *elongation* and *termination*. - *[initiation]*: the small ribosomal subunit binds to the 5' end of the mRNA; initiation factors help guide the small subunit to the mRNA; the small subunit moves towards the start codon and the initiator tRNA (met) binds at the AUG; then the large subunit binds. - *[elongation]*: the ribosome moves down the mRNA, and the appropriate tRNA enters the ribosome. It is during this process that the peptide bond is formed by an enzyme in the ribosome called the **peptidyl transferase.** Once the peptide bond is made, the ribosome moves down one codon called *translocation*, the tRNA in the P site moves to the E site and exits the ribosome. Elongation continues until the ribosome reaches a stop codon. - *[termination]*: proteins called *releasing factors* will separate the two subunits and translation will end. **[2.5 Regulation of Gene Expression ]** The term **gene expression** refers to the production of mRNA by a cell. Not all genes are expressed at the same time. Cells regulate when they will produce a gene product in a process called **gene regulation**. In a multi cellular organism, like humans, all somatic cells have the same genes but each cells expresses a different set of genes. Genes can be "turned on" under a set of certain growth conditions. Gene regulation can be "positive" or "negative". Prokaryotic and eukaryotic can regulate their genes in a variety of ways (Fig. 2.13). One way to regulate gene expression is by **transcriptional regulation** -- controlling transcription. There can also be *post-transcriptional regulation*, translational regulation and post-translational regulation. **Transcriptional Regulation of Gene Expression** The important component to transcriptional regulation is at the promoter. The nucleotide sequences in a promoter are different for prokaryotes and eukaryotes. In a eukaryote, common promoter sequences are **TATA box** and **CAAT box** (Fig. 2.14). Transcription factors are important in a eukaryote to allow the RNA polymerase to bind at the promoter. There are unique sets of transcription factors for different promoters in eukaryotic and prokaryotic cells. **Enhancers** help to tightly regulate transcription. Some enhancers can help to recruit other proteins called *activators*. These activators will work to stimulate transcription. Some genes have repressor sequences that will stop/reduce gene expression. There are cell and tissue specific gene expression. Identifying all of the components that are important for gene expression is critical in biotechnology to make products that are needed for human health. **Noncoding RNAs and Their Roles in Regulating Gene Expression** Noncoding RNAs, like tRNA and rRNA, do not make protein products (Table 2.4). There are **long noncoding RNAs** **(lncRNA)** and **small noncoding RNAs (sncRNA)**, each serving a different function. **Short interfering RNA (siRNA)** and **microRNAs (miRNA)** both regulation gene expression, such as preventing translation from happening (Fig. 2.25). RNA mechanisms of gene silencing are called **RNA interference (RNAi)**. Understanding the function of RNAi is important in understanding the nature of certain human diseases. **Bacteria Use Operons to Regulate Gene Expression** Bacteria are the historical basis of biotechnology. Understanding how bacteria regulate their genes is important. Bacteria organize their genes in a unit called an **operon**. The classic study of an operon is the *lac* operon (Fig. 2.16). The *lac* operon has three genes, *lacZ*, *lacY* and *lacA*. These genes are involved in lactose degradation. The *lac* operon is controlled by a ***lac* repressor**, when bound to the **operator**. When the *lac* repressor is bound to the operator, transcription of the *lac* operon is prevented. **[2.6 Mutations: Causes and Consequences ]** Changes in the nucleotide sequence of DNA is called a **mutation**. Mutations can lead to genetic diversity. Some mutations can cause diseases. **Types of Mutations** Mutations can happen because of spontaneous events, like the slippage of DNA polymerase during DNA replication. If the mutation is the result of an environmental cause, then that is done by **mutagens**, many of which can be physical (UV light) or chemical. Mutations may or may not affect the protein expression, depending on the location of the mutation in the gene / codon. A very common mutation is called **point mutations**, also known as **single-nucleotide polymorphisms (SNP)** (Fig. 2.17). Mutations can affect the function of proteins. Types of mutations: - **silent mutation**: change in the nucleotide sequence, but does not change the amino acid - **missense mutation**: change in the nucleotide sequence, and changes the amino acid - **nonsense mutation**: change in the nucleotide sequence that codes for a stop codon - **frameshift mutation**: caused by base pair insertions and deletions **[Mutations can be inherited or acquired]** **Inherited mutations** are passed to offspring through the gametes. **Acquired mutations** happen in somatic cells and are not passed on to offspring. However, acquired mutations can lead to conditions like cancer. **Mutations Are the Basis of Variation in Genomes and a Cause of Human Genetic Diseases** Some human genetic diseases are the result of a mutation, like sickle cell anemia (Fig. 2.18). Sickle cell anemia is the results of a single base mutation in the **hemoglobin** gene. The slight variations in the human genome are caused by SNPs. Most SNPs are in the introns, but if they are in the exons, that can affect the outcome of the protein. Scientists are working on **gene therapy** to address a lot of these genetic conditions (Fig. 2.19). **[2.7 Revealing the Epigenome ]** The study of genomes also involves the **epigenome**, the modification of chromosome structure that does not involve mutations in the DNA sequence. Diet and the environment can influence the epigenome. Also, the addition of methyl groups to cytosine and histone proteins can affect gene expression (Fig. 2.20). Epigenetic modifications can affect how accessible the DNA is for transcription. Epigenetics is of great interests to pharmaceutical and biotech companies. **[2.8 Immune Response Mechanism in Prokaryotes Results in Extraordinary New Technology for Editing Genes *In Vitro* and *In Vivo* ]** A simplified immune response in bacteria shows promise to edit genes *in vitro* and *in vivo*. This simple immune response is the **CRISPR-Cas system (Clustered Regularly Interspaced Palindromic Repeats)** (Fig. 2.21). The CRISPR-Cas system in bacteria is used to prevent viral infections. Cas nucleases, like Cas9, rely on ncRNAs called **CRISPR-derived RNAs (crRNAs)** to target specific viral sequences for destruction. The CRISPR system in bacteria can target viral DNA and destroy it. The CRISPR-Cas system is now being used to edit DNA in a process called **gene or genome editing**.