Honors Biology 2A: Gene Expression - McCarthy 24-25 PDF

# Honors Biology - 2A: Gene Expression ## Additional Information on Proteins - Like the 26 letters of the alphabet, 20 amino acids can be arranged in different ways to form many different types of proteins. - 11 of the amino acids can be made by humans, however, 9 (called essential amino acids) mu...

# Honors Biology - 2A: Gene Expression ## Additional Information on Proteins - Like the 26 letters of the alphabet, 20 amino acids can be arranged in different ways to form many different types of proteins. - 11 of the amino acids can be made by humans, however, 9 (called essential amino acids) must be obtained through food. ### What differs from one protein to another? 1. Number of amino acids (length) 2. Type of amino acid 3. Sequence or order of amino acid 4. Number of polypeptides ## Closer Look at the 20 Amino Acids - The 20 amino acids can be grouped according to the chemical properties of their variable groups. | Amino Acid Group | Properties | |----------------------------|------------------------------| | **Hydrophobic** (Non-polar) | - Most frequently behaves non-polar. <br>- Can form disulfide bridges with other cysteines. | | **Hydrophilic** (Polar) | - Have polar groups (–OH, –NH2). <br>- Can form hydrogen bonds with other polar molecules. | | **Charged** (Acids) | - Donate H+ (overall negative charge). | | **Charged** (Bases) | - Accept H+ (overall positive charge). | ## The Three-Dimensional Structure of Proteins - After amino acids are bound by peptide bonds, they interact with each other, causing the molecule to fold into a three-dimensional shape. - A protein can be made up of one or several polypeptides. ### Primary Structure (1°) - A straight, single chain of amino acids held together by peptide bonds. - This structure is not functional yet. ### Secondary Structure (2°) - H-bonds form between O in a carboxyl and H-bonds from an amino forming alpha helices and beta sheets. - This structure is also not functional yet, but it establishes the overall shape of the protein. ### Tertiary Structure (3°) - Folding into a 3D shape due to R-group interactions. - R-group interactions can be nonpolar/nonpolar, polar/polar, acid/base, or cysteine/cysteine. - This is the final functional product of the protein. ### Quaternary Structure (4°) - Only occurs if two or more polypeptide chains are needed to form the final structure. - For example, hemoglobin ## Amino Acids can be grouped according to the chemical properties of their variable groups. 1. **Nonpolar** (hydrophobic) 2. **Polar** (hydrophilic) 3. **Cysteine** 4. **Charged -** (Acids) 5. **Charged +** (Bases) ## If just one amino acid is changed in a protein, this will usually result in a change in the protein's structure. - This change can also affect the function of the protein. ## An example of a change in structure that leads to disease: - **Sickle-cell anemia**. This is caused by a single change in the amino acid sequence of the protein hemoglobin. ## Denaturation - The loss of a protein's secondary, tertiary, and/or quaternary structure. ### What factors might denature a protein? - High temperature, extreme pH, and extreme salt concentration. ### How do these factors denature proteins? - **High temperature:** Interferes with H-bonds (2°) and R-groups (3°) causing the protein to unfold. - **Extreme pH:** Changes in ions interfere with ionic bonding (3°) causing the protein to unfold. - **Extreme salt concentration:** Salt dissociates into ions interfering with acid/base interactions (3°) causing the protein to unfold. ## Proteins Determine Traits - All cells contain genetic information in the form of DNA molecules. - **Genes** are regions in the DNA that contain the instructions that code for the formation of proteins. - Therefore, **genes** determine traits. - **Genes** influence an organism's characteristics by determining which types of proteins the organism makes. ## Why do you think some people have harmful traits such as albinism, lactose intolerance, sickle cell anemia, or hemophilia, and other people don't? - **It depends on the genes or mutations they inherit, giving rise to proteins that do not function properly.** ## Changes to genes located on chromosomes may affect proteins and may result in harmful, beneficial, or neutral effects to the structure and function of the organism. ## Brainstorm for each protein function: - What would happen if the protein was missing or defective? | Protein Function | Effect if this protein is missing or defective | |----------------------------------------------------|-------------------------------------------------------| | Enzyme for synthesizing melanin (pigment that gives our skin and hair color) | Lack of color in the skin and hair (albinism) | | Lactase (breaks down lactose) | Inability to break down lactose found in milk (lactose intolerance) | | Acetaldehyde dehydrogenase (breaks down acetaldehyde, a harmful product of alcohol metabolism) | Alcohol sensitivity (skin flushing and unpleasant symptoms from drinking alcohol) | | Hemoglobin (protein in red blood cells which transports oxygen in the blood) | Inability to properly transport oxygen (i.e., sickle cell anemia) | | Clotting proteins in the blood | Excessive bleeding/ wounds don't heal (hemophilia) | # Nucleic Acids - There are two kinds of nucleic acids: - **DNA** (deoxyribonucleic acid) - **RNA** (ribonucleic acid). - Nucleic acids are large polymers made up of repeating monomers called nucleotides. ## Nucleotides consist of three parts: 1. **Sugar** (ribose or deoxyribose) 2. **Nitrogenous base** (4 types) 3. **Phosphate group** ### Sugar - DNA contains **deoxyribose** - RNA contains **ribose** ### Nitrogenous Bases **Purines** - two rings 1. **Adenine (A)** 2. **Guanine (G)** **Pyrimidines** - one ring 1. **Cytosine (C)** (in DNA and RNA) 2. **Thymine (T)** (only in DNA) 3. **Uracil (U)** (only in RNA) ## DNA structure - DNA is a **double-stranded** molecule, meaning that it is made up of two strands of nucleotides. - The two strands are held together by **hydrogen bonds** between the bases. - Hydrogen bonds are very weak, but the **double-stranded structure** of DNA is very stable because there are so many of them within this large molecule. - Within a single strand, each nucleotide is connected to the next one by **covalent bonds** to form long polymers. - Each of the 46 pieces of DNA in your cell nucleus is actually millions of nucleotides long. - If you look closely, especially at the deoxyribose molecules, you can see that the two strands of nucleotides in DNA are oriented in opposite directions. Therefore, the two strands are said to be **antiparallel**. - DNA is often represented as a ladder where the sides of the ladder are made up of the phosphate and sugar molecules, and the steps (or rungs) of the ladder are made up of the bases. The ladder structure of DNA is then twisted into a spiral shape called a **double helix**. - The shapes of the bases fit into each other, where **T will only bind with A**, and **C will only bind with G**. This is called **complementary base pairing**, and it is dependent upon the three-dimensional structure of the bases. ## DNA by the numbers... - 46 (23 pairs) = Number of chromosomes (pieces of DNA) in a human body cell. - 20,000 = The estimated number of genes in the human genome. - ~3 billion base pairs = Number of nucleotides in the genome of a human sperm or egg cell (= 6 billion base pairs per a human body cell). ## DNA Replication - The process of making an exact copy of the DNA. - Takes place in the nucleus of eukaryotic cells. - DNA is replicated prior to cell division, so that both new daughter cells receive the same amount and identical copies of DNA. ## In DNA Replication, the following steps occur: 1. **DNA helicase** enzyme helps DNA unwind and unzip as hydrogen bonds break between complementary base pairs. 2. The two separated strands act as templates to produce two new strands. 3. **Free floating nucleotides** in the nucleus pair up with the complementary nucleotides on the existing template strands. The enzyme **DNA polymerase** adds the new nucleotides. Covalent bonds form between the sugars and phosphates of the new nucleotides to form new strands. 4. **Hydrogen bonds** form between the complementary base pairs. 5. The result is **two identical DNA molecules** (one for each new cell). Each molecule contains one old and one new strand. 6. **Proofreader enzymes** check the new molecules for mistakes (genetic mutations). ## In reality, DNA replication in your cells is a more complex process than what was described above. - DNA is replicated in many places at once, making the process faster. ## Organization of DNA in Cells - Each cell in your body contains 46 very long pieces of DNA, each being millions of nucleotide pairs long. - In order for these extremely long molecules to be packaged in the nucleus of your cell, each piece of DNA is wrapped around a series of proteins called **histones**, similar to the way thread is wound around a spool. - **DNA wound around proteins** in this way is called **chromatin**. - During the life of your cell, the DNA is usually in the form of chromatin. It is only after replication, when the cell is going to divide, that the chromatin condenses even further to form a doubled-armed structure called a **chromosome**. ## Differences Between Chromatin and Chromosomes | Characteristic | Chromatin | Chromosomes | |---------------------------|-------------------------------|-----------------------------------| | Coiling of DNA | Loosely coiled DNA | Tightly coiled DNA | | Accessibility | Nucleotide sequences are more accessible | Nucleotide sequences are less accessible | | Cell Function | "Working DNA" | Involved in cell division | | Cellular Presence | Present in cells at all times | Only present in cells about to divide| ## Transitioning from Chromatin to Chromosome and Back: 1. The cell gets the signal to divide. DNA uncoils from chromatin structure. 2. DNA is replicated. 3. 2 identical pieces of DNA coil back up into chromatin by wrapping back around the histones. 4. Chromatin coils on itself further to form chromosomes. Each of the identical pieces of DNA becomes one of the two arms of a double arm chromosome. These are called **sister chromatids**. 5. Sister chromatids split and the cell divides putting one copy of each chromosome into each daughter cell,. 6. Chromosomes in daughter cells unravel back to chromatin so the nucleotides are once again readable for protein production and future DNA replication. **Note:** The word chromosome is often used to refer to DNA in any of its forms, but a true chromosome is a double-armed structure that exists only when the cell is dividing. ## The Function of DNA - To code for **all of our characteristics/traits** and to enable these traits to be passed from one generation to the next. - The **sequence of nucleotides** creates a code that is the “recipe” for a protein. - **Proteins** lead to traits. ## What is a gene? - A segment of the DNA molecules that codes for a polypeptide which leads to a trait. ## How does one gene differ structurally from the next? - Each gene has a different number and sequence of nucleotides. - This means that each gene codes for a different number of amino acids in a protein/polypeptide. ## A genome is an organism's complete set of deoxyribonucleic acid (DNA). - It could also be described as all the unique DNA in one cell on one organism. ## The Human Genome Project - In the year 2000, the **Human Genome Project** published the completed sequence of all the nucleotides that make up human chromosomes. - This information will contribute to the ability to treat human disease and improve the quality of life for humans. ## A Closer Look at DNA and Genes - Of all the 3 billion base pairs that make up your genome, only a small fraction (approximately 3-5%) actually constitute the ~20,000 genes that code for protein. - The other ~97% make up **non-coding regions** and were once thought to be “Junk” DNA. Many functions for junk DNA have been determined and further research is ongoing. - “Noncoding” DNA can be located **BETWEEN genes or WITHIN genes**. ## Genes themselves can be broken down into two main regions: 1. **Protein Coding Region** 2. **Regulatory Region** ### Protein Coding Region - Triplets of nucleotides that code for the sequence of amino acids within a protein. - This region is transcribed and translated. ### Regulatory Region - The nucleotide sequence that precedes the protein coding region, regulating whether or not the gene will be transcribed. - Includes several regions, such as the promoter region. ### Promoter - A sequence of nucleotides on the DNA that the RNA polymerase binds to. - This marks the beginning of transcription. ### Transcription Factors - Special proteins that bind to promoter regions. - These factors help position the RNA polymerase at the correct gene to make the mRNAs that the cell needs. - Transcription factors determine if a gene will be "turned on" or "turned off" ## The Production of a Protein from a Gene (Gene Expression) - The sequence of nucleotides in a gene will determine the sequence of amino acids that will be in the protein that the gene is coding for. - DNA must remain in the nucleus, but proteins are assembled at the ribosomes. ## Two processes are necessary in order for a protein to be produced from a gene: 1. **Transcription** 2. **Translation** ### Transcription - The process in which a section of the DNA code is used to produce a complementary RNA molecule (could be mRNA, tRNA, or rRNA). ### Translation - The process by which the sequence of bases of an mRNA is converted into the sequence of amino acids of a protein. ## Central Dogma of Molecular Biology: DNA -> RNA -> PROTEIN -> TRAIT ## The Central Dogma (in more detail): 1. **Transcription**: DNA is transcribed into mRNA 2. **Translation**: mRNA is translated into a polypeptide 3. The polypeptide may either be a functional protein or it may need to fold into its final three-dimensional shape. 4. **Protein folding** leads to traits. ## Summary of the Differences Between DNA and RNA: | Characteristic | DNA | RNA | |---------------------------|---------------------------------------|---------------------------------------| | Structure | Double-stranded | Single-stranded | | Sugar | Deoxyribose | Ribose | | Nitrogenous Bases | Adenine (A), Thymine (T), Cytosine (C), Guanine (G) | Adenine (A), Uracil (U), Cytosine (C), Guanine (G) | ## Transcription - The process that produces mRNA from a gene. - The enzyme **RNA polymerase** opens the gene and makes RNA. - The RNA transcript is a copy of the gene but **uracil (U)** is used in the RNA instead of **thymine (T)**. ## In Transcription, the following steps occur: 1. **RNA polymerase** enzymes cause a gene segment (part of the DNA) to unwind from chromatin structure. 2. **Hydrogen bonds** break between complementary base pairs on the two DNA strands. 3. **One side of the DNA** is used as a "template" to produce a single-stranded RNA molecule. **RNA polymerase** does this by matching up free-floating RNA nucleotides in the nucleus and covalently bonding the RNA nucleotides to each other to make the RNA molecule. 4. The **RNA molecule breaks away** from the DNA template strand. 5. **The original DNA strands reconnect** by H-bonding and the molecule recoils into chromatin. ## What happens to mRNA after it has been transcribed from DNA? - It is processed, leaves the nucleus, and travels to the ribosome for translation. ## mRNA Processing - mRNA is modified in order to produce the Final Transcript. ### The following events occur during mRNA processing: 1. **Removal of introns (mRNA splicing)** 2. **Addition of Guanine Cap and Poly A tail:** - A **guanine cap** is added to one end of the transcript and a series of **adenine nucleotides** known as a **poly A tail** is added to the other end of the transcript. - These nucleotides are added to help prevent the breakdown of the mRNA until after it has been translated. ## RNA Processing in Eukaryotes - mRNA processing takes place in the nucleus before leaving to travel to the ribosomes. 1. **5' Capping:** A specialized guanine nucleotide (called the 5' cap) is added to the 5' end of the primary transcript. 2. **Splicing:** Introns are removed and exons are spliced together to form the mature mRNA transcript. 3. **PolyA tail addition:** A poly A tail is added to the 3' end of the transcript. The mRNA then travels to the ribosome where it is translated into a protein. ## Regions of DNA | Region | Transcribed Only | Transcribed and Translated | Neither | |-------------------------|------------------|-----------------------------|---------| | Exons | ✓ | ✓ | | | Ribosome Binding Region | ✓ | ✓ | | | Start Codon | ✓ | ✓ | | | Other Coding Triplets | ✓ | ✓ | | | Stop Codon | ✓ | ✓ | | | Nucleotides after the Stop Codon | ✓ | | | | Intron Regions | ✓ | | | | Promoter | ✓ | | | | Guamine Cap | ✓ | | | | Poly A Tail | ✓ | | | ## Primary mRNA Transcript: - Includes exons and introns, with a guanine cap. ## Mature/Final mRNA Transcript: - Includes exons, a poly A tail, and a guanine cap. ## The DNA Code - The DNA code is in the sequence of bases (or the sequence of nucleotides) in a gene. ## The DNA code is universal. - This means that all living things store information in DNA that can be transcribed and translated using the same 20 amino acids. ## Triplet Code - Every 3 nucleotides (bases) in DNA codes for **one** of the 20 different amino acids. - The **sequence of bases** in a gene segment codes for the **sequence of amino acids in a protein**. ## Codon - A triplet of nucleotides in mRNA that codes for an amino acid. ## Translation - The process where the mRNA code is used to assemble or build a specific sequence of amino acids to form a specific polypeptide. ## Translation takes place at an organelle called the ribosome. - Ribosomes are small organelles with a two subunit structure (“small” and “large” subunits) composed of rRNA (ribosomal RNA) and ribosomal proteins. - Formed in the nucleus – migrate to the cytoplasm where they help to synthesize proteins. ## In addition to mRNA and the rRNA of the ribosome, another type of RNA called tRNA is important for the translation process. ### tRNA 1. **Structure:** A single-stranded molecule of RNA that folds into a clover leaf shape due to hydrogen bonding between complementary base pairs. It is about 80 nucleotides long. 2. **Amino Acid Attachment:** One end of tRNA binds with an amino acid. There is a specific tRNA for each amino acid. 3. **Anticodon:** The bottom loop of tRNA contains an anticodon. An anticodon is a triplet of nucleotides complementary to the codon on the mRNA. It forms H-bonds with the codon to orient the amino acid so the peptide bond can form. tRNA is not directly involved in the formation of peptide bonds. ## Fill in the following chart (use codon chart): | DNA Triplet Code | mRNA Codon | tRNA Anticodon | Amino Acid | |-------------------|-------------|----------------|------------------| | TTG | AAC | UUG | Asparagine | | AAA | UUU | AAA | Phenylalanine | | ACT | UGA | ACU | Stop | | ACC | UGG | ACC | Tryptophan | ## Initiation of Translation: 1. The small ribosomal subunit binds to its recognition sequence on mRNA, and the methionine-charged tRNA binds the AUG start initiation codon, completing the initiation complex. 2. The large ribosomal subunit joins the initiation complex, with methionine-charged tRNA now occupying the P site. ## Translation Continues: 1. The ribosome moves along the mRNA one codon at a time. 2. tRNA molecules carrying their associated amino acids bind to the codons in the A site of the ribosome. 3. Peptide bonds are formed between the amino acids in the A site and the P site. 4. The tRNA in the P site is released, and the ribosome moves to the next codon. 5. This process continues until a stop codon is reached. 6. The polypeptide chain is released from the ribosome. ## Events that occur in the process of translation: 1. **mRNA binds** to a ribosome (2 codons positioned at a time for translation). Ribosome binding region (RBR) of mRNA H-bonds to rRNA of ribosome. 2. **tRNA's with help of enzymes** attach to amino acids in the cytoplasm. Beginning at the start codon (AUG) the first two tRNA's bind with mRNA (anticodon to codon). 3. **Peptide bond forms**(with help of enzyme) between 2 amino acids on tRNA. 4. **First tRNA released** (can bind with another aa and be used again). 5. **Second tRNA** (now carrying the aa's) moves 1 spot down on the ribosome. 6. **Because tRNA is H-bonded to a codon of mRNA, it drags the mRNA along one position placing the next codon in position on the ribosome.** 7. **The next tRNA aa, complementary to the open position, will link w/ mRNA codon to anticodon and the process continues, peptide bond → tRNA released → moves down.** 8. **Eventually a stop codon** is reached (UAA, UGA, UAG) on mRNA and there is no tRNA to match so translation stops. 9. **Polypeptide is released** (into cytoplasm or RER lumen). 10. **The 2 parts of the ribosome come apart** and the mRNA is released and eventually degraded. ## Polyribosomes - Clusters of ribosomes that trail each other on the same piece of mRNA. - Average sized polypeptide made in ~1 minute. - More than one ribosome can use a single mRNA. - Each ribosome makes a copy of the polypeptide. ## After Translation: 1. **The polypeptide folds** into its final shape (secondary, tertiary, quaternary structure). 2. **Post-translational modifications** occur (removal of methionine or addition of other molecules to the proteins). ## A Note on Ribosome Production - **rRNA** is produced in the nucleus in the **nucleolus region** (portion of DNA that contains the sequences for rRNA transcription). - **Ribosomal proteins** must also be made. If proteins are required to make ribosomes and ribosomes make proteins, then you need a ribosome to make a ribosome! ## Summary - The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein. **DNA -> RNA -> PROTEIN -> TRAIT** ## DNA-RNA-PROTEIN-TRAIT(S) Relationship | Component | Function | |-----------------------------|--------------------------------| | Nucleotide sequence in the DNA of a gene | Stores the genetic code | | Nucleotide sequence in messenger RNA (mRNA) | Carries the genetic code from the nucleus to the ribosomes. | | Amino acid sequence in a polypeptide (rRNA and tRNA are required for production) | Determines the protein's structure and function. | | Protein Folding, Structure and Function of a protein (e.g., normal hemoglobin vs. sickle cell hemoglobin) | Contribute to the organism's traits. | | An individual's characteristics or traits (e.g., normal health vs. sickle cell anemia) | Ultimately results in the organism's characteristics. | ## Mutations - **A change in the DNA sequence.** - Most mutations are not harmful, but some mutations can be harmful because they can cause diseases. ## Why are most mutations harmful? - Because we are well adapted to our environment, any change is likely to decrease our survival. - Mutations in coding regions are more harmful than mutations in non-coding regions. - A **mutation** in a gene can lead to an altered protein with impacted function, leading to a genetic disease. - For example, a mutation in the gene for hemoglobin can cause sickle-cell anemia. ## Mutations can occur in several ways: 1. **DNA Replication Errors:** DNA polymerase incorrectly pairs bases, leading to a change in the sequence. 2. **Mutagens** (environmental factors that cause DNA damage): - Chemicals (smoking) - UV radiation - X-rays - Viruses ## Why is it that all these mutations don't accumulate to any great degree in one genome? - **We have many different repair enzymes that move up & down the DNA looking for damaged regions, or mismatched base pairs, and try to correct the error(s).** - **DNA Polymerase** does this as it adds nucleotides! - **Fewer than 1 in 1,000 base changes leads to a mutation** due to the success of repair mechanisms. ## Point Mutation - A change in just **one base pair of a gene**. ## There are several different types of point mutations that will change the base sequence in different ways. 1. **Nucleotide Substitution**: - Changing one base to another. - May do nothing at all. - May change the amino acid. - A change to a stop codon results in a premature stop to translation, which can be harmful. 2. **Nucleotide Deletion**: - Removing one base. - Causes a **frameshift mutation**, which changes the reading frame of the gene. - This can lead to a nonfunctional protein. 3. **Nucleotide Insertion**: - Adding one base. - Causes a **frameshift mutation**, which changes the reading frame of the gene. - This can lead to a nonfunctional protein. ## Of the three kinds of DNA point mutations: substitution, deletion, and additions, which one or ones do you think would most often cause the greatest problems? Explain. - **Deletions and additions** are more likely to cause problems because they can **shift the reading frame**, leading to the production of a nonfunctional protein. ## In contrast to these point mutations, there can also be chromosomal mutations. - Large sections of a chromosome can be moved, flipped, deleted, or added.