GEN BIO 1 Endterm Reviewer PDF

GEN BIO 1 ENDTERM REVIEWER LESSON 1: Enzyme Structure and Function **Enzymes** \- are biological catalysts (catalysts are substances that speed up that rate of reactions) \- speed up all biochemical reactions such as respiration and photosynthesis \- are synthesized inside living cells **Extra...

GEN BIO 1 ENDTERM REVIEWER LESSON 1: Enzyme Structure and Function **Enzymes** \- are biological catalysts (catalysts are substances that speed up that rate of reactions) \- speed up all biochemical reactions such as respiration and photosynthesis \- are synthesized inside living cells **Extracellular enzymes** - leaves a cell and functions outside the cell Intracellular enzymes - remains in the cell and functions inside the cell \- Most enzymes are globular proteins. Some are RNAs called ribozymes. \- Remain unchanged at the end of the reaction \- The substance the enzyme works on is called a substrate. \- Once a reaction has occurred, the enzyme-substrate complex breaks into products and enzyme \- Each enzyme catalyzes only one type of reaction **What if there were no enzymes?** -YOU DIE In the absence of enzymes, reactions in a cell would be too slow to sustain life and we would cease to exist. Properties of Enzymes 1\. Enzymes are **biological catalysts** 2\. **Highly specific** (acts only on a specific substrate) 3**. Can be used over and over again** for similar reactions 4\. **Required in small amounts** 5\. **Lower the activation energy needed** for the reaction 6\. **Does not alter the nature or properties** of the end products 7\. The **catalyzed reactions is reversible** (the same enzyme usually catalyzes both the forward and reverse of a reversible reaction) 8\. **Speeds up the rate of reaction** 9\. **Can be affected by factors such as temperature, pH, inhibitors, substrate concentration and enzyme concentration** Classifications of Enzymes **1. Oxidoreductases** \- This type of enzyme is involved in redox reactions \- Includes dehydrogenases (transfer H\*)\' oxidases (e transfer from molecular oxygen) and peroxidases (electron transfer to peroxide) **Redox reactions** (Reduction and Oxidation) - reactions in which hydrogen atoms, oxygen atoms or electrons are transferred between molecule **Reduction** - the half reaction that involves the gain of e /H\* **Oxidation** - the half reaction that involves the loss of e /H\* **Oxidizing** **agent** (**OA**) - gains the e\*/H+ **Reducing agent (RA)** - losses the e /H\* Example: **2. Transferases** \- Catalyze the transfer of an atom or group of atoms from a donor molecule to an acceptor molecule Example: **3. Hydrolases** \- Catalyze hydrolytic reactions and their reverse reaction, condensation Most common class of enzymes and includes **esterases, glycosidases lipases, and proteases** Example: **4. Lyases** \- Involved in the elimination or addition reactions in which group of atoms is removed or added to a substrate -new groups are added or removed by breaking a double bond or catalyzing the formation of a double bond in the substrate \- Includes **decarboxylases** Example: **5. Isomerases** \- Catalyze molecular isomerization. They catalyze the internal arrangement of atoms in a substrate and convert one isomer to another  Example: **6. Ligases** \- Are also known as **synthetases**. \- Involved in the formation of covalent bonds that join two molecules together such as C - 0, C - S, C - N, or C - C \- ATP is needed to form these bonds Example: Mechanism of Action **Active Site** When a substrate molecule meets an enzyme molecule, it fits in to a depression on the surface of the enzyme molecule. This depression is called the active site. The active site is formed due to the particular way the polypeptide chain of the enzyme is folded. The active site has a specific shape into which only one type Of substrate will fit. In the same way, substrates have a surface region that is complementary in terms of size, shape, Solubility, and charge to the active site of its enzyme molecule. When an enzyme is denatured by heat or a change in pH, the shape of the active site is changed and the substrate can no longer fit into the active site. **Activation Energy** The energy required for substances to react is called activation energy (Ea) or free energy of activation. This energy is required to break or make bonds. It can be provided in the form of heat that substrates absorbs from the surroundings. Enzymes speed up reaction rates by lowering the activation required. Without enzyme, high temp is required. With an enzyme, the reaction can take place at a lower temperature.  Hypotheses for mechanism of action There are two ways to explain how enzyme-substrate complexes are formed: **1. Lock and Key Mechanism** **2. Induced Fit Mechanism** **Lock and Key Mechanism** *An enzyme is specific because the structure of its active site is complementary to that of its substrate.* Therefore, only substrates that can fit into the active site of the enzyme can combine with the enzyme to form an enzyme-substrate complex. When an enzyme-substrate complex is formed, some bonds are broken within the substrate and the shape of the substrate molecule become slightly distorted. This distortion lowers the activation of energy of the reaction. Once old bonds are broken and new bonds are formed, the resulting product will have a different shape and structure. This will cause the product to be released from the enzyme molecule leaving the enzyme to reattach itself to another substrate molecule. **Induced Fit Mechanism** The induced fit mechanism suggested by Koshland in 1959 is a modified version of the lock and key model. The active site in an enzyme molecule is not rigid but is flexible. The shape of the active site is not exactly complementary to the substrate. The binding of the substrate induces the enzyme to change its shape slightly leading to a better fit between its active site and the substrate. There is also a slight alteration to the shape of the substrate. The products that are formed move away from the enzyme and the enzyme is free to catalyze the reaction of another substrate molecule. LESSON 2: Cell Theory **What is a cell?** The cell is the smallest structural unit of an organism that is capable of independent functioning. Classical Cell Theory *The three postulates of the cell theory are the following:* 1\. The cell is the basic structural and functional unit of all living organisms. 2\. All living organisms (plants and animals) are made up of cells. 3\. All cells arise from pre-existing cells. Origin of the Cell Theory **Zacharias Janssen and Hans Lippershey (1590s)** \* contributors on the discovery of the cell \* known for their invention the compound optical microscope \* the microscope invented by Janssen and Hans was used by *Robert Hooke*, the earliest scientist to study living things under a microscope. **Robert Hooke (1665)** \* made an important discovery under a compound optical microscope \* looked at a thin slice of cork under his microscope \* saw tiny little shapes that looked like little rooms with walls around each of them and named them *cellulae* which is Latin for \"little rooms\" **Anton van Leeuwenhoek (1674)** \* became the first to observe live cells of human and bacteria \* he invented a microscope with improved lenses that could magnify objects from 270 to 300-fold **Matthias Jakob Schleiden (1838)** first to state that cells are the building blocks of all plants and that an embryonic plant arose from one single cell **Theodor Schwann (1839)** stated that cells are the fundamental units of animals too **Rudolf Virchow (1855)** stated in German \'Omnis cellula e cellula\' which means that new cells come from already existing cells Modern Cell Theory *Four postulates were added to form the modern cell theory:* 1\. Cells contain genetic material (DNA) which is passed on to new cells during cell division. 2\. All cells are similar in their chemical composition. 3\. All energy flow occurs within the cell. 4\. Activities of the organisms are a result of combined actions of individual cells. LESSON 3: Prokaryotic and Eukaryotic Cells **Prokaryotes** Prokaryotes, (pro - before; karyon - nucleus) are *single-celled* organisms and the earliest and most primitive forms of life on earth. They comprise *archaebacteria* and *bacteria.* They can be found almost everywhere and are part of the human microbiota. They live on your skin, in your body, in your environment, and on everyday objects. Examples: \* Cyanobacteria - photosynthetic bacteria (also known as \* blue-green algae) \* Escherichia coli - commonly found in the lower intestine \* Thermus aquaticus - can withstand extreme temperatures **Outer Structure:** \- enclosed by a slimy **capsule** which helps them to cling to each other and prevents them from drying out \- have a **cell** **wall** made of **peptidoglycan** (except in archaebacteria) \- have a **single** **compartment** enclosed by a plasma membrane **Appendages:** \- many prokaryotes have a **flagellum** (pl. **flagella**). It is a tail-like structure that they use for **motility** (cell movement) \- they **do not have cilia**, but they have a **pilus** (pl. **pili**) which are hair-like protrusions that comes in several types with each having different roles: \* **Attachment pilus** (short), also known as **fimbria** (pl. **fimbriae**), allow them to stick to surfaces \* **Sex pilus** (long) holds the two bacteria together during sexual reproduction (**conjugation**) **Inner Structure:** \- have **no membrane-bound organelles** (all the cell components are not separated from each other) \- have **no real nucleus**; their DNA is found in a region called the **nucleoid** \- have one circular chromosome composed of DNA but **not associated with histones**, but some bacteria **have** **plasmids** (small loops of DNA that are separate from the chromosomal DNA) Reproduction/Cell Division: \- they reproduce either through **binary fission (asexual)**, or **conjugation (sexual):** \* **Binary fission** - the formation of two daughter cells from a parent cell. \* **Conjugation** - DNA is transferred between prokaryotes by means of a pilus. **Eukaryotes** Eukaryotes, (eu - true; karyon - nucleus) can either be *unicellular (protists/protozoa)* or *multicellular organisms (fungi, plants, animals)*. The most distinguishing characteristic of eukaryotes is the compartmentalization (membrane-bound) of the organelles in their cells. **Outer Structure:** \- **cell walls** are found in plants (cellulose), and fungi (chitin), while animals and protozoans lack cell walls. \- all eukaryotes **have a plasma membrane** **Appendages:** \- may have **flagellum** or **cilium** (pl. **cilia**), which is a membrane-bound thread-like protrusion that extends from the surface of the eukaryotic cell **Inner Structure:** \- have **membrane-bound organelles** \- have a **true nucleus** bounded by a double membrane and containing a nucleoli \- has one or **more paired, linear chromosome** composed of **DNA** associated with **histones** \- **no plasmids** Reproduction/Cell Division: \- cells divide either through mitosis **(asexual) or meiosis (sexual)**