BIO105 Final Review Practice Flashcards

BIO105 Final Review: Assignment Parameters and Introductory Chemistry

The documentation presented here serves as the exhaustive study guide and final review for BIO105, authored by Manama Lopez. This specific assignment is designated as extra credit, with a firm submission deadline established for May 13th at 9:00am. In pursuit of a successful semester, the requirements for this assignment are stringent: every blank must be populated, as points are exclusively awarded to submissions that are 100% complete. No late submissions are permitted under any circumstances.

The chemical foundations of life begins with the structure of the atom. Atoms are composed of subatomic particles including positively charged protons and neutrally charged neutrons, both of which are localized within the nucleus. Negatively charged electrons are found orbiting the nucleus within valence shells. The innermost valence shell reaches capacity at 2 electrons, while the outermost shells may contain up to 8 electrons.

Chemical bonds are categorized by their methods of formation and strength. Ionic bonds result from the weak attraction between a positively charged ion and a negatively charged ion; these bonds are characterized by their tendency to break easily when molecules are introduced to water. Covalent bonds are formed when electrons are shared between molecules to fill their outer valence shells. If electrons are shared equally, the bond is nonpolar; if shared unequally, the bond is polar. Within the context of proteins, these bonds are identified as peptide bonds, which are critical in establishing the primary structure. They also facilitate the connection between the sugar and phosphate molecules in DNA and RNA.

Hydrogen bonds play a vital role in molecular stability and structure. In a strand of DNA, hydrogen bonds form between the nucleotides, causing the molecule to twist into its characteristic double helix. Within a singular molecule of water, polar covalent bonds exist between the hydrogen and oxygen atoms. However, hydrogen bonds are the forces that exist between multiple different molecules of water. These interactions are possible because the hydrogen atoms possess a positive charge while the oxygen atom possesses a negative charge.

Chemical Reactions and the Four Classes of Macromolecules

Chemical reactions categorized by the role of water include hydrolysis and dehydration synthesis. A hydrolysis reaction describes a process where water is utilized to break a larger molecule into smaller components; in this instance, the reactants are larger than the products. Conversely, a dehydration reaction involves the removal of water to join two molecules together, resulting in products that are larger than the initial reactants.

Macromolecules are divided into four primary categories: proteins, carbohydrates, triglycerides (lipids), and nucleic acids. Triglycerides are composed of a single glycerol molecule bound to 3 fatty acids and can exist in both saturated and unsaturated forms. Nucleic acids include essential biological molecules such as DNA, RNA, and ATP. Carbohydrates include simple forms like monosaccharides and can be converted into glycogen for long-term storage within the body.

Proteins are a diverse group of macromolecules composed of amino acids linked by peptide bonds. They include enzymes, which act as biological catalysts. Proteins can be denatured into their constituent amino acids under certain environmental conditions. Their primary structure is defined simply as an amino acid chain.

Protein Hierarchy and the Mechanics of Enzymatic Catalysis

Protein structure is organized into four distinct levels of complexity. The primary protein structure is a string of amino acids linked by peptide bonds, a process facilitated by the ribosome. The secondary protein structure occurs when hydrogen bonds fold the protein into specific shapes such as alpha helices and beta pleated sheets. The tertiary protein structure represents the final 3-dimensional configuration of the protein. Finally, the quaternary protein structure involves the binding of several distinct protein subunits into a single, larger protein complex.

Enzymes are specialized proteins that are essential for life. Contrary to being non-specific, enzymes are highly specific to certain substrates and will only bind to the molecules they are designed to process. Their primary functions are to increase the speed of chemical reactions and to catalyze them while reducing the total amount of energy required for the reaction to proceed. Enzymes are not used up by the reactions they facilitate; they can be reused repeatedly. However, if an enzyme is denatured, it loses its functional shape and will stop working. Although they are macromolecules, they belong strictly to the protein group, not the carbohydrate group.

Cellular Form, Function, and Organelle Specialization

The cell is composed of various organelles, each with specialized functions. The nucleus serves as the site of transcription and houses the cell's DNA. The cytoplasm is a gel-like substance that fills the cell and provides an environment for the organelles. The cell membrane is composed of a phospholipid bilayer and acts as a selective barrier. The mitochondria are responsible for the synthesis of ATP from glucose to provide cellular energy.

Endoplasmic reticulum (ER) comes in two forms: rough ER is a studded membranous organelle that assembles proteins, while smooth ER acts as a storage site for intracellular lipids, cholesterol, and calcium. Ribosomes assemble the primary protein structures from mRNA. The Golgi complex is responsible for packaging and modifying proteins for transport out of the cell. Lysosomes are vesicles filled with hydrolytic enzymes used for digestion, and the general term for structures used to spill contents into extracellular fluid is exocytosis.

Dynamics of Membrane Transport, Osmosis, and Tonicity

Membrane transport is the movement of molecules into and out of the cell. Diffusion is defined as the movement of molecules from an area of high concentration to an area of low concentration. The rate of diffusion can be increased by several factors: an increase in temperature, an increase in the concentration gradient, or an increase in the permeability of the membrane. Conversely, increasing the size of the diffusing molecule typically decreases the rate of diffusion.

There are four primary types of membrane transport. Simple diffusion is a passive process used by small nonpolar molecules like oxygen ($O_2$) and carbon dioxide ($CO_2$). Facilitated diffusion is also a passive process that utilizes membrane proteins to move substances such as glucose and various ions. Carrier-mediated transport is a process that can be either active or passive, used typically for sodium ($Na^+$), potassium ($K^+$), and other ions. Vesicular transport is an active process used to move large molecules and proteins across the membrane.

Osmosis is the specific movement of water across a selectively permeable membrane, moving from an area of low solute concentration to high solute concentration. The tonicity of a cell's environment affects its volume. In a hypertonic environment (e.g., 20% $NaCl$ outside vs 10% $NaCl$ inside), the cell volume decreases. In a hypotonic environment (e.g., 0% $NaCl$ outside vs 10% $NaCl$ inside), the cell volume increases as water enters. In an isotonic environment (e.g., 10% $NaCl$ outside and inside), there is no change in cell volume.

Genes, Nuclear Functions, and Cellular Respiration

DNA molecules are double-stranded helices composed of sugar-phosphate backbones and four types of nucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G). The process of converting DNA into mRNA is known as transcription, which takes place within the nucleus. Complementary DNA strands are formed by matching base pairs (A with T, C with G). For a template strand sequence of TAC CCA CGA GAT TTG GTA, the complementary strand is ATG GGT GCT CTA AAC CAT. Translation subsequently occurs at the ribosomes to form the primary structure of proteins.

Cellular respiration is the process of creating ATP for the cell, consisting of three sequential stages: Glycolysis, the Kreb's Cycle, and the Electron Transport Chain. Glycolysis begins with one molecule of glucose. If oxygen is present ($O_2$), the Kreb's Cycle follows. If oxygen is absent, the body undergoes lactic acid fermentation, which only produces an additional 2 molecules of ATP. The final products of cellular respiration include ATP and carbon dioxide ($CO_2$), the latter of which is eliminated via the respiratory system.

Histology: Epithelial and Connective Tissues

Epithelial tissues are classified by their layering and cell shape. A single layer is called simple epithelium, while multiple layers are stratified epithelium. Pseudostratified epithelium appears to have multiple layers but every cell reaches the basement membrane. Transitional epithelium (urothelium) lines the bladder and can stretch, appearing simple when full and stratified when empty. Cell shapes include squamous (flat), cuboidal (round or square), and columnar (rectangular).

Connective tissues are diverse in structure and function. Spongy bone is composed of trabeculae and spicules, while compact bone is composed of osteons and osteocytes. Areolar tissue is a loose tissue containing elastic, reticular, and collagen fibers. Dense connective tissue forms tendons and ligaments. Blood is a unique connective tissue containing red blood cells, white blood cells, and platelets. Cartilage contains chondrocytes housed within the lacuna. Adipose tissue is composed of adipocytes for fat storage.

Physiology of Muscular and Nervous Systems

Muscle tissue's primary function is moving the body, while nervous tissue is responsible for generating electrical impulses. In skeletal muscle, contraction requires the presence of ATP and the calcium ion ($Ca^{2+}$). The sarcomere contains thick myofilaments known as myosin and thin myofilaments known as actin. Shortening of the sarcomere occurs when actin binds to myosin.

The Central Nervous System (CNS) consists of the brain and spinal cord, whereas the Autonomic Nervous System (ANS) is divided into the Sympathetic and Parasympathetic branches. Neurons use the axon to send signals. For an action potential to fire, the membrane voltage must reach a specific threshold. The resting membrane potential of a neuron is $-70\,mV$. Depolarization occurs as the voltage becomes more positive due to sodium ($Na^+$) ions entering the cell. Repolarization happens when sodium channels close and potassium ($K^+$) channels open. The sodium-potassium ATPase pump restores balance by moving ions against their gradients.

The parasympathetic system is identified as the "rest and digest" system, using the neurotransmitter acetylcholine (though some sources mention varying signals). The sympathetic system is the "fight and flight" system, utilizing norepinephrine and epinephrine as chemical signals.

Neuroanatomy and Sensory Organs

The brain is divided into various lobes and regions. The cerebellum maintains balance and coordination. The cerebrum includes the frontal lobe (higher order mental function, decision making), parietal lobe, temporal lobe (auditory processing), and occipital lobe (visual processing). The hypothalamus regulates hunger, thirst, and temperature. The corpus callosum allows communication between the right and left hemispheres. Grey matter consists of cell bodies and dendrites, while white matter is composed mostly of myelinated axons.

Sensory organs like the eye and ear involve complex structures. In the eye, the sclera is the white part, the cornea is the clear covering, and the iris is the colored part that contracts in response to light. The pupil is the opening where light enters, which then passes through the lens to be focused on the retina, where photoreceptors (rods and cones) reside. The blind spot is where the optic nerve meets the retina. In the ear, the tympanic membrane vibrates in response to sound, passing vibrations to the ossicles and eventually the cochlea, which communicates auditory information to the nerve.

Cardiovascular, Respiratory, and Digestive Systems

Arteries carry blood away from the heart, while veins carry it toward the heart. The right side of the heart pumps to the lungs; the left side pumps to the systemic circuit. Upper chambers are atria, and lower are ventricles. The tricuspid valve is on the right, and the bicuspid (mitral) is on the left. Atrioventricular (AV) valves sit between atria and ventricles, while semilunar valves (aortic and pulmonary) sit between ventricles and arteries. Gas exchange occurs in the capillaries. Heart contraction is initiated by the sinoatrial (SA) node; contraction is termed systole and relaxation is diastole. Oxygen is transported via hemoglobin in red blood cells.

External respiration is gas exchange between the lungs and blood, while internal respiration occurs between the blood and tissues. Inspiration involves the diaphragm, external intercostals, and scalenes. Forced expiration uses internal intercostals and abdominal muscles. The trachea is lined with ciliated pseudostratified columnar epithelium and supported by C-shaped hyaline cartilage rings.

The digestive system involves the esophagus (transport), stomach (acid and protein digestion), small intestine (absorption), and colon (water absorption). The liver synthesizes bile, while the gallbladder stores it. The pancreas releases enzymes and hormones like insulin and glucagon. The pharynx is superior to the esophagus, and the epiglottis prevents food from entering the trachea.

The Urinary, Endocrine, and Reproductive Systems

The kidney consists of the renal cortex (outer) and renal medulla (inner, containing pyramids). Urine flows through the renal pelvis, ureters, bladder (composed of detrusor muscle), and finally the urethra. The external urethral sphincter is voluntary, while the internal is involuntary. The nephron processes include filtration (at the glomerulus/capsule), reabsorption, and secretion. The order of the nephron segments is the proximal convoluted tubule, nephron loop, distal convoluted tubule, and collecting duct.

Hormones regulate body functions: Growth hormone ($GH$) stimulates mitosis; insulin decreases blood sugar while glucagon increases it; parathyroid hormone ($PTH$) increases calcium via osteoclast action; calcitonin decreases calcium via osteoblasts. Aldosterone promotes sodium reabsorption, while atrial natriuretic hormone ($ANH$) promotes sodium excretion. Endocrine glands are made of epithelial tissue. Diabetes mellitus is characterized by uncontrolled high blood sugar; Type 1 involves a lack of insulin production, while Type 2 is characterized by insulin resistance. Gigantism occurs before growth plates close, and acromegaly occurs after.

In the male reproductive system, sperm mature in the epididymis and travel through the vas deferens. Leydig cells produce testosterone, while Sertoli cells support sperm production. Seminal vesicles and the prostate gland secrete alkaline fluids for the semen. In the female system, the uterus houses the embryo, with the endometrium being the layer lost during menstruation and the myometrium being the muscle layer. Fertilization typically occurs in the fallopian tubes. The cervix is the opening superior to the vaginal canal. External genitalia include the labia majora, labia minora, and clitoris.