BIO Final Exam (2) PDF

Five fundamental characteristics of all living organisms 1. Everything is made up of cells 2. replication/reproduction = GOAL of organisms 3. Process information (read genes) 4. Must acquire and use energy (ATP) 5. All are products of evolution Hierarchy of Life (including defini...

Five fundamental characteristics of all living organisms 1. Everything is made up of cells 2. replication/reproduction = GOAL of organisms 3. Process information (read genes) 4. Must acquire and use energy (ATP) 5. All are products of evolution Hierarchy of Life (including definition, function, location) - From smallest to biggest: - Atom - molecule - macromolecule - organelle - cell - tissue - organ - organ system - organism - population - community - ecosystem - biosphere Definitions - Atom- the smallest identifiable unit of matter - Molecule- a substance made up of two or more atoms held together by covalent bonds - Macromolecules- large, complex molecules that are essential for life. They are made up of smaller molecular subunits called monomers, which are bonded together to form polymers organelle - specialized structures within eukaryotic cells that perform distinct functions - Cell- membrane bound units that are the fundamental structural and functional unit of life - Tissue- a group of cells that function as a unit. These cells are specialized and work together to perform a specific function - Organ- - Organ system- Organ systems are groups of organs that work together to perform one or more functions - Organism- - Population- - Community- - Ecosystem- - Biosphere- Organ Systems - Endocrine- hormone production (thyroid, pituitary, and adrenal) - Lymphatic/immune- helps keep body fluid levels balance and defends the body against infections (white blood cells, thymus, bone marrow) - Respiratory- absorption of oxygen and discharge of carbon dioxide (nose, lungs, bronchi) - Reproductive- to reproduce (uterus, ovaries, fallopian tubes) - Cardiovascular- distribution of nutrients, oxygen, wastes, hormones, electrolytes, etc. (heart, blood vessels) - Digestive- nutrient breakdown and absorption (mouth, pharynx, esophagus, stomach, intestines, liver, gallbladder) - Urinary-waste elimination (kidneys and bladder) - Skeletal- support, movement, and protection; blood formation (bones, cartilage, ligaments - Muscular- responsible for movement and stability (muscles) - Nervous- rapid internal communication, coordination, and motor control (brain, spinal cord, nerves) - 2 kinds of nervous system (central and peripheral)  - Central: includes brain and spinal cord - Peripheral: consists of the nerves that come from the brain and spine - Integumentary- protects against damage (skin, hair, nails) Functional groups (6)- groups found in organic compounds - Many molecules that contain carbon bonded to other elements, such as hydrogen, are called organic compounds - In general, the carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape. But the chemical behavior of the compound—meaning the types of reactions that it participates in—is dictated by groups of H, N, O, P, or S atoms that are bonded to one of the carbon atoms in a specific way - Amino- acts as a base; attracts protons (contains Nitrogen) - Carboxyl- acts as an acid; tends to lose protons (contains COOH-) - Carbonyl- have sites that link molecules into more-complex compounds (contains C=O - found on molecules such as acetaldehyde and acetone - Hydroxyl - act as weak acids; highly polar and makes compounds more soluble through hydrogen bonding with water (contains OH-) - Phosphate- have two negative charges; help store lots of chemical energy (contains P with oxygens around it) - Sulfhydryl- form disulfide bonds that help contribute to protein structure (contains S—S) DNA/RNA Overall Structures DNA ○ deoxyribonucleic acid is a molecule that contains the genetic code that is unique to every individual and is responsible for making all the proteins that form our bodies ○ The information coded in DNA is hereditary meaning that it passes from parent to child. ○ Double helix  ○ DNA and other nucleic acids are polymers of nucleotides Each nucleotide consists of: One sugar—deoxyribose One phosphate group One nitrogenous base ○ Found in the nucleus ○ Bases are Purines and pyrimidines Purine: double ring (Pure As Gold) (adenine, guanine) Pyrimidines: single ring (Cut The Pie) (thymine, cytosine) ○ 46 DNA molecules in the nucleus of most human cells ○ Total length of 2 meters Average DNA molecule 2 inches long ○ Made up of sugar and phosphate backbone Deoxyribose (5 carbon sugar) Phosphate group ○ 2 hydrogen bonds between Adenine and thymine ○ 3 hydrogen bonds between guanine and cytosine RNA ○ Ribonucleic acid (RNA) is a molecule that is present in the majority of living organisms and viruses. ○ It is made up of nucleotides Nucleotides consist of 1. ribose sugars (has an OH group deoxyribose lacks) 2. phosphate groups 3. attached to nitrogenous bases ○ The nitrogenous bases include adenine, guanine, uracil, and cytosine. ○ Single helix ○ Smaller than DNA ○ In cytoplasm ○ Three different types mRNA Transmits genetic information from DNA to the ribosome, where proteins are synthesized. Single-stranded and carries codons that specify amino acids. Exons—“sense” portions of the immature RNA ○ Will be translated to protein Introns—“nonsense” portions of the immature RNA ○ Must be removed before translation tRNA Brings amino acids to the ribosome during protein synthesis. tRNA has an L-shaped tertiary structure with two crucial ends:  ○ Anticodon End: Contains a three-base anticodon that pairs with the complementary mRNA codon. ○ Amino Acid Attachment Site: Located at the 3' end, where the specific amino acid is attached. rRNA Forms the core of the ribosome's structure and catalyzes protein synthesis. Combines with proteins to form ribosomes. DNA Replication Before a cell divides, it must duplicate its DNA so it can give a complete copy of all its genes to each daughter cell; Since DNA controls all cellular function, this replication process must be very exact Law of complementary base pairing—we can predict the base sequence of one DNA strand if we know the sequence of the other ○ Enables a cell to reproduce one strand based on the information in another Enzymes Involved ○ DNA Helicase an enzyme that functions by melting the hydrogen bonds that hold the DNA into the double helix structure. The area of the DNA where the DNA helicase has unzipped the DNA is known as a replication fork. Replication fork- a Y-shaped structure where a DNA double helix splits into two strands for copying ○ DNA polymerase does make mistakes Multiple modes for correction of replication errors Double checks the new base pair and tends to replace incorrect, biochemically unstable pairs with more stable correct pairs Result is only one error per 1 billion bases replicated DNA polymerase is a crucial enzyme in DNA replication. Its primary function is to add deoxyribonucleotides to the 3′ end of a newly forming DNA strand, ensuring the accurate copying of the DNA template. This process occurs in the 5′ to 3′ direction. ○ DNA ligase an enzyme that joins together DNA fragments by forming a phosphodiester bond between the 5' phosphate group of one fragment and the 3' hydroxyl group of another, playing a crucial role in DNA replication and repair processes within cells essentially, it acts like a "molecular glue" to seal breaks in the DNA strand Okazaki fragments ○ short pieces of DNA synthesized discontinuously on the lagging strand during DNA replication, essentially forming small segments that are later joined together to create a continuous strand; they are named after the scientists who discovered them, Reiji and Tsuneko Okazaki Transcription and translation (DNA → RNA → Protein)  Transcription ○ The process by which a cell makes an RNA copy from a segment of DNA ○ RNA copy, called messenger RNA (mRNA), carries the genetic information needed to make proteins in a cell. It carries the information from the DNA in the nucleus of the cell to the cytoplasm, where proteins are made ○ Occurs in nucleus ○ RNA polymerase —enzyme that binds to the DNA and assembles the mRNA Base sequences TATATA or TATAAA inform the polymerase where to begin RNA polymerase opens up the DNA helix about 17 base pairs at a time RNA polymerase rewinds the DNA helix behind it Gene can be transcribed by several polymerase molecules at once Terminator: base sequence at the end of a gene which signals polymerase to stop ○ Pre-mRNA—immature RNA produced by transcription that includes both introns and exons Exons—“sense” portions of the immature RNA Will be translated to protein Introns—“nonsense” portions of the immature RNA Must be removed before translation ○ Alternative splicing—removing the introns by enzymes and splicing the exons together into a functional RNA molecule One gene can code for more than one protein Translation ○ the process that converts the language of nucleotides into the language of amino acids' ○ Ribosomes—translate sequence of nucleotides into the sequence of amino acids Consists of two granular subunits, large and small Each made of several rRNA and enzyme molecules ○ Happens in cytoplasm Occur mainly in cytosol, on surface of rough ER, and nuclear envelope ○ mRNA molecule begins with leader sequence Acts as binding site for small ribosomal subunit Large subunit attaches to small subunit Ribosome pulls mRNA molecule through it like a ribbon, reading the bases as it goes When start codon (AUG) is reached, protein synthesis begins All proteins begin with methionine when first synthesized ○ Each tRNA picks up specific amino acids from pool of free amino acids in cytosol One ATP molecule is used to bind amino acid to site on tRNA Provides energy for peptide bond formation ○ Large ribosomal subunit contains an enzyme that forms peptide bond that links amino acids together First tRNA released from ribosome Second tRNA temporarily anchors growing peptide chain Ribosome shifts and third tRNA brings its amino acid to the site ○ Codon A codon is a mRNA sequence of three nucleotides (a trinucleotide) that forms a unit of genomic information encoding a particular amino acid. Start codon= AUG Stop codon= UAG,UGA, UAA The genetic code consists of 64 codons, 61 of which specify amino acids, and 3 are stop codons. The code is nearly universal and redundant, meaning multiple codons can code for the same amino acid. 20 amino acids correspond with all 64 codons ○ Anticodon a sequence of three nucleotides located on a transfer RNA (tRNA) molecule that is complementary to a specific codon on a messenger RNA (mRNA) strand, allowing the tRNA to bring the correct amino acid to the growing polypeptide chain during protein synthesis (translation) Examples UUC: The anticodon for the amino acid lysine, whose codon is AAG UUU: The anticodon for the amino acid lysine, whose codon is AAA  Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution ○ Four types of atoms make up 96% of matter in organisms—Hydrogen, carbon, nitrogen, and oxygen ○ C, H, N, O, P and S make up over 99% of atoms in body Basic Atomic Structure ○ Nucleus made up of protons and neutrons: Protons—positive charge (+1) Neutrons—neutral charge ○ Surrounded by orbiting electrons: Negative charge ○ Atom with equal number of protons and electrons: Charges balance Electrically neutral ○ Elements: Consist entirely of a single type of atom ○ Atomic number: Characteristic number of protons in nucleus of any atom Written as subscript left of its symbol ○ Mass number: Sum of protons and neutrons in atom ○ Number of protons in element does not vary but neutrons in element may vary Forms element with different numbers of neutrons (isotope): Isotopes of element have different masses ○ Example: All carbon atoms have 6 protons: ○ Carbon-12 has 6 neutrons; atomic mass 12 D a ○ Carbon-13 has 7 neutrons; atomic mass 13 D a ○ Carbon 14 has 8 neutrons; atomic mass 14 D a ○ Atomic weight of element—Average of all masses of naturally occurring isotopes based on their abundance Example: Atomic weight of carbon is 12.01 since carbon-12 is most abundant isotope ○ Radioactive isotopes—Unstable isotopes that decay over time ○ Electron shells Each electron shell contains specific number of orbitals Electron shell comprising single orbital can hold up to two electrons Shell with four orbitals can contain up to eight electrons ○ Electrons of an atom fill innermost shells first, then fill outer shells ○ Outermost shells of elements Atom’s valence shell is outermost shell  Electrons in this shell called valence electrons Number of unpaired valence electrons is called the valence of an atom ○ Different atoms have different numbers of unpaired electrons ○ Atoms most stable when their valence shells are full Shells can be filled by formation of chemical bonds—Attractions that bind atoms together Covalent bonds form when unpaired valence electrons are shared by two atoms Connected atoms termed molecule Polar and nonpolar covalent bonds ○ Electrons in covalent bond not always shared equally Compounds are molecules in which atoms of different elements are bonded together Pull shared electrons toward their nuclei with varying strengths (electronegativity) ○ Electronegativity— Strength with which atoms pull electrons toward themselves Atom’s electronegativity determined by: Number of protons Distance of valence shell from nucleus ○ Moving up and to the right on periodic table electronegativity O > N > S,C,H,P ○ Nonpolar covalent bond: Electrons are evenly shared between two atoms Bond is symmetrical Example: H2 ○ Polar covalent bond: Electrons are shared unevenly (asymmetrical) Electrons in polar covalent bonds spend most of their time close to nucleus of more electronegative atom Example: H2O Ionic Bonds and Bonding ○ Unlink covalent bond, electron is not shared; it is completely transferred from one atom to another Transfer gives each atom a full valence shell ○ Ions—atom or molecule that carries charge: Cation—Atom loses electron and becomes positively charged Anion—Atom gains an electron and becomes negatively charged pH and buffer Role of water in acid/base- ○ Acids- Substances that give up protons during chemical reactions and raise the hydrogen ion concentration of water (H+ increases) ○ Bases substances that acquire protons during chemical reactions and lower the hydrogen ion concentration of water (OH- increases)  (H+ + OH- ->