CH2 CHEM PT 6 - Nucleic Acids and ATP Vocabulary flashcards -

Nucleic Acids and ATP: Structure, Function, and Energy

• Topics covered: nucleic acids (DNA and RNA) and cellular energy in the form of ATP.
• Visual aid described: a segment of DNA represented as a ladder with backbones and rungs.

DNA: structure and components

• DNA stands for deoxyribonucleic acid.
• Backbone composition: alternating phosphates (P) and sugars (deoxyribose). The backbone forms the sides of the ladder in a double helix.
• Rungs of the ladder: nitrogen bases. The four bases are guanine (G), cytosine (C), thymine (T), and adenine (A).
• Base-pairing rules in DNA:
  • Adenine pairs with thymine (A–T).
  • Cytosine pairs with guanine (C–G).
  • This pairing creates the ladder-like structure with complementary strands.
• A nucleotide is the basic unit of DNA consisting of a phosphate, a sugar (deoxyribose), and a nitrogen base. DNA is made up of a series of nucleotides.
• RNA differs from DNA in three main ways (see below).

Nucleotides and bases

• Nucleotides: phosphate + sugar + nitrogen base.
• DNA bases: G, C, T, A.
• RNA bases: G, C, A, and uracil (U) instead of thymine; RNA uses ribose instead of deoxyribose.
• Importance of sugar type and strand structure:
  • DNA: deoxyribose, double-stranded.
  • RNA: ribose, single-stranded; thymine is replaced by uracil.
• Example model details (from the class model):
  • The white parts of the model represent sugar; the black parts represent phosphate.
  • The rungs (colored pairs) represent base pairs: thymine–adenine (e.g., orange with red) or cytosine–guanine (e.g., blue with green).
  • A base pair rule: red is never with orange; blue is never with green (a visual cue aligning to A–T and C–G pairing).

DNA as a double helix and its function

• DNA is a very long molecule that forms a double helix, not a straight ladder.
• The helix has two long sugar–phosphate backbones and the rungs are base pairs.
• Function of DNA: to code for the body’s proteins.
• DNA coding regions are read as triplets (three bases at a time). Example triplets on one strand: GTT, AGC, CCG, etc. Each triplet codes for a specific amino acid.
• Some triplets are explicitly mapped in the transcript example:
  • GTT codes for the amino acid glutamine (as given in the transcript).
  • AGC codes for the amino acid serine.
  • CCG codes for the amino acid glycine.
• A codon (triplet) corresponds to one amino acid; multiple triplets along DNA code for a sequence of amino acids, forming a protein.
• The central dogma (as presented): DNA is copied into RNA, and RNA is used to make protein.
• In a typical human cell:
  • There are 46 chromosomes (the transcript says 46 strands of DNA inside the nucleus).
  • The human genome codes for over more than 20,000 different proteins.

How DNA codes for proteins: transcription and translation (central dogma in action)

• DNA contains the code for amino acids, which are the building blocks of proteins.
• The code in DNA is transcribed into RNA, which then carries the code to the site of protein synthesis.
• An RNA copy is complementary to the DNA sequence it was transcribed from.
• RNA (specifically mRNA) is used to assemble amino acids into a protein at the ribosome.
• Proteins include structural proteins (e.g., collagen), enzymes, hemoglobin, and many hormones.
• Start/stop signals: the body uses start codons to indicate where a protein-coding sequence begins and stop codons to indicate where it ends; the transcript notes that there are signals that mark the beginning and end of the coding region.
• The significance of the 3-base code: three nucleotides (a triplet) code for one amino acid, which then links together to form a protein.
• Why this matters: the sequence of amino acids (the primary structure) determines how the protein will fold and function.
• If a base is mutated (e.g., a sun-induced mutation changing one base), the triplet changes, potentially altering the amino acid and folding, which can disrupt protein function. Example discussed: a mutation affecting hemoglobin can lead to sickle cell disease when red blood cells sickle under low oxygen.
• Mutations and inheritance: if such a mutation exists in germ cells (egg or sperm), it can be passed to offspring, potentially transmitting a faulty protein and disease.
• Practical points:
  • A few triplets map to specific amino acids; the examples given (GTT → glutamine, AGC → serine, CCG → glycine) illustrate the concept that triplets code for amino acids rather than representing amino acids themselves.
  • The number of amino acids in a protein is determined by how many triplets are present; for example, 300 bases could encode 100 amino acids (since 300 / 3 = 100).
• Protein complexity: some proteins have primary structures that lead to folding into complex three-dimensional shapes; function depends on proper folding.
• Hemoglobin example highlights quaternary structure (four protein subunits) and how mutations in DNA can affect the structure and function of a protein that has crucial biological roles (like oxygen transport).

Summary of DNA’s significance and the protein code

• DNA holds the recipe for assembling amino acids into proteins.
• The triplet code within DNA (and its RNA complement) determines the sequence of amino acids and thereby the primary structure of proteins.
• Proper DNA coding and protein folding are essential for normal physiology; mutations can lead to diseases and can be inherited.
• The central dogma connects DNA to RNA to protein, with RNA acting as the messenger and translator of genetic information.

Extra: a note on numbers and genetics mentioned in the transcript

• Chromosome count/ DNA strands in nucleus mentioned as 46 strands (note: in human cells this corresponds to 23 pairs of chromosomes in diploid cells; transcription uses this as a teaching simplification).
• The genome codes for over 20,000 proteins.

ATP: the usable energy currency of the cell

• ATP stands for adenosine triphosphate.
• Structure of ATP: an adenosine moiety (adenine + ribose) connected to a triphosphate group; the bond between the second and third phosphate (the triphosphate tail) stores a large amount of energy.
• Usable energy in ATP is stored in the high-energy phosphate bond between the last two phosphates of the tail.
• ATP hydrolysis releases energy: the hydrolysis of ATP to ADP and P releases energy that cells use to power cellular processes.
  • Simplified reaction (per transcript):
    ext{ATP}
    ightarrow ext{ADP} + ext{P} + ext{energy}
  • This is an exergonic reaction (energy is released).
• ATPase enzymes can catalyze the hydrolysis of the terminal phosphate bond.
• The energy from ATP is used to power various cellular processes, including ion pumps that move ions across membranes and, more broadly, muscle contraction.
• Reversibility: the breakdown is reversible. The cell can re-synthesize ATP from ADP and P using energy from nutrients (dehydration synthesis in the reverse direction):
  ext{ADP} + ext{P} + ext{energy}
  ightarrow ext{ATP} + ext{H}_2 ext{O}
• Where does the energy come from to re-form ATP? From nutrients in the diet; energy-rich molecules like glucose store energy that can be converted into ATP.
• The energy currency concept: glucose contains energy in chemical bonds but cannot be used directly by cells to do work; it must be converted to ATP. This conversion is accomplished through cellular respiration, a series of reactions that break glucose with the help of oxygen to yield ATP, carbon dioxide, and water.
• Cellular respiration (as described in the transcript):
  • Overall reaction: ext{Glucose} + ext{O}2 ightarrow ext{CO}2 + ext{H}_2 ext{O} + ext{ATP} + ext{heat}.
  • Glucose is a monosaccharide; oxygen is required; this process captures energy from glucose in the form of ATP.
  • The complete process yields about 36 ext{ or } 38 ext{ ATP} per molecule of glucose, depending on counting methods.
• Analogy used to illustrate energy transfer: bringing currency into a store (e.g., Mexican pesos vs. dollars) to buy goods. Glucose has energy, but it must be converted to ATP (the usable currency) before it can be used for energy-demanding tasks.
• Practical implications: ATP is essential for all cellular processes; a muscle contraction example (e.g., bending the elbow) uses ATP; energy is required for many activities such as pumping ions and moving molecules across membranes.
• Core takeaway objectives for this unit:
  • Understand the structure and significance of DNA and its role in coding for proteins.
  • Understand the role of ATP as the usable energy currency and how energy flows from food (glucose) to ATP via cellular respiration.
  • Recognize the central dogma and the connection between DNA, RNA, and protein synthesis.