BIO202 Exam 1 lec 1-3

sbu lec 1 - lec 3

What are the three subatomic particles and their charges?

Protons: +1 charge, Neutrons: 0 charge (neutral), Electrons: -1 charge

What is atomic number?

The number of protons in an atom's nucleus (also equals the number of electrons in a neutral atom)

What is mass number?

The sum of protons + neutrons in an atom's nucleus

What are isotopes?

Atoms of the same element with the same number of protons but different numbers of neutrons (different mass)

What is a radioactive isotope? Give an example.

An isotope that decays by releasing particles. Example: Carbon-14 (¹⁴C) has a half-life of 5,715 years and decays to Nitrogen-14

What are 4 uses of radioactive isotopes in biology?

1. Determining age of samples, 2. Cytotoxic agents (cancer treatment), 3. Inducing mutations in DNA, 4. Biological tracers (labeling molecules)

What is a covalent bond?

A bond formed by the sharing of electron pairs between atoms

What is the difference between polar and nonpolar covalent bonds?

Polar: unequal sharing of electrons (electrons pulled toward more electronegative atom); Nonpolar: equal sharing of electrons

What is an ionic bond?

A bond formed by the attraction between oppositely charged ions (cations and anions) after complete electron transfer

What are cations and anions?

Cations: positively charged ions; Anions: negatively charged ions

Give an example of an ionic compound.

NaCl (sodium chloride) - Na⁺ (cation) and Cl⁻ (anion)

What is electronegativity?

A measure of an atom's attraction for electrons in a chemical bond

Which element is most electronegative in living cells?

Oxygen (O)

What are hydrogen bonds?

Weak bonds that occur when a hydrogen atom covalently bonded to one electronegative atom (usually N or O) is attracted to another electronegative atom

What are Van der Waals bonds?

Weak, transient interactions between molecules caused by temporary charge fluctuations ("hot spots") from electron movement

Why are weak bonds important in cells?

They allow temporary associations between molecules, important for processes like signaling where molecules need to bind and then release

What are the 4 key properties of water?

1. Cohesive behavior, 2. Ability to stabilize temperature, 3. Expansion upon freezing, 4. Solvent versatility

What is cohesion in water?

The ability of water molecules to stick together through hydrogen bonds, creating properties like surface tension

Why does water have high specific heat?

It requires a lot of energy to break the many hydrogen bonds in water, so it can absorb and store heat without large temperature changes

Why does ice float?

Ice has more hydrogen bonds than liquid water, keeping molecules farther apart. This makes ice less dense than liquid water.

What is the difference between hydrophilic and hydrophobic substances?

Hydrophilic: "water-loving" - substances that dissolve in water (have ionic or polar bonds); Hydrophobic: "water-fearing" - substances that don't dissolve in water (have mostly nonpolar bonds, like oils and fats)

What is pH?

pH = -log[H⁺]. It's a logarithmic scale measuring hydrogen ion concentration

What is neutral pH?

pH 7 (equal concentrations of H⁺ and OH⁻ at 10⁻⁷ M each)

What is the difference between acids and bases?

Acids: increase H⁺ concentration (pH < 7); Bases: increase OH⁻ concentration (pH > 7)

What is a buffer?

A substance that minimizes pH changes by absorbing excess H⁺ or donating H⁺ when depleted

Give an example of a biological buffer system.

Carbonic acid-bicarbonate system in blood: H₂CO₃ ⇌ HCO₃⁻ + H⁺

What is molarity (M)?

The number of moles per liter of solution

What is a mole?

The amount of substance equal to its molecular weight in grams (contains ~6.022 × 10²³ molecules - Avogadro's number)

What are the 6 major functional groups in biology?

1. Hydroxyl (-OH), 2. Carbonyl (-CO), 3. Carboxyl (-COOH), 4. Amino (-NH₂), 5. Sulfhydryl (-SH), 6. Phosphate (-PO₄)

What are the properties of hydroxyl, carbonyl, and carboxyl groups?

Hydroxyl: polar; Carbonyl: polar; Carboxyl: negatively charged

What are the properties of amino, sulfhydryl, and phosphate groups?

Amino: positively charged; Sulfhydryl: polar, participates in S-S bonds (disulfide bonds); Phosphate: negatively charged and bulky

What are the 4 building blocks of macromolecules?

1. Simple sugars, 2. Fatty acids, 3. Amino acids, 4. Nucleotides

What is the general formula for carbohydrates?

(C)n(H₂O)m where the C:H:O ratio is n:(2:1)m

What is glucose's molecular formula?

C₆H₁₂O₆

What are the two main functions of glucose?

1. Energy source: C₆H₁₂O₆ + 3O₂ → 6CO₂ + 6H₂O + energy; 2. Structural component: cellulose in cell walls, glycolipids and glycoproteins in membranes

What is condensation synthesis (dehydration synthesis)?

The process of joining monomers by removing water to form polymers

What is cellulose?

A polysaccharide made from glucose monomers, forming plant cell walls

Why doesn't cellulose dissolve in water?

Most of its chemical bonds are covalent carbon-to-hydrogen bonds, making it hydrophobic

What is the structure of a fatty acid? Give an example.

Long hydrocarbon chain with a carboxyl group. Example: Palmitic acid CH₃-(CH₂)₁₄-COOH

What are fatty acids composed of?

Hydrophobic region: long hydrocarbon chain; Hydrophilic region: carboxyl group (-COOH)

What is the difference between saturated and unsaturated fatty acids?

Saturated: no double bonds (C=C) in the fatty acid chain; Unsaturated: contains double bonds (C=C) in the chain

What are the 3 main functions of fatty acids?

1. Energy sources (produce more energy than glucose), 2. Components of phospholipids (essential for membranes), 3. Stored as fats/triglycerides

What is a triglyceride (fat)?

Glycerol backbone bonded to 3 fatty acid chains through ester linkages (formed by removal of water)

What is the structure of a phospholipid?

Hydrophilic head: phosphate group attached to glycerol; Hydrophobic tails: 2 fatty acid chains

What happens to unsaturated fatty acids in phospholipids?

The double bond creates a "kink" or bend that prevents close packing of phospholipids in membranes, increasing fluidity

How do phospholipids arrange themselves in water?

They form bilayers or micelles with hydrophobic tails facing each other and hydrophilic heads facing the water

What is the significance of phospholipid bilayers?

They are the major component of biological membranes

What are sterols? Give an example.

A class of lipids characterized by 4 fused rings. Example: Cholesterol

What are the functions of sterols?

1. Components of plasma membrane (contribute to fluidity and rigidity), 2. Precursors of steroid hormones

What are the 3 functions of nucleotides?

1. Energy carriers (ATP, GTP), 2. Signals (cAMP), 3. Building blocks of DNA and RNA

What are the 2 groups of nitrogenous bases?

1. Purines (2 rings): Adenine, Guanine; 2. Pyrimidines (1 ring): Cytosine, Thymine, Uracil

What is a nucleoside?

Base + Sugar (ribose or deoxyribose)

What is a nucleotide?

Nucleoside + Phosphate group(s) = Base + Sugar + Phosphate

What are the chemical differences between DNA and RNA?

DNA: deoxyribose sugar (lacks oxygen at position 2), contains thymine; RNA: ribose sugar (has oxygen at position 2), contains uracil instead of thymine

What are the 5' and 3' ends of DNA/RNA?

5' end: free phosphate group; 3' end: free hydroxyl (-OH) group

What is the DNA backbone made of?

Sugar-phosphate backbone connected by phosphodiester bonds

What are the base pairing rules (Chargaff's rules)?

A pairs with T (2 hydrogen bonds), C pairs with G (3 hydrogen bonds)

Why are C-G pairs more stable than A-T pairs?

C-G pairs have 3 hydrogen bonds vs. 2 for A-T pairs

What is the structure of double-stranded DNA?

Double helix; Sugar-phosphate backbone outside; Bases inside; Antiparallel strands (one 5'→3', one 3'→5')

What are the 3 uses of base pairing?

1. Preserve information (DNA replication), 2. Repair mistakes (DNA replication), 3. Transfer information (transcription, translation)

How much information can DNA encode?

4 nucleotides in n-nucleotide length = 4ⁿ combinations. Human genome has ~3 × 10⁹ nucleotides

What are the types of RNA?

mRNA (messenger RNA), tRNA (transfer RNA), rRNA (ribosomal RNA), microRNA, siRNA (regulation), snRNA (splicing)

What is transcription?

DNA → RNA by DNA-dependent RNA polymerase (same language: nucleotides)

What is translation?

RNA → Protein (language change: nucleotides to amino acids)

How much amplification occurs from gene to protein?

Example: 1 gene → 10⁴ copies of RNA → 10⁵ protein molecules per RNA → 10⁹ total protein molecules

What is the genetic code?

3 nucleotides (codon) = 1 amino acid. (4 nucleotides)³ = 64 possible codons for 20 amino acids

What are stop codons?

3 of the 64 codons that signal termination of translation (UAA, UAG, UGG)

What is degeneracy of the genetic code?

Multiple codons can code for the same amino acid (61 codons for 20 amino acids)

What is a reading frame?

The way codons are read in groups of 3. Usually only 1 of 3 possible reading frames is correct

What is an Open Reading Frame (ORF)?

The correct reading frame that starts with AUG (start codon) and continues until a stop codon

What is the function of ribosomes?

Organelles that read mRNA, set the reading frame, and synthesize proteins by adding amino acids

What is tRNA?

Transfer RNA - adaptor molecule that brings amino acids to the ribosome during translation

What is an anticodon?

The 3-nucleotide sequence on tRNA that is complementary to the mRNA codon

What is the basic structure of an amino acid?

Central carbon (α-carbon) bonded to: Amino group (-NH₂), Carboxyl group (-COOH), Hydrogen atom, Side chain (R group) - variable

What are the 3 classifications of amino acids based on their side chains?

1. Polar (uncharged), 2. Charged: Basic (+) or Acidic (-), 3. Nonpolar

What functional roles do charged amino acids play?

Basic (+): Found in DNA-binding proteins, nuclear localization signals; Acidic (-): Various functions

Where are nonpolar amino acids often found?

In hydrophobic membrane domains of proteins

What is a peptide bond?

A covalent bond between the carboxyl group of one amino acid and the amino group of another (formed by condensation - removal of water)

What are the N-terminus and C-terminus of a protein?

N-terminus: amino end (corresponds to 5' end of gene); C-terminus: carboxyl end (corresponds to 3' end of gene)

What are the 4 levels of protein structure?

1. Primary: amino acid sequence, 2. Secondary: chemical bonds in peptide backbone (α-helix, β-sheet), 3. Tertiary: bonds between side chains, 4. Quaternary: association of multiple subunits

What bonds maintain secondary structure?

Hydrogen bonds within the peptide backbone

What is an α-helix?

A protein coil held together by hydrogen bonds every 4th peptide bond. (secondary) structural level

What is a β-sheet?

A protein chain folded on itself with two regions parallel to each other, held by hydrogen bonds - forms very rigid structures

What 4 types of interactions form tertiary structure?

1. Hydrogen bonds, 2. Ionic bonds, 3. Disulfide bonds (covalent, between cysteine residues), 4. Hydrophobic interactions

What is quaternary structure? Give an example.

The association of multiple protein subunits. Example: Immunoglobulin G (IgG) has 2 heavy chains and 2 light chains

What are the functions of proteins?

Structure (collagen, keratin), Storage (casein, ovalbumin), Transport (hemoglobin), Hormones (insulin), Receptors, Contraction (actin, myosin), Defense (antibodies), Enzymes (catalysis)

How many possible combinations can 20 amino acids produce?

For a protein of length n: 20ⁿ combinations (for 300 amino acids: 20³⁰⁰ possibilities)

Give an example of how a single amino acid change affects protein function.

Sickle-cell anemia: Glutamic acid → Valine substitution at position 6 of hemoglobin causes red blood cells to become sickle-shaped

What is the N-rule for protein half-life?

N-terminal Arg, Lys, Leu, Phe, Tyr, Trp: half-life ~1 minute; Other N-terminal amino acids: half-life >10 hours

What are 2 methods for determining primary structure?

1. Protein micro-sequencing: Hydrolyze protein, separate pieces, determine amino acid composition (~20 amino acids), 2. DNA sequencing: sequence the gene and deduce protein sequence using genetic code (any length, but indirect)

What corresponds to the N-terminus and C-terminus in the gene?

N-terminus corresponds to 5' end of coding region; C-terminus corresponds to 3' end of coding region

What mediates molecular motion in cells?

Cytoskeletal proteins (NOT cytoskeletal lipids - these don't exist)

What type of bond holds oxygen atoms together in O₂?

Nonpolar covalent bonds (equal sharing of electrons)

What type of bond holds oxygen and hydrogen together in H₂O?

Polar covalent bonds (unequal sharing - oxygen is more electronegative)

If an element has atomic number 76 and mass number varies between 152-160, what varies?

Number of neutrons (between 76 and 84 neutrons)

Why does water evaporate faster on hot, dry days for cooling?

Lower humidity allows faster evaporation, which removes heat energy from the skin

What is the pathway for secretion of a newly synthesized protein?

Rough ER → Golgi → transport vesicle → plasma membrane

If a molecule contains carboxyl groups as its predominant functional group, what property does it have?

It will form hydrogen bonds with water molecules (hydrophilic) because carboxyl groups are polar and negatively charged

How do you make a hydrocarbon more flexible?

Fewer double bonds (more single bonds allow rotation and flexibility)

Which parts of amino acids form peptide bonds between tyrosine and isoleucine?

Carboxyl group of tyrosine and amino group of isoleucine