Exam 1 Flashcards
Weak interactions between non polar molecules that are close
Van der waals forces
Accepts H+
Bases
Donates H+
Acid
Acts as both acid and base
Water
Mix of weak acid and it’s conjugate base (vice versa)
Buffer
Measure of H+
pH
pH formula
-log[H+]
Hydrochloric Acid (HCl)
Strong Acid; fully dissociates to make H+ and Cl- in water
Carbonic Acid (H2CO3)
Weak Acid; partially dissociates in water to form H+ and HCO3-
Nitric Acid
Strong Acid; fully dissociates to make H+ and NO3-
Acetic Acid
Weak Acid; partially dissociates to make H+ and CH3COO-
Phosphoric Acid (H3PO4)
Weak acid; partially dissociates into H+ ions and H2PO4-, HPO4(2-), and PO4(3-)
Sulfuric Acid (H2SO4)
Strong Acid; Fully dissociates to form HSO4- and H+
Ammonia (NH3)
Weak base; partially dissociates in water to form NH4+ and OH-
Sodium Hydroxide (NaOH)
Strong base; fully dissociates to form Na+ and OH-
Potassium Hydroxide (KOH)
Strong base; fully dissociates to form K+ and OH-
Methyl Amine (CH3NH2)
Weak base; partially dissociates in water to form CH3NH3+ and OH-
Sodium Hypochlorite (NaOCL)
Weak base
Functional Group
Determines how molecules interact with others
Carbohydrates
Variably sized sugar molecules usually with formula (C1H2O1)n. Characterized by number of sugars.
Carbohydrate functions include
Storing energy
Transporting stored energy
Be arranged to form other molecules
Form extra cellular support structures
Monosaccharides
Simple sugars; monomer of complex carbs; used as energy source; exists as ring or chain
Disaccharides
Two simple sugars linked by covalent bonds
Oligosaccharides
Formed by several monosaccharides; often covalently bonded to proteins and lipids on cell surfaces where they serve as recognition signals
Polysaccharides
Larger polymers of monosaccharides; some are branched
Glycosidic Bonds
Bonds by which di, oligo, and polysaccharides are held together
Condensation Reaction
Results in formation of covalent bonds between monomers; forms polymers and creates water; new covalent bond between monomers and water is created
Hydrolysis Reaction
Breaks down polymers into monomers and consume water
Lipids
Nonpolar hydrocarbons that have various roles in cells; defined by insolubility in water
Fats and Oils
Type of lipid; triglycerides that store energy
Triglyceride
3 fatty acids and 1 glycerol connected with an ester linkage (formed through condensation reaction)
Fats are
Solid at room temp
Oils are
Liquid at room temp
Phospholipid
Type of lipid; 2 fatty acids bound to glycerol with a phosphate; amphipathic: head is hydrophilic phosphate group and tail is hydrophobic fatty acid chains
Carotenoids
type of lipid; light absorbing pigments
Steroids
Multiple rings that share carbon atoms; cholesterol, messenger molecules, hormones, etc
Wax
Long chain alcohol bound ton an unsaturated fatty acid
Nucleic Acids
Informational macromolecules
Monomer of nucleic acids
Nucleotides
Polymer of nucleic acids
DNA and RNA
DNA molecules vary in their
sequence of bases
Chargaff’s Rule
[A]=[T], [C]=[G]= 50%
Purines
Type of nitrogenous base; double ringed; adenine and guanine
Pyrimidines
Type of nitrogenous base; single ringed; cytosine and thymine
What kind of backbone do oligonucleotides have?
Sugar-phosphate backbone; always attaches to carbon #5
Differences between RNA and DNA
RNA single-stranded vs DNA double
RNA has 2 OH groups, DNA has OH and H (RNA more reactive)
Sugar in RNA is ribose vs sugar in DNA is deoxyribose
Nucleotide ATP
Adenine monomer of RNA; used as energy carrier
Phosphodiester Bond
Links nucleotides in a strand of DNA (covalent bonds); between phosphate group at 5 carbon location and hydroxyl at 3 carbon location
What did Rosalind Franklin’s Photo 51 reveal about DNA?
Double helix
Bases are on inside of each strand and sugar-phosphate groups are on inside
Diameter: 2nm
Number of nucleotides per turn=10
Chain is antiparallel
Key features of DNA
Double Helix
Right-handed (turns to right)
Antiparallel (one strand has free 3’ hydroxyl group other strand has free 5’ phosphate group)
Strands are held together by hydrogen bonding between complementary bases
Outer edges of the bases are exposed in major and minor grooves (major=bigger)
Monomers of Protein
Amino Acids
Gene
A sequence of DNA that contains the info to make one protein
One gene, one enzyme hypothesis
Each gene contains the info needed to make a single enzyme
RNA polymerase
The enzyme that synthesizes RNA according to the information provided by the sequence of bases in a particular stretch of DNA; transcription
Coding strand of DNA
Has same polarity and sequence as mRNA
mRNA
Carries info from DNA to site of protein synthesis
Template strand of DNA
Complementary to RNA
What reads mRNA to produce protein?
Ribosomes
Transcription
First process in gene expression; is the process by which hereditary info in DNA is copied to mRNA
Translation
Second process in gene expression; process by which info in mRNA is used to synthesize proteins
What determines the sequence of amino acids in a protein
The sequence of bases in the mRNA
Genetic code
A triplet code, with a three base sequence called a codon specifying a single amino acid
Four characteristics of the genetic code
Redundant; all amino acids except Met and TRP are coded for by more than one codon
Conservative; when several codons specify the same amino acid, the first two bases of the codons are almost always identical
Unambiguous; a single codon never codes for more than one amino acid
Universal; With few exceptions, all organisms have the same genetic code
Start Codon
AUG
Stop Codons
UAA, UAG, UGA
What dictates protein’s functions
Folding of its polypeptide chains into specific shapes
Primary Structure of protein
The sequence of the amino acids in a polypeptide chain
Which of the two isomers of amino acids are found in physiological contexts?
L-alanine, not D-alanine
What dictates amino acid’s properties
Amino acid side chains aka r-groups
Which amino acids have polar, hydrophilic side chains that are uncharged?
Serine, Threonine, Asparagine, Glutamine, Tyrosine
Which amino acids have charged hydrophilic side chains
Arginine, Histidine, Lysine, Aspartic Acid (-), Glutamic Acid (-)
Which amino acids have hydrophobic side chains
Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Tryptophan, Valine
Which amino acids don’t fit any categories
Cysteine, Glycine, Proline
Amino groups in amino acids
Accept H+ (basic)
Carboxyl groups in amino acids
Donates H+(acidic)
Influences to protein folding include
H bonds
pH
temp
van dar waals forces
hydrophobic interactions
Secondary structure of a protein
Determined and stabilized by hydrogen bonding with the backbone of amino acids (may form alpha helix or beta pleated sheets)
Tertiary structure
How a protein folds in 3D because of interactions between R groups; stabilized by hydrogen bonds, disulfide bridges, hydrophobic interactions
Quaternary Structure
Association of polypeptides with other polypeptides
What happens if a chemical treatment were used to disrupt the secondary and tertiary structure of a protein
It would become denatured (unfolded) and it won’t function
Urea
Highly polar molecule that disrupts hydrogen and ionic bonds
B-mercaptoethanol
Can reduce/break disulfide bridges
Proteins have very specific binding partners to which they bind
Non-covalently
What is specificity in binding of protein partners determined by
Shape: should be general fit between protein and other molecule
Chemistry: surface R groups can interact with other molecule through non-covalent interactions
Chaperone Proteins
Protects proteins from inappropriate binding and also helps new proteins with folding