BIOL 1406 Exam 2

DNA molecule

a double-stranded molecule made of nucleotides that stores all of your genetic information; shaped like a double helix with sugar-phosphate backbones and paired bases in the middle

RNA molecule

a single-stranded molecule made of nucleotides that helps carry out the instructions stored in DNA; uses ribose sugar and uracil instead of thymine

Polypeptide

a chain of more than 50 amino acids linked together by peptide bonds; folds up to become a functional protein

Protein

the complete, functional form of one or more polypeptide chains; largely determines what a cell looks like and how it functions

Gene expression

a series of steps that takes the information in the sequence of bases in DNA, transcribes it into mRNA, and then translates the mRNA into amino acids to make the cell's proteins

Nucleotide

the monomer of nucleic acids; made up of three basic parts: a 5-carbon sugar, a phosphate group, and a nitrogenous base

Polynucleotide

a long chain of nucleotides bonded together by phosphodiester bonds; DNA and RNA are both polynucleotides

Antiparallel

the two DNA strands run in opposite directions — one goes 5' to 3' and the other goes 3' to 5'

5' end

the end of a DNA or RNA strand that has a free phosphate group attached to the 5th carbon of the sugar

3' end

the end of a DNA or RNA strand that has a free hydroxyl (-OH) group on the 3rd carbon of the sugar; new nucleotides are always added to the 3' end

Complementary base pairing rule

A pairs with T (or U in RNA) and C pairs with G; this is how the two strands of DNA hold together and how RNA is built from a DNA template

Transcription

the process of using a DNA template to make a complementary RNA copy of the information; occurs in the nucleus in eukaryotes

Translation

the process of using the information in mRNA to synthesize proteins; it interprets the nucleotide "language" into amino acids at the ribosome

mRNA (messenger RNA)

messenger RNA; carries the code from DNA to the ribosome

tRNA (transfer RNA)

transfer RNA; brings amino acids to the ribosome and matches its anticodon to the mRNA codon

rRNA (ribosomal RNA)

forms the core of ribosomes and helps catalyze protein synthesis

Ribose

the 5-carbon sugar found in RNA nucleotides; has one more oxygen than deoxyribose (the sugar in DNA)

Uracil

the nitrogenous base found in RNA that replaces thymine; it pairs with adenine

Codon

a group of 3 mRNA bases that specifies a particular amino acid; there are 64 possible codons (4³ = 64), and more than one codon can specify the same amino acid; AUG is the start codon, and UAA/UAG/UGA are stop codons

RNA polymerase

the enzyme that binds to DNA at the promoter and synthesizes RNA using the template strand; RNA Pol I makes rRNA (large subunit), RNA Pol II makes mRNA, RNA Pol III makes rRNA (small subunit) and tRNA

RNA transcript

the newly made RNA strand produced during transcription before any processing has occurred

Promoter region

a specific DNA sequence where RNA polymerase recognizes and binds to start transcription; it signals "start here"

Termination sequence

a DNA sequence that causes both the polymerase and newly-made RNA transcript to dissociate from DNA, ending transcription

Protein encoding region

the section of a gene that actually codes for the amino acid sequence of a protein

Aminoacyl-tRNA synthetase

the enzyme that attaches the correct amino acid to its matching tRNA molecule; makes sure the right amino acid gets paired with the right tRNA

Ribosome E, P, A sites

the three sites on a ribosome during translation — A site (acceptor site where an aminoacyl tRNA enters), P site (peptidyl site where a peptide bond forms), E site (exit site where empty tRNAs leave the ribosome)

Immature mRNA (pre-mRNA)

precursor mRNA that contains both introns and exons; it hasn't been processed yet — still needs the 5' cap, poly-A tail, and splicing

Mature mRNA

fully processed mRNA ready to leave the nucleus; introns removed, exons spliced together, 5' cap and poly-A tail added

Poly-A tail

100-250 adenine nucleotides added to the 3' end of mRNA; helps export mRNA from the nucleus, protects against degradation, and facilitates initiation of translation

5' cap (7-methylguanosine cap)

a modified guanine nucleotide (7-methylguanylate) added to the 5' end of mRNA; the eukaryotic ribosome cannot bind to uncapped mRNA, and capping protects mRNA from degradation

snRNPs

small nuclear ribonucleoprotein complexes that bind to introns and cut them out, then splice together the exons during RNA processing

Posttranscriptional modifications

changes made to pre-mRNA after transcription — includes adding the 5' cap, adding the poly-A tail, and removing introns and splicing exons together

Posttranslational modifications

changes made to a polypeptide after translation that help it become active — includes folding, adding carbohydrate groups (glycosylation), cleaving off amino acids, phosphorylation, transport, activation, or degradation of protein

Base substitution mutation

a type of point mutation where one base is replaced by another; may or may not change the amino acid produced

Frameshift mutation

a mutation caused by inserting or deleting nucleotides that shifts the reading frame, often changing many amino acids and usually producing a nonfunctional protein

Missense mutation

a point mutation that changes one amino acid in the protein to a different amino acid

Nonsense mutation

a point mutation that changes a codon that specifies an amino acid into a premature stop codon, causing the protein to be cut short

Amino acid

the monomer of proteins; composed of a central carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and an R-group (side chain) that makes each of the 20 amino acids unique

Constitutive genes

genes that are neither inducible nor repressible — they are active at all times; examples include regulatory proteins like CAP and repressor proteins

Regulated genes

genes that are turned on or off depending on conditions; the cell only expresses them when their products are needed

Lac operon

a cluster of genes in E. coli for lactose metabolism under transcriptional control of one promoter; contains lacZ (β-galactosidase — breaks down lactose), lacY (lactose permease — transports lactose into the cell), and lacA (galactoside transacetylase); it is an inducible operon — normally turned off, turned on when lactose is present and glucose is absent

CAP (catabolite activator protein)

an activator protein that, when bound to cAMP, binds to the CAP site near the lac promoter; the resulting bend in DNA enhances RNA polymerase binding, which increases transcription (positive control)

CAP site

the DNA region on the lac operon where the CAP-cAMP complex binds; located near the lac promoter, upstream of the operator

Promoter

the DNA sequence where RNA polymerase recognizes and binds to begin transcription of a gene or operon

Operator

a regulatory DNA sequence in an operon (like lacO) that provides a binding site for the repressor protein; when the repressor binds here, it prevents RNA polymerase from transcribing the genes

Lac genes

the three structural genes of the lac operon — lacZ (β-galactosidase), lacY (lactose permease), and lacA (galactoside transacetylase); they are transcribed together as a polycistronic mRNA

Repressor

a regulatory protein that binds to the operator and inhibits transcription (negative control); in the lac operon, when lactose is present, allolactose binds to the repressor, changes its shape, and prevents it from binding to the operator — so transcription can occur

trp operon

a repressible operon in E. coli that encodes enzymes required to make the amino acid tryptophan; when tryptophan levels are low, the trp repressor is inactive and the operon is transcribed; when tryptophan levels are high, tryptophan acts as a corepressor that binds to the repressor, allowing it to bind the operator and shut off transcription

R group (side chain)

the variable part of an amino acid that makes each one unique; determines whether the amino acid is polar, nonpolar, charged, etc.; charged and polar side chains are hydrophilic, nonpolar side chains are hydrophobic

Hydrophilic

"water-loving" — describes molecules or parts of molecules that interact readily with water, usually because they are polar or charged

Hydrophobic

"water-fearing" — describes nonpolar molecules or parts of molecules that do not interact with water and tend to cluster together

Monomer

a single small molecule ("one-part") that can be bonded to other identical or similar molecules to form a polymer

Polymer

a large molecule ("many-parts") made of many repeating monomer subunits linked together

Macromolecule

a very large, complex molecule important for life — the four main types are carbohydrates, proteins, lipids, and nucleic acids

Peptide bond

a covalent bond that forms when the amino group of one amino acid shares electrons with the carboxyl group of another amino acid; links amino acids in a chain

Dipeptide

two amino acids joined together by a single peptide bond

Four levels of protein folding

primary (amino acid sequence), secondary (alpha helices and beta-pleated sheets from hydrogen bonds between backbone groups), tertiary (3D folding from R-group interactions), quaternary (two or more independently folded polypeptide chains fit together)

Catalyst

a substance that lowers the activation energy of a reaction and speeds it up, without being used up in the process

Enzyme

a protein that catalyzes (speeds up) chemical reactions in the cell by lowering the activation energy; most enzymes are globular shaped and reactants bind in the active site

Substrate

the specific reactant molecule that binds to the active site of an enzyme; only certain substrates fit into the active site of an enzyme (lock and key model)

Product

the molecule(s) that result from an enzyme-catalyzed reaction

Activation energy

the amount of energy required to reach the transition state and start a chemical reaction; enzymes lower this amount so reactions happen faster in cells

Competitive inhibition

when a molecule similar in shape to the substrate competes with it for the enzyme's active site, blocking the substrate from binding

Allosteric regulation

when a molecule binds to a spot on the enzyme that is NOT the active site, which changes the enzyme's shape and either activates or inhibits it; ex: allolactose binds to the lac repressor and changes its shape

Reversible inhibition

enzyme inhibition that can be undone — the inhibitor can detach and the enzyme goes back to normal

Irreversible inhibition

enzyme inhibition where the inhibitor permanently alters or destroys the enzyme so it can never function again

Denatured

loss of a protein's secondary through quaternary structure (and therefore its function) caused by heat, pH changes, or organic solvents; the primary amino acid sequence is still intact but the protein can't work anymore

Acid

a substance that releases hydrogen ions (H+) in solution, lowering the pH below 7

Base

a substance that accepts hydrogen ions (H+) or releases hydroxide ions (OH-) in solution, raising the pH above 7

pH

a scale from 0-14 that measures how acidic or basic a solution is; 7 is neutral, below 7 is acidic, above 7 is basic

Cell membrane (plasma membrane)

selectively permeable boundary between the cell and its environment; only allows certain molecules to pass through — small/large nonpolar molecules cross quickly, charged molecules or ions cross slowly or not at all

Phospholipid

an amphipathic molecule with a hydrophilic phosphate head and two hydrophobic fatty acid tails; kinked tails (from double bonds) keep adjacent phospholipids from packing tightly, making membranes more fluid

Intracellular

inside the cell

Extracellular

outside the cell

Peripheral protein

membrane proteins that are not embedded in the lipid bilayer; located on the inner or outer surface of the plasma membrane

Integral (transmembrane) protein

membrane proteins firmly bound to the membrane; they are amphipathic and transmembrane proteins extend all the way through the membrane

Fluid mosaic model

Singer and Nicolson's model — the membrane is a "mosaic" of many different kinds of molecules (phospholipids, protein channels and pumps, carbohydrate ID tags, cholesterol) that is not static but fluid because the positions of proteins are constantly changing

Amphipathic

describes a molecule that has distinct hydrophobic ("water-fearing") and hydrophilic ("water-loving") regions; phospholipids are a key example

Selectively permeable

describes a membrane that only allows certain molecules to pass through while blocking others; also called semipermeable

Diffusion

the movement of particles from an area of higher concentration to an area of lower concentration; passive transport, no energy required

Osmosis

the diffusion of water across a selectively permeable membrane from high water concentration to low water concentration (toward higher solute); helps maintain homeostasis

Isotonic

"same strength" — the concentration of dissolved substances outside the cell is the same as inside; no net water movement; cell size stays the same

Hypertonic

"above strength" — the concentration of dissolved substances (solute) outside the cell is higher than inside; water flows out of the cell by osmosis; cell shrinks (crenates)

Hypotonic

"below strength" — the concentration of dissolved substances (solute) outside the cell is lower than inside; water flows into the cell by osmosis; cell swells and may burst (lyse)

Facilitated diffusion

membrane proteins help (facilitate) the movement of certain molecules across the cell membrane by diffusion (high to low concentration) that can't diffuse through the lipid bilayer directly; passive transport, does not require energy; can occur through channels or carrier proteins

Active transport

the movement of materials through a membrane against a concentration gradient (low to high); requires energy from the cell (ATP); carrier protein binds with the substance and changes shape to release it on the other side

Sodium-potassium pump

a membrane protein pump that uses ATP to transport Na+ and K+ against their concentration gradients; an example of active transport

Exocytosis

a type of active transport in which large amounts of materials leave the cell in membrane-bound vesicles

Endocytosis

a type of active transport in which large amounts of materials enter the cell in membrane-bound vesicles

Phagocytosis

"cell eating" — a type of endocytosis where the cell engulfs large solid particles

Pinocytosis

"cell drinking" — a type of endocytosis where the cell takes in tiny droplets of fluid

Pathogens

parasitic microbes that cause disease symptoms; examples include bacteria and viruses

Prokaryote Bacteria

single-celled organisms that lack a nucleus and membrane-enclosed organelles; cell wall made of peptidoglycan

Cocci

sphere-shaped bacteria

Bacillus

rod-shaped bacteria

Spirochaetes

spiral-shaped bacteria; some _____ are flexible, spirilli are rigid

Vibrio

comma-shaped bacteria

Pili

threadlike structures on the surface of a bacterial cell; used to twitch or glide across surfaces and play important roles in bacterial reproduction (conjugation) and disease processes

Flagellum

structure used for swimming; made of the protein flagellin; has three parts — the motor (anchored in the membrane), the hook (connects motor to filament), and the filament (the long external part that spins); different from eukaryotic flagella, works like an outboard motor

Plasmid

small, circular pieces of DNA that exist independently of the bacterial chromosome; have their own origin of replication; not usually necessary for survival but can provide growth advantages like antibiotic resistance; an episome is a plasmid that can integrate into the bacterial chromosome