Chapter 1 bio Flashcards
Matter
anything that takes up space and has mass
Element
A pure substance that has specific physical/chemical properties and can’t be broken down into a simpler substance
Atom
the smallest unit of matter that still retains the chemical properties of the element
Molecule
two or more atoms joined together
Intramolecular forces
attractive forces that act on atoms within a molecule
Intermolecular forces
forces that exist between molecules and affect physical properties of the substance
Monomers
single molecules that can polymerize, or bond with one another
Polymers
substance made up of many monomers joined together in chains
Dehydration (condensation) reaction
creates a covalent bond between monomers and releases water
Hydrolysis
a reaction that breaks a covalent bond using water
Carbohydrates
- used as fuel and structural support
- they contain carbon, hydrogen, and oxygen atoms (CHO)
- they can come in the form of monosaccharides, disaccharides, and polysaccharides
Monosaccharides
carbohydrate monomers
Ribose
a 5 carbon monosaccharide
Fructose
a 6 carbon monosaccharide
Glucose
a 6 carbon monosaccharide
What is an example of 2 carbohydrate isomers?
glucose and fructose (different arrangement of atoms)
Disaccharides
- contain 2 monosaccharides joined together by a glycosidic bond
- the result of a dehydration reaction
- Ex: sucrose, lactose, and maltose
Glycosidic bond
a covalent bond that joins a carbohydrate molecule to another group
Polysaccharides
contain multiple monosaccharides connected by glycosidic bonds to form long polymers (Ex: starch and glycogen)
Starch
form of energy storage for plants
Glycogen
form of energy storage in animals
Proteins
- contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON)
- these atoms combine to form amino acids, which link together to build polypeptides (or proteins)
Amino acids
- are monomers of proteins
- have an amino, carboxy;, and R-group side chain
- there are 20 different kinds of amino acids, each with a different R-group
Polypeptides
- are polymers of amino acids and are joined by peptide bonds through dehydration reactions
- Hydrolysis reactions break peptide bonds
Primary structure of protein
Sequence of amino acids connected through peptide bonds
Secondary structure of protein
- intermolecular forces between the polypeptide backbone (not R-groups) due to hydrogen bonding
- forms a-helices and B-pleated sheets
Tertiary structure of protein
- 3-dimensional structure due to interactions between R-groups
- can create hydrophobic interactions based on the R-groups
- Disulfide bonds are created by covalent bonding between the R-groups of two cysteine amino acids
- hydrogen bonding and ionic bonding between R groups also hold together the tertiary structure
Protein denaturation
- describes the loss of protein function and higher order structure
- only the primary structure is unaffected
- proteins will denature as a result of high or low temperatures, pH changes, and salt concentrations
- Ex: cooking an egg in high heat will disrupt the intermolecular forces in the egg’s proteins, causing it to coagulate
Quaternary structure of protein
multiple polypeptide chains come together to form one protein
What are examples of protein function?
Storage, hormones, receptors, structure, immunity, and enzymes
Catalysts
- increase reaction rates by lowering the activation energy of a reaction
- transition state is the unstable conformation between the reactants and the products
- they reduce the energy of the transition state
- they do not shift a chemical reaction or affect spontaneity
Enzymes
- act as biological catalysts by binding to substrates (reactants) and converting them into products
- enzymes bind to substrates at an active site, which is specific for the substrate that it acts upon
- most enzymes are proteins
- protein enzymes are susceptible to denaturation
- they require optimal temperatures and pH for function
Induced fit theory
describes how the active site molds itself and changes shape to fit the substrate when it binds
ribozyme
an RNA molecule that can act as an enzyme (a non-protein enzyme)
Cofactor
a non-protein molecule that helps enzymes perform reactions
Coenzyme
an organic cofactor (i.e., vitamins), inorganic cofactors are usually metal ions
How do enzymes catalyze reactions?
- conformational changes that bring reactive groups closer
- the presence of acidic or basic groups
- induced fit of the enzyme-substrate complex
- electrostatic attractions between the enzyme and substrate
Phosphatase
cleave a phosphate group off of a substrate molecule
Phosphorylase
directly adds a phosphate group to a substrate molecule by breaking bonds within a substrate molecule
Kinase
- indirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from an ATP molecule
- these enzymes do not break bonds to add the phosphate group
Feedback regulation of enzymes
occurs when the end product of an enzyme-catalyzed reaction inhibits the enzyme’s activity by binding to an allosteric site
Competitive inhibition
- occurs when the competitive inhibitor competes directly with the substrate for active site binding
- can be outcompeted by adding more substrate
Noncompetitive inhibition
- occurs when the noncompetitive inhibitor binds to an allosteric site that modifies the active site
- cannot be outcompeted by adding more substrate
Allosteric site
a location on an enzyme that is different from the active site
Enzyme kinetics plot
can be used to visualize how inhibitors affect enzymes
Michaelis Constant (Km)
is the substate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax)
Saturation
occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus)
How does competitive inhibition compare to normal enzyme on enzyme kinetics plot?
Vmax stays the same while Km increases
How does noncompetitive inhibition compare to normal enzyme on enzyme kinetics plot?
Vmax decreases while Km stays the same
Lipids
- contain carbons, hydrogen, and oxygen atoms (CHO), like carbohydrates
- they have long hydrocarbon tails that make them very hydrophobic
Triacylglycerol (triglyceride)
- is a lipid molecule with a glycerol backbone (3 carbons and 3 hydroxyl groups) and 3 fatty acids (long hydrocarbon tails)
- glycerol and the 3 fatty acids are connected by ester linkages
Saturated fatty acids
have no double bonds and as a result pack tightly (solid at room temperature)
Unsaturated fatty acids
- have double bonds
- double bonds create kinks in the fatty acid chain, preventing tight packing and increasing membrane fluidity
Phospholipids
- are lipid molecules that have a glycerol backbone, one phosphate group, and 2 fatty acid tails
- the phosphate group is polar, while the fatty acids are nonpolar
- as a result, they are amphipathic (both hydrophobic and hydrophilic)
- they spontaneously assemble to form lipid bilayers
Cholesterol
- an amphipathic lipid molecule that is a component of the cell membranes
- it is the precursor to steroid hormones (lipids with 4 hydrocarbon rings)
- it is the starting material for vitamin D and bile acids
Lipoproteins
allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins
Waxes
are simple lipids with long fatty acid chains connected to alcohols
Carotenoids
are lipid derivatives containing long carbon chains with double bonds and function mainly as pigments
Sphingolipids
- have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognition
Glycolipids
- are lipids found in the cell membrane with a carbohydrate group attached instead of a phosphate group in phospholipids
- like phospholipids, they are amphipathic and contain a polar head and a fatty acid chain
Nucleic acids
- contain nucleotide monomers that build into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) polymers
Nucleosides
contain a 5 carbon sugar and a nitrogenous base
Nucleotides
contain a 5 carbon sugar, a nitrogenous base, and a phosphate group
Deoxyribose vs ribose
Deoxyribose sugars have a hydrogen at the 2’ carbon while ribose have a hydroxyl group at the 2’ carbon
Phosphodiester bonds
- are formed through a condensation reaction where the phosphate group of one nucleotide (at the 5’ carbons) connects to the hydroxyl group of another nucleotide (at the 3’ carbon) and release a water molecule as a by-product
- a series of phosphodiester bonds create the sugar-phosphate backbone, with a 5’ end (free phosphate) and a 3’ end (free hydroxyl)
Nucleic acid polymerization
proceeds as nucleoside triphosphates are added to the 3’ end of the sugar-phosphate backbone
DNA
- is an antiparallel double helix, in which two complementary strands with opposite directionalities (positioning of 5’ ends and 3’ ends) twist around each other
miRNA (microRNA)
small RNA molecules that can silence gene expression by base pairing to complementary sequences in mRNA
mRNA
is single-stranded after being copied from DNA during transcription
rRNA (ribosomal RNA)
it is formed in the nucleolus of the cell and helps ribosomes translate mRNA
dsRNA (double stranded RNA)
- some viruses carry their code as double stranded RNA
- dsRNA must pair its nucleotide, so it must have equal amounts of A/U, and C/G
tRNA (transfer RNA)
small RNA molecule that participates in protein synthesis
How old is the universe?
approximately 13.8 billion years old
When did the first cells appear on Earth?
3.5 billion years ago
Primordial Earth
- Earth’s primordial atmosphere was comprised of inorganic compounds and was a reducing environment (little O2 gas)
- as Earth cooled, gases condensed, forming the primordial sea
- simple compounds evolved into more complex organic compounds
- organic monomers linked into polymers
- protobionts emerged as precursors to cells
- heterotrophic, obligate anaerobic prokaryotes developed
- autotrophic prokaryotes, such as cyanobacteria capable of photosynthesis, formed. This led to oxygen production and accumulation, creating an oxidizing environment (high O2 gas)
- Primitive eukaryotes emerged, supporting the endosymbiotic theory where membrane bound organelles (mitochondria, chloroplasts), originally free-living, were engulfed by other prokaryotes, leading to a symbiotic relationship
- more complex eukaryotes and multicellular organisms began to evolve
Modern Cell Theory
- all lifeforms have one or more cells
- the cell is the basic structural, functional, and organizational unit of life
- all cells come from other cells (cell division)
- genetic information is stored and passed down through DNA
- an organism’s activity is dependent on the total activity of its independent cells
- metabolism and biochemistry (energy flow) occurs within cells
- all cells have the same chemical composition within organisms of similar species
Central dogma of genetics
- states that information is passed from DNA->RNA->proteins
- there are a few exceptions (reverse transcriptase and prions)
RNA world hypothesis
the theory that early life forms relied on self-replicating RNA both to store genetic information and to catalyze chemical reactions before the evolution of DNA and proteins
What happens because RNA is reactive and unstable?
- DNA replaced RNA in how genetic information is stored
- proteins largely replaced RNA in catalyzing reactions (ribozymes being a notable exception)
Endosymbiotic theory
states that eukaryotes developed when aerobic bacteria were internalized as mitochondria while the photosynthetic bacteria became chloroplasts
