Chapter 1 bio Flashcards
(82 cards)
1
Q
Matter
A
anything that takes up space and has mass
2
Q
Element
A
A pure substance that has specific physical/chemical properties and can’t be broken down into a simpler substance
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Q
Atom
A
the smallest unit of matter that still retains the chemical properties of the element
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Q
Molecule
A
two or more atoms joined together
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Q
Intramolecular forces
A
attractive forces that act on atoms within a molecule
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Q
Intermolecular forces
A
forces that exist between molecules and affect physical properties of the substance
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Q
Monomers
A
single molecules that can polymerize, or bond with one another
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Q
Polymers
A
substance made up of many monomers joined together in chains
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Q
Dehydration (condensation) reaction
A
creates a covalent bond between monomers and releases water
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Q
Hydrolysis
A
a reaction that breaks a covalent bond using water
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Q
Carbohydrates
A
- 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
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Q
Monosaccharides
A
carbohydrate monomers
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Q
Ribose
A
a 5 carbon monosaccharide
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Q
Fructose
A
a 6 carbon monosaccharide
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Q
Glucose
A
a 6 carbon monosaccharide
16
Q
What is an example of 2 carbohydrate isomers?
A
glucose and fructose (different arrangement of atoms)
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Q
Disaccharides
A
- contain 2 monosaccharides joined together by a glycosidic bond
- the result of a dehydration reaction
- Ex: sucrose, lactose, and maltose
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Q
Glycosidic bond
A
a covalent bond that joins a carbohydrate molecule to another group
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Polysaccharides
A
contain multiple monosaccharides connected by glycosidic bonds to form long polymers (Ex: starch and glycogen)
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Q
Starch
A
form of energy storage for plants
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Q
Glycogen
A
form of energy storage in animals
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Q
Proteins
A
- contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON)
- these atoms combine to form amino acids, which link together to build polypeptides (or proteins)
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Q
Amino acids
A
- 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
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Q
Polypeptides
A
- are polymers of amino acids and are joined by peptide bonds through dehydration reactions
- Hydrolysis reactions break peptide bonds
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Primary structure of protein
Sequence of amino acids connected through peptide bonds
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Secondary structure of protein
- intermolecular forces between the polypeptide backbone (not R-groups) due to hydrogen bonding
- forms a-helices and B-pleated sheets
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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
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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
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Quaternary structure of protein
multiple polypeptide chains come together to form one protein
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What are examples of protein function?
Storage, hormones, receptors, structure, immunity, and enzymes
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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
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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
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Induced fit theory
describes how the active site molds itself and changes shape to fit the substrate when it binds
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ribozyme
an RNA molecule that can act as an enzyme (a non-protein enzyme)
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Cofactor
a non-protein molecule that helps enzymes perform reactions
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Coenzyme
an organic cofactor (i.e., vitamins), inorganic cofactors are usually metal ions
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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
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Phosphatase
cleave a phosphate group off of a substrate molecule
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Phosphorylase
directly adds a phosphate group to a substrate molecule by breaking bonds within a substrate molecule
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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
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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
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Competitive inhibition
- occurs when the competitive inhibitor competes directly with the substrate for active site binding
- can be outcompeted by adding more substrate
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Noncompetitive inhibition
- occurs when the noncompetitive inhibitor binds to an allosteric site that modifies the active site
- cannot be outcompeted by adding more substrate
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Allosteric site
a location on an enzyme that is different from the active site
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Enzyme kinetics plot
can be used to visualize how inhibitors affect enzymes
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Michaelis Constant (Km)
is the substate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax)
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Saturation
occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus)
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How does competitive inhibition compare to normal enzyme on enzyme kinetics plot?
Vmax stays the same while Km increases
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How does noncompetitive inhibition compare to normal enzyme on enzyme kinetics plot?
Vmax decreases while Km stays the same
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Lipids
- contain carbons, hydrogen, and oxygen atoms (CHO), like carbohydrates
- they have long hydrocarbon tails that make them very hydrophobic
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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
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Saturated fatty acids
have no double bonds and as a result pack tightly (solid at room temperature)
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Unsaturated fatty acids
- have double bonds
- double bonds create kinks in the fatty acid chain, preventing tight packing and increasing membrane fluidity
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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
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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
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Lipoproteins
allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins
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Waxes
are simple lipids with long fatty acid chains connected to alcohols
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Carotenoids
are lipid derivatives containing long carbon chains with double bonds and function mainly as pigments
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Sphingolipids
- have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognition
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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
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Nucleic acids
- contain nucleotide monomers that build into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) polymers
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Nucleosides
contain a 5 carbon sugar and a nitrogenous base
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Nucleotides
contain a 5 carbon sugar, a nitrogenous base, and a phosphate group
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Deoxyribose vs ribose
Deoxyribose sugars have a hydrogen at the 2' carbon while ribose have a hydroxyl group at the 2' carbon
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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)
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Nucleic acid polymerization
proceeds as nucleoside triphosphates are added to the 3' end of the sugar-phosphate backbone
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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
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miRNA (microRNA)
small RNA molecules that can silence gene expression by base pairing to complementary sequences in mRNA
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mRNA
is single-stranded after being copied from DNA during transcription
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rRNA (ribosomal RNA)
it is formed in the nucleolus of the cell and helps ribosomes translate mRNA
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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
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tRNA (transfer RNA)
small RNA molecule that participates in protein synthesis
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How old is the universe?
approximately 13.8 billion years old
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When did the first cells appear on Earth?
3.5 billion years ago
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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
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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
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Central dogma of genetics
- states that information is passed from DNA->RNA->proteins
- there are a few exceptions (reverse transcriptase and prions)
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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
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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)
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Endosymbiotic theory
states that eukaryotes developed when aerobic bacteria were internalized as mitochondria while the photosynthetic bacteria became chloroplasts
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