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Bio Test 2 Study Set
Biology
| Question | Answer |
|---|---|
| Molarity | The amount of solute molecules per volume of solution (it is a measure of concentration) |
| Can the same volume have different molarities? | Yes, if the amount of solute in them is different. |
| What is the molarity (M) equation? | M = (moles of solute) / (Liters of solution) |
| What is a mole? | A unit to measure the number of particles of a particular substance (can be used to refer to atoms or molecules). |
| What is avogadro's number (moles to amount of atoms)? | 1 mole = 6.022 x 10^23 atoms |
| Molar mass | the weight of a mole of a particular substance |
| What are the units of molar mass? | (g/mol) |
| What are the 2 ways to make solutions containing a specific concentration? | 1) Start with a solid substance, weigh out a specific amount, and dissolve it in a liquid solvent. 2) Start with a more concentrated solution, and dilute it with water or another liquid |
| What are H+'s refered to as? | Protons |
| What is pH? | a specific measure of the concentration of H+ in a solution |
| What amount/difference would a change of 1 pH be in H+ concentration? | A 10-fold difference in H+ concentration |
| What is the equation for pH? | pH = -log[H+] |
| T or F: the less hydrogen ions (H+), the lower the pH? | False, the less hydrogen ions, the higher the pH... the more hydrogen atoms the lower the pH. |
| Are pH's of 0-6.9 considered acidic, neutral or basic? | Acidic |
| What pH represents a neutral solution? | A pH of 7 |
| Are pH's of 7.1-14 considered acidic, neutral, or basic? | Basic |
| What makes a reactant an acid? | If it is a proton (H+) donor |
| What makes a reactant a base? | If it is a proton (H+) acceptor |
| Is water an acid or a base? | It can be both! |
| What are the 4 types of macromolecules? | Proteins, carbohydrates, lipids, and nucleic acids |
| T or F: a macromolecule's shape determines its biological function. | True |
| What are most of the macromolecules? | Polymers |
| How are polymers created? | By linking/bonding monomers together in codensation (dehydration synethesis) reactions |
| Monomer | a single molecular unit |
| Polymer | molecule or macromolecule composed of many repeating monomer units |
| What is the polymer associated with amino acids? | Proteins |
| What is the monomer associated with proteins? | amino acids |
| What else can proteins be referred to as (its other names)? | Peptides, polypeptides, or anything that has to do with the substances bound to them or their function |
| List some of the functions of proteins? (8) | Contractile, hormonal, protection, transport, enzyme, storage, structural, receptor |
| What 3 things make up an amino acid? | An amine group, a carboxyl group, and a side chain |
| What are the other names for the side chain in amino acids? | Variable region/chain, or R-group |
| How does the amino acid exist inside the neutral pH of cells? | The amine group has a positvely charged nitrogen after accpeting a proton (acted as a base) and the carboxl has a negatively charged oxygen after donating a proton (acted as an acid) |
| What is the non-variable region of an amino acid? | The region including the amine, carboxyl, and central carbon (everything except the side chain) |
| What are the 3 types of R-groups? | 1) Charged 2)Polar 3) Nonpolar |
| How do you identify a charged R-group? | Simply recognize if the side chain contains an atom with a charge (could be positive or negative) |
| What type of interactions would you expect charged R-groups to make? | Ionic bonds |
| How do you identify a polar side chain? | If there is a polar covalent pond between any atoms in the side chain it is polar |
| What type of interactions would you expect polar R-groups to make? | H-bonds |
| How do you identify a nonpolar side chain? | If the side chain does not have a single charge and all bonds between atoms are nonpolar covalent then it is nonpolar |
| What type of interactions would you expect nonpolar R-groups to make? | hydrophobic interactions and Van der Waals |
| What are the 3 special case R-groups? | Cysteine, Glycine, and Proline (see slide 14 of macromolecules part 1 for more details) |
| How are many biological polymers formed? | Via condensation (or dehydration synthesis) reactions |
| What is a biproduct (also created) of condensation reactions? | Water is formed during the reaction |
| What type of bond forms between the monomers when they link to form a polymer during a condensation reaction? | A covalent bond forms between the monomers |
| What is the covalent bond between amino acids called? | a peptide bond |
| What are the distinct ends of proteins called? | The N-terminus and the C-terminus |
| What is the N-terminus? | The amine group on the first amino acid that does not participate in peptide bond formation (remains with a positvely charged nitrogen) |
| What is the C-terminus? | The final carboxyl group that does not participate and in peptide bond formation, remaining unmodified (remains with a negatively charged oxygen) |
| How are many biological polymers broken? | Via hydrolysis reactions |
| What reagent is necessary in order for hydrolysis reactions to occur? | Water needs to be added |
| What are the 3 ways to represent the 3D structure/folding of proteins? | 1) Space-filling model 2) Stick model 3) Ribbon model |
| What are the 4 levels of protein structure? | primary, secondary, tertiary, and quaternary |
| What is the primary structure of proteins? | The order of amino acids in the polypeptide formed by covalent bonds between amino acids (straight chain) |
| How is the secondary structure of proteins formed? Give the specifics. | Formed by hydrogen bonds between non-variable parts of non-adjacent amino acids... the partially negative oxygen of a carbonyl can H-bond with the partially positive hydrogen of an amino group (most be non-adjacent amino acids of the same protein) |
| What are the 2 types of secondary protein structures that can be formed? | An alpha helix and a beta sheet |
| How is the tertiary structure of proteins formed? | By interactions and bonds between side chains (R groups) of different amino acids within one polypeptide/protein or interactions and bonds between side chains and the environment |
| What two R-groups can form a disulfide bridge with one another, and what effect does the disulfide bridge have? | Two cysteines can form a strong covalent S-S bond, the disulfide bridge, which is important to protein structure |
| How is the quaternary structure of proteins formed? | By interactions and bonds between side chains (R groups) of different amino acids in different polypeptides/proteins |
| What are the individual polypeptide chains called in the quaternary structure? | Subunits |
| T or F: The multi-subunit protein complex (the complete/total quaternary structure) only functions once the subunits come together. | True |
| T or F: Proteins are rigid and unable to change shape. | False, proteins are dynamic and have constant variation |
| T or F: Biological function is determined by the precise protein shape. | True |
| What is the monomer of carbohydrates? | Monosaccharides |
| What is the polymers of carbohydrates? | Disaccharides, Oligosaccharides, and Polysaccharides |
| What is the typical formula for carbohydrates? | (CH2O)n (H having double whatever C has, typically) |
| What are carbohydrates also referred to as? | saccharides |
| What are mono- and di-saccharides often called? | sugars |
| What do endings with "-ose" typically signify? | A sugar--> a carbohydrate |
| Are monosaccharides typically found in ring form or linear open chains? | Ring form |
| When a carbohydrate forms a ring, what are the two orientations it could have and what distinguishes them? | 1) The alpha orientation--> the hydroxyl groups on both sides of the ring point in the same direction 2) The beta orientation--> the hydroxyl groups on each side of the ring point in opposite directions |
| What could the different orientations of carbohydrate rings affect? (Think back to pre-exam 2 Q) | Their ability to react, be broken down by enzymes, etc. |
| What are the covalent bonds that link monosaccharides called? | Glycosidic linkages |
| What type of reaction forms glycosidic linkages? | Condensation (dehydration) reactions |
| How are di- and poly-saccharides broken up back into monosaccharides? | Hydrolysis reactions |
| What are the two major roles of carbohydrates we discussed in the slides? | Energy storage and structural support |
| What branched polymer of glucose stores energy in animals? | Glycogen |
| What branched polymer of glucose stores energy in plants? | Amylopectin (a type of starch) |
| What happens when the energy stored by carbohydrates is needed? | Hydrolysis reactions release glucose molecules to be broken down during metabolism |
| What unbranched polymer of glucose is used for structural support (for ex. in plants)? | Cellulose |
| What does the orientation of the glycosidic linkages allow cellulose to do/oportunize for it? | Creates a straight polymer that allows it to form H-bonds between different polymers of cellulose |
| How can you modify a carbohydrate to alter its function? | By attaching a functional group to a monomer (ex Chitin) |
| What is chitin? | A modified carbohydrate stemming from functional groups added to its monomers that is the main constituent of fungal cell walls and exoskeletons of arthropods |
| What are the 3 important properties of lipids? | 1) They can be broken down to release energy 2) They primarily contain C-C and C-H bonds 3) They are hydrophobic (the tails) |
| What are the 2 categories of lipids? | 1) Fats 2) Steroids |
| What are the building blocks for fats? | Fatty acids are the "building block" mono-, di-, and triglyceride polar fats (phospholipids) |
| What are steroids? | Type of lipid that includes 4 infused hydrocarbon rings |
| What are the 2 types of fatty acid tails> | Saturated and unsaturated |
| What is an unsaturated tail? | If there are 1 or more double bonds in the tail |
| What is a saturated tail? | All/only single bonds in the tail |
| Are saturated fatty acids or unsaturated fatty acids more tightly packed together? Why? | Sat. fatty acid tails are more tightly packed because the double bonds in unsat. tails create a bend in the tail that prevents them from getting close and forming van der waals, whereas sat. tails are straight, allowing them to get closer and form v.d.w. |
| How are the fatty acid tails joined to a glycerol molecule to form triglyceride for example? | Through ester linkages , a covalent bond that attaches the tails to the glycerol (3 ester linkages in the case of triglyceride) |
| What does the substitution of polar groups onto the hydrophobic lipid result in? | An amphipathic molecule |
| What is an amphipathic molecule? | A molecule that is hydrophilic at one end and hydrophobic at the other |
| What is an example of a amphipathic molecule? | Phospholipids |
| How do phospholipids create the bilayer structure of cell and organelle membranes? | They position their hydrophilic heads to the water outside the cell in one row and in the second row their orientation is flipped so the heads interact with the water inside the cell |
| What is the monomer of nucleic acids? | Nucleotides |
| What is the polymer of nucleotides? | Nucleic acid |
| What are the 3 components of nucleotides? | 1) a phosphate group 2) a 5-carbon (pentose) sugar 3) a nitrogenous base |
| What is the 5-carbon sugar called in RNA and what makes it distinct from its counterpart in DNA? | Ribose which has hydroxyl groups (OHs) on both C2 and C3 |
| What is the 5 carbon sugar called in DNA and what makes it distinct from its counterpart in RNA? | Deoxyribose which lacks a hydroxyl group (OH) at C2 (only has one at C3) |
| What are the 2 types of nitrogenous bases? | Purines and pyridines |
| Do purines or pyridines have 2 rings? | Purines have 2 rings |
| What are the purine nitrogenous bases? | A (Adenine) and G (Guanine) |
| What are the pyridine nitorgenous bases? | C (Cytosine), U (Uracil) in RNA, and T (Thymine) in DNA |
| What are the 3 major roles of nucleotides? | Information storage (most obvious and important), singaling, and energy |
| How are the nucleotide monomers linked together to form nucleic acid? | Through covalent phosphodiester bonds |
| How can you tell a nucleic acid's 5' end? | The 5' end has a free phosphate group on the 5' carbon of the sugar |
| How can you tell a nucleic acid's 3' end? | The 3' end has a free hydroxyl group on the 3' carbon of the sugar |
| Should double-stranded nucleic acids be parallel to one another or anti-parallel? | Antiparallel |
| How are the two strands of nucleid acids held together? | By complementary base-pairing H-bonds |
| Between what types of nucleic acids could base-pairing occur? | Between DNA and DNA, between DNA and RNA, and between RNA and RNA |
| What is the double helix structure of paired DNA strands? | There is a sugar-phosphate backbone on the outside and the nitrogenous bases face in towards each other |
| How many H-bonds are needed to base-pair A and U/T? | 2 H-bonds |
| How many H-bonds are needed to base-pair G and C? | 3 H-bonds |
| What is the order of events from the DNA structure to the Protein? | DNA structure---(Transcription)---> RNA ---(Translation)---> Amino Acids ---(Protein folding)---> Protein |
| T or F: Changing, adding, or deleting nucleotide(s) will not alter the amino acid sequence of a protein. | False, the order and identity of nucleotides in protein coding genes specifies the order and idenity of amino acids in a protein, thus changing, adding, or deleting them would alter the amino acid sequence of the protein (ex Sickle Cell) |
| What is the first rule of nucleic acid synthesis? | Two strands of nucleic acid must be anti-parallel in order to base pair. |
| How is the template strand read? | Always from the 3' to the 5' end |
| What is the second rule of nucleic acid synthesis? | New nucleotides can only be added to a free 3' hydroxyl (OH) group. Thus the new strand will be built in the 5' to 3' direction. (Remeber: template ALWAYS read from 3' to 5', new strand ALWAYS built 5' to 3') |
| What is the third rule of nucleic acid synthesis? | The enzyme making the new strand of DNA or RNA determines which nucleotide (base) to insert by reading the template strand. They are complementary! |
| What is the RNA created in transcritption? | mRNA, a sequence of nucleotides complementary to the gene's DNA code that will code for a protein |
| Genome | All the DNA of an organism |
| Chromosome | Long DNA molecule coiled around proteins and compacted |
| Gene | Segment of DNA that codes for a product (only some DNA is genes ~1-2% , much is non-coding) |
| What encodes RNA? | Genes |
| Messanger RNAs (mRNAs) | Serve the function of coding for a protein |
| Non-coding RNAs | Serve their function as RNAs and are not made into proteins |
| What are the differences between DNA and RNA? | DNA: -double stranded -A,C,G,T as bases -H on C2 of sugar (deoxyribose) RNA: -single strand -A,C,G,U as bases -OH on C2 (ribose sugar) |
| Where in the cell does transcription occur? | In the nucleus |
| Where in the cell does RNA processing (only in Eukaryotes) occur? | In the nucleus |
| Where in the cell does translation occur? | In the cytoplasm |
| What happens during transcription? | Creates an RNA whose nucleotides are complementary to those of the DNA template strand of a gene |
| What enzyme carries out transcription? | RNA polymerase |
| What is an enzyme? | Molecules (usually proteins) that catlyze and speed up chemical reactions |
| What are the phases of transcription? (3) | 1) Initiation 2) Elongation 3) Termination |
| What are the 4 basic parts of a gene? | 1) promoter 2) initiation site 3) transcribed region 4) termination site |
| What is the promoter of a gene? | The DNA region where RNA polymerase initially binds. This area is not copied into RNA |
| What is the initiation site of a gene? | Where transcription begins: the first DNA nucleotide copied into RNA |
| What is the transcribed region of a gene? | The DNA region with nucleotides that are copied into RNA |
| What is the termination site of a gene? | Where transcription ends: the signal for RNA polymerase to cease copying to DNA |
| What enzyme does RNA polymerase contain? | Helicase |
| What does helicase do? | It is an enzyme that facilitates the breaking of hydrigen bonds between the DNA strands to expose the template strand for use. (forms a "transcription bubble"). |
| What occurs during transcription initiation? | RNA polymerase binds to the promoter DNA region |
| What happens during transcription elongation? | RNA polymerase moves along the template DNA strand, synthesizing a complementary RNA strand using ribonucleotide triphosphates (NTPs) |
| T or F: Both strands of DNA are used to make the RNA in transcription. | False, just the one template DNA strand is used |
| What occurs during transcription termination? | The RNA polymerase reaches the termination site and falls of the DNA, as the new RNA is released |
| T or F: Many RNA transcripts are produced from a single gene. | True |
| What does RNA processing in Eukaryotes entail? | Splicing, capping, and tailing the RNA |
| What is added to the 5' end in RNA processing? | A 5' cap is added |
| What is added to the 3' end in RNA processing? | A 3' tail of many A (adenine) nucleotides is added |
| What does splicing do to the pre-mRNA during processing? | Removes any introns |
| What are the purpose of the 5' cap and the 3' tail (more generally, RNA processing)? | To stabalize the mRNA and facilitate its export from the nucleus |
| What are snRNPs? | particles that are complexes of proteins and snRNAs (a non-coding RNA) that bind exon/intron boundaries and together several can form the spliceosome |
| What is the spliceosome? | Made up of several snRNPs, it removes introns (which are degraded) from the pre-mRNA, then it ligates the exons together |
| Where and through what does the mature mRNA made in RNA processing go? | Exported from the nucleus to the cytoplasm through nuclear pores |
| Where in the cell does translation (mRNA to protein) occur? | In the cytoplasm |
| What are the requirements necessary for translation? (4) | -mRNA -tRNA with the appropriate amino acids attached -Ribsomes -Release factor proteins |
| What is a codon? | 3 mRNA nucleotides that code for 1 amino acid |
| How does the ribsome find the correct codon to begin translation? | It scans the mRNA from the 5' end until it finds the start codon (AUG), and it begins with that codon, setting the reading frame |
| What is a codon table? | Shows the triplets (codons) in mRNA that will result in specific amino acids being added to a protein |
| What are the 5' and 3' UTRs (untranslated regions) | Parts of the mRNA that have been transcribed, but do not get translated (region outside the start and stop codons) |
| Do stop codons encode amino acids? | No |
| What do transfer RNAs (tRNAs) do? | Translate between the language of codons and the language of amino acids |
| What is a charged tRNA? | tRNA with its bound amino acid |
| What does the tRNA structure consist of? | An anticodon that binds to the mRNA strand (complementary and antiparallel) and an amino acid that matches the codon presented by the mRNA (NOT ITS OWN ANTI-CODON) |
| Where in the cytoplasm does translation occur? | Within a ribosome, a huge complex of proteins and ribsomal RNAs (rRNAs) |
| What are the 3 tRNA binding sites? | The E site, the P site, and the A site |
| What happens during translation initiation? | The small ribosomal subunit attaches to the 5' cap of mRNA and scans base by base until it finds AUG (start codon) which allows the large subunit to bind and set the reading frame |
| What happens during translation elongation? | Charged tRNAs drift in and out of the A site until the correct tRNA bonds with the mRNA codon through complementary base pairing. Peptide bonds will form between amino acids. |
| T or F: The cytoplasm contains a pool of every possible tRNA. | True |
| How are the peptide bonds formed during translation? | The ribosome's peptidyl transferase activity catalyzes the condensation reaction between the amino acids |
| How does the ribsome and tRNA shift during translation elongation? | After forming the peptide bond, the ribsome shifts down the tRNA as the first tRNA is shifted from the P to the E site, Exiting the ribosome, and the second tRNA is shifted from the A to the P site |
| What occurs at each binding site (w/ tRNA and the amino acids attached)? | E--> No amino acid attached to tRNA anymore and tRNA begins to dissociate from the ribosome P--> Has growing chain of amino acids attached to its tRNA and tRNA is attached to mRNA strand A---> has amino acid and is arriving to be bonded to the m-RNA |
| What happens during translation termination? | A release factor binds to the mRNA in the A-site at the stop codon and releases the created polypeptide chain, while the ribsome and mRNA separate |
| T or F: A single mRNA translates to one copy of a polypeptide. | False, a signle mRNA can be used to translate many copies of the same polypeptide |
| What does the amount of protein produced from a single strand of mRNA depend on? (3) | 1) The amount of transcription 2) The stability of the mRNA transcript 3) How efficiently ribosomes can bind to and translate mRNA |
| T or F: All proteins are complete after translation? | False, proteins fold into their 3D shape and could undergo modifications that are essential to their function |
| What are 3 examples of post-translation modification in proteins? | 1) Phosphorylation--> added phosphate groups that alter the shape of the prot. 2) Glycosylation --> adding sugars, important for prot.'s targeting and recognition 3) Proteolysis--> Cleaving the polypeptide, allows prot. fragments to fold in new shapes |
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