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DNA rep/tran
biol 1210 DNA replication, transcription & translation
| Question | Answer |
|---|---|
| (review) what parts of nucleotides form the backbone of polynucleotides? | phosphate groups & pentose sugar |
| (review) what is the name of the connection between nucleotides? | phosphodiester linkage (type of dehydration synthesis) |
| (review) during synthesis of polynucleotides, are nucleotides added to the 5' or 3'? | 3' end |
| (review) what is the direction of polynucleotide synthesis? | 5' to 3' |
| (review) why do purines only pair up with pyrimidines? | due to the bases' structural shape. Pyimidines x pyrimidines = too much space, purine x purine = not enough space, purine x pyrimidine = perfect fit |
| (review) why does adenine pair specifically with thymine or uracil, while guanine pairs with cytosine? | due to the # of hydrogen bonds between nitrogenous bases (H - - O or H - - N). A & T/U = 2 bonds, G & C = 3 bonds |
| (review) list 3 differences between DNA & RNA molecules | DNA - 2 strands, thymine, deoxyribose. RNA - 1 strand, uracil, ribose |
| (review) in DNA molecule, 15% of bases are adenine. Can you calculate the rest? If yes, what are each of the bases %? | yes. 15% A = 15% T, 100% - 30% = 60% -> 30% G, 30% C |
| (review) in RNA molecule, 15% of the bases are adenine. Can you calculate the rest? If yes, what are each of the bases %? | no. RNA is single stranded (no complementary base pairing) so we cannot calculate it |
| draw a DNA molecule 4 pentoses long, labelling: nucleotide & its parts, phosphodiester linkage, sugar-phosphate backbone, hydrogen bonds btwn bases, Van der Waals interactions, and indicate 3' to 5' or 5' to 3' direction | see notes p. 3 |
| (review) in which phase of cell cycle does DNA get replicated, and in which phase are the copies separated | replicated: S-phase of interphase. Separated: Anaphase of mitosis of M-phase |
| what feature of DNA makes replication possible? | complementary base pairing |
| describe semi-conservative model of DNA replication | 2 strands are complementary - each strand acts as a template for building new strand. Parent molecule unwinds, 2 new daughter strands are built based on base-pairing rules, each consisting of 1 parent (old) and 1 new strand |
| origins of replication | special sites where DNA replication starts and the two parental strands are separated, opening up "replication bubble" |
| how many origins of replication are there? | prokaryote - 1, eukaryote - 10k to 100k |
| direction of replication in "bubble" | replication proceeds in both directions from each origin until the entire molecule is complete |
| replication fork | a Y-shaped region at the end of each replication bubble where new DNA strands are elongating |
| DNA helicase | enzymes that separate the 2 strands of the double helix at the replication forks |
| single-strand DNA binding protein (SSBP) | binds to and stabilizes single-stranded DNA until it can be used as a template |
| topoisomerase | enzyme that corrects "overwinding" ahead of replication forks by breaking, swiveling and rejoining DNA strands |
| DNA polymerase | catalyze the elongation of new DNA at a replication fork. They cannot add if there is no -OH group on the end of pentose, therefore, need an RNA primer on the DNA template strand & cannot initiate synthesis of a polynucleotide |
| (review) what does 3' and 5' end of polynucleotide mean? | Carbon 3' on the pentose of a nucleotide has OH where the nucleotide is added, and the 5' carbon of the pentose had a phosphate group |
| primase | starts an RNA chain from scratch and adds RNA nucleotides one at a time using parental DNA as template. The RNA Primer is short (5-10 nucleotides), added at the 5' end of each new strand and its 3' end is the starting point for new DNA strand |
| why do we need a primer? | when the DNA molecule is initially unzipped, there is no -OH group on the 3' carbon = DNA polymerase cannot add nucleotides. Therefore, need a primer first |
| in which directions is the DNA molecule read vs grown? | Read 3' to 5', grows 5' to 3' |
| nucleoside triphosphate + examples | each nucleotide added to a growing DNA strand initially starts as a nucleoside triphosphate (base + ribose + 3 phosphate groups). Ex. Adenosine triphosphate (dATP), dCTP, dGTP, dTTP. As each monomer joins DNA strand, it loses 2 phosphate groups in process |
| difference between ATP & dATP | dATP - deoxyribose, ATP - ribose |
| describe how antiparallel structure of double helix affects replication | DNA polymerases add nucleotides only to free 3' end of growing strand, therefore DNA only elongates in 5' to 3' direction. Results in a leading & lagging strand in the replication bubble growing in opposite directions |
| leading strand | DNA polymerase III synthesizes continuously, moving towards the replication fork (towards direction of DNA unwinding) |
| lagging strand | DNA polymerase III must work in direction away from the replication fork, leaving behind regions of single-stranded DNA. Hence it is synthesizes as series of Okazaki fragments joined by DNA ligase |
| describe DNA replication by #s in bacteria | genome of 5 million base pairs, 1 circular chromosome, 1 origin of replication, 2k nucleotides in Okazaki fragment, 500 nucleotides/second, 20-40 min duration |
| describe DNA replication by #s in humans | genome of 3 billion base pairs, 46 linear chromosomes, 10k-100k origins of replication, 200 nucleotides per Okazaki fragment, 50 nucleotides/sec, 20 hours duration |
| DNA polymerase III | using parental DNA as template, synthesizes new DNA strand by adding nucleotides to an RNA primer or growing strand |
| DNA polymerase I | removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides |
| DNA ligase | joins Okazaki fragments of lagging strand & on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA |
| (review) central dogma of molecular biology | describes the flow of information in the cell. DNA (gene storing info) -> mRNA (delivering info) -> proteins (machine using info) |
| (review) where do transcription and translation take place in the human cell? | transcription - nucleus, translation - cytoplasm |
| steps of transcription | initiation (RNA polymerase binds to promoter and pries apart DNA strands) elongation (RNA polymerase moves along DNA, untwists double helix, adds RNA nucleotides to 3' end following base pairing rules), termination (terminator signals end of transcription |
| genetic code | specifies how a sequence of nucleotides codes for a sequence of amino acids. This occurs in triplet code; codons: a group of 3 bases that specifies for a particular amino acid |
| why does the genetic code have to be in triplets? | to translate nucleotides -> amino acids we need 3 nucleotides:1 amino acid. We only have 4 bases but need to make 20 dif. amino acids, so we need to make combinations. 2 nucleotides/amino acid is not enough (16 possible), 3 nucleotides = 64 possible |
| describe types of the 64 codons | 61 code for amino acids, 1 codes for the start of an amino acid sequence (AUG), 3 are "stop" signals to end translation |
| genetic code is "redundant but not ambiguous" | more than 1 codon codes for 1 specific amino acid, but not ambiguous - 1 codon does not code for 2+ amino acids. Ex. CUU, UUG, UUA, CUG = leucine and each only leucine |
| genetic code is "conservative" | usually, codons coding for the same amino acid have the same first 2 amino acids ex. UC_ _ = serine |
| what does it mean codons are read in the correct frame? how is this achieved? | codons must be read in the proper groupings in order for a specified polypeptide to be produced, and for this they need to know where to start -> start codons. |
| genetic code is "nearly universal" | almost all species (not just animals) have the same genetic code (same genes specifying for the same amino acids). Hence, we can transplant genes and make cats glow in the dark! |
| genetic code is "non-overlapping" | they don't read the codon twice or mix the nucleotides - it is always in the sequence of 3 nucleotides. Ex. AUGAAACCC = AUG AAA CCC not AU GAAA CC C |
| translate mRNA using chart in notes: 5' AUGGGCCAGUAG 3' | AUG = start, GGC = Gly, CAG = Gln, UAG = stop |
| which 3' to 5' sequence of nucleotides in DNA template strand codes for polypeptide Phe-Pro-Lys? AAAGGGUUU, TTCCCCAAG, TTTCCAAAA, AAGGGCTTC or UUUCCCAAA | see notes for answer |
| where does transcription occur? what enzymes are involved? | in the nucleus only (where the DNA strands are). Completed almost solely by RNA polymerase, which unwinds, replicates, and rewinds the DNA inside itself |
| during transcription, how are the nucleotides produced? | one of the two DNA strands (template strand) orders the sequence of nucleotides in the RNA transcript. DNA is read 3' to 5', mRNA is produced 5' to 3' |
| during translation, mRNA base triplets (codons) are read in _ to _ direction. Each codon specifies for a specific ___ to be placed along a polypeptide | 5' to 3, amino acid |
| how many different amino acids are there? | 20 |
| list the 3 major types of RNA | mRNA, tRNA, rRNA |
| transcription & translation in prok vs. euk | prok: both occur in cytoplasm, often concurrently, many polyribosomes, euk: transcript in nucleus, translate in cytoplasm, transcript & translate r separate |
| overview of translation | sequences of bases in mRNA is decoded to synthesize the amino acid sequence in a protein, ribosomes catalyze translation, often forming polyribosomes. tRNAs bind to amino acids and transfer them to polypeptide |
| polyribosome | form where multiple ribosomes are attached to a single mRNA at a single time. Many copies of a protein are produced from one mRNA |
| why is transcription/translation different in prok & euk? | eukaryotes' DNA is in the nucleus and no ribosomes are in the nucleus, whereas prokaryotes' DNA is open in the nucleoid region of cytoplasm |
| tRNA structure | 75-85 nucleotides long, flattened into one plane is like cloverleaf, but hydrogen bonds twists into 3D molecule that is ~L shaped. CCA sequence at 3' end binds to amino acids, loop at opposite end is anticodon |
| aminoacyl tRNA | an enzyme made of a tRNA linked to its amino acid |
| anticodon | sequence of 3 nucleotides that base-pairs with the mRNA codon & brings amino acid to ribosome |
| describe how amino acids attach to tRNA | aminoacyl tRNA synthetases enzymes "charge" the tRNA by catalyzing the addition of amino acids to tRNAs (requires ATP). For each of 20 amino acids: different aminoacyl tRNA synthetase & 1 or more tRNA |
| wobble hypothesis | there are 61 diff. codons but only ~40 tRNAs, so the anticodon of tRNAs can still bind successfully to a codon whose third position requires nonstandard base pairing - one tRNA is able to base-pair with more than 1 codon |
| how is the wobble hypothesis possible? | the genetic code is conservative. The 1st 2 nucleotides almost always code for the same amino acid |
| ribosome structure | ribosomes contain many proteins & rRNA, made of small subunit - holds mRNA in place, & large subunit - reactions where peptide bonds form. 3 tRNAs line up inside ribosome during translation |
| tRNA sites in the ribosome | tRNAs only fit when anticodon binds to corresponding codon in mRNA. Incl: A site - arriving for aminoacyl tRNA, P site - peptide bond forms, E - where tRNAs without amino acids exit |
| steps of translation | 1. aminoacyl tRNA carrying correct anticodon for mRNA codon enters A site 2. peptide bond forms btwn amino acid on A-site tRNA & polypeptide on P-site tRNA 3. ribosome moves down mRNA by one codon and all 3 tRNAs move down 1 position |
| how do proteins grow and where is the amino acid added? | proteins grow by 1 amino acid with each repeat of the steps, amino acids always added to carboxyl (C- terminus) of polypeptide (grows Amino group -> Carboxyl end) |
| describe initiation phase of translation | begins near AUG start codon, small ribosomal subunit binds to mRNA at ribosome binding site (6 bases up from start) w initiation factors |
| initiator tRNA | 1st tRNA called initiator RNA carrying a modified methionine (start codon, f-Met) |
| translation initiation steps | 1. mRNA binds to ribosomal subunit 2. initiator tRNA bearing f-Met binds to start codon 3. large ribosomal subunit binds so initiatior is in P site |
| describe elongation phase of translation | at start: initiator tRNA in P site, E & A sites empty, aminoacyl tRNA binds to codon in A site. Peptide bond forms btwn P tRNA amino acid and A tRNA amino acid. Translocation occurs & starts growing the protein |
| translocation | ribosome slides one codon towards 3' end of mRNA w help of elongation factors. Uncharged tRNA from P site moves into E site & leaves, tRNA attached to growing peptide moves into P site & A site opened to expose new codon & able to accept new aminoacyl tRN |
| termination phase of translation | when A site encounters stop codon, release factor protein enters A site - looks like tRNAs, but doesn't carry amino acid and hydrolyzes (breaks) bond linking the P-site tRNA to polypeptide chain |
Created by:
AntBanana
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