Bio Exam 2

Bio exam 2

similarities of the structures of DNA and RNA

• nucleotide monomers: both molecules are polymers made of repeating units called nucleotides

• every nucleotide has three identical base component

  • phosphate group

  • 5 Carbon sugar

  • nitrogenous base

• sugar phosphate backbone

  • individual nucleotides in both chains link together via covalent phosphodiester bonds connecting phosphate group of one sugar to the hydroxyl group of the other

• shared nitrogenous bases

  • adenine

  • guanine

  • cytosine

• complementary base pairings

  • both molecules use hydrogen bonding for complementary base interactions

  • A - U/T

  • G - C

similarities in DNA replication and transcription

• requires DNA template

• occurs in nucleus of eukaryotic cells

• DNA helix must be opened

• specific DNA sequences act as start signals

• new nucleic acids strand is complementary to DNA template

• polymerase enzyme connects nucleotides via covalent bonds (phosphodiester bonds)

• nucleic acid strands formed in specific directions by polymerase enzyme

  • phosphate group end to -OH end

Differences in DNA replication and transcription

Transcription

• start signal = promoter

• stop signal = terminator

• no primer needed

• one strand transcribed (one DNA strand serves as template)

• RNA polymerase

• forms RNA strands (RNA nucleotides. U)

• a gene can be transcribed many time or not at all before cell division

DNA Replication

• start signal = origin of replication

• no stop signal

• requires RNA primers

• both strands are replicated and both serve as template

• DNA polymerase

• forms DNA strand (uses DNA nucleotide. T)

• all DNA replicated only once before cell division)

Mutations are

• not always harmful

what is a mutation that changes a base pair but the amino acid produced in translation stays the same

• silent mutation

a frameshift mutation (insertion or deletion) of one nucleotide at the beginning of a coding region causes a ___ impact than a frameshift mutation at end of coding region

Bigger

add or delete early will affect every codon afterwords

causes polypeptide folding to change

an error made by RNA polymerase during transcription is less harmful to an organism than a mutation in DNA because the faulty RNA is temporary and not passed on to daughter

true

different types of mutation

substitution

• silent

  • changes base pair but amino acid produced in translation is the same

• nonsense

  • codon that codes for something else is turned into a stop codon earlier on

• missense

  • one nucleotide is changed

  • alter a codon that specifies a specific amino acid and changes the codon to one that specifies a different amino acid

insertions and deletions

• lose or add a nucleotide

• messes up everything else after the mutation

• unless multiple of 3 nucleotides are added or deleted nothing changes and only adds an amino acid

what type of mutation is occurring is occurring when UAC changes into a UAA (stop)

Nonsense mutation

redundancy principle

• different(multiple) codons can produce same amino acid

• helps transcription and translation because small errors might not be bigger errors

mice experiment

• griffiths 1920s findings

• information required for bacteria to cause pneumonia can be passed from dead to living and cannot be destroyed by boiling

mice experiment group and control groups

• controls

  • live harmless

  • live pathogenic

  • heat killed pathogenic

• experimental

  • heat killed pathogenic + live harmless

what information did each control in the mice experiment provide

if heat actually killed the pathogenic bacteria

tRNA

attaches amino acids and anticodons

anticodons are three nucleotides tRNA that interact with complementary mRNA codon

translation occurs ____ transcription

• after

• lallygagging or late

• translating from a different language

• transcribe to get the new mRNA

• mRNA is translated into a new language

enzymes attach Amino acids to trna. these are then used in translation with a ribosome to create a polypeptide chain. what is special about these enzymes?

they are almost always accurate

what bonds form between complementary nucleotides, codon and anticodons, strands of DNA

hydrogen bonds

what are two ways you can figure out the mRNA sequence when the DNA sequence is given to you

• coding vs template strand

• mRNA is compliment to template strand A in template = U

• Exact same as coding strand but swap T for U

Rna polymerase copies off the ___ strand

template

deoxyribose vs Ribose

• only 1 hydroxyl

• full hydroxyl group = 2

how many ORIs are there in prokaryotic vs eukaryotic

• multiple in eukaryotic

• one in prokaryotic

why does the enzyme ligase only work on one strand (formed away from replication fork)

• needs to connect the section

• leading strand is continuous DNA replication with DNA polymerase and has no fragments

• lagging strand has fragments because it is going the wrong way so more nucleotides are being put out so DNA polymerase has to go back up to helicase

• ligase acts as glue that holds it together

• fragments are Okazaki fragments

DNA helicase unwinds in the DNA strands

• DNA polymerase attaches these strands and needs a RNA primer

• two DNA polymerase attach to each replication fork - two template strands to copy

• DNA ligase links the separate strands together on lagging strand

• bonds being added to connect nucleotides are covalent bonds

steps of DNA replication

• ORI opens

• DNA helicase unwinds DNA

• DNA polymerase forms the new strands

• DNA ligase glues together the fragments from lagging strands

transcription

• transcribing DNA and turning it into mRNA

• RNA polymerase takes DNA and turns it into RNA

transcription steps

• RNA polymerase binds to the promoter sequence

• DNA helix must be opened to allow transcription

• new RNA strand Is formed from phosphate group end to hydroxyl group end

• RNA strand separates from DNA template as RNA travels along the gene sequence

• RNA polymerase transcribes terminator sequence

• RNA polymerase releases DNA and RNA and can transcribes gene again

eukaryotic mRNA processing/splicing

• what happens first in mRNA processing: five prime cap and a poly-a tail

  • why does this happen: so it is more durable and won’t be degraded as it is moved into the cytoplasm and so it can be exported and translated efficiently

splicing

it allows one gene to make different versions of mRNA

mRNA leaves nucleus and goes to cytoplasm where translation happens

translation

• mRNA needs to be found by a ribosome and attaches to it

• initiation - start signal = AUG

• tRNA and the amino acid

• tRNA has the anticodon UAC it is the complement of AUG

Translation steps

initiation: Ribosome and first tRNA assemble at the start codon

• tRNA with anticodon complementary to start codon interacts with mRNA (AUG signals start)

elongation: polypeptide chain formed as ribosomes move along the mRNA

• moves from phosphate end to hydroxyl end

• tRNA with anticodon complementary to second codon interacts with mRNA

• Met attached by covalent bond next to amino acid (catalyzed by rRNA)

• ribosome shifts one codon (toward hydroxyl group end)

• chain of Amino acids are connected by covalent bond

• empty tRNA ejected (enzymes pick it up and attach to new amino acid)

termination: stop codon reached

• no tRNAs in cells with anticodons complementary to stop codons (no stop codon corresponds with Amino acids)

• components disassemble

  • finished polypeptide

  • ribosome (unchanged)

  • mRNA (unchanged)

Termination

• stops transcription

Why is it important that the enzymes that bond amino acids to the tRNAs are correct and what happens if the enzymes set the genetic code incorrectly

• the protein will not work properly

• the proteins will not function correctly and organisms cannot survive with incorrect enzyme

why is it important that the enzymes that bond amino acids to the tRNA are correct and what happens if the enzymes set the genetic code incorrectly

• the protein will not properly

• the proteins will not function correctly and organism cannot survive with incorrect enzyme

what’s the sequence of the polypeptide produced by expression of this gene (whole region of DNA that gets transcribed is show)

• complementary to template strand

• the coding strand but swap t for u

stop codons

UGA

UAG

UAA

nonsense mutation

• genetic change in DNA that turns amino acid into premature stop codon

silent mutation

• change in DNA nucleotide sequence but it does not alter the resulting amino acid sequence

• DNA and mRNA will be different but structure of polypeptide will not

missense mutation

• change in a single nucleotide base causes a different amino acid to be encoded at the position

splicing allows different polypeptides to be produced under different conditions by expression of the same gene

DNA replication vs transcription

DNA replication: copies entire genome using both strands as templates to produce identical daughter helices

transcription: only uses a single template strand of DNA to synthesize a specific RNA molecule

start and stop signals for DNA replication, Transcription, translation

DNA replication: ORI (start) and there is no stop signal

Transcription: promoter (start) and terminator (stop)

Translation: AUG/met/start and stop/no amino acid

what does it mean that genetic code is unambiguous

• each codonspecifies only one amino acid

genetic code is non overlapping

• each nucleotide in mRNA is part of only one codon (triplet)

distinction of unambiguous and redundancy

• while multiple different codons can point to the same amino acid a single codon never codes for two or more different amino acids

translation statements

• ribosomes move along mRNA

• covalent bonds are formed between amino acids

• mRNA is translated in a specific direction

why do enzymes that attach amino acids to tRNAs determine which codons correspond to which amino acids

• tRNA will interact with a complementary codon during translation

• whatever amino acid is attached gets added at that codon

what does antiparallel mean

• base pairing: the opposite orientation allows nitrogenous bases to face inward and form stable hydrogen bonds

• DNA replication: DNA polymerases only add new nucleotides and the template runs in opposite directions

type of bond that connects nucleotides within a strand

phosphodiester

type of bond that holds two stands of DNA molecule together

• hydrogen bonds

Differences in DNA and RNA

• DNA

  • double stranded and has double helix

  • contains deoxyribose

  • pairs A with T

  • extremely long molecules that are stable and forever

  • built for error resistant archival storage thats permanent

• RNA

  • temporary shorter molecules

  • pairs A with U

  • contains ribose

  • single stranded

  • built for temporary, versatile execution

gene

specific segment of DNA that contains instructions to make a protein or molecule

Genome

• genome is the complete set of all genetic material in an organism

difference between coding and template strand

• they are two complementary dna strands in transcription

• template strand

  • actual strand that RNA polymerase reads to build mRNA transcript

  • nucleotide sequence is complementary to both mRNA and coding

• coding strand

  • strand that is not read directly by RNA polymerase

  • matches mRNA besides Ts

  • nucleotide sequence is identical to mRNA transcript but T is replaced by U

why do DNA strands of double helix have to be separated for transcription

• so that the enzyme RNA polymerase can access the nucleotide sequence and use one strand as a template to build complementary mRNA

nucleotide

• fundamental building blocks of nucleic acids

• contains three parts

  • five carbon pentose sugar

  • phosphate group

  • nitrogenous base

nucleic acid

• express genetic information in living cells and viruses

nitrogenous base

• pair up to form rungs of nucleic acid ladder/double helix

• store genetic information

• building blocks of DNA and RNA

phosphodiester bond

strong covalent chemical bond

formed between the sugar phosphate backbone

antiparallel

• two strands of double helix run in opposite directions

• sugar phosphate backbone

• interior base pairs

• opposite orientation

origin of replication

• where DNA replication starts

• multiple in eukaryotic cells (multiple linear chromosomes)

• one in prokaryotic cells (circular singular chromosome)

rna primer

• short strand that serves as necessary starting point for DNA synthesis during DNA replication

• binds to a single stranded DNA template

if one eukaryotic gene produces different proteins through mRNA splicing the proteins would

likely share some similarities

describe both DNA replication and transcription

• a polymerase enzyme forms a complementary strand

• new strands are formed in a specific direction

• a specific DNA sequence indicates start

why is it important that the genetic code is unambiguous

• it ensures that translation of a specific mRNA sequence always generates the same amino acid sequence

what correctly describes tRNAs in cells

• specific type of tRNA can only be attached to one type of amino acid

• the anticodon of a tRNA determines with which codon of mRNA it interacts

• the enzymes that attach amino acids to tRNAs determine which codons correspond to which amino acids

• a tRNA only has one anticodon

insertions and deletions cause

more structural and functional alteration in a protein than a substitution mutation

if something is added prior to the start codon

it will not affect transcription and cause the least amount of protein structural alteration

insertion has the potential to alter

• only amino acids specified by codons AFTER the inserted nucleotide

• insertion can alter the length of the polypeptide

mutation that changes UGU to UGG

• missense mutation

• polypeptide will have one different amino acid

mutation that changes UGU to UGC

silent mutation

no difference in polypeptide chain

mutation that changes UGU to UGA

• nonsense mutation

• shorter polypeptide chain

what type of substitution mutation alters both DNA sequence and polypeptide sequence

• nonsense and missense

how the structural differences of DNA and RNA relate to their respective roles

why can transcription occur without translation but not vice versa

• transcription has to copy a segment of DNA into mRNA

• Translation is only built to read and accept mRNA strand not the DNA

why do the enzymes that attach amino acids to tRNAs determine which codons correspond to which amino acid cells

• aminoacyl-tRNA syntheses determine which codons correspond to which amino acids because they act as the physical translator of the genetic code

mutation affects DNA not

mRNA or RNA. It is a affect on DNA

cap and poly-a tail

added to pre-mRNA during processing to create a stable and mature messenger RNA (mRNA) ready for translation

tRNAs

• reads mRNA codons and delivers the matching amino acid to the ribosome

• each tRNA has a three nucleotide sequence of an anticodon that base pairs with a codon

• the opposite end of the tRNA covalently binds to a specific amino acid which was previously loaded onto it by an aminoacyl-tRNA synthetase enzyme

• polypeptide synthesis is where inside the ribosome the tRNA places its amino acid next to the growing protein chain and help them link to peptide bond

___ bonds connect nucleotides within a strand of DNA and the two strands of DNA molecule are held together by __ bonds

covalent, hydrogen

in DNA replication

100% of the chromosome is copied

it occurs only once

what part of DNAs structure allows it to be copied

nucleotides paired up in a specific way

transcription involves using DNA as a template to form a new RNA strand. in what ways are DNA and RNA similar?

• complementary nucleotides can interact via hydrogen bonds

• strands have a direction because the two ends are different

• nucleotides in a strand are connected by covalent bonds (phosphodiester)

which correctly describes transcription in eukaryotic vs prokaryotic

• transcription occurs in the nucleus in eukaryotic cells and in the cytoplasm in prokaryotic

is it possible for two protiens to have the exact same amino acid composition but different structures?

yes

amino acids in translation also include

the start (AUG)/met

what would happen if a particular type of tRNA could be connected to different types of amino acids

• a specific mRNA sequence could be translated into different amino acid sequences