BIOL 200

what are informational polymers

polymers with more than one kind of polymer

3 examples of informational polymers

DNA, RNA, protein

what are the 2 components of an informational biopolymer

a common element and a characteristic element

where does the backbone form in an informational polymer and what kind of bond is it

between the common elements; covalent bond

what do the characteristic elements become in informational polymers

side chains

what determines the information in an informational biopolymer

the sequence of the monomer elements

what happens if a monomer has 1 joining site

it can only make a dimer (2 monomers)

what happens if a monomer has 2 joining sites

they can form linear polymers of infinite length

when is a monomer symmetrical

when both joining sites are chemically identical

what happens when a monomer has 3 joining sites

it can form branched polymers

why aren’t informational biopolymers branched

because linear molecules are easier to pack tightly (ex: DNA packing)

when are informational polymers circular

when 2 ends are joined, but they are usually linear

what kind of monomers are informational biopolymers made of

asymmetric monomers

what are asymmetric monomers

when a monomer has 2 chemically different joining sites

what is the main condition of informational biopolymers

growth of the chain only occurs at one end, unidirectionally

what is the polymer and chain length for nucleotides

nucleic acids; 1000 to 10^8

what is the polymer and chain length for amino acids

protein; 100-1000

what is the characteristic element of a nucleotide monomer

heterocyclic base

what is a heterocyclic base

a ring that contains more than one kind of atom (ex: N and C)

what is the common element of a nucleotide monomer

pentose sugar phosphate

what is a pentose

a 5 carbon sugar

what are the 2 joining sites on the common element of nucleotides

the 5’ phosphate and the 3’ hydroxyl on the pentose

which end do monomers add onto a nucleic acid polymer

3’

what is the structural difference between DNA and RNA

RNA has a hydroxyl group on the 2’ carbon, DNA just has a hydrogen on the 2’ carbon

why is DNA more stable than RNA in water

because the absence of the oxygen on the 2’ carbon, so it is less reactive to hydrolysis

which came first RNA or DNA

RNA

what are the purines

adenine and guanine

what are the pyrimidines

uracil, thymine, cytosine

where does the N glycosidic bond occur and why is it important

between the 1’ carbon of the ribose and the nitrogen on the 9’ carbon of the base. it is a key linkage in DNA repair

what is the difference between thymine and uracil

thymine has a methyl group on the 5’ carbon

why is thymine found in DNA and uracil found in RNA

because damage in DNA is more easily repairable with thymine

what links 2 adjacent nucleotides together in a DNA molecule

phosphodiester bond

which end of a DNA chain would a nucleotide be added to

3’

what is the characteristic element of an amino acid monomer

the amino acid side chain (R)

what is the common element of an amino acid monomer

the alpha carbon, carboxyl group, and amino group

is the amino acid group basic or acidic

basic

is the carboxyl group basic or acidic

acidic

what kind of stereoisomers are used in protein synthesis

L

where are the 2 joining sites in protein polymers

the amino group and the carboxyl group

which end do monomers add onto a protein chain

carboxyl end (c-terminus)

what is the link between adjacent amino acids

peptide bond

how are monomers added to a polymer chain

they are energized when a high energy bond is broken

which way is favoured when energy is released via a breaking bond

forwards reaction/growing polymer chain

what is a nucleoside

a heterocyclic base with just the pentose sugar

what happens when the nucleoside triphosphate is incorporated into the nucleic acid chain

the 2 outer phosphates are kicked out

what form are amino acid monomers

high energy amino acyl-tRNA esters

what happens when amino acid monomers are being added

the high energy ester bond is broken and the tRNA molecule is kicked out so the next amino acid can connect

why can’t energized monomers join a chain by themselves

an enzyme needs to catalyze the linkage reaction

what is the template, enzyme, and energized monomer for DNA

DNA; DNA polymerase, dNTP

what is the template, enzyme, and energized monomer for RNA

DNA; RNA polymerase, rNTP

what is the template, enzyme, and energized monomer for protein

mRNA; ribosome, aminoacyl tRNA

what holds together 2 DNA strands

hydrogen bonds

what is the general structure of the DNA strands

sugar phosphate backbone on outside, base pairs on inside

what is the significance of major and minor grooves

DNA binding proteins can make contact with base pairs at the major or minor grooves without separating the strands

what is denaturation and how does it occur

DNA strand separation when DNA is heated in water to break the hydrogen bonds

what is renaturation

when denaturated DNA strands can reform complementary base pairs by cooling down DNA

what is the Tm of DNA

the temperature where half of the DNA is separated

what is the relationship between Tm and base pairs

the more G-C base pairs, the higher the Tm

what is the central dogma of molecular biology

DNA to RNA to protein

what is transcription

when DNA gets turned into RNA

what is translation

when RNA turns into protein

what is local melting

when a region of DNA is separated into 2

how do rNTPs diffuse

randomly; any base pair can approach the template base, but RNA polymerase will only link them if they are compatible

what happens at the 3’ end of the RNA chain during transcription

the 3’ OH attacks the alpha phosphate of the incoming rNTP, and the gamma diphosphate is dropped

what is the difference between the new RNA strand formed in transcription and the nontemplate strand

they are identical except the RNA strand contains U instead of T, and has a ribose sugar backbone. they are both complementary and antiparallel to the template strand.

what is a transcription bubble

a loop of the nontemplate strand that is unwound by helicase

what is the promoter

the region where RNA polymerase initially binds to the DNA to start transcription

how does DNA helicase separate strands

it uses the energy of ATP to separate the strands

what happens as RNA polymerase moves down the DNA chain

the original DNA strands reconnect behind RNA polymerase and kicks out the new RNA strand.

what happens at a stop site

RNA polymerase is destabilized and falls off the DNA chain, releasing the newly RNA chain

what are some similarities between transcription and DNA replication

DNA is used as the template strand, the new strand is synthesized 5’ to 3’, helicase is used to expose the template, same reaction of 3’ OH attacking alpha phosphate and dropping gamma diphosphate.

what are some differences between transcription and DNA replication

monomer for transcription are rNTPs, monomer for replication are dNTPs, transcription has promoters and stop sites, replication has replication origins but no stop sites, in transcription the new RNA strand separates from the template strand but in replication the new DNA never separates from the template strand.

what is the start and result of transcription

start with one molecule of double sided DNA and end with one molecule of double stranded DNA and the RNA single strand

what is the start and result of DNA replication

start with one molecule of double stranded DNA and end with 2 molecules of double stranded DNA

what are 2 examples of direct interaction

during replication and translation DNA has physical interaction with the next monomer via the dNTP and rNTP

what is an example of indirect interaction

mRNA does not touch aminoacyl tRNA to make proteins during translation

what are 2 functions of tRNA

acts as an adaptor between the template and growing chain, and adding tRNA adds a high energy version of amino acids

what form of amino acid monomers are used to form proteins

high energy amino acyl-tRNA esters

what is the difference between codons and anticodons and where are they located

a codon codes for the amino acid, located on the mRNA, an anticodon is attached to the tRNA which matches with the codon.

what is a ribozyme

a half RNA and half protein molecule that facilitates protein synthesis

what is the peptidyl transferase reaction and what is it catalyzed by

when amino acids are added to the polypeptide chain, catalyzed by the large subunit of the rRNA molecule

what is the RNA world hypothesis

that RNA evolved before DNA and proteins, because ribozyme functions as a protein and contains RNA

what is the basic biological point of DNA and RNA

to allow the synthesis of specific proteins which carry out the physical and chemical functions of cells

what is the largest known protein and its length

titin, a muscle protein, 30 000 amino acids

what is the primary structure of a protein

the sequence of amino acids which determines its shape via amino acid side chains

what determines the primary structure of a protein

DNA from your genome

what are the 2 classes of amino acid side chains

hydrophilic and hydrophobic

what are the main characteristics of hydrophilic amino acids

have a polar charge and interact well with water

what is the hydrophobic effect

water molecules around a hydrophobic molecule forms a cage like low entropy structure. when hydrophobic molecules join, some water molecules are released freely increasing the entropy, causing the formation of hydrophobic and aqueous phases.

why do oil and water separate over time

because entropy increases over time, which favours the congregation of hydrophobic molecules surrounded by water

what is the oil drop model of protein folding

an infinite number of possible structures can exist, but each protein only has one true conformation, where hydrophilic side chains are on the outside and hydrophobic on inside

what are the 5 main kinds of functions of proteins

structure, movement, molecular transformation, signalling, transport

what kinds of shapes do secondary structures of proteins form

alpha helix and beta pleated sheets

what is a domain

a 40 amino acid long region that is compactly folded and made of various motifs, which can hold its structure independently

what is a homodimer

a structure that is made up of 2 of the same molecule

why do multiple polypeptides bind together

because they have complementary surfaces

what is the role of DNA in protein function

DNA indirectly determines protein function because it determines the amino acid sequence, which determines the 3D shape

what is the secondary structure of a protein

local conformations of the peptide chain backbone which form alpha helices and beta sheets

what is the general structure of an alpha helix or beta sheet

the hydrogen bonding between peptide bond carbonyl oxygen atoms on AA1 and amino group hydrogens on AA2

how much of a polypeptide chain is made of alpha helices or beta sheets

60%