Molecular Bio Aparicio - Midterm 1

what are nucleotides composed of?

base, sugar, phosphate

what is a nucleoside?

base + sugar

what are the main differences between RNA and DNA?

1. DNA does not have a hydroxyl group at the 2' carbon (ribose replaces deoxyribose)

2. Uracil replaces Thymine

3. RNA is almost always single stranded

what bond attached the base to the sugar in DNA and RNA?

glycosidic bond

where is the OH group found in both DNA and RNA?

3' position

where is the phosphate group found in both DNA and RNA?

5' position

purines

bases with a double ring structure, adenine and guanine

pyrimidines

bases with a single ring structure, cytosine, thymine, and uracil

where is the glycosidic bond of the base and sugar found in purines?

9 position

where is the glycosidic bond of the base and sugar found in pyrimidines?

1 position

how are nucleotides joined?

phosphodiester bonds between 3' hydroxyl of one sugar and the phosphate attached to the 5' hydroxyl of the next sugar

what charge does the backbone of DNA and RNA have?

negative

How are the two DNA strands held together?

non-covalent hydrogen bonds

how many hydrogen bonds form when A pairs with T?

2

how many hydrogen bonds form when C pairs with G?

3

what is the most energetically favorable formation of DNA?

right handed helix, helix turns in a clockwise direction

where are bases found in DNA strands?

in the center

where are sugar-phosphate backbones found in DNA strands?

outside

B-DNA

right handed helix, 10.5 base pairs per turn, base pairs are 3.4 Angstroms apart vertically

DNA is more flexible when what bases are present?

A and T

major and minor grooves

allow DNA binding proteins to recognize specific sequences without separating DNA strands

A-DNA

right handed, 11 base pairs per turn, grooves are evenly sized

Z-DNA

left handed helix, looks like a ladder

negative supercoiling

results from DNA helix being unwinded to compensate for the strain of the molecule

Toroidal supercoiling

the DNA wraps around another molecule in the cell

Interwound supercoiling

The DNA interwinds and wraps about itself

why is DNA less reactive than RNA?

because of the absence of the hydroxyl group

linkage number

number of times one strand of dna wraps around another

can linkage number change in closed circular DNA?

no

twist

the number of turns in a fragment of DNA

what does a positive twist number denote?

a right handed helix

what does a negative twist number denote?

a left handed helix

writhe

describes supercoiling of closed circular or constrained linear DNA

supercoiling formula

Lk= Tw+ Wr

Wr>0

positively coiled DNA

Wr<0

negatively coiled DNA

topoisomerases

enzymes that introduce or remove supercoils from DNA

post transcriptional modification

changes that occur to a newly transcribed primary RNA transcript, functional RNA rather than mRNA

are chemical modifications reversible?

usually permanent

why is the 2' OH in ribose so important?

it facilitates a reaction that can break phosphodiester bonds

why is DNA better for long-term information storage?

because it is more stable because it lacks the hydroxyl group on the 2' carbon

why is RNA better for dynamic information changes?

because it has the 2' hydroxyl group and because it is single stranded and thus more flexible and less constrained than DNA

what type of helix does RNA favor when double stranded, and why?

A type helix due to steric hindrance and sugar pucker

sugar pucker conformation RNA

C3' endo, favors A type helix

sugar pucker conformation DNA

C2' end form, favors B type helix

why does RNA have more inter and intra molecular interactions than DNA?

due to the 2' OH allowing RNA to form hydrogen bonds

secondary RNA structure

created by short stretches of intra molecular base pairing usually with Watson-crick base pairing and G-U, antiparallel direction

tertiary RNA structure

overall three dimensional arrangement of secondary structures and single stranded regions of the entire RNA

non Watson-crick base pairing

can occur in RNA, usually involves chemically modified bases and can introduce structural differences

Uracil and Guanine pairings

doubles uracil's chance of pairing, allows anti-codon to recognize two different codons

why is the U-G pairing known as a wobble base pair?

because the structure can wobble when sitting on mRNA

Base triple interaction

extra H bonds that form at side groups and stabilize the structure, bring three strands together for short stretches

why do RNA molecules bind to large numbers of cations?

to counteract the negative charge of the backbone, otherwise nucleotides wouldn't wanna come near DNA and it wouldn't be able to be translated

co-variations

differences that occur between species, yet conserve secondary interactions

what part of ribosomal RNA is conserved?

the ability for the sequence to make a secondary structure

what is the role of ribosomal RNA?

it catalyzes the formation of peptide bonds between amino acids in order to produce proteins by making sure tRNA and mRNA line up

proteins

made up of covalently joined amino acids

what is an amino acid made up of?

a central carbon atom (chiral), an amino group (NH3+), a carboxylate group (COO-), and an R group

what form are all amino acids in biology?

L form (amino group on left hand side)

all amino acids exist as isomers except which one?

glycine

amino acid ionization

amino acid R groups can gain or lose a proton and have a charged state, to adapt to the PH of the environment they are in

what amino acids can be ionized?

Love His Art, As God Lysine Histidine Arginine Aspartic Acid Glutamic Acid

how are peptide bonds formed?

dehydration synthesis

what is the peptide backbone made up of?

a repeated series of C and N atoms, with side chains protruding

N-terminus

the end of a polypeptide with an exposed amino group

C-terminus

the exposed carboxyl group at the other end of a peptide chain

amino acid residue

what remains of each amino acid after water is removed

can peptide bonds rotate?

no, due to partial double bond character that exerts resonance

what type of bond character do peptide bonds have?

partial double bond character

what atoms share electrons in peptide bonds?

O and C (carboxyl group) N (amino group)

why does histidine act as a proton donor and/or acceptor?

because its Pka is close to the neutral PH of a cell

what parts of the polypeptide can still rotate?

the N-central carbon bond and the C-central carbon bond

primary protein structure

amino acid sequence

secondary protein structure

occurs when the sequence of amino acids are linked by hydrogen bonds, beta strands and alpha helices

tertiary protein structure

3D folding pattern of a protein due to side chain interactions, held together by covalent bonds

quaternary protein structure

protein consisting of more than one amino acid chain

what bonds occur in alpha helices?

H bonding between C--O of one peptide bond and N-H of another

alpha helices structure

3.6 amino acids per turn, diameter of 12 Angstroms, R groups protrude out the sides to interacts with proteins

how are beta sheets formed?

when peptide bonds hydrogen bond to one and other through carbonyl and amide groups

beta sheet structure

slightly twisted, largely planar, side chains protrude outward and behind

what amino acids are often found in helices?

Leucine, Methionine, Glutamine, and Glutamic Acid

what amino acids are often found in beta sheets?

Valine, Isoleucine, Phenylaline

what amino acids are often found in beta turns?

Glycine (small side chains and flexible) and proline (usual structure that introduces kinks in polypeptide chain (helix breaker))

what type of chemical interactions drive protein folding?

hydrophobic interactions

what is it called when a protein is unfolded?

denaturing: often done by changing conditions such as heat, detergents or solvents

what enables us to predict secondary structures?

conservation of amino acid sequence

how do you know if two proteins will have a similar function?

conservation of the same critical amino acids

polypeptide domain

compact region of a polypeptide which can fold on its own

why is protein structure viewed as being modular?

because proteins can have multiple domains that fold independently and carry out specific functions

protein motif

specific amino acid sequences that make specific contacts with each other or ions that coordinate charges

Helix-Turn-Helix DNA Binding Motif

recognition helix lies in the major groove and makes H bonds with base groups

Zinc-finger DNA Binding Motif

two cysteines and two histidines coordinate a Zn ion to form the finger, each finger recognizes about 3 base pairs of DNA

what is powerful about a few zinc fingers in tandem?

they can recognize much longer, more unique sequences which is much more specific

where do DNA binding proteins most frequently bind?

major groove

what type of structures can fit in the major groove?

alpha helices and beta sheets

how does binding in the minor groove work?

introduces distortion to DNA which can be beneficial in specific reactions

do chemical groups vary more in the major or minor groove? why?

the major groove T-A and A-T are the same, and G-C and C-G are the same, so these can't be distinguished by binding proteins

Covalent post-translational modifications

phosphorylation, acetylation, and methylation can switch proteins on, off, cause them to be destructed, cause allosteric change, and can directly affect ligand binding

Ubiquitination

small protein that can be covalently linked to lysine

mono-Ub

regulates activity of a protein