Molecular biology exam 2

Erwin Chargaff

A=T, G=C, disproved the tetranucleotide hypothesis

SUMOylation

Added to a lysine for transcription and nuclear transport

Ubiquitination

Added to a lysine to target a protein to the proteasome for destruction

Acetylation

Added to lysine, often found on histones

purines

Adenine and Guanine

Identify the properties and structure of peptide bonds.

1-3 letter code N--> C Primary covalent linkage between amino acids in polypeptides

Domain

A folded section of a protein, typically functional, continuous chain. offer: compartmentalization, specialization, and substrate channeling through multidomain complexes, reduce folding time and enhance protein stability.

Phosphorylation

A high-energy group added to a ser, thr, or tyr for protein activation

Helix-turn-helix

A long α-helical dimer connected by a short turn. The helices can both interact with DNA, or one can act as a stabilization helix

SNARE

Membrane fusion

Heme groups

Metals

Define coiled coils, explaining how they form and how they are held together.

The nonpolar side chains along each a-helix can be arranged so that their side groups contact another helix •This allows side groups to pack neatly together only when the a-helices interact at 18° angle from parallel. If a-helices remained parallel, could stay in contact for only few residues

Linking number

The number of times one strand has to pass over the other to separate completely. It equals twist + writhe.

Twist

The number of turns of one strand over the other, as in dsDNA.

Writhe

The overall supercoiling of the dsDNA across itself.

Define melting temperature

The temperature at which denaturing occurs for half of the double helix's

What factors contribute to melting temp. (Tm)

Tm increases with GC%, DNA length & salt concentration

Proteins that read both major and minor codes are called

Zinc fingers

I-motif

cytosine rich. Found in promoters & telomeres involved in regulation.

Fatty acid synthase

is a large protein with multiple domains, each with a specific enzymatic role in the addition of two carbons to a growing fatty acid chain.

Phosphofructokinase-2 / fructose bisphosphatase-2

is a single polypeptide with 2 domains

Major groove

larger and carries more info about functional grous

shuttle component

mRNA transfers genetic info from DNA to ribosomes. No tertiary structure

solenoidal supercoiling

mechanism by which underwinding contributes to DNA compaction in the cells

regulation

miRNA, siRNA, riboswitches, RNase P (generates tRNA), spliceosome, hammerhead, introns

Nucleotide

nitrogenous base + pentose (nucleoside) + 1 or more phosphate

Nucleoside

nitrogenous base + pentose sugar

Transmembrane have proteins that are

nonpolar amino acids to cross the membrane with hydrophobic amino acids on the outside

type l beta turns

proline

a-helix breaking

proline, glycine supercoild around one another called coiled coil

quaternary structure of protein

proteins consist of multiple polypeptide (subunits)

Hoogsteen base pairing

purine and pyrimidine form different hydrogen bonds

structural component

rRNA is a component of ribosome, catalyzes peptide bond formation, tertiary structure

sequence specific DNA binding proteins

read DNA in the major groove, a-helices also have dipole moment that gives them partial + charge at the N-terminus which allows for interactions with phosphate backbone

Enzyme active sites have amnio acids that are

scattered across the primary sequence

Helicase:

separate double strands during dna synthesis

Primary Strucutre of Protein

sequence of amino acids in a polypeptide chain (covalent)

Topo l

ssDNA cuts, steps of +/-1, works at the replication fork and transcription, removes +/- supercoils and produces right handed solenoid.

ds DNA can form

supercoils

RNA tertiary structure example

tRNA

Phosphofructokinase-2 / fructose bisphosphatase-2 if DEPHOSPHOYLATED then?

the phosphofructokinase domain catalyzes the formation of fructose-2,6-bisphosphate, which activates glycolysis.

Pos supercoiling

tighter winding overwinding restricted access. Found in thermophites store energy to help keep DNA wound up under high temp.

AND gate

two phosphorylation's are required to activate a target protein

Neg supercoiling

unwinding , underwinding . Stored free energy that aids speedster ion in replication, recombination & transcription. Found in b to x snap conversation for regulation.

Listeria riboswitch does what

uses RNA structure to control expression

Murine Leukemia virus does what

uses RNA switch to control translation

Differentiate between Watson and Crick's first model of DNA and later models.

watson 1st model: a-helix, ignored side chains. Mg2+ would be bound by water and hydrophillic phosphates on outside watson later DNA: left handed DNA, 0.34nm distance between pairs

protein domains that recognize specific sequence are

Leucine zipper, Helix-loop-helix, Helix-turn-helix, zinc finger

Riboswitches example

Listeria, Murine leukemia virus and S-adensoyl-methionine,

Phoebus Levene

Discovered the base-sugar-phosphate, proposed the Tetranucleotide Hypothesis for DNA

Frederick Griffith

Discovered transformation while studying pneumonia

Topoisomerase inhibitors

doxorubicin, camptothecin, topotecan, and fluoroquinolones.

teritery structure of protein

3D final folding stabilized by weak interaction

Ribosomes

1. example of quaternary structure 2.Divalent cations shield the neg-charged backbone & stabilize the structure 3. Protein components assist in tertiary structure & protection, regulation 4. Universally conserved nucleotides in the ribosome's catalytic site support the RNA world hypothesis.

DNA properties

1.AT base pairs are less stable than GC base pairs and are more likely to break. 2.ssDNA absorbs more than dsDNA. 3.ATATAT has a lower Tm than GCGCGC. 4, AAAAAA+TTTTTT will reanneal more quickly than ATGCTC+TACGAG.

DNA 4 characteristics

1.DNA is 2nm wide 2.DNA periodicity is 10.5 3.Sugar protrude at 120 or 240 degrees from the phosphate back bone produces major/minor grooves 4.major groove is nearly twice the width of minor groove

Describe α-helices and their properties

1.Most stable arrangement due to H-bonds between carbonyl (c=o) and Amide (n-h) 2.right handed helix 3.side chains away from helix [perpendicular]

B form DNA

10bp turn. Watson-Crick model DNA. Deep, wide and longer major groove. ANTI

A form DNA

11bp tuen. Condensed form of DNA. Deeper major groove and shallower minor groove. ex: bacteriA ANTI

Z-form DNA

12bp turn longest left handed often repetitive. ANTI-> pyrimidines SYN-> purines

A & T have how many hydrogen bonds?

2 hydrogen bonds

Describe the structure of RNA and the factors that impact its stability

2' OH of RNA, Divalent metals- Mg2+ can shield -charged backbone, unique base pairs can form

A single zinc finger can recognize _______ unique pairs?

3

C and G have how many hydrogen bonds?

3 hydrogen bonds (stronger)

Motif

A small protein fold, typically not functional on its own

plectonemic supercoiling

A structure in a molecular polymer that has a net twisting of strands about each other in some simple and regular way.

Glycosylation

A sugar added to ser, thr, or asn for protein folding or membrane secretion

Helix-loop-helix

An α-helical dimer separated by a flexible loop that allows them to pack together

Topo ll

dsDNA cuts, Steps of +/-2, dimer, requires ATP, untangling of daughter DNA after replication, involved in transcription , recombination.

Alfred Hershey and Martha Chase

Bacteriophage 32P enters host, 35S does not

Explain the unique RNA structures including the unique bases and base pairing, as well as its ability to form secondary and tertiary structures.

Base stacking and G=U pair, wobble base pairing and glycosidic bonds can be in trans parallel

Bromo

Binds to acetylated lysine

Chromo

Binds to methylated lysine

SH2 and PTB

Binds to phosphotyrosine

SH3

Binds to proline

EF-Hand

Calcium binding

ATP Hydrolysis

Can create large structural movements, such as myosin walking on actin

Describe the Ribonuclease Experiment and what it demonstrated

It was the first experimental evidence that primary amino acid sequence of polypeptide contains all the information needed to specify the folding of polypeptide into native 3D structure

where are coiled coils are found?

Keratin, myosin & collagen

Leucine zipper

Coiled coil dimers with a repeating appearance of hydrophobic amino acids. The open end has basic amino acids which H-bond to DNA.

Mechanical Activation

Converting a physical force into a biochemical signal

subunit

Correct match: An individual polypeptide chain of a larger quaternary structure

Pyrimidines

Cytosine and Thymine

Common conformation for Guanine & thymine

Keto rarely in enol

Quadruple helix

Guanine rich has parallel/Antiparallel conformations found in telomeres, replicates quickly, turn on/off genes. Linked to unstable DNA cancer

Rosalind Franklin

Her Photo 51 provided important clues about DNA's structure being helical and antiparallel

Phosphofructokinase-2 / fructose bisphosphatase-2 if PHOSPHOYLATED then?

If phosphorylated at a serine, the bisphosphatase domain catalyzes the reverse step, activating gluconeogenesis

Polar

Interact with DNA bases in the major groove, and are in the active site of serine proteases

Positively-Charged

Interact with DNA's phosphate backbone and bases (basic)

Aromatic amino acid

Interact with the rings of ssDNA and ssRNA via base stacking, absorb UV light at 280

Zinc finger code

Interacting with half zinc fingers can recognize every possible sequence

Gyrase (bacteria)

Introduces net supercoils or relaxes Pos supercoils

The Mica Experiment

Involved binding DNA to mica and digesting with an enzyme to determine the periodicity of DNA helix = 10.5 bp/turn

RING Finger

Involved in ubiquitin-dependent degradation

Explain how phosphorylation by ATP can activate

Kinases: adds phosphates to target proteins (serine, threonine or tyrosine)

Compare the structure of RNA with DNA.

OH replaces an H 2' Carbon of sugar Uracil: absence of CH3 compared to thymine Single stranded, double stand (A form only) Adapter between DNA & Amino acids Not genetic material Can have 2 and 3 structures Divalent metals like Mg2+ often bind to shield charges (tight packing) Unique bases and base pairs

Nonpolar amino acid

Often buried inside a protein, contributing greatly to folding. Aliphatic open chains

XOR gate

One or the other but not both inputs are required for activation

Explain how phosphorylation by ATP can inactivate

Phosphatases: remove phosphates, and are also important for regulating pathways.

Types of supercoils

Plectonemic & solenoidal (toriodal)

Why is melting temperature important?

Primer annealing in DNA hybridization

Proteolytic Cleavage

Protein cleavage for activation or destruction

Proteins also interact with RNA through the

RNA recognition motif

RNA quaternary structure example

Ribosome

NADH/FADH

Rossmann fold

Domain examples

SH2 ,SH3,snare, EF-hand, bromo, chromo, ring finger found in protein structure

p53 transcription factor

Senses cell stress and initiates DNA damage response pathways, and apoptosis if the cell cannot be repaired

Oswald Avery

Showed DNA was the genetic material via transformation

Protein components of ribosomes

Shuttle, adaptor, structural, enzymatic activity, regulation

Watson and Crick

Solved the double helical structure of DNA

Negatively-Charged

Stabilize cations like Mg2+ in an enzyme's active site, interact with DNA bases. (acidic) ex: aspartate, glutamate ionic in cells

Describe Levinthal's paradox.

States it's impossible for proteins to try every combination, yet folding occurs in seconds stepwise manner.

Define the tetranucleotide hypothesis.

Suggested that bases were in equimolar quantities in chromosomes, in the same order.

parallel beta sheet

adj. chain run in the same n->c direction

antiparallel beta sheet

adj. chain runs opp. (More stable

secondary structure of protein

alpha helix and beta sheet max hydrogen binding

Common conformation for Adenine & cytosine

amino rarely in imino

Describe β-sheets, highlighting their structure

are extended pleated sheet-like strucutres, parallel runs in same direction & are weak due to bent bonds. Antiparallel b-sheets run opp directions and are strong due to linear H-bonds.

OR gate

at least one of the two inputs is required for the protein to activate

Eukaryotic domains are larger than

bacterial proteins and bacteria synthesize them SEPARATELY as multidomain in eukaryotes.

Zinc fingers work by?

bind with zinc with cysteines ad histidines to hold domain together, use polar side chains to interact with H-bond donors and acceptors in the major groove.

enzymatic activity

can form tertiary structure, ribozymes can catalyze rxns

adaptor component

decoded info (tRNA), tertiary structure due to intramolecular interactions

type ll beta turns

glycine

Pyruvate kinase

has 3 domains & catalyzes the last step of glycolysis (PEP-> pyruvate)

Motifs example

helix hairpin, beta hairpin

topoisomerases

help to maintain the integrity of the chromosomes. breaks changed supercoiling ss/ds

α-helices and β-sheets both maximize H-bonds to allow polypeptides to transverse the__________ interior of protien

hydrophobic

Protien fold to the lowest energy a strong influcence is the burial of

hydrophobic side chains

Protrusion

indentation

Riboswitches

involve metabolites binding to RNA to regulate transcription or translation.