Protien Structure Flashcards
Primary DNA structure
Polymer of nucleotides which consist of:
5 Carbon sugar (deoxyribose)
Nitrogenous Bases (ATGC)
Phosphate group
DNA chain formation
DNA and RNA chains formed through 3 step process
Bases attach to sugars = Nucleosides
Nucleoside + 1(+) phosphate = Nucleotides
Nucleotides are linked 5 prime to 3 prime by phosphodiester bonds (covalent)
Length of DNA
Double stranded
Number of bases = measurement of length
1000=kilobase pair 1000000=megabase pair
Oglionucleosides = short chains of single stranded DNA <50 bases
Secondary DNA structure
Hydrogen bonds (weak interactions) Nitrogenous bases = hydrophobic Insoluble = water imposes strong constraints on overall conformation of DNA in solution
Base stacking
Base pairs can stacked onto each other which forms helical twist
Eliminates any gaps between bases and prevents water from being inside the helix
High number of weak hydrophobic interaction (VDV forces)
One complete turn of Helix
3.4nm or 10.5 base pairs
Minor and major spacing
A-DNA
Important in dsRNA and may be present in DNA- RNA hybrid molecules (R loops)
Z-DNA
Present in short DNA region- role in DNA expression
Unusual DNA secondary structures
Slipped structures
Triple helix DNA
Tertiary structure
Supercoiling of DNA
DNA loops domains
Quaternary structure
DNA-Protein structure
DNA function = regulated by DNA binding proteins
Types of DNA protein interactions
Specific e.g Trans Factors
Unspecific e.g Histones
DNA packaging in eukaryotes
Nucleosomes are basic unit Composed of: Protein core= Histones DNA wrapped around Histones Linker: DNA between nucleosomes
Types of histones
Core- (11-16 kDa)
Linker- (20 kDa)
Histones: small, positively charged basic proteins
Tails of histones
Amino (N) terminal tails: Long but variable in length Lysine-rich = positively charged Carbonyl (C) terminal end: Three histone folding domains Histone-Histone interactions Histone-DNA interactions
Histones fold and dimerisation
Handshake
H2A+H2B
H3+H4
Nucleosome assembly - Core
Octamer of two molecules of each core histone:
H3 & H4 form tertamer (binds to dna)
H2A & H2B form dimer
H3 & H4 tetramer binds to the above dimer
N-Terminal is exposed
Where do histones bind?
The Minor groove of DNA
Bonds between protein and DNA
H-bonds between proteins and oxygen of phosphate backbone
Facilitates bending
Masks negative charge of phosphates
No base recognition
Three major binding domains in TFs
DNA- binding domain (N-terminal) Activation domain (C-terminal) Dimerisation domain
Dimerisation domain
The majority of transcription factors bind DNA as homodimers or heterodimers
TF structures
Helix-Turn-Helix
Zinc finger
Basic leucine zipper
Basic Helix-loop-Helix
Helix-Turn-Helix
Composed of 3 alpha helixes with linkers
3rd helix contains DNA
Often developmental genes
Zinc finger
One of most prevalent DNA-binding domains
Name due to 2D structure
-Zn ion integrates with Cys and His residues
-Alpha helix inserts int the major groove of DNA
Example-Gal4 is an acidic zinc finger involved in galactose metabolism
Basic leucine Zipper
Less common
Dimer of 2 long Alpha-Helices
Leucine residues in central region of helix aid dimerisation
Hetero or homo dimers ‘pincer’ DNA contact
Basic Helix-loop-Helix
Similar structure to Helix turn Helix
Similar mechanism to leucine finger (dimerisation)
DNA binding domain= rich in basic amino acids
TFs recognise DNA
Using alpha helices inserted into the MAJOR groove of DNA
Proteins recognise and bind to DNA
Recognise the chemical properties in the major and minor groove of DNA
Patterns of bases in the sequences are specific to a DNA binding protein
Major groove is the only groove that patterns are marked differently so gene regulatory proteins often use major groove
RNA versatility
Much greater structural versatility compared to DNA
RNA chains fold Ito unique three dimensional structures that act similarly to globular proteins
Folding patterns decide..
Chemical reactivity Specific interactions (with proteins etc)
Non protein coding RNAs
RNPs
May act as a scaffold for assembly of proteins
RNA-protein interactions can influence the catalytic activity of proteins (e.g Telomerase)
Example of RNPs
Telomerase- adds telomeric repeat t chromosomes during replication
Composed of- RNA and protein (RT)
RNA may be catalytic = Rybozimes
Small RNAs can control gene expression = miRNAs
Levels of RNA structure
Primary: Ribonucleoside sequence
Secondary: Base paired regions v.s single stranded
Tertiary: 3D structure(long range interactions)
Quaternary: Complex of two or more strands
Difference in primary To DNA
Ribose instead of deoxyribose
Uracil instead of thymine
RNA secondary structure
Includes bulges, stems, hairpins and junctions
Prediction of RNA secondary structure
1-Thermodynamic data for free energy
2-Comparative sequence analysis
Covariance
Comparing conservation of RNA secondary structure
Non canonical base pairs
Not conventional=
G-U C-A
RNA tertiary structure -Psuedoknot
Single stranded loop base pairs with complimentary sequence outside of the loop
This folds into 3D shape by COAXIAL STACKING
The A-Minor Motif
One of the most abundant long range interactions in large RNA molecules
Single stranded adenosines make tertiary contact with minor groups of RNA double helixes by hydrogen bonding and VDW forces
Tetra loop Motif
This motif Enhances the stability of stem loop structures
A stem loop with the tetra loop sequence UUUU is particularly stable due to special base stacking
The kink turn motif
This motif is an unsymmetrical internal loop embedded in RNA double helix
Striking feature is the sharp bend or kink in the phosphodiester backbone of the three-nucleotide bulge
Kissing hairpin loop motif
Two hairpin loops form a kissing interaction
Bound by: two single strands of hairpin loops with complimentary sequences.
