Protien Structure

Question 1

Primary DNA structure

Answer 1

Polymer of nucleotides which consist of:
5 Carbon sugar (deoxyribose)
Nitrogenous Bases (ATGC)
Phosphate group

Question 2

DNA chain formation

Answer 2

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)

Question 3

Length of DNA

Answer 3

Double stranded
Number of bases = measurement of length
1000=kilobase pair 1000000=megabase pair
Oglionucleosides = short chains of single stranded DNA <50 bases

Question 4

Secondary DNA structure

Answer 4

Hydrogen bonds (weak interactions)
Nitrogenous bases = hydrophobic 
Insoluble = water imposes strong constraints on overall conformation of DNA in solution

Question 5

Base stacking

Answer 5

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)

Question 6

One complete turn of Helix

Answer 6

3.4nm or 10.5 base pairs

Minor and major spacing

Question 7

A-DNA

Answer 7

Important in dsRNA and may be present in DNA- RNA hybrid molecules (R loops)

Question 8

Z-DNA

Answer 8

Present in short DNA region- role in DNA expression

Question 9

Unusual DNA secondary structures

Answer 9

Slipped structures

Triple helix DNA

Question 10

Tertiary structure

Answer 10

Supercoiling of DNA

DNA loops domains

Question 11

Quaternary structure

Answer 11

DNA-Protein structure

DNA function = regulated by DNA binding proteins

Question 12

Types of DNA protein interactions

Answer 12

Specific e.g Trans Factors

Unspecific e.g Histones

Question 13

DNA packaging in eukaryotes

Answer 13

Nucleosomes are basic unit 
Composed of: 
Protein core= Histones 
DNA wrapped around Histones 
Linker: DNA between nucleosomes

Question 14

Types of histones

Answer 14

Core- (11-16 kDa)
Linker- (20 kDa)

Histones: small, positively charged basic proteins

Question 15

Tails of histones

Answer 15

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

Question 16

Histones fold and dimerisation

Answer 16

Handshake
H2A+H2B
H3+H4

Question 17

Nucleosome assembly - Core

Answer 17

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

Question 18

Where do histones bind?

Answer 18

The Minor groove of DNA

Question 19

Bonds between protein and DNA

Answer 19

H-bonds between proteins and oxygen of phosphate backbone
Facilitates bending
Masks negative charge of phosphates
No base recognition

Question 20

Three major binding domains in TFs

Answer 20

DNA- binding domain (N-terminal)
Activation domain (C-terminal)
Dimerisation domain

Question 21

Dimerisation domain

Answer 21

The majority of transcription factors bind DNA as homodimers or heterodimers

Question 22

TF structures

Answer 22

Helix-Turn-Helix
Zinc finger
Basic leucine zipper
Basic Helix-loop-Helix

Question 23

Helix-Turn-Helix

Answer 23

Composed of 3 alpha helixes with linkers
3rd helix contains DNA
Often developmental genes

Question 24

Zinc finger

Answer 24

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

Question 25

Basic leucine Zipper

Answer 25

Less common Dimer of 2 long Alpha-Helices Leucine residues in central region of helix aid dimerisation Hetero or homo dimers ‘pincer’ DNA contact

Question 26

Basic Helix-loop-Helix

Answer 26

Similar structure to Helix turn Helix Similar mechanism to leucine finger (dimerisation) DNA binding domain= rich in basic amino acids

Question 27

TFs recognise DNA

Answer 27

Using alpha helices inserted into the MAJOR groove of DNA

Question 28

Proteins recognise and bind to DNA

Answer 28

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

Question 29

RNA versatility

Answer 29

Much greater structural versatility compared to DNA | RNA chains fold Ito unique three dimensional structures that act similarly to globular proteins

Question 30

Folding patterns decide..

Answer 30

``` Chemical reactivity Specific interactions (with proteins etc) ```

Question 31

Non protein coding RNAs

Answer 31

RNPs May act as a scaffold for assembly of proteins RNA-protein interactions can influence the catalytic activity of proteins (e.g Telomerase)

Question 32

Example of RNPs

Answer 32

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

Question 33

Levels of RNA structure

Answer 33

Primary: Ribonucleoside sequence Secondary: Base paired regions v.s single stranded Tertiary: 3D structure(long range interactions) Quaternary: Complex of two or more strands

Question 34

Difference in primary To DNA

Answer 34

Ribose instead of deoxyribose Uracil instead of thymine

Question 35

RNA secondary structure

Answer 35

Includes bulges, stems, hairpins and junctions Prediction of RNA secondary structure 1-Thermodynamic data for free energy 2-Comparative sequence analysis

Question 36

Covariance

Answer 36

Comparing conservation of RNA secondary structure

Question 37

Non canonical base pairs

Answer 37

Not conventional= | G-U C-A

Question 38

RNA tertiary structure -Psuedoknot

Answer 38

Single stranded loop base pairs with complimentary sequence outside of the loop This folds into 3D shape by COAXIAL STACKING

Question 39

The A-Minor Motif

Answer 39

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

Question 40

Tetra loop Motif

Answer 40

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

Question 41

The kink turn motif

Answer 41

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

Question 42

Kissing hairpin loop motif

Answer 42

Two hairpin loops form a kissing interaction | Bound by: two single strands of hairpin loops with complimentary sequences.