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Biochem > Protien Structure > Flashcards

Protien Structure Flashcards

1
Q

Primary DNA structure

A

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

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2
Q

DNA chain formation

A

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)

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3
Q

Length of DNA

A

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

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4
Q

Secondary DNA structure

A 
Hydrogen bonds (weak interactions)
Nitrogenous bases = hydrophobic 
Insoluble = water imposes strong constraints on overall conformation of DNA in solution
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5
Q

Base stacking

A

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)

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6
Q

One complete turn of Helix

A

3.4nm or 10.5 base pairs

Minor and major spacing

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7
Q

A-DNA

A

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

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8
Q

Z-DNA

A

Present in short DNA region- role in DNA expression

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9
Q

Unusual DNA secondary structures

A

Slipped structures

Triple helix DNA

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10
Q

Tertiary structure

A

Supercoiling of DNA

DNA loops domains

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11
Q

Quaternary structure

A

DNA-Protein structure

DNA function = regulated by DNA binding proteins

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12
Q

Types of DNA protein interactions

A

Specific e.g Trans Factors

Unspecific e.g Histones

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13
Q

DNA packaging in eukaryotes

A 
Nucleosomes are basic unit 
Composed of: 
Protein core= Histones 
DNA wrapped around Histones 
Linker: DNA between nucleosomes
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14
Q

Types of histones

A

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

Histones: small, positively charged basic proteins

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15
Q

Tails of histones

A 
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
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16
Q

Histones fold and dimerisation

A

Handshake
H2A+H2B
H3+H4

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17
Q

Nucleosome assembly - Core

A

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

18
Q

Where do histones bind?

A

The Minor groove of DNA

19
Q

Bonds between protein and DNA

A

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

20
Q

Three major binding domains in TFs

A 
DNA- binding domain (N-terminal)
Activation domain (C-terminal)
Dimerisation domain
21
Q

Dimerisation domain

A

The majority of transcription factors bind DNA as homodimers or heterodimers

22
Q

TF structures

A

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

23
Q

Helix-Turn-Helix

A

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

24
Q

Zinc finger

A

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

25
Q

Basic leucine Zipper

A

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

26
Q

Basic Helix-loop-Helix

A

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

27
Q

TFs recognise DNA

A

Using alpha helices inserted into the MAJOR groove of DNA

28
Q

Proteins recognise and bind to DNA

A

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

29
Q

RNA versatility

A

Much greater structural versatility compared to DNA

RNA chains fold Ito unique three dimensional structures that act similarly to globular proteins

30
Q

Folding patterns decide..

A 
Chemical reactivity 
Specific interactions (with proteins etc)
31
Q

Non protein coding RNAs

A

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

32
Q

Example of RNPs

A

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

33
Q

Levels of RNA structure

A

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

34
Q

Difference in primary To DNA

A

Ribose instead of deoxyribose

Uracil instead of thymine

35
Q

RNA secondary structure

A

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

36
Q

Covariance

A

Comparing conservation of RNA secondary structure

37
Q

Non canonical base pairs

A

Not conventional=

G-U C-A

38
Q

RNA tertiary structure -Psuedoknot

A

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

39
Q

The A-Minor Motif

A

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

40
Q

Tetra loop Motif

A

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

41
Q

The kink turn motif

A

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

42
Q

Kissing hairpin loop motif

A

Two hairpin loops form a kissing interaction

Bound by: two single strands of hairpin loops with complimentary sequences.

Biochem (5 decks)

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