BIOL 200 midterm quizlet

Central Dogma

DNA > RNA > Protein

Nucleotides

base, sugar, phosphate

Glycosidic Bond

Base and sugar bond

Nucleotide monomers

phosphates = acidic characteristics, covalently bonded to suger (phosphodiester bond)

Hydrogenous base = covalently bond to sugar

Sugar

Purines

2 ring base, Adenine, Guanine

Pyramidines

1 ring base, RNA = uracil, cytosine, DNA = thymine, cytosine

Nucleoside

base, sugar

Amino Acid

building blocks of polypeptides, determines the shape of the polypeptide, 20 types

Protein functions

catlysis, transport, signalling, structure, motor, regulatory (control protein activity/gene function)

Amino Acid Structure

Amino end (N-terminus), Carboxyl end (C-terminus), R groups

Special a.a.

Cysteine, glycine, proline

Cysteine

special a.a with sulfhydryl group, form disulfide bonds

Glycine

special a.a. with H symmetrical, intra/inter cross linking

Proline

special a.a. rigid ring structure

DNA shape

5' end: free phosphate group attached to sugar phosphodiester bond: links nucleotides

3' end: free hydroxyl group on terminal end sugar

DNA "backbone"

repeating phosphate-pentose units, holds no info

outside of dbl bond

within DNA structure

3D structure of DNA

watson and crick, 2 polynucleotide strands wound together to form dbl helix (anti //), bases stacked

Base pairing

complementary base

T dbl bonds to A, C triple bonds to G (stronger = more H bonds)

Right-handed Helix DNA

most DNA in cells

B DNA

major and minor groove, important for DNA-protein interactions, ex: TBP

R-H helix

A DNA

low humidity or high [salt], B DNA turns into A DNA

RNA-DNA, RNA-RNA exist in this form

R-H helix

• smaller, wider

Z DNA

short DNA molecule of alternating purines and pyramidines

formed after transcription, tag for transcribed genes

L-H helix

• taller, longer

DNA denaturation and renaturation

important for DNA replication/transcription

unzipping and re-annealing of DNA

RNA secondary structures

hairpin, stem-loop

RNA tertiary structure

pseudoknot

Primary structure of protein

a.a. sequence

amino end, amide groups, r groups, carboxyl ends

Peptide Bond

linkange of one a.a. to another, on C terminus linking to next N terminus

Residue

amino acid

Secondary structure of protein

local folding

alpha-helix: stabilized by H bonds

beta sheet: 5-8 residues, r groups away/toward you, laterally packed beta strands, // or anti //

Beta turn: most common, 3-4 residues, glycine/proline twists and turns

Tertiary structure of protein

long range folding

stabilized by hydrophobic interactions b/w non-polar side chains

H bonds b/w polar side chains

Disulfide bonds b/w cysteine residues (covalent bond)

Quaternary structure of protein

multi-meric structure

pores (4 proteins) = potassium ion channel protein

Supramolecule structure of protein

large-scale assembly

10-100 polypeptides chains

general transcription factors: RNA polymerase, mediator complex, promotor, pre-initiation transcription complex

Motifs

combos of secondary structure proteins

Coil-Coil Motif

hydrophobic interactions

fibrous proteins

ex: collagen

Helix-loop-helix Motif

ionic bonds involving Ca2+

ex: Ca2+ binding proteins

Zinc-finger Motif

contains Zn2+

ex: RNA, DNA, binding proteins

Domains

need these for certain proteins to function

ex: pyruvate kinase needs 3 domains

Reshuffling of motifs and domains

new proteins made

Ingredients for transcription in bacteria

DNA template, ribonucleotides (monomers for RNA polymerization), RNA polymerase (catalyze synthesis of RNA

Ist step of transcription

Initiation

• polymerase binds to promoter (upstream of gene) in duplex DNA

forms "closed complex"

• polymerase melts duplex DNA

forms "open complex"

• polymerase catalyzes phosphodiester linkage of two initial rNTPs

rNTP

ribonucleotide tri-phosphate, building blocks of RNA synthesis

N = G, C, A, U

2nd step of transcription

Elongation

• polymerase goes from 3' to 5'

• continues to melt DNA

• adds rNTPS to growing RNA

• formation of phosphodiester bonds b/w 3' OH and alpha phosphate group of incoming rNTP

3rd step of transcription

Termination

• at stop site, polymerase releases completed RNA and dissociates from DNA

Holoenzyme

subunit of RNA polymerase

consists of core enzyme + sigma factor

alpha: loading entire onto transcript

beta: helps with phosphodiester linkage

Sigma factor

subunit of RNA polymerase

scans DNA until encounters promoter to bind with and form "closed complex"/to start transcription

How does sigma factor recognize promoter region?

RNA polymerase subunit

binds to specific sequence motifs (-10, -35 regions = start, stop site)

Messenger RNA

mRNA

genetic info from DNA in form of codons

Transfer RNA

tRNA

key to decipher codons in mRNA

each tRNA has an associated a.a. and anticodon

Ribosomal RNA

rRNA

assiciates with proteins to from ribosomes

tRNA structure

folds with itself

acceptor stem, loop, anticodon, loop