BIO130 first half

Week 1: cellular diversity: Cell Theory

• The cell is the basic unit of life

• All organisms 1 or more cells

• Cells arise from pre-exsisting cells

Prokarotic cell

• No membrane-bound organelles

• Smaller than eukaryotes

• Less DNA

DNA is compartmentalized but no membrane —> nucleoid

Eukaryotic cell

• Nucleus

• Membrane-bound organelles

• Larger and more complex

Origins of mitochondria

Entangle-engulf-endogenize (E³ ) model

Ancient anaerobic archeal cell and ancient aerobic bacterium

• started as ectosymbiote (outside)

• then engulfed as endosymbiote

• then bacteria membrane broken

(other model show predatory mechanism)

Ancient cell folding protusions

Give way for nuclear envelope and endoplasmic reticulum

Origins of eukaryotes graph

mitochondria first —→ eukaryotes

chloroplast second —→ plants

Endosymbiont hypothesis for mitochondria and chloroplasts — evidence

1. Both have remnants of own genome which resemble modern prokaryotes

2. Both have kept some of own protein and DNA synthesis components, also resemble prokaryotes

3. Membranes are similar to prokaryotes and derived from bacteria ancestor

Model organisms and Humans — general attributes of model organisms

1. Fast development and short life cycles

2. Small reproductive (adult) size

3. Readily available

4. Tractability (manipulation or modification)

5. Understandable genetics

Examples of model organisms

• Ecoli

• Brewer’s yeast — simple eukaryote

• Arabidopsis — plant

• Nematode, drosophila, zebrafish, mice — animals

Lec 2: The Central Dogma of Molecular Biology

Information flow is always in one direction

DNA (transcription) —→ RNA (translation) —→ Protein

.

Refined:

• messengerRNA: translation for protein

• transferRNA: transport amino acids

• rRNA: heart of ribosome, breaking and forming of bonds

Antiparallel and genetic code

• DNA, RNA, and proteins are synthesized as linear chains of info with intrinsic directtion

• RNA translating to amino acid is universal through the genetic code

What are nucleic acids?

1. Genetic material in a cell

2. DNA & RNA

Three parts of a nucleotide

1. Pentose sugar

2. Phosphate group (1, 2, or 3)

3. Nitrogenous base

Nucleotide bases

Pyrimidine

• Cytosine

• Thymine

• Uracil

Purines

• Adenine

• Guanine

Differences between DNA and RNA

RNA:

• ribose

• OH on 2’ carbon

• uracil

DNA:

• deoxyribose

• H on 2’ carbon

• thymine (extra methyl)

Differences between bases

Nucleic acid nomenclature

Nucleoside: sugar + base

Nucleotide: sugar + base + 1, 2, 3 phosphate

1. Nucleoside monophosphate

2. Nucleoside diphosphate

3. Nucleoside triphosphate

Nucleic acid chains

1. DNA is synthesized from deoxyribonucleoside triphosphates (dNTPs)

2. RNA is synthesized from ribonucleoside triphosphates (NTPs)

3. Nucleotides linked by phosphodiester bonds

Molecular interactions

1. Electrostatic attrations (charges attract)

2. Hydrogen bonds

3. Van der waals attractions

4. Hydrophobic force

(Individually weak, sum to be strong)

Three forces that keep DNA strands together

1. H-bonds (base pairing, G-C stronger cause 3 bonds)

2. Hydrophobic interactions (phosphate backbone hydrophylic, bases hydrophobic

3. Van der waals attractions

DNA structure

• DNA will naturally come together, energetically favourable

• Proteins can recognize and make contact with specfic sequences in major & minor grooves

Separating DNA strands

DNA can unravel and return to double helix

• use energy or enzymes to denature

• useful for replication, transcription, or PCR

Lec 3: intro to protein structure

Quaternary: more than 1 polypeptide chain, subunits

Multiprotein complexes: many chains and subunits, machine

Amino acid structure

1. proteins composed of amino acids

2. side-chain/R group is variable and determines the type of amino acid

3. three major categories

   1. acidic ( - charge)

   2. basic ( + charge)

   3. uncharged polar

   4. nonpolar

classification system for amino acids

• half are polar

• 5 charged polar

• 5 uncharged polar

Amino acids and the genetic code

AUG — start codon methione

UAA, UAG, UGA — stop codon

Degenerative code: more codons than AA, more than one can code for the same AA

Flexibility: similar codons for similar AA, can tolerate mutations better

Unique amino acid: cysteine

• can form disulfide bonds — (oxidation form, reduction break)

  • both interchain and intrachain

• covalent bond creates stability

• “staple”

• often used in structural proteins

Primary structure: Peptide bonds

• catalyzed by ribosome

• peptide backbone of C-C-N-C-C-N

Polarity: always grow in the same direction, starting at N-terminus

Differences in primary AA sequence matter - vasopressin example

• both vasopressin and oxytocin are 9 AA long

• both are identical except at two locations

  • vasopressin controls urine production

  • oxytocin involved in birth, lactation, and pair bonding

Order of AA is important too - Leu-enkephalin

• natural opioid

• the opposite order of AA has no pharmalogical effects

• the amine-carboxyl orientation essential to function

Secondary structure: Alpha-helix

• Forms independantly of side chains

• carboxyl h-bonds with amino of AA 4 after

• n — n+4

(helical structures are common in biology because they are stable

Beta sheet

Forms independtly to R groups (but they alternatively point up and down, interactions)

• H-bond of carbonyl (C=O) with amide hydrogen (N-H) of neighbouring strand

• typically contain 4-5 strands but can have more

• can be antiparallel or parallel

  • anti only needs small sequence between

  • parallel needs more

Counting polypeptide chains

Always count from N-terminus (amino end)

Coiled coil

Alpha helices twisting together

• Only form with amphipathic — protein with both hydrophobic and hydrophilic parts

  • repeating hydrophobic molecule every 4 peptide bonds — hydrophobic stripe

  • 2 helices will wrap together, push hydrophobic parts into middle

• very stable and strong

  • keratin in hair

  • myosin motor proteins

Amyloid structure

Beta sheets stacked together

Misfolded proteins can form amyloid structure — neurodegenerative diseases

• prions: converts properly folded molecules

Lec 4: Tertiary structure

Overall 3D structure of a protein

Held together by:

• hydrophobic forces

• non-covalent bonds

• covalent disulfide bonds

Hydrophobic force

• non-polar AA in interior of folds

• polar AA on exterior

Tertiary structure — continued

1. Proteins fold into conformation that is most energetically favourable — spontaneous

   • H-bonding in:

   • backbone/backbone

   • backbone/side chain

   • side chain/side chain

2. Chaperone proteins can also help make process more efficient and reliable in living cells

   • misfolded proteins cant function

Tertiary structure can have large variety of shapes

• globular, filament, etc

But few of the possible chains will be useful

• majority 50—2000 AA long

• well-behaved, stable

Models for proteins

• Backbone model — only backbones

• Ribbon model — shows folding

• Wire model — shows positions of bonds

• Space-filling model — contour map

Protein domains

Regions of proteins that have specialized functions

single polypeptide

• each domain has own tertiary structure and function semi-independently

.

eukaryotic proteins often have 2 or more

• connected by intrinsically disordered sequences (flexible regions)

• domains are important for the evolution of proteins

Protein domains — extra example: Src protein kinase

Kinase — phosphorylate proteins (changes activity)

Src protein kinase has 3 domains

• SH2 and SH3 regulates kinase

Protein families

Way to organize proteins — a protein can belong in more than one

• Similar AA sequences and tertiary structures

• Members have evolved different functions

• Most proteins belong to families with similar structural domains

Quaternary structure

More than1 polypeptide chain

• not all proteins

• subunit = separate polypeptide

• can get really big

Quaternary structure example: Hemoglobin

1. Each hemoglobin has 4 subunits (2 alpha, 2 beta)

2. Sickle cell anemia is caused by mutation in beta subunit

Multiprotein complexes and molecular machines

Can be:

• many identical subunits (actin filaments)

• mixtures of proteins and DNA/RNA (ribosomes)

• dynamic assemblies of proteins to form machines (DNA replication)

Multiprotein complexes and molecular machines

conformational changes

• perform job

• often need ATP

.

scaffold proteins

• binds proteins together

How are proteins studied?

Past

• purify proteins

• electrophoresis & affinity chromatography

.

Now

• Mass spectrometry

  • sequenced many genomes

  • find mass and match to predictions

• discover precise 3D structure with other techniques

• can also use AI to predict structure using only polypeptide

Protein separation

separate using size, shape, charge, hydrophobicity

Proteomics

Large scale study of proteins

• structure

• interactions

• abundance and turnover

• location