Mcc Week 1

Front 1

Protein folding Gen Info

1. Primary Structure
2. Secondary Structure
3. Tertiary Structure
4. Quarternary Structure

Back 1

Gen: Stabilized by non-covalent bonds (H-bonds) Folding occurs to energetically favorable state.

1. Amino Acid residues
2. Beta sheets and Alpha Helices, turn
3. Folded petptide
4. Assembled polypeptide subunits - usually bury the majority of hydrophobic side chains

Front 2

Oxygen binding by myoglobin

Back 2

Myoglobin binding mechanism means it needs really low pO2 to unbind. Typical capillary O2 concentration is 30mmHg. Typically during vigorous exercise will dip below 10mmHg. Allowing myoglobin to release O2.

Front 3

Oxygen binding by hemoglobin

Back 3

Small change in oxygen concentration results in a large change in oxygen binding. Cooperative Binding.

Front 4

Bohr Effect

Back 4

Lowering pH favors the T-State. Tissues in need of O2 have lower pH. Releasing more O2.

Front 5

CO2 - Hemoglobin -

Back 5

80% of CO2 travels in plasma as HCO3- > catalyzed by carbonic anyhdrase

Front 6

2,3- BPG

Back 6

Upregulated by glycolysis, in higher altitude. 2,3 BPG binds to partially deoxygenated hemoglobin, allosterically upregulating bound O2

Front 7

Transcription

Back 7

RNA Polymerase I II III - add onto the 3' end of nascent product.

Read template strand.mRNA builds in a 5' to 3' direction.

Complimentarity - anti parallel double stranded helix.

Front 8

DNA Binding Proteins

Back 8

Short recognition molecules on DNA.
Interact with each other. (More at the party longer they stay)
Not necessarily enhancers or silencers. They just bind, then the complex they form will recruit co-activators or co-repressors

Multiple factors therefore cooperate to increase or decrease the probability that a polymerase will be recruited and transcription will occur.

Allows the level of transcription to be controlled over a wide range of values.

Front 9

Beta globin locus

Back 9

Regulated so that subsets come on and then are repressed in a developmental pattern.

A single enhancer or control locus is the key to regulation.

Front 10

Mutations in genes can occur....

Back 10

-Promoter mutations lead to decreased transcription
-Splice site recognition or splice junction mutations lead to inappropriate splicing of the primary transcript into mRNA
-Exon mutations lead to decreased translation,
decreased protein stability, or altered protein function

Front 11

Consider where mutations occur in gene and how that would play out clinically.

Back 11

Hemoglobin as an example.

Things to consider: missense mutations in introns and exons. Splice-site mutations, promoter mutations, nonsense mutations, frameshift mutations, more?

Front 12

Discuss the regulation of Transcription

Back 12

Front 13

Discuss 4 ways to regulate transcription and how they interact.

Back 13

Front 14

Complex Diagrams and how to easily understand them

Back 14

Front 15

Diagramming Example

Back 15

We can use the wiring diagram to generate hypotheses:The effect of the HDAC inhibitor suggests that some cancers result from altered expression of tumor suppressor genes.

Front 16

Explain the delta-ALA Synthase Mechanism

Back 16

Vitamin B6 = Pyridoxal Phosphate (PLP)
Binds to Lysine248 of delta-ALA-Synthase.
Activates Glycine to neutrophillically attack succinyl CoA

Front 17

Enzyme Catalysis: Substrates bind to enzyme ________.

Back 17

active sites

Where chemical transformations occur.

Front 18

Active site amino acids often act as_____ and_____ in the reaction.

Back 18

acids and bases

enzyme activity is often pH dependent

Front 19

Reaction specificity depends on _________.

Back 19

active site structure.

Front 20

Many reactions require more chemical capabilities than amino acids can provide. These are called:

Back 20

cofactors or coenzymes. (often vitamins and minerals) B6 and B5 in delta ALA is an example.

Front 21

Enzyme Catalysis: Define - Transient intermediate

Back 21

During reaction intermediates can form which contain covalent bonds.

Front 22

Define - Catalysis

Back 22

lowering the free energy of the transition state.

Enzymes alter the kinetics, not the thermodynamics of the reaction. Thus the speed at which the products and substrates reach equilibrium.

Front 23

Define: Vmax

Back 23

the rate at which a particular enzyme, at a particular concentration, catalyzes a reaction when it is saturated with substrate.

varies with the concentration of the enzyme present

Front 24

Define: Km

Back 24

The concentration of substrate required for a particular enzyme to catalyze the reaction at half the maximal rate. This is a constant and does NOT vary with enzyme concentration.

Front 25

Define: kcat

Back 25

turnover number for an enzyme

kcat is independent of enzyme concentration.

Front 26

Define: kcat (again)

Back 26