Biochemistry Chapter 1

What is the definition of Biochemistry?

The chemistry of life.

What are the four key elements of science?

1. Focus on the natural universe

2. Honest reporting in results

3. Results can be reproduced by protocol

4. Carried out in scientific context

What are the 5 types of scientific methods?

1. Observation → Hypothesis → Experiment

2. Serendpity

3. Inspiration

4. Model building for deduction

5. Exploration and observation

What is the two classifications of cells?

Unicellular and Multicellular

What are specific to Eukaryotes?

Membrane bound organelles, membrane enclosed nucleus,

What is specific to prokaryotes?

Nucleoid, flagella, pili, smaller in size

How do Eukaryotes deal with their diffusion issue?

Extensive folding on surface

What does a ribosome do?

Create proteins

What does a peroxisome do?

oxidizes fatty acids

What does a lysosome do?

Degrades intracellular debris

What does Golgi do?

Packages proteins to be moved to organelles or outside the cell itself

What does the cytoskeleton do?

Support the cell and move organelles

what does the SER do?

Produce lipids

What does RER do?

Produce proteins

What are the three domains?

Bacteria, Archaea, Eukarya

Which two domains are considered to be extremophiles?

Bacteria and Eukarya

Which two domains came first?

Bacteria and Archaea

Which two domains are only unicellular?

Archaea and Bacteria

Name the structural hierarchy for chromatin.

Chromatin → DNA/Protein → Nucleotides

Name the structural hierarchy for plasma membrane?

Plasma membrane → Protein → amino acid

Name the structural hierarchy for cell wall.

cell wall → cellulose → sugars

What is the central dogma?

DNA → transcription → mRNA → translation → unfolded protein → folded → folded protein

What happens if DNA is copied wrong?

Mutations will likely occur or death.

What causes evolution?

Mutations that are better suited for their environment.

What is the difference between genome vs genes?

Genome is the total bp in the chromosomes.

Genes are the amount of bp that are actually used. Most of the genome is never used,

What are the important elements? (DONT MEMORIZE ALL)

C, H, N, O, Na, K, Cl, P, S, Cl

What are the trace elements? DO NOT MEMORIZE

Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, W

How is molecular mass measured?

Daltons

What is the definition of a nucleophile?

Anything that has a lone pair or negative charge, Wants to get rid of electrons

What is definition of an electrophile?

Something that wants to take electrons. It’s positive or near something that is electronegative.

What are enzymes?

They are biological catalysts, mainly proteins

What is a cofactor?

A small molecule (usually coenzyme or metal ion) that helps enzymes work.

What are the three ways cofactors work?

Ox/red, one-carbon, group transfer

What’s the relationship between thermodynamics and kinetics?

Inversely Proportionate

What can lower a transition state?

Enzyme

All life is fundamentally _____.

Aqueous

Why is all life need water?

Because of the weak chemical interactions from hydrogen bonding from water

What shape is water? Why is it important?

Water is a bent molecule because of its polarity.

In water, how many H bonds does each H2O make?

3.4

In ice, how much Hbonds does each H2O molecule make?

4

is water or ice more dense?

Water

What does it mean if water melts and evaporates at room temp

the delta H is >0 and then delta S must be > 0. (Entropy focused)

What is the strongest shape for an H bond?

linear

Water does water form with ionic compounds?

Ion-dipole moments

What helps nonpolar gases bond with water?

Carrier proteins

What do hydrophobic molecules do to water?

Break the H-bonds apart

What type of bonds does water form by itself?

dynamic and fleeting

What does water become when forced to interact with hydrophobic molecules?

Highly ordered

What is the hydrophobic effect?

Clustering of nonpolar groups due to an increase in entropy for hydrophilic which offsets the decrease entropy in water,

What happens in amphipathic molecules in water?

The hydrophobic parts huddle while hydrophilic touches water. Aka micelles