Chapter 1: Biochemistry Concepts and Themes

What is science?

A way of gaining new knowledge and the knowledge we gain from that process

What does “natural universe” mean

It focuses on things that people can observe and measure.

What are the 4 key elements that make an idea or experiment scientific?

• Natural universe

• Honest results

• Reproducible

• Scientific context

What does “honest results” mean in science?

Results are reported truthfully, without changing or hiding information.

What does “reproducible” mean in science?

Other scientists can repeat the experiment and get similar results.

What is the scientific method?

A way of gaining new knowledge that follows the four conditions of science.

Is there only one scientific method?

No. There are many different approaches that can be used in science.

What is a scientist?

Someone who uses the scientific method to answer questions about the natural world.

What is the postulate of objectivity?

The assumption that a natural phenomenon does not randomly change. If an experiment gets different results when repeated, there is a reason.

What is a hypothesis?

A possible explanation for one or more observations that has not yet been thoroughly tested

What is a theory?

A well-supported explanation based on many experimental observations

What is the classic scientific method?

Hypothesis —> experiment —> answer

What are cells?

Organized systems of molecules and macromolecules.

What are the three domains of life?

• Bacteria

• Archaea

• Eukarya

What is catalysis?

When a substance changes the rate of a chemical reaction without being chemically changed itself.

What is an enzyme?

A protein or RNA that speeds up a specific chemical reaction by lowering the activiation energy.

What are Bacteria?

Organisms that have a plasma membrane but no nucleus or internal organelles.

What are the organelles in bacterial cell?

• Cytoplasm

• Plasma membrane

• Ribosomes

• Nucleoid

What are Archaea?

Organisms that often live in extreme environments, such as very hot, acidic, or salty places.

What are Eukarya?

Organisms whose cells have a nucleus, multiple chromosomes, and internal organelles. They can be single-celled or multicellular.

What are the organelles of a eukaryotic cell?

• Cytoplasm

• Plasma membrane

• Ribosomes

• Nucleus

• Nuclear membrane

• Membrane-bounded organelles

Which domain of life has the most organisms?

Bacteria

What does a phylogeny show?

A phylogeny shows the evolutionary relationships between organisms.

Where is the DNA located in a bacterial cell?

In a nucleoid region, rather than inside a nucleus.

Where is the DNA located in a eukaryotic cell?

The nucleus

Are viruses part of the three domains of life?

No

Why do viruses need host cells?

They depend on the enzymes and resources of the host cell to make new viruses.

How often do E. coli cells divide?

Every 20–40 minutes.

What are ribosomes?

Structures that make proteins from an RNA message.

What are pili?

Short structures that help bacteria attach to other cells or surfaces.

What are flagella?

Long structures that help bacteria move through their environment.

What is the nucleolus?

The site where ribosomal RNA is made.

What does the rough ER do?

It is a major site of protein synthesis.

What does the smooth ER do?

It is involved in lipid synthesis and drug metabolism.

What does the Golgi complex do?

It processes, packages, and sends proteins to other parts of the cell or outside the cell.

What do transport vesicles do?

They move proteins and lipids between the ER, Golgi, and plasma membrane.

What does a peroxisome do?

It helps break down fatty acids.

What does a lysosome do?

It breaks down cellular waste and debris.

What structures are unique to plant cells?

Cell wall, chloroplasts, vacuole, and glyoxysomes.

What structure is unique to animal cells?

Lysosomes

What are plasmodesmata?

Openings that provide a path between neighboring plant cells.

What does the large vacuole do?

It stores substances and helps degrade and recycle macromolecules.

What do chloroplasts do?

They capture sunlight and make ATP and carbohydrates during photosynthesis.

What are thylakoids?

Structures inside chloroplasts where light-driven ATP production occurs.

What are starch granules?

They temporarily store carbohydrates made during photosynthesis.

What is a glyoxysome?

An organelle containing enzymes involved in the glyoxylate cycle.

What are the three levels of organization?

Monomers → macromolecules → supramolecular structures.

What are supramolecules?

Groups of molecules that are held together to form larger structures.

What are model organisms?

Organisms that are easy to maintain and study in a laboratory.

What is a genome?

The complete set of genetic information (DNA) in an organism.

What is a mutation?

A change in DNA that can sometimes be inherited.

What is a chromosome?

A large DNA molecule with associated proteins that contains many genes and stores genetic information.

What is a gene?

A segment of DNA that codes for a functional protein (polypeptide) or RNA molecule.

What is the central dogma of molecular biology?

DNA → RNA → Protein.

What laws does biochemistry follow?

The laws of chemistry and physics.

What do biological processes involve?

Chemical reactions.

What four elements make up over 99% of most cells?

Hydrogen, oxygen, nitrogen, and carbon.

What element is the chemistry of living organisms centered around?

Carbon

What do functional groups do?

They give molecules specific chemical properties.

What is a dalton (Da)?

A unit used to measure molecular mass.

What are nucleophiles?

Electron-rich molecules or atoms that donate electrons.

What are electrophiles?

Electron-deficient molecules or atoms that accept electrons.

What usually starts a biochemical reaction mechanism?

An unshared pair of electrons from a nucleophile.

What do enzymes do in biochemical reactions?

They catalyze (speed up) biochemical reactions.

What is a cofactor?

An inorganic ion or coenzyme needed for an enzyme to work.

What is free energy (G)?

The part of a system's energy that can do work at constant temperature and pressure.

What is a transition state?

The highest-energy, temporary state of a molecule during a chemical reaction.

What is activation energy (ΔG‡)?

The energy needed to reach the transition state and start a reaction.

What happens when activation energy is high?

The reaction is slower

How can reaction rates be increased?

By increasing temperature or pressure or by adding a catalyst.

What does a catalyst do?

It lowers the activation energy, making a reaction happen faster.

What is an equilibrium constant (Keq)?

A value that describes the relative amounts of reactants and products at equilibrium.

What is the difference between ΔG and ΔG‡?

ΔG tells you whether a reaction is energetically favorable, while ΔG‡ tells you how much energy is needed to get the reaction started.

What does a negative ΔG mean?

The reaction is favorable and releases free energy.

What three things is free energy related to?

Enthalpy (H), entropy (S), and temperature (T).

What is entropy (S)?

A measure of randomness or disorder in a system.

What is enthalpy (H)?

The heat content of a system.