BIOCHEMISTRY – PRELIM REVIEWER

BSN – 1

To my humble students!!

Good day!! Prelim exam is coming fast, and I am sure that you are cramming to study subjects
all at once. Remember that you are taking the exam to measure your understanding with the
lessons not that you are taking it to be judged. Your scores will not define your capabilities
rather it will be a result of how rigorous you study. Not everyone has the same resources, time,
and opportunities to study for this exam, there are some who needs to do chores, business,
and attend personal matters which may contribute to your preparation. Still, I am proud of
how you are trying to be great, to be the version you envision yourself. I am proud of the efforts,
sacrifices, and perseverance to learn and succeed. If you need help studying our subject, feel
free to reach out.

Good luck everyone!!!

Teacher Ali

What is Biochemistry?

• “Chemistry of the living cell”

• The science in which chemistry is applied to the study of living organisms and the atoms
and molecules which comprise living organisms.

Chemistry of Life

• Most biological compounds are made of only SIX elements: C, H, O, N, P, S.

• Only 31 chemical elements occur naturally in plants and animals.
• All organisms have similar biochemical pathways.
• All organisms use the same genetic code.

Four Major Classes of Biomolecules

o Carbohydrates
o Lipids
o Proteins
o Nucleic Acid
Foundations of biochemistry

Cellular Foundations

o Metabolism is the building and breaking down of life-sustaining chemicals within an

organism.
 o Three Purposes of Metabolism
▪ The conversion of food to energy.
▪ The conversion of food to building blocks.
▪ The elimination of waste products.
▪
o Catabolic – the breaking down of compounds.
o Anabolic – the building up (synthesis) of compounds.
o Enzymes are crucial to metabolism because enzymes act as catalysts – they allow a
reaction to proceed more rapidly.

o Two types of Enzyme Model

▪ Lock and Key Model - substrate is the exact shape of the enzyme binding
site.

▪ Induced-fit Model - the shape of the enzyme change to bind to the

substrate.

o Two types of Cells

o Prokaryotic Cells
▪ are simplistic cells.
▪ All prokaryotes have a single, circular chromosome located in a nucleoid
region of the cell, as well as ribosomes that produce proteins that perform
cellular metabolic functions.
o Eukaryotic Cells
▪ much larger and require more compartmentalization to adequately
perform metabolic functions.
▪ They have a true nucleus surrounded by a complex nuclear membrane
that houses multiple, linear chromosomes.

o The design for a cell mostly resides in the blueprint for the cell, the genetic code, which
is comprised of deoxyribonucleic acid (DNA) housed in the cell nucleus and a small
amount in the mitochondria.

Membrane Transport
o Molecules can move into the cell by two major processes.
 o diffusion or active transport.
▪ In passive diffusion, small, non-polar move across the membrane directly
across the membrane. Larger and/or polar molecules move by facilitated
diffusion, which requires a channel or carrier protein.

o The transport of molecules can also occur through the processes of.
o exocytosis and endocytosis.
▪ Exocytosis occurs when the secretory vesicle fuses with the plasma
membrane causing the contents of the vesicle to be exposed to the
outside of the cell.
▪ New proteins can also be introduced into the plasma membrane during
this fusion process. In the reverse process, called endocytosis, very large
particles can be engulfed into the cell.

Membrane Transport
• Solvent + Solute = Solution
• Intracellular fluid – inside the cell
• Extracellular fluid – outside the cell

Two Methods of Transport

• Passive – does not need energy
• Active – needs ATP

Types of Passive Transport

• Diffusion – Assisted by a channel protein
• Filtration – Separating through a membrane
•
Physical Foundations

o Living cells are open systems, exchanging matter and energy with their surroundings,
extracting and channeling energy to maintain themselves in a dynamic steady state
distant from equilibrium.
o free-energy change, ∆G, enthalpy change, ∆H, and entropy change, ∆S. These
variables are related by the equation ∆G = ∆H - T ∆S.

Genetic Foundations

o Genetic information is encoded in the linear sequence of four deoxyribonucleotides in

DNA.
o Transcription – from DNA to RNA
o Translation – from mRNA to Protein
Evolutionary Foundations

o Occasional inheritable mutations yield an organism that is better suited for survival in an
ecological niche and progeny that are preferentially selected.
 o Knowledge of the complete genomic nucleotide sequences of organisms from different
branches of the phylogenetic tree provides insights into the evolution and function of
extant organisms and offers great opportunities in human medicine.

Cells

o Cell Theory
o All organisms are composed of cells.
o Cells are the basic unit of all organisms.
o Cells arise only from pre-existing cells.

o All cells have certain structures in common.

o genetic material – in a nucleoid or nucleus.
o cytoplasm – a semifluid matrix.
o plasma membrane – a phospholipid bilayer.

o Cells were discovered in 1665 by Robert Hooke.

o Early studies of cells were conducted by:
• Mathias Schleiden (1838) – All plants are composed of cells
• Theodor Schwann (1839) – All plants and animals are composed of cells.
• Rudolf Virchow (1958) – All cells come from pre-existing cells.

Parts of the Cell

Nucleus
• Nuclear Membrane – bounds the nucleus
• Nucleolus – Site of Ribosome
• Chromatin – Combination of DNA and Proteins

Cytoplasm
• Cytosol – Fluid substance
• Inclusions – Substances inside the cell that are not organelles
• Organelles – Specific parts of the cell that carry out the processes.

Plasma Membrane
• Hydrophobic tails – placed between two hydrophilic heads
• Hydrophilic heads – placed in front of watery environment
• Proteins – serves as a channel or carrier of molecules
• Sugars – provides energy to cells
• Cholesterol – aids with the permeability of the membrane

The Organelles
• Nucleus - DNA Storage
• Mitochondrion - Energy production
• Ribosome - Protein synthesis
• Rough ER - Protein production and modification
 • Smooth ER - Lipid production and Detoxification
• Golgi apparatus - Protein transportation and export
• Peroxisome - Lipid breakdown; redox reactions
• Lysosome - Protein destruction

The Organelles
• Cytoskeleton - Cell movement; intracellular transportation
• Cell membrane - Define the inside and outside of a cell
• Cytosol - Cellular fluid

Surface Extensions
• Cilia – hair-like structure to filter air
• Flagella – whip-like structure for movement
• Microvilli – for surface area
Microscopy
Antoine van Leeuwenhoek - 1st to see single-celled organisms in pond water

Types of Microscope
1. Compound Light Microscope
• 1st type of microscope, most widely used
• light passes through 2 lenses
• Can magnify up to 2000x

2. Electron Microscope
• Used to observe VERY small objects: viruses, DNA, parts of cells
• Uses beams of electrons rather than light
• Much more powerful

Types of Electron Microscope

• Transmission Electron Microscope (TEM)
o Can magnify up to 250,000x
• Scanning Electron Microscope (SEM)
o Can magnify up to 100,000x

Guidelines for use

• Always carry with 2 hands
• Only use lens paper for cleaning
• Do not force knobs
• Always store covered

Vocabulary
• Magnification: increase of an object’s apparent size
• Resolution: power to show details clearly
• Both are needed to see a clear image