UNIT 1 – INTRODUCTION TO BIOCHEMISTRY

Biochemistry

is the study of the chemical substances

found in living organisms and the chemical interactions of

these substances with each other.

• It also deals with the application of the principles and

methods of chemistry to the fields of biology and

physiology.

STRUCTURAL CHEMISTRY

looks into the relationship of the molecular structure of

biochemical substances to their biological functions.

METABOLISM

studies the totality of chemical reactions that occur in living

organisms.

3. MOLECULAR GENETICS

seeks to understand the chemistry of the processes and

substances that store and transmit biological information.

• aims to understand heredity and the expression of genetic

information in molecular terms.

Biochemistry

is both a multidisciplinary and an

interdisciplinary science. As a multidisciplinary science, it

draws on many disciplines and use their results to answer

the questions about the molecular nature of life processes.

For example, the magnetic resonance imaging (MRI) tests

originated with physicists, but became a vital tool for

chemists in biochemical research.

ORGANIC

CHEMISTRY

describes the properties of

bioorganic substances and their role

in living organisms.

MICROBIOLOGY

the use of single-celled organisms

and viruses in the elucidation of

many metabolic pathways and

regulatory mechanisms.

GENETICS

understanding mechanisms that

gives a particular cell or organism its

biochemical identity.

MEDICINE

understand disease states in

molecular terms for proper diagnosis

and therapy.

BIOTECHNOLOGY

the use of organisms or their parts to

manufacture or modify products.

NUTRITION

understanding metabolism and

dietary requirements as a key

component in the maintenance of

good health.

CELL BIOLOGY

understanding the biochemical

division of labor within the cell as well

as the different mechanisms

involved.

PHYSIOLOGY

investigating life processes at the

tissue and organism levels.

Livings systems are all made up of cells,

typically many types. In turn, these cells

possess subcellular structure known as

organelles, which are complex

assemblies of very large polymeric

molecules, called macromolecules.

Biological structures play a role in the organism’s

existence.

• From parts of organisms, such as limbs and organs,

down to the chemical agents of metabolism, such as

enzymes and metabolic intermediates, a biological

purpose can be given for each component.

• Indeed, it is this functional characteristic of biological

structures that separates the science of biology from

studies of the inanimate world such as chemistry, physics,

and geology.

• In biology, it is always meaningful to seek the purpose of

observed structures, organizations, or patterns, that is, to

ask what functional role they serve within the organism.

extract energy from the environment. (Sun) (Solar energy) (herbivores) (carnivorous predators)

Maintenance of the highly organized structure and activity

of living systems depends on their ability to (______________________)

• The ultimate source of energy is the (___).

• (______) flows from photosynthetic organisms

(organisms able to capture light energy by the process of

photosynthesis) through food chains to (_________) and

ultimately to (_________________) at the apex of the

food pyramid (See figure below).

(biosphere) (photosynthesis) (metabolism) (ATP) (NADPH) (useful forms of stored

energy)

The (__________) is thus a system through which energy

flows.

• Organisms capture some of this energy, be it from

(_____________) or the (__________) of food, by forming

special energized biomolecules, of which (___) and

(______) are the two most prominent examples.

(unfavorable processes)

When these molecules react with other molecules in the

cell, the energy released can be used to drive

(_____________).

That is, ATP, NADPH, and related compounds are the

power sources that drive the energy-requiring activities

of the cell, including biosynthesis, movement, osmotic

work against concentration gradients, and in special

instances, light emission (bioluminescence).

(constancy over time)

At the expense of this energy flow, the organism can

maintain its intricate order and activity far removed from

equilibrium with its surroundings, yet exist in a state of

apparent (_____________).

steady state

This state of apparent constancy, or so-called (_________), is actually a very dynamic condition.

• Energy and material are consumed by the organism and

used to maintain its stability and order.

• In contrast, inanimate matter, as exemplified by the

universe in totality, is moving to a condition of increasing

disorder or, in thermodynamic terms, maximum entropy.

(deoxyribonucleic acid, or DNA)

This substance consists of polymeric chains of

(_____________), which are structurally

complementary to one another.

Biomolecules

the molecules that make up life are specialized

organic compounds present

in living systems

(stable covalent bonds) (electron-pair sharing)

Like organic compounds, biomolecules are all carbon

compounds.

• The prevalence of C is due to its unparalleled versatility in

forming (__________) through (____________).

(four covalent bonds) (C itself, H, O, and N.)

Carbon can form as many as (_____________) by

sharing each of the four electrons in its outer shell with

electrons contributed by other atoms.

• Atoms commonly found in covalent linkage to C are (_________)

(Hydrogen) (Oxygen) (three

covalent bonds)

(_______) can form one covalent bond by contributing

its single electron to the formation of an electron pair.

• (______), with two unpaired electrons in its outer shell,

can participate in two covalent bonds, and nitrogen,

which has three unshared electrons, can form (__________).

(triple bonds)

Carbon and nitrogen can even share three electron

pairs to form (________).

(catenation) (tetrahedral nature of the four covalent

bonds) (linear, branched), (cyclic compounds of C).

Two properties of carbon covalent bonds merit particular

attention.

• One is the ability of carbon to form covalent bonds with

itself (_________).

• The other is the (________________________) when carbon atoms form only single bonds.

• Together these properties hold the potential for an

incredible variety of (____________) and (____________).

functional

groups

Recall that organic compounds are classified according

groups of atoms within their structure that have

characteristic chemical behaviors, known as (_________).

water,

o carbon dioxide, and

o three inorganic nitrogen compounds—

▪ ammonium (NH4+),

▪ nitrate (NO3-) and

▪ dinitrogen (N2).

The major precursors for the formation of biomolecules

are:

metabolites,

which are simple organic compounds that are

intermediates in cellular energy transformation and in the

biosynthesis of various sets of building blocks.

BUILDING BLOCKS

o amino acids,

o sugars,

o nucleotides,

o fatty acids, and

o glycerol.

(polymers) (monomers)

All macromolecules, except lipids, are considered

(________) because they are composed of chains of their

corresponding building blocks (________).

supramolecular complexes

Interactions among macromolecules lead to the next level

of structural organization, (____________).

• Here, various members of one or more of the classes of

macromolecules come together to form specific

assemblies that serve important subcellular functions.

(organelles)

In eukaryotes (higher organisms), these

supramolecular complexes are further organized into what

is known as (__________).

noncovalent forces

These supramolecular assemblies are an interesting

contrast to their components because their structural

integrity is maintained by (_________), not by

covalent bonds.

(cellular inclusions) (membrane

bounded)

These are entities present in the cell.

• Organelles share two attributes:

o They are (_______), usually (________),

(cells and organelles)

Membranes define the boundaries of (________).

cell

All living things are made up of

cell

The (____) is the simplest functional unit of living organisms.

• Most chemical reactions that are needed to sustain life

takes place within the cell.

• As mentioned, the cell is smallest entity capable of

displaying attributes associated uniquely with the living

states. Although the cellular level may be considered as

one of the simple levels of structures, understanding the

mechanisms involved within it may help elucidate how the

higher levels of structure works and functions.

(prokaryotes and eukaryotes) (prokaryotic cell) (eukaryotic cell)

There are two types of cells, (__________).

• The simplest way to distinguish these two types is that a

(___________) contains no well-defined nucleus,

whereas the opposite is true for a (___________).

(Prokaryotes) (cell wall, an outer membrane, and a plasma membrane.) (cytoplasm)

• (_______) are mostly bacteria.

• Besides the lack of a nucleus, there are few well-defined

structures inside a prokaryotic cell.

• The exterior of a prokaryotic cell has three components:

(______/_____/______)

• These components allow controlled passage of material

into or out of the cell.

• The materials necessary for proper functioning of the cell

float about inside it, in a soup known as the (________).

• The illustration below shows a simplified version of a

prokaryotic cell.

(Eukaryotes) (organelles)

• (__________) are animals, plants, fungi, and protists. You

are a eukaryote.

• As mentioned earlier, in addition to having a nucleus,

eukaryotic cells have a number of membrane-bound

components known as (_________).

• In general, (________) contain much more genetic

material than prokaryotic cells.

• The illustration below shows a typical animal and plant

cells, which are basically eukaryotes.

(nucleus) (deoxyribonucleic

acid (DNA). (DNA)

is the most obvious organelle in any

eukaryotic cell.

• It is enclosed in a double membrane and communicates

with the surrounding cytosol via numerous nuclear pores.

• Within each (______) is nuclear chromatin that contains the

organism’s genome.

• The chromatin is efficiently packaged within the small

nuclear space.

• Genes within the chromatin are made of
(__________)

• The DNA stores the organism’s entire encoded genetic

information.

• The (_____) is similar in every cell of the body, but depending

on the specific cell type, some genes may be turned on or

off - that's why a liver cell is different from a muscle cell,

and a muscle cell is different from a fat cell.

• When a cell is dividing, the nuclear chromatin (DNA and

surrounding protein) condenses into chromosomes that

are easily seen by microscopy.

Nucleolus

The prominent structure in the nucleus is the (_________).

• The (1) ————- produces ribosomes, which move out of the

nucleus and take positions on the rough endoplasmic

reticulum where they are critical in protein synthesis.

(cytosol)

is the "soup" within which all the other cell

organelles reside and where most of the cellular

metabolism occurs.

• Though mostly water, the (_____) is full of proteins that

control cell metabolism including signal transduction

pathways, glycolysis, intracellular receptors, and

transcription factors.

Cytoplasm

This is a collective term for the cytosol plus the organelles

suspended within the cytosol.

centrosome, or MICROTUBULE ORGANIZING

CENTER (MTOC)

The (____________), is an area in the cell where

microtubules are produced.

(spindle)

The two centrosomes move to opposite ends of the

nucleus, and from each centrosome, microtubules grow

into a "(_______)" which is responsible for separating

replicated chromosomes into the two daughter cells.

Centriole

is a ring of nine groups of fused

microtubules.

• There are three microtubules in each group.

• Microtubules (________) are part of the cytoskeleton.

• In the complete animal cell centrosome, the two (_________)

are arranged such that one is perpendicular to the other.

7. Golgi:

is a membrane-bound structure with

a single membrane.

• It is actually a stack of membrane-bound vesicles that are

important in packaging macromolecules for transport

elsewhere in the cell.

• The stack of larger vesicles is surrounded by numerous

smaller vesicles containing those packaged

macromolecules.

• The enzymatic or hormonal contents of lysosomes,

peroxisomes and secretory vesicles are packaged in

membrane-bound vesicles at the periphery of the (_________)

Lysosome:

contain hydrolytic enzymes necessary for

intracellular digestion.

• They are common in animal cells, but rare in plant cells.

• Hydrolytic enzymes of plant cells are more often found in

the vacuole.

are membrane-bound packets of oxidative

enzymes.

• In plant cells, peroxisomes play a variety of roles including

converting fatty acids to sugar and assisting chloroplasts

in photorespiration.

• In animal cells, peroxisomes protect the cell from its own

production of toxic hydrogen peroxide.

• As an example, white blood cells produce hydrogen

peroxide to kill bacteria.

• The oxidative enzymes in peroxisomes break down the

hydrogen peroxide into water and oxygen.

Secretory Vesicle

Cell secretions - e.g. hormones, neurotransmitters - are

packaged in secretory vesicles at the Golgi apparatus.

• The secretory vesicles are then transported to the cell

surface for release.

(Cell membrane) (hydrophilic) (hydrophobic)

Every cell is enclosed in a membrane, a double layer of

phospholipids (lipid bilayer).

• The exposed heads of the bilayer are "(_________)" (water

loving), meaning that they are compatible with water both

within the cytosol and outside of the cell.

• However, the hidden tails of the phosopholipids are

"(_________)" (water fearing), so the cell membrane acts

as a protective barrier to the uncontrolled flow of water.

• The membrane is made more complex by the presence of

numerous proteins that are crucial to cell activity.

• These proteins include receptors for odors, tastes and

hormones, as well as pores responsible for the controlled

entry and exit of ions like sodium (Na+) potassium (K+),

calcium (Ca2+) and chloride (Cl-).

Mitochondria

provide the energy a cell needs to move,

divide, produce secretory products, contract - in short, they

are the power centers of the cell.

• They are about the size of bacteria but may have different

shapes depending on the cell type.

• are membrane-bound organelles, and like

the nucleus have a double membrane.

• The outer membrane is fairly smooth.

• But the inner membrane is highly convoluted, forming folds

(cristae) when viewed in cross-section.

• The cristae greatly increase the inner membrane's surface

area.

• It is on these cristae that food (sugar) is combined with

oxygen to produce ATP - the primary energy source for

the cell.

(vacuole) (cell vacuole)

is a membrane-bound sac that plays roles in

intracellular digestion and the release of cellular waste

products.

• In animal cells, (1) (_______) are generally small.

• tend to be large in plant cells and play several

roles: storing nutrients and waste products, helping

increase cell size during growth, and even acting much like

lysosomes of animal cells.

• The plant (__________) also regulates turgor pressure in the

cell.

• Water collects in cell (1), pressing outward against

the cell wall and producing rigidity in the plant.

• Without sufficient water, turgor pressure drops and the

plant wilts.

(Cell walls) (cellulose) (turgor pressure)

Plant cells have a rigid, protective (_______) made up of

polysaccharides.

• In higher plant cells, that polysaccharide is usually

(_________).

• The cell wall provides and maintains the shape of these

cells and serves as a protective barrier.

• Fluid collects in the plant cell vacuole and pushes out

against the (________).

• This (______________) is responsible for the crispness of

fresh vegetables.

(Chloroplast) (grana)

(____________) are specialized organelles found in all higher

plant cells.

• These organelles contain the plant cell's chlorophyll

responsible for the plant's green color and the ability to

absorb energy from sunlight.

• This energy is used to convert water plus atmospheric

carbon dioxide into metabolizable sugars by the

biochemical process of photosynthesis.

•have a double outer membrane.

• Within the stroma are other membrane structures - the

thylakoids.

• Thylakoids appear in stacks called "(____)" (singular =

granum).

(endoplasmic reticulum, or ER)

Throughout the eukaryotic cell, especially those

responsible for the production of hormones and other

secretory products, is a vast network of membrane-bound

vesicles and tubules called the (___________________) for short.

ER

The (__) is a continuation of the outer nuclear membrane

and its varied functions suggest the complexity of the

eukaryotic cell.

smooth endoplasmic reticulum

The (________________) is so named because

it appears smooth by electron microscopy.

• plays different functions depending on the

specific cell type including lipid and steroid hormone

synthesis, breakdown of lipid-soluble toxins in liver cells,

and control of calcium release in muscle cell contraction.

Rough endoplasmic reticulum

(________) appears "pebbled" by

electron microscopy due to the presence of numerous

ribosomes on its surface.

• Proteins synthesized on these ribosomes collect in the

endoplasmic reticulum for transport throughout the cell.

(Ribosomes) (large subunit) (small subunit)

(_________) are packets of RNA and protein that play a

crucial role in both prokaryotic and eukaryotic cells.

• They are the site of protein synthesis.

• Each ribosome comprises two parts, a (_________) and a

(________).

• Messenger RNA from the cell nucleus is moved

systematically along the ribosome where transfer RNA

adds individual amino acid molecules to the lengthening

protein chain.

(cytoskeleton) (Microtubules, Actin filaments (microfilaments), Intermediate fibers)

As its name implies, the (_________) helps to maintain cell

shape.

• But the primary importance of the (________) is in cell

motility.

• The internal movement of cell organelles, as well as cell

locomotion and muscle fiber contraction could not take

place without the (_________).

• The (___________) is an organized network of three primary

protein filaments:

(________)

(________)

(________)

unicellular or multicellular

Eukaryotic organisms may be (______/_______).