Chapter 1 Cell Function And DNA RNA Organism – Biochemistry

This lesson covers Cell Function And DNA RNA Organism – Biochemistry.

What determines the lower limit of cell size

set by the minimum number of each type of biomolecule required by the cell

What is the upper limit of cell size

set by the rate of diffusion of solute molecules in aqueous systems

Who showed up first in evolution: autotrophs or heterotrophs?


Who showed up first in evolution: anaerobic or aerobic?


An organism that uses reduced inorganic compounds as its electron source


obtain electrons from organic compounds


Are Eukaryotes more closely related to archaea or bacteria?


which domain showed up first?

archaea. They were able to live in harsh or extreme environments


trap and use sunlight


derive their energy from the oxidation of chemical fuel


Organisms that make their own food


An organism that cannot make its own food.


Process that requires oxygen


Process that does not require oxygen

Four major building blocks

Amino acids, Nucleic acids, lipids, sugar

secondary metabolites

pathways that lead to specialized products not found in every living cell


systemic characterization of the metabolome under very specific conditions


systematic characterization of protein complements under specific conditions

Three major functions of polysaccharides

1. energy-rich fuel stores
2. rigid structural components of cell walls
3. extracellular recognition elements that bind to proteins on other cells


all of a cell’s carbohydrate-containing molecules

Function of lipids

serve as structural components of membranes, long term energy storage, pigments, and intracellular signals

Which is the only amino acid that occurs as its D isomer?


chiral center

carbon with four different substituents and lack a plane of symmetry


Compounds with the same structural formula but with a different arrangement of the atoms in space.


isomers that are mirror images of each other


stereoisomers that are not mirror images


The particular three-dimentional shape of a protein molecule

cis configuration

the configuration in which substituent groups are on the same side of a double bond

trans configuration

the configuration in which substituent groups are on the opposite sides of a double bond


The heat content of a system at constant pressure


A measure of disorder or randomness.

free energy

energy that is available to do work

how do unfavorable reactions occur?

coupling them with a favorable reaction

Reaction coupling allows for:

unfavorable reactions to happen

Is a living organism an isolated, closed or open thermodynamic system?

open system

Organisms obtain energy from their surroundings in two ways:

1. they take up chemical fuels (such as glucose) from their environment and extract energy by oxidizing them
2. They absorb energy from sunlight

What elements are essential elements for life?

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


no bond breaking between changes. This is achieved through rotating


need to break a bond between changes
Ex. changing from cis to trans


without water


a molecule that is not superimposable on its mirror image


A molecule that is superimposable on its mirror image


Two different molecules that have the same chemical formula

Are Amino acids L or D conformation?


Are sugars L or D conformation


racemic mixture

A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.

steady state

a state in which inputs equal outputs, so that the system is not changing over time

Law of Conservation of Energy

In any physical or chemical change, the total amount of energy in the universe remains constant although form of the energy may change

Law of Increasing Entropy

the total entropy of the universe is continually increasing.

Is the human body an open or closed system?



loss of electrons


gain of electrons


The removal of hydrogen from a molecule

If change in G is less than 0 what does that indicate?

-exergonic reaction
-it is favorable
-reaction is spontaneous

If change in G is more than 0 what does that indicate?

-not spontaneous

energy coupling

The use of an exergonic process to drive an endergonic one.


proteins (sometimes RNA) that increase the rate (kinetic) of a chemical reaction

Do enzymes alter free energy? (thermodynamic)


Do enzymes affect the kinetic or thermodynamic process of a reaction?

Kinetic. They speed up the reaction by lowering activation energy

Are enzymes consumed during a reaction?



Metabolic pathways that break down molecules, releasing energy.


Metabolic pathways that construct molecules, requiring energy.

Central Dogma of Biology

DNA -> RNA -> Protein


Matching Chromosomes that are similar but not identical


homologous genes within a single species


homologous genes separated by a speciation event


An organism that makes its own food


an organism that gets its energy from sunlight


Organisms that get energy from chemicals taken from the environment


A part of the cell containing DNA and RNA and responsible for growth and reproduction


A dense region of DNA in a prokaryotic cell.


An organism whose cells do not have an enclosed nucleus, such as bacteria.


organism whose cells contain a nucleus

Four major types of building blocks

Amino acids, Nucleic acids, lipids, sugar

activation energy

Energy needed to get a reaction started


The carriers for energy and high energy electrons during glycolysis


organism that makes organic carbon molecules from carbon dioxide using energy from chemical reactions


Organisms that use light as a source of energy to synthesize organic substances and that use carbon dioxide as their carbon source


An organism that must consume organic molecules for both energy and carbon.


An organism that uses light to generate ATP but that must obtain carbon in organic form.

Three types of cytoplasmic filaments

actin filaments, microtubules, and intermediate filaments


Process by which a cell releases large amounts of material


process by which a cell takes material into the cell by infolding of the cell membrane

how are the monomeric subunits of proteins, nucleic acids, and polysaccharides joined

by covalent bonds

How are macromolecules held together

by noncovalent interactions such as hydrogen bonds, ionic interactions, van der waal interactions, and hydrophobic effects

Most abundant elements in living organisms

carbon, hydrogen, oxygen, nitrogen

amine group

the nitrogen-containing portion of an amino acid

carbonyl group

a chemical group consisting of a carbon atom linked by a double bond to an oxygen atom


molecules with the same chemical bonds and same chemical formula but different spatial arrangement of atoms


fixed spatial arrangement of atoms

How is configuration conferred?

1. double bonds around which there is little or no freedom of rotation
2. chiral centers, around which substituent groups are arranged in a specific orientation

geometric isomers

differ in the arrangement of their substituent groups with respect to the nonrotating double bond
cis-trans isomers


spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds

dynamic steady state

when the gains and losses of ecological systems are in balance

isolated system

if the system exchanges neither matter nor energy

closed system

if the system exchanges energy but not matter with its surroundings

open system

if the system exchanges both energy and matter

first law of thermodynamics

Energy cannot be created or destroyed. Amount of energy is constant, although the form of the energy may change

The free energy of formation of proteins is positive. To carry out these thermodynamically unfavorable, energy-requiring reactions, what does the cell do?

couple them to other reactions that liberate free energy

Adenosine Triphosphate (ATP)

compound used by cells to store and release energy

Keq > 1

G is large and negative
products are favored


G is large and positive

Why is the breakdown of ATP in cells an exergonic process

all living cells maintain a concentration of ATP far above its equilibrium concentration


All of the chemical reactions that occur within an organism (both catabolic and anabolic)

which came first: DNA, RNA, or protein. Why?

RNA. It can act as catalysts in their own formation meaning RNA may have been the first gene and the first catalyst

Life is characterized by: (5)

1. high degree of complexity
2. Extraction, transformation, and systematic use of energy to create and maintain structures and to do work
3. structure, function and interactions
4. Responsively interact with the surroundings
5. Replication and evolution

Is a living organism considered stable or dynamic


who showed up first in evolution?


where do prokaryotes contain their DNA

in the nucleoid

what is the cell wall of prokaryotes composed of


what is the function of the cytoskeleton (3)

-cell shape
-transport paths

Protein: monomeric, oligomeric, macromolecule, and total collection

amino acid->peptide->protein->proteome

DNA: monomeric, oligomeric, macromolecule, and total collection

Nucleic acid-> polymer or nucelotide-> DNA or RNA-> genome

Sugar: monomeric, oligomeric, macromolecule, and total collection

monosaccharide->oligo-/poly-saccharide-> Glycan-> Glycome

Lipids: monomeric, oligomeric, macromolecule, and total collection

Fatty acid-> lipid->membrane-> lipidome

conformation vs confirguation

Conformation does not require bond breaking between changes
Configuration needs to break a bond between changes

When two acids condense together and lose water (anhydride) are they stable? why or why not?

No, the negative charges will repel

What are the two possible geometric isomers?

cis and trans

The lower the potential energy the [more/less] stable the molecule


Which has the higher probability of forming, a conformation with high potential energy or with low potential energy?

low potential energy

Do isomers have the same chemical composition?


Enantiomers have [different/identical] physical properties


what is the only physical property that is not identical in enantiomers?

how they rotate in polarized light

Diasteromers have [different/identical] physical and chemical properties


What is the difference between chemical synthetic compounds and biosynthetic compounds

chemical synthetic compounds produce a racemic mixture but a biosynthetic compound is normally single handed

why dont cells make L and D amino acids

Macromolecules have unique binding pockets so only certain molecules fit in well and can bind. If the wrong configuration is present, they will not be able to bind. This is called stereospecificity

When an organism is dead, what is its state in accordance to the surroundings

It is equilibrium, no net energy change

How do organisms maintain homeostasis?

By keeping the concentrations of most metabolites at steady state

In steady state, the rate of synthesis of a metabolite […] the rate of breakdown of this metabolite


Which is the measure of number and kinds of bonds or interaction that are made and broken

Enthalpy (H)


Exergonic, thermodynamically favorable, spontaneously move forward


Endergonic, thermodynamically unfavorable, will not move forward spontaneously (move backward)

What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= –
S= +

G= –


What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= +
S= –

G= +

not spontaneous

What is the sign of G? Will this reaction be spontaneous or not spontaneous:
H= +
S= +

G= +/-

Favorable at high temperature (G=-)
unfavorable at low temperature (G=+)

can entropically unfavorable reactions still be spontaneous? How? give an example

yes. Soap forms micelles, which are ordered structures due to hydrophobic interactions

A kinetic or nonspontaneous reaction is one in which the most stable state is that of the…


A thermodynamic reaction favors the [products/reactants], resulting in a spontaneous reaction that occurs without the need to constantly supply energy


What are the most stable states of a kinetic reaction

Those of reactants, in which an input of energy is required to move the reaction from a state of stability, to that of reacting and converting itself into products

What are the most stable states of a thermodynamic reaction

Those of products, because the reaction occurs spontaneously, without the need for energy to be added

An endergonic reaction is kinetically [stable/unstable] and thermodyncamically [favorable/unfavorable]

stable/ unfavorable

An exergonic reaction is kinetically [stable/unstable] and thermodyncamically [favorable/unfavorable]

unstable/ favorable

If all the concentrations of products and reactants are 1, what would G be? why?



If all concentrations of reactants and products are 1 then k=[products]/[reactants]= 1


If k>1 then G is[pos/neg] and the reaction proceeds [forwards/backwards]

negative/ forward

If k<1 then G is[pos/neg] and the reaction proceeds [forwards/backwards]

positive/ backwards

Two reactions can be coupled if they share..

a common intermediate

What do DNA, RNA and Protein do?

DNA: stores information
RNA:transmits information
Proteins:; function manifests information

The 3D structure of a protein is determined by

DNa sequence (that determines the amino acid sequence)

key goal of biochemistry

understand what it means to be alive at the molecular level

2nd key goal of biochemistry

understand the effects of the molecular manipulations on the life that an organism leads

unity of biochemistry

organisms are remarkably uniform at the molecular level

Jacques Monod

“anything found to be true of the bacterium e.coli must also be true of elephants”


This uniformity reveals that all organisms on earth came from a common ancestor

a core of essential biochemical processes, common to all organisms, appeared ________ in the evolution of life.


the diversity of life in the modern world has been generated by:

evolutionary processes acting on these biochemical processes common to all organisms

which three elements make up 98% of atoms in an organism?

oxygen, hydrogen, and carbon

all life requires


fuel molecules are made entirely of:

carbon hydrogen and oxygen

biological fuels, like the fuels that power machinery, react with __________ to produce ________________ ______________ and _________________

oxygen, carbon dioxide, water

reactions in which biological fuels reacting with oxygen to produce carbon dioxide and water are called:

combustion reactions

biological fuels that undergo combustion provide energy to power the:


the four classes of biomolecules

proteins, nucleic acids, lipids, carbohydrates

proteins are constructed of _____ building blocks called:

20, amino acids

amino acids are linked by__________ ___________

peptide bonds

proteins serve as:

signal molecules, receptors for signal molecules, structural roles, allow mobility, provide defenses against environmental dangers, and are catalysts


agents that enhance the rate of a chemical reaction without being permanently affected themselves

proteins catalysts are called


every process that takes place in living systems depends on:


primary function of nucleic acids:

store and transfer information

what do nucleic acids contain?

the instructions for all cellular functions and interactions

nucleic acids are constructed from only four building blocks called:


a nucleotide is made up of:

five carbon sugar either deoxyribose or ribose, attatched to a heterocyclic ring stucture called a base,
and at least one phosphoryl group

there are two types of nucleic acids:

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

genetic information is stored in:

DNA, the “parts list” that determines the nature of the organism

DNA is constructed from __________ deoxyribonucleotides. differing from one another only in the __________ structure of the __________

4 ,ring, bases

the four bases of DNA are:

Adenine, Guanine, Thymine, Cytosine

the information content of DNA is the sequence of nucleotides linked together by ________________ linkages.


In the double helix, bases interact with one another such that:

A with T and C with G

some regions of DNA are copied as a special class of RNA molecules called______________ ________

messenger RNA

mRNA is a template for the synthesis of __________


unlike DNA, mRNA is :

frequently broken down after use

RNA is similar to DNA in composition with two exceptions:

1. the base thymine (T) is replaced with uracil (U)
2. the sugar component of the ribonucleotides contain an additional hydroxyl (-OH) group

among the key biomolecules, ___________ are much smaller than proteins or nucleic acids


lipids are not polymers made of ____________ ___________, as are proteins and nucleic acids

repeating units

a key characteristic of many biochemically important lipids is their dual chemical nature: part of the molecule is _____________ and the other part of the molecule is ___________

hydophillic, hydrophobic


it can dissolve in water


cannot dissolve in water

the dual nature of lipids allows:

lipids to form barriers that delineate the cell from its environment and to establish intracellular componentsl allows an “inside” and “outside” at biochemical level

lipids are also an important ___________ form of energy


the hydrophobic component of lipids can undergo _____________ to provide large amounts of cellular energy.


the most common carbohydrate fuel

glucose the simple sugar

glucose is stored in animals as:


what does glycogen consist of:

many glucose molecules linked end to end and having occasional branches

in plants, the storage form of glucose is


central dogma

proposed by Francis Crick: information flows from DNA to RNA to protein

DNA constitutes the heritable information – the __________


the information of the genome is packed in discrete units called


the process of copying the genome is called


DNA polymerase

a group of enzymes that catalyze the replication process

Translation takes place on large macromolecular complexes called ____________, consisting of RNA and protein


The _______ is the basic unit of life


A ____________ is a lipid bilayer: two layers of lipids organized with their hydrophobic chains interacting with one another and the hydrophilic head groups interacting with the environment


There are two basic types of cells: ___________ cells and ____________ cells

eukaryotic, prokaryotic

The main difference between the two basic cell types is the existence of membrane-enclosed compartments in ______________ and the absence of such compartments in ________________.

eukaryotes, prokaryotes

—two biochemical features minimally constitute a cell: there must be :

(1) a barrier that separates the cell from its environment and
(2) an inside that is chemically differ- ent from the environment and that accommodates the biochemistry of living.

The _____________ ______________ separates the inside of the cell from the outside, one cell from another cell.

plasma membrane

the membrane must be rendered semipermeable but in a very selective way. This ______________ ______________is the work of proteins that are embedded in the plasma membrane or associated with it

selective permeability

The plasma membrane of a plant is itself surrounded by a ______ _______

cell wall

The cell wall is constructed largely from ___________, a long, linear polymer of glucose molecules


The inner substance of the cell, the material that is surrounded by the plasma membrane, is called the ___________.


The cytoplasm is the site of a host of biochemical processes, including the:

initial stage of glucose metabolism, fatty acid synthesis, and protein synthesis.

the cytoskeleton is a network of three kinds of protein fibers—________ _____________, __________________ _____________, and ________________—that support the structure of the cell, help to localize certain biochemical activities, and even serve as “molecular highways” by which molecules can be shuttled around the cell

actin filaments, intermediate filaments, microtubules

a key difference between eukaryotic cells and prokaryotic cells is the presence of a complex array of intracellular, membrane-bounded compartments called ____________ in eukaryotes


The largest organelle is the_____________, which is a double-membrane-bounded organelle


The ___________ is the information center of the cell, the location of an organism’s genome.


The nuclear membrane is punctuated with ________ that allow transport into and out of the nucleus.