Cell Function And DNA RNA Organism – Biochemistry

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?

autotrophs


Who showed up first in evolution: anaerobic or aerobic?

anaerobic


An organism that uses reduced inorganic compounds as its electron source

Litotrophs


obtain electrons from organic compounds

organotrophs


Are Eukaryotes more closely related to archaea or bacteria?

Archaea


which domain showed up first?

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


Phototrophs

trap and use sunlight


chemotrophs

derive their energy from the oxidation of chemical fuel


Autotrophs

Organisms that make their own food


Heterotroph

An organism that cannot make its own food.


Aerobic

Process that requires oxygen


Anaerobic

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


metabolomics

systemic characterization of the metabolome under very specific conditions


Proteomics

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


Glycome

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?

glycine


chiral center

carbon with four different substituents and lack a plane of symmetry


Stereoisomers

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


Enantiomers

isomers that are mirror images of each other


Diastereomers

stereoisomers that are not mirror images


conformation

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


Enthalpy

The heat content of a system at constant pressure


Entropy

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


Conformation

no bond breaking between changes. This is achieved through rotating


Configuration

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


Anyhydride

without water


chiral

a molecule that is not superimposable on its mirror image


achiral

A molecule that is superimposable on its mirror image


isomers

Two different molecules that have the same chemical formula


Are Amino acids L or D conformation?

L


Are sugars L or D conformation

D


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?

open


oxidation

loss of electrons


reduction

gain of electrons


Dehydrogenation

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?

-Endergonic
-unfavorable
-not spontaneous


energy coupling

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


Enzymes

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


Do enzymes alter free energy? (thermodynamic)

No


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?

No


Catabolism

Metabolic pathways that break down molecules, releasing energy.


Anabolism

Metabolic pathways that construct molecules, requiring energy.


Central Dogma of Biology

DNA -> RNA -> Protein


Homologs

Matching Chromosomes that are similar but not identical


Paralogs

homologous genes within a single species


orthologs

homologous genes separated by a speciation event


Autotroph

An organism that makes its own food


Phototroph

an organism that gets its energy from sunlight


Chemotrophs

Organisms that get energy from chemicals taken from the environment


Nucleus

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


Nucleoid

A dense region of DNA in a prokaryotic cell.


Prokaryotic

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


Eukaryote

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


ATP/NADH

The carriers for energy and high energy electrons during glycolysis


Chemoautotrophs

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


Photoautotrophs

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


Chemoheterotrophs

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


Photoheterotrophs

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


Exocytosis

Process by which a cell releases large amounts of material


Endocytosis

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


Steroisomers

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


configuration

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


conformation

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


Keq<1

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


Metabolism

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

Dynamic


who showed up first in evolution?

Bacteria


where do prokaryotes contain their DNA

in the nucleoid


what is the cell wall of prokaryotes composed of

peptidoglycan


what is the function of the cytoskeleton (3)

-cell shape
-transport paths
-movement


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

more


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?

yes


Enantiomers have [different/identical] physical properties

identical


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

different


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

equals


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

Enthalpy (H)


G<0

Exergonic, thermodynamically favorable, spontaneously move forward


G>0

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= –


spontaneous


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…

reactants


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

products


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?

0

G=-RTlnK

————-



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


ln(1)=0
G=-RT*0=0


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.

early,


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

water


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:

cell


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


catalysts

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


proteins catalysts are called

enzymes


every process that takes place in living systems depends on:

enzymes


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:

nucleotides


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.

phosphodiester


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 __________

proteins


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


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


hydrophillic

it can dissolve in water


hydrophobic

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

storage


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

combustion


the most common carbohydrate fuel

glucose the simple sugar


glucose is stored in animals as:

glycogen


what does glycogen consist of:

many glucose molecules linked end to end and having occasional branches


in plants, the storage form of glucose is

starch,


central dogma

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


DNA constitutes the heritable information – the __________

genome


the information of the genome is packed in discrete units called

genes


the process of copying the genome is called

replication


DNA polymerase

a group of enzymes that catalyze the replication process


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

ribosomes


The _______ is the basic unit of life

cell


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

membrane


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

cellulose


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

cytoplasm


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

organelles


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

nucleus


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

nucleus


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

pores


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