BASIC THEMES: INTRODUCTION TO BIOCHEMISTRY Flashcards
=the branch of science concerned with the
chemical and physicochemical processes and substances that occur within living
organisms.
= governs all living organisms and living
processes.
BIOCHEMISTRY
=are macromolecules or "giant molecules" They are giant because they are polymers made of hundreds or even thousands of smaller molecules. smaller molecules. = Molecules of life.
BIOMOLECULES
Types of biomolecules
1) Proteins
2) Nucleic Acid
3) Nucleotides
4) Carbohydrates
5) Lipids
most prominent for its ability to self- bonding. It is notable because it is tetravalent, it can form bonds with itself and with other elements giving rile to different monomers such as amino acids, nucleotides, and sugar monomers (monosaccharides)
CARBON
what are the 6 elements that make up biomolecules?
Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, Phosphorous
It pertains to any organism or a life form that possesses or shows the characteristics of life or being alive.
LIVING THINGS
It is the study of compounds of carbon and hydrogen and their derivatives.
ORGANIC CHEMISTRY
Substance that undergo same reaction belong to the same functional groups.
INORGANIC CHEMISTRY
=German chemist who disapproved the vital force in 1828
=experimenting synthesized urea
=waste product of animal metabolism, from ammonium cyanate
FREDRICH WOHLER
a numerous combination of atoms that form parts of chemical molecules, that undergo characteristic reactions themselves, and that in many cases influence the reactivity of the remainder of each molecule.
FUNCTION GROUPS
=Reaction of phosphoric acid with a hydroxyl group.
ESTER
=P-O-R LINKAGE
ESTER
Red spheres:__
White:___
Green:___
Orange:____
RED: OXYGEN
WHITE: HYDROGEN
GREEN: CARBON
ORANGE: PHOSPHORUS
reaction of two molecules of phosphoric acid.
ANHYDRIDE
Contains a P-O-P linkage
ANHYDRIDE
two anhydride linkages and one ester.
ADENOSINE TRIPHOSPHATE (ATP)
is mainly attempt to understand the behavior of entire biological systems.
SYSTEM BIOLOGY
is one that test experimental and control groups in parallel
CONTROLLED EXPERIMENT
origin of the Universe; cataclysmic explosion.
BIG BANG
elements formed in the original big bang
explosion:
HYDROGEN, HELIUM AND SOME LITHIUM
Most abundant isotopes:
CARBON, OXYGEN, NITROGEN, PHOSPHORUS, AND SULFUR
How does the chemical elements formed? (3 WAYS)
(1) by thermonuclear reactions that normally take place in stars.
(2) Explosions of stars.
(3) by the action of cosmic rays outside the
stars since the formation of the galaxy.
the original stars produced after the beginning of the Universe.
FIRST GENERATION STARS
destroyed the first generation stars.
SUPERNOVAS
uses the decay of unstable nuclei.
RADIOACTIVE DATING
What is the age of the Earth?
4 BILLION TO 5 BILLION YEARS
There is a lot of free oxygen existed in the early stages. T OR F?
FALSE.
When did CO2 existed in the atmosphere?
3.8 BILLION YEARS AGO
most abundant elements in Earth’s crust.
Silicon (26%) and Aluminum (7.5%)
When substances such as proteins and nucleic acids are produced abiotically (from the Greek “abios”, meaning “not alive”), they are physiologically significant.
BIOMOLECULES
typical products of such reactions; amino
acids; building blocks of proteins.
FORMALDEHYDE (HCHO) AND HYDROGEN CYANIDE (HCN)
smaller molecules; amino acids, nucleotides, and monosaccharides
MONOMERS
are polymers macromolecules? YES OR NO
YES
combine by polymerization to form proteins.
AMINO ACIDS (MONOMERS)
=polymerization of sugar
=Many monosaccharides linked together
POLYSACCHARIDES
Monomers of carbohydrates.
MONOSACCHARIDES
Monomers of nucleotides. Its sequence
encodes genetic code and they are called molecules of heredity.
NUCLEIC ACIDS
Where can you find ribosomes?
Cytosol
total DNA of a cell
GENOME
individual units of relativity which controls the expression of individual traits.
GENES
DNA stands for?
deoxyribonucleic acids.
RNA stands for?
ribonucleic acids.
How can you determine a protein’s properties?
by the amino acids sequence
The effect of monomers sequence on the properties of polymers.
CATALYTIC ACTIVITY
=increases the rates of chemical reactions compared with uncatalyzed reactions
CATALYSIS
Refers to the relationship between nucleotide sequences in nucleic acids and amino acid sequences in proteins
GENETIC CODE
How do monomers form?
by smaller molecules
How do polymers form?
EU hundreds or thousands of monomers are linked to produce polymers
How do proteins form?
amino acids (the monomers)combine by polymerization to form protein
How do nucleic acids form?
Nucleotides combine`
How do polysaccharides form?
polymerization of sugar monomers produces polysaccharides
“true nucleus”
more complex organisms
can be multicellular or single-celled.
Are part of the cell that has its own membrane within the cell. Plasma membrane is the only membrane in this
EUKARYOTES
What is the respiratory organelles?
Mitochondria
What is the internal membrane in eukaryote?
Endoplasmic reticulum
The sites of protein synthesis in all livingorganisms are called?
ribosomes
=no well-defined nucleus is present
the DNA of the cell is concentrated in one region called the nuclear region.
PROKARYOTES
Part of the cell that has distinct function
ORGANELLE
are made up of linked smaller molecules called monomers, that can be linked together to form polymers, also called macromolecules.
CELLS`
From the beginning, smaller, simpler types of cells were also seen floating around in the experimental broths. These cells were more primitive and had no obvious sub cellular components, so they were called prokaryotes meaning “before nucleus”
PRIMITIVE CELLS
➡Single strand
➡ has a backbone made ofalternating sugar (ribose)and phosphate groups
➡has four bases adenine(A), uracil (U), cytosine (C)or guanine (G)
RNA (RIBONUCLEIC ACID)
➡ contains the genetic information
➡NA molecules allow this information to be passed from one generation to the next
- double-stranded helix-
Nucleotide base pairs:adenine (A) paired withthymine (T), and guanine(G) paired with cytosine (C)
DNA (DEOXYRIBONUCLEIC ACID)
To survive, organisms learn or change or get new/lose traits suitable to their environment. Those that can survive will reproduce to pass the traits to the next generation
EVOLUTION
Genes are made up of?
DNA
is the basic physical and functional unit of heredity
GENES
is the most important part of the cell with anuclear membrane
NUCLEUS
contain enzymes that catalyze important energy-yielding reactions.
MITOCHONDRIA
which are found in green plants and green algae, are the sites of photosynthesis.
CHLOROPLASTS
=Is a DNA-based thread-like structure
=it is responsible for the transmission of inherited traits.
CHROMOSOMES
=aggregate of DNA and protein
=is a DNA and protein-based material foundwithin chromosomes
CHROMATIN
➡Each of the partial partitions in a mitochondrion formed by infoldings of the inner membrane.
➡give a signature, wrinkled shape to the inner membrane of the mitochondria.
➡contains proteins, including ATP synthase and a range of cytochromes
CRISTAE
- Space within the inner membrane.-
- generally used as a jelly-like structure instead of cytoplasm in connective tissue
MATRIX
Smooth Endoplasmic Reticulum does not have ribosomes bound to it. T or F
True
- involved in the secretion of proteins from the cell.
- is a central intracellular membrane-bound organelle with key functions in trafficking, processing, and sorting.
- Series of flattened membranes- usually involved in secretion of the protein
GOLGI APPARATUS
- Acts as the waste disposal system of the cell by digesting unwanted materials in the cytoplasm.
- membrane enclosed sacs contained hydrolytic enzymes.
- fuse with endosomes, aiding the digestion of materials inside endosome
LYSOSOMES
- are small, membrane enclosed organelles that containsenzymes involved in a variety of metabolic reactions.
PEROXISOMES
- It is an anabolic pathway occurring in plants, and several microorganisms but not in animals.
- they have a single membrane.
- they have high equilibrium density in sucrose gradient configuration.
- their matrix (internal content) is finely granular.
Glyoxysomes
portion of the cell that lies outside the nucleus and the other membrane-enclosed
CYTOSOL
lattice of fine strands, consisting mostly of protein, that pervades the cytosol
CYTOSKELETON
Enclosed by a single membrane a cavity within the cytoplasm
- isolate waste substances that are toxic to the plan
VACUOLES
Single celled organism
Unicellular organisms
→ consists only of prokaryotic organisms
→ consist of bacteria and cyanobacteria
KINGDOM MONERA
→ Unicellular
→ Eukaryotic
→ includes unicellular organisms such as Euglena, Volvox, Amoeba, and Paramecium
PROTISTA
→ Multicellular
→ Eukaryotic
→ Insects, animal, human, etc
ANIMALIA
→ Multicellular
→ Eukaryotic
→ yeast, mushrooms, etc
FUNGI
The Fungi is under Domain Eukarya with Animalia and Plantae. T OR F?
TRUE
→ Multicellular
→ Eukaryotic
→ Plants, trees, etc.
PLANTAE
→ Unicellular
→ Prokaryotic organisms
→ Consist of bacteria and cyanobacteria
MONERA
→ association between two organisms is seen as giving rise to a new organism that combines the traits of both the original ones.
Symbiotic
→ One species gains at the other’s expense.
Parasitic Symbiosis
→ A relationship that benefits both speciesinvolved.
Mutualism
→ Live in extreme environments
Also called extremophiles
Archae Bacteria
Strict anaerobes that produce methane (CH4) fromcarbon dioxide (CO2) and hydrogen (H2)
METHANOGENS
→ Require very high salt concentrations, such as those found in the Dead Sea, for growth
HALOPHILES
→ Require high temperatures and acid conditions forgrowth—typically, 80°C– 90°C and pH 2.
THERMOACIDOPHILES
These organisms are called archaebacteria (early bacteria) to distinguish them from eubacteria (true bacteria) because there are marked differences between the two kinds of organisms.
EUBACTERIE
→ a larger host cell contains a genetically determined number of smaller organisms.
ENDOSYMBIOSIS
It is important in many reactions that take placein the cell, particularly those involving synthesisof large molecules.
ENERGY
The ____ is the ultimate source of energy. It provides the energy for photosynthesis, which produces carbohydrates as well as oxygen.
sun
trap light energy and use it to drive the energy-requiring reactions that convert carbon dioxide and water to carbohydrates and oxygen.
photosynthetic Organisms
Such as animals that consume these carbohydrates, use them as energy sources.
Non-photosynthetic organisms
→ A branch of science that predicts the likelihoodof reactions.
THERMODYNAMICS
A _______ is one that will take place without outside intervention. This point does not specify the reaction rate.
Spontaneous reaction
What does the he first law, also known as Law of conservation of Energy states?
that energy can not be created or destroyed in an isolated system.
=you cant win
states that the entropy of any isolated system always increases
=you cant break even
The second law of thermodynamics
states that the entropy of a system approaches a constant value as the temperature approaches absolute zero.
The third law of thermodynamics
→ most useful criterion for spontaneity of a process.
→ requires conditions of constant temperature andpressure
FREE ENERGY
→ free energy of a system decreases (negative).
→ it is called exergonic (ENERGY IS RELEASED)
Spontaneous process
→ the change in free energy is positive
→ energy must be supplied to occur.
→ It is called endergonic (ENERGY IS ABSORBED)
Nonspontaneous process
→ free energy change is zero
Equilibrium
→ Symbol G is given to free energy in his honor
→ His work is the basis of biochemical thermodynamics
→ Greatest scientist born in the United States.
J. Williard Gibbs
His equation for entropy was one of his supreme achievements.
- His equation is carved on his tombstone.
Ludwig Boltzmann
aims to understand the behavior of entire biological systems
SYSTEMS BIOLOGY
ACID - BASE BALANCE
Regulation of Free Hydrogen Ion Concentrations
It is an ionic compound
- A bond between opposite charge that contains hydrogen and other elements
- Also known as the proton donor, wherein it hasno electron
ACID
Difference bet. strong and weak acid
Strong acid dissociates in equilibrium on a solution and the H+ and negative ions liberate freely in the concentration of a solution. Unlike weak acid, wherein it dissociates only in aqueous solution which makes the majority remain undissociated with little liberation in a concentration of the solution.
it signifies hydrogen concentration and determines the acidity or alkalinity of a solution
pH scale (power of Hydrogen)
Arterial blood: pH level=___
Venous blood: pH level=___
Arterial blood: pH level=7.45
Venous blood: pH level=7.35
Why is venous blood more acidic than the arterial blood?
because of the carbonic acid formation from carbon dioxide wherein both have different route that resulted in indifferent encounter of substance which affect the pH level of arterial blood to the venous blood
What is the reference/Average point for body acid-base value?)
And for someone who is dead?
pH= 7.4 (blood)
death: ph=8.0
Too much acid in the blood. Below7.35 pH level.
Acidosis
Too much base in the blood. Above7.45 pH level
Alkalosis
= Also known as proton acceptor
= Combine with free hydrogen ion (H+)
= Strong base can bind more H+
BASE
Effects of acidosis in our body:
depression and disorientation of CNS leading to coma.
Effects of Alkalosis in our body:
Overexcitability of the peripheral (tingling sensation) and central (twitches and muscle spasm)nervous system. Death may occur in the muscle spasm in respiratory muscles that depends on breathing
Disturb metabolic activities and deviation alter the shape and activity of protein molecules
Enzyme Activity
more H+ eliminated by thekidney, less K+ is excreted that can result to cardiac arrestand other detrimental in the body.
Potassium level in the body
is a protein molecule that is made up of amino acids joined in a long chain
ENZYME
= Drinkable water with a pH level of 8-9
= reduces lactate concentration, an indirect marker or fatigue which means that alkaline water can accelerate muscle fatigue recovery.
= can maintain the body’s health by neutralizing acids in the body that can help eliminate the chance of obesity due to acid levels in the body.
Alkaline water
is an acid with acidity greater than pure sulfuric acid. (Billion times stronger than sulfuric acid)
SUPERACID
The world’s strongest superacid
=Formed by mixing hydrogen fluoride (HF) and antimony pentafluoride (SbF5).
Fluoroantimonic Acid
= It is important in the body for it manages the acid and base imbalances produced by both normal and abnormal physiology
= Maintains optimal pH levels and regulates the carbon dioxide concentration.
= Primary ECF buffer against noncarbonic acid changes.
Carbonic acid- Bicarbonate
= Helps to maintain acidity and around the cells.
= Maintains constant H+ ions. Without these buffer systems, cellular pH and the pH of fluids outside the cells would fall
= Primary ICF and ECF buffer
PROTEIN
=Helps to maintain the normal pH of the human body
= Takes part as the principal protein inside the red blood cells. It is the primary buffer against carbonic acid.
=The CO2 transport in the form of bicarbonate is also facilitated by the buffer action and the Haldane effect of hemoglobin.
HEMOGLOBIN
= Normally operates in the internal fluids of all cells.
= Maintains the intracellular pH.
= An effective physiological buffer because it’s near in the physiological.
= It is a urinary buffer
PHOSPHATE
= Addition or removal of acid or base
= Minimize pH system
CHEMICAL BUFFER SYSTEM
= Difficulty of breathing
= Due to lack of oxygen and carbon dioxide concentration
= Carbonic Acid- produced when the carbon dioxide on lungs react with water
Hypoventilation
T or F. Respiratory and Renal Compensation DO NOT partially regulates each other
False
is a critical condition that occurs when waste products linked with impaired kidney function accumulate in the bloodstream.
UREMIC ACIDOSIS
refers to the effects of waste product accumulation and implies “urine in the blood”
UREMIA
What can cause uremia?
Diabetes mellitus, Hypertension. Glomerulonephritis, Polycystic disease, Obstruction of infection in kidney and Analgesic nephropathy
Uremic acidosis is most commonly caused by:
chronic kidney disease (CKD), which can lead to end-stage renal (kidney) disease (ESKD), although it can also happen suddenly, resulting in possibly reversible acute kidney injury and failure (AKI).
