Chemical & Biochemical foundations of Pathophysiology

Question 1

Atomic Structure

Answer 1

atoms are divided into two regions: a nucleus, and a cloud of electrons that orbit around the nucleus.

Question 2

Nucleus of atoms

Answer 2

The nucleus of an atom contains protons that are positive and neutrons that are neither negative nor positive.

Question 3

Electrons

Answer 3

Electrons have a negative charge and orbit the nucleus

Question 4

Why do atoms have a neutral charge

Answer 4

Protons are positive, neutrons have no charge, and electrons have a negative charge. Atoms are neutral because they have an equal amount of protons and electrons

Question 5

Carbon

Answer 5

carbon- is the only element in the body that is in IVA/A. It has four electrons in its outer shell (valence). Carbon has 6 protons, 6 neutrons, 2 electrons in the inner shell, and 4 electrons in its outer shell.

Question 6

Carbon and the Octet Rule

Answer 6

Carbon uses the 4 electrons in its valence shell to interact with other atoms. Carbon needs 4 more electrons to fulfill the octet rule.

Question 7

Carbons interaction with hydrogen

Answer 7

Hydrogen has only 1 electron. Carbon can share 1 electron with 4 hydrogen atoms, and each of the hydrogen atoms shares 1 electron with the carbon atom. The sharing results in a carbon atom with 8 electrons in the valence shell and four hydrogen atoms with two electrons each. The bonds formed between the carbon atom and each hydrogen atom are called single covalent bonds, and the resulting compound is a molecule.

Question 8

Oxygen and the Octet Rule

Answer 8

Oxygen belongs to the 6th group of the periodic table. It contains six electrons in the outermost shell. In molecular oxygen (o2), each atom has six electrons plus two additional electrons from the other oxygen atom. This allows oxygen atoms to fulfill the octet rule. The two electrons shared between bonding atoms are called a bonding pair, and each pair of electrons that is not contributing t the formation of a bond is called a lone pair. Therefore, each atom has two bonding pairs and two lone pairs in molecular oxygen.

Question 9

Electronegativity

Answer 9

The tendency of an element to attract a bonding pair of electrons. The electronegativity depends on the number of protons in the nucleus; thus, an element with more protons will be more electronegative than an element with fewer protons. Elements with higher proton numbers also have a higher group number; electronegativity increases across a period in the periodic table. Oxygen in group 6A is more electronegative than carbon in group 4A.

Question 10

Ionic Molecules

Answer 10

Ionic molecules are those in which one or more atoms have lost or gained an electron to have a full charge of 1+,2+,3+,1-,2-,3-. These ions will attract other molecules and single-atom ions of opposite charge and are stabilized when surrounded by polar water molecules in aqueous solutions. Example: sodium chloride NaCl is ionic >2.0

Question 11

nonpolar molecules

Answer 11

Those in which there is equal electron sharing across the covalent bonds. When a molecule is made up of elements with differing electronegativity (the strength of attraction on electrons shared in a covalent bond), partial charges develop within the molecule. The element with stronger electronegativity develops partial positive charges. Biological molecules rich in carbon-hydrogen bonds ( such as fatty acid chains are based or based on cholesterol molecules) tend to have a relatively equal electron sharing and are nonpolar.

Question 12

examples of polar molecules

Answer 12

carbohydrates, amino acids, and nucleic acids containing hydrogen bonds and nitrogen-hydrogen bonds tend to have unequal electron sharing and tend to be polar molecules.

nonpolar covalent o2 0-.4
polar H2o .4-2.0
Ionic NaCl >2

Question 13

Carbon

Answer 13

Carbon is the basic building block required to form proteins, carbohydrates, and fats. It plays a crucial role in the regulation physiology of the body. Its central role is because it has four bonding sites that allow for building long, complex chains of molecules. Carbon bonds can be formed and broken with a modest amount of energy, allowing for the dynamic organic chemistry that goes on in our cells. Carbon’s four valence electrons enable carbon to covalently bond to oxygen, hydrogen, and nitrogen to form many molecules important for cellular function. Methyl, and carboxy, are groups of atoms that give specific properties to hydrocarbon chains or rings that define their overall chemical characteristics and function.

Question 14

Macromolecules

Answer 14

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids ( RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules( any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to four different atoms, making this versatile element ideal for serving as the backbone of macromolecules.

Question 15

Hydrocarbons

Answer 15

Organic molecules consist entirely of carbon and hydrogen, such as methane (CH4). We often use hydrocarbons in our daily lives as fuels, such as propane and butane. The many covalent bonds between the atoms in hydrocarbons store tremendous energy, which is realized when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms.
Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or nonbranched.

Question 16

Carbohydrates

Answer 16

Carbohydrate molecules contain multiple polar hydroxyl groups that can easily form hydrogen bonds in water and aqueous fluids. Carbohydrates’ biological functions of carbohydrates include energy source for cells, modification of cell membrane proteins and lipids, modification of plasma proteins and hormones, cell recognition sites ( like blood group antigens), attachment sites, and support within cell membranes, and mediation of host-pathogen interactions.

Question 17

Carbohydrates’ role in brain function

Answer 17

The brain essentially depends upon glucose (glycemia) for its energy needs. Because neurons have the highest energy demand in the adult brain, they require continuous glucose delivery from the blood. Tight regulation of glucose metabolism is critical for brain physiology.
Carbohydrates also modify components of the cell membrane.

Question 18

lactose intolerance

Answer 18

Lactose is made of glucose and galactose. During digestion of milk and dairy products, lactose is broken down into its monomers, which are then assimilated. The enzyme lactase is responsible for this hydrolysis reaction; individuals who cannot produce lactase during adulthood suffer from lactose intolerance. Persistent disaccharides in the intestine cause signs and symptoms associated with the condition (abdominal pain, bloating, and diarrhea).

Question 19

The duet rule

Answer 19

The duet rule applies to hydrogen, helium, and lithium. The innermost valence shell can only hold two electrons. Hydrogen can empty the shell by losing one electron, leaving only a proton in the nucleus. For this reason, hydrogen ions are often referred to as protons (think about the acid-secreting proton pump of the stomach). Helium is a noble gas-having two electrons that completely fill the electron shell and satisfy the duet rule; therefore, it does not have chemical reactivity. Lithium is in group 1 below hydrogen. The most stable state of lithium is to lose one electron in the outer shell, becoming Li and having two electrons to fulfill the duet role.

Question 20

The major elements of the body

Answer 20

Carbon
oxygen
hydrogen
nitrogen

Question 21

The minor elements of the body

Answer 21

Sodium
potassium
chlorine
calcium
phosphorus
sulfur
magnesium
iron
copper
zinc

Question 22

How may electrons are in the valence shell of major elements?

Answer 22

The first shell can hold only two electrons, the second shell can hold eight electrons, and the third shell can hold eight electrons. Hydrogen has one electron in the first shell. Carbon has four electrons in the second shell, nitrogen has five electrons in the second shell, and oxygen has six electrons in the second shell.

Question 23

What are the main ions found in the body, and where are they found? Are they in the extracellular fluid or intracellular fluid?

Answer 23

Most ions in the body are dissolved in aqueous intracellular and extracellular fluids. The main ions in the body are sodium, chloride, bicarbonate, potassium, phosphate, hydrogen, magnesium, and calcium ions. Several amino acids found in proteins can also be ionized, and soluble proteins found in the intracellular and extracellular fluids are often negatively charged.
Sodium chloride and bicarbonate are concentrated in extracellular fluid.
Potassium, and protein anions, are more concentrated in the intracellular.

Question 24

Chylomicron

Answer 24

Carries products of dietary fat digestion from the intestine to the liver and other organ tissues

Question 25

VLDL

Answer 25

Carries newly synthesized triglycerides from the liver to adipose tissue, as well as other organs. VDLS coated with apolipoprotein B-100, which are responsible for delivering triglycerides to the tissue.

Question 26

IDLS

Answer 26

The particles left after VLDL release triglycerides to peripheral cells are IDLS. The liver is responsible for clearing some IDLY particles while other IDL particles are converted to LDL by hepatic lipase.

Question 27

LDL

Answer 27

LDL particles are mostly made of cholesterol, and their main purpose is to release cholesterol to cells throughout the body before being cleared by the liver. Individuals who consume excessive amounts of Chol, and saturated fat accumulate excessive amounts of LDL in the circulation, which eventually migrate to the arterial walls promoting atherogenesis and the development of atherosclerosis.

Question 28

HDL

Answer 28

HDL particles have the highest density of all lipoproteins as they contain a large amount of proteins. They also contain the highest phospholipid content, as well as some cholesterol, and very little triglycerides. HDL particles are synthesized in the liver and intestine to be released into the circulation, where they are responsible for transferring apolipoproteins to nascent chylomicrons and VLDL, and collecting cholesterol from IDL, and chylomicron remnants. Clinically low HDL levels are markers of increased cardiovascular risk.

Question 29

Amino acid's role in biological signal

Answer 29

R groups are radical, meaning it is the variable part of amino acids. Amino acids have three main groups, carboxyl groups, amino groups, and a radical which can change. They are ae important because their properties determine protein structure and function. The size, polarity, acidity, and reactivity drive the folding and function of proteins due to the proteins trying to fold into their most energy-efficient conformations given the solvent. In enzymes, the pocket where the substrates are reacted needs to have certain radial expressions to bind and weak the bonds to substrates. The side chains are extremely important for this.

Question 30

Cell functions of nucleotide

Answer 30

Nucleotides play a pivotal role in cell signaling cascades. Cyclic versions of both amp and guanosine monophosphate (GMP) serve as intracellular second messengers. Historically, the first of these to be described as cyclic AMP. cAMP is formed when ATP undergoes a reaction that converts it into a ring structure. This reaction is catalyzed by adenylyl cyclase and is often activated in response to a ligand-receptor interaction on the plasma membrane. cAMP acts as an intracellular second messenger, turning on a signaling cascade, often through the activation of downstream kinases. Like cAMP, cyclic GMP can also serve as an intracellular second messenger. Guanosine triphosphate plays a key role in signal transduction as its hydrolysis to guanosine diphosphate (GDP) provides a timing switch for many membrane receptors. For this reason, many receptors in this category are referred to as G protein-coupled receptors.

Question 31

Tyrosine role in PKU

Answer 31

Tyrosine is the precursor for the neurotransmitters dopamine, norepinephrine, and for thyroid hormones. When the enzyme phenylalanine hydroxylase is defective in the autosomal-recessive fashion infants develop PKU because tyrosine cannot be synthesized so they develop hyperphenylalaninemia. The lack of tyrosine may cause hypopigmentation because melanin is produced from tyrosine.

Question 32

RNA

Answer 32

RNa Rna is single stranded Rna has ribose sugar Bases present are adenine, guanine, cytosine, uracil Adenine pairs with uracil Purine is not equal to pyrimidine Regions have complementary nucleotides. Pairs. And form hairpin loop like structure and helical RNA is genetic material for some viruses. The length of RNA is short and consist of only a few thousand of nucleotides.

Question 33

Three types of RNA present in organisms

Answer 33

mRNA rRNA tRNA mRNA occurs in the nucleolus, rRNA, tRNA occur in cytoplasma

Question 34

DNA

Answer 34

DNA is double stranded except in a few viruses. DNA has deoxyribose sugar Bases present are adenine, guanine, cytosine, and thymine Adenine pairs with thymine Purine is equal to pyrimidine (Chargaff’s rule) Complementary nucleotides are present throughout the length of DNA DNA is the genetic material in all living organisms The length of DNA is quite large consisting of millions of nucleotides DNA occurs only in one form in an organism. DNA occurs in the nucleus, nucleolus, and extrachromosomal DNA in mitochondria and chloroplast

Question 35

Octet rule

Answer 35

The Octet rule means there are eight electrons in the outer valence shell. To satisfy the octet rule, electrons may be lost or acquired. This process results in an ion-acquiring an electron forms an anion, a negatively charged ion while losing an electron forms a cation, a positively charged ion. Ions are stable in aqueous intracellular and extracellular fluids, as their electrical changes are surrounded by polar water molecules. The other way of satisfying the octet rule is by electron-sharing between atoms in the process of covalent bond formation.

Question 36

RNA role in protein synthesis

Answer 36

RNA has a major role in transporting the information stored in DNA to the ribosome where protein synthesis occurs. The primary function of RNA is to create proteins via translation. RNA carries genetic information that is translated by ribosomes into various proteins necessary for cellular processes. mRNA, rRNA, and tRNA are the three main types of RNA involved in protein synthesis The synthesis of proteins includes several steps and uses a different nucleic acid to do this work. RNA is essential to the process of protein synthesis. The steps in the process include transcription of a gene into pre-mRNA, post transcriptional processing to create mRNA, transport of the mRNA out of the cell nucleus, translation of mRNA into a polypeptide chain of amino acids, and finally, post-translational processing to create a finished, and functional protein.

Question 37

What role does DNA polymerase play in the replication process?

Answer 37

DNA polymerase is an enzyme that is responsible for synthesizing DNA, they add nucleotides one by one to the growing DNA chain, incorporating only those that are complementary to the template. DNA polymerases are responsible for the process of DNA repair during the replication process. The enzymes proofread the sequence of nucleotides and, when an error is located, excise the incorrect nucleotide and replace it with the correct one.

Question 38

What are some of the roles individual nucleotides play in cell function?

Answer 38

Adenosine triphosphate (ATP) is the energy currency of the body. The cyclic forms of adenosine monophosphate (cAMP) and guanosine monophosphate (cGMP) are intracellular second messengers. Guanosine Triphosphate (GTP) is involved in single transduction by membrane receptors.

Question 39

Importance of screening newborns wit PKU

Answer 39

Early intervention is key to improving outcomes, as infants maintained on a low-protein/low-phenylalanine diet can avoid many cognitive delays in infants before t screening. People with PKU are typically treated with a strict dietary regimen that limits food intake containing phenylalanine to prevent hyperphenylalaninemia and the associated mental retardation.

Question 40

Which DNA base pairs participate in complementary base pairing through hydrogen bonds?

Answer 40

Adenine and thymine form a base pair and are connected by two hydrogen bonds. Guanine and cytosine form a base pair and are connected by three hydrogen bonds.

Question 41

Endogenous pathway

Answer 41

After digestion and absorption of a meal the liver produces, and packages triglyceride-rich VLDLS coated with apolipoprotein B-100, which is also responsible for delivering triglycerides to the tissue. HDL also transfers additional apolipoproteins to VLDL in the circulation. Because VLDL carries lipids produced by the liver, this pathway of lipid delivery is known as the endogenous pathway

Question 42

Why might a person need to have a laboratory assay to determine their lipoprotein levels?

Answer 42

Lipid panels are assessed as a marker of cardiovascular risk. Excessive amounts of low-density lipoproteins migrate into arterial walls and promote atherogenesis which causes atherosclerosis. Higher levels of high-density lipoproteins are generally associated with lower cardiovascular risks.

Question 43

Nitrogen

Answer 43

Nitrogen has five electrons in its valence and needs three more to reach stability and fulfill the octet rule. Two nitrogen atoms can share three pairs of electrons to form a triple bond. In molecular nitrogen, each nitrogen atom also has one lone pair(N2). When double or triple bonds are formed, the molecule becomes planar, as multiple bonds between two atoms limit the movement of the two atoms involved. planar, as multiple bonds between two atoms, limits the movement of the two atoms involved.

Question 44

Principles of base pairing

Answer 44

The base on one strand of the DNA makes hydrogen bonds with the bases on the other strand. Each purine bonds with a pyrimidine: guanine always makes three hydrogen bonds with cytosine, and adenine always makes two hydrogen bonds with thymine. Although individual hydrogen bonds lack strength, the billions of hydrogen bonds holding together the antiparallel strands of DNA give it extraordinary structural stability. During the process of gene transcription, the double-stranded DNA separates, allowing access to transcription factors and to the RNA polymerase, which catalyzes the production of a messenger RNA. This product is synthesized using DNA as a template to establish nucleotide sequence and synthesize a complementary RNA sequence.

Question 45

Define three different amino acids that are associated with specific body functions and identify those functions.

Answer 45

Tyrosine is used in the synthesis of thyroid hormones (thyroxine, triiodothyronine) and neural and endocrine catecholamines (dopamine, norepinephrine, and epinephrine). Tryptophan- is used to synthesize serotonin, melatonin, and the coenzyme Nicotinamide adenine dinucleotide, which are used in metabolic functions. Histidine- used to synthesize histamine, an inflammatory mediator. Glycine- used in the production of porphyrins, precursors to heme. Glutamate-neurotransmitter and precursor of y-aminobutyric acid (GABA), another transmitter.

Question 46

What are some hydrophobic amino acids that might be found in the core of a folded protein?

Answer 46

``` Protein folding tends to cluster hydrophobic amino acids in the core of the protein, hidden away from the aqueous extracellular or intracellular fluid. these include: alanine valine leucine isoleucine methionine proline tryptophan phenylalanine. ```

Question 47

How does hydrogen bonding contribute to secondary protein structures?

Answer 47

Hydrogen bonds between the carbonyl (C-O) and amino (N-H) portions of peptide bonds stabilize the secondary structures of alpha-helices and beta-pleated sheets within proteins.

Question 48

Genetic red flags

Answer 48

Red flags are diseases or characteristics of diseases that lead the clinicians to reasonably conclude the higher likely hood of a strong genetic component to the disease. g- groups of anomalies- the presence of multiple anomalies. e-early or extreme presentation of illnesses- earlier than expected age of onset or in uncharacteristic sex. n-Neurodevelopmental delay or neurodegenerative disease. especially combined with other red flags such as congenital dysmorphologies. e-exceptional pathology- found in organs or structures of paired or bilateral organs. ex-several different cancers in the same patient simultaneously. s - surprising laboratory values.