NHM 361 - EXAM 3

LIPID METABOLISM, PROTEIN METABOLISM, NUCLEIC ACIDS, CENTRAL DOGMA

during lipid digestion, what enzyme hydrolyzes triglycerides?

lipase hydrolyzes triglycerides to glycerol, fatty acids, and monoglycerides

phosphoglycerides are hydrolyzed to what?

their component substances

where are triglycerides and phosphoglycerides resynthesized?

in the cells of intestinal mucosa

insoluble lipids are complexed with ____ to form _________

proteins to form lipoproteins

why are insoluble lipids complexed with proteins to form lipoproteins?

To facilitate transport in the lymph and bloodstream and ensure solubility

what are lipoproteins consisted of?

lipids (phospholipids + cholesterols + triglycerides) and proteins

what are the four classifications of lipoproteins?

1. chylomicrons

2. VLDL (very low density lipoprotein)

3. LDL (low density lipoprotein)

4. HDL (high density lipoprotein)

what are chylomicrons, where are they produced, and what are their characteristics?

chylomicrons are a type of lipoprotein produced by the small intestine

chylomicrons are the highest level of triglycerides (>85%) with the lowest density and lowest proteins

what is VLDL, where is it located, and what is its percentage of triglycerides?

VLDL stands for Very Low Density Lipoprotein (a type of lipoprotein) and is produced by the liver

they have a high level of triglycerides (>50%)

what is LDL and its characteristics?

LDL stands for low density lipoproteins (a type of lipoprotein)

it is the highest level of cholesterol and increases the risk of CVD

what is HDL and its characteristics?

HDL stands for high density lipoprotein (a type of lipoprotein)

it has the highest level of proteins and the highest density with the lowest triglycerides

HDL decreases the risk of CVD

what happens when the body’s stores of glycogen are depleted?

fatty acids are called on as energy sources

fat mobilization helps do what?

fat mobilization helps conserve glycogen stores and glucose for use by the brain cells and RBCs

talk about fat mobilization in relation to brain cells

fat mobilization helps conserve glycogen stores and glucose for use by the brain cells because the brain cannot directly obtain nutrients from the blood because of the blood-brain barrier

talk about fat mobilization in relation to red blood cells

fat mobilization helps conserve glycogen stores and glucose for use by red blood cells because RBCs do not have mitochondria and therefore cannot oxidize fatty acids

hydrolysis of stored triglycerides is followed by what?

the entry of fatty acids and glycerol into the bloodstream

what are the two components of the hydrolysis of fat?

glycerol: water-soluble and dissolves in blood and is transported to cells that need it

fatty acids: in blood, mobilized fatty acids form a lipoprotein with the plasma protein and are transported to tissue cells in this form

what is the plasma protein called when fatty acids are mobilized in the blood?

serum albumin

discuss the process of glycerol metabolism

glycerol is converted in the cytoplasm to dihydroxyacetone phosphate (a chemical intermediate of glycolysis)

by entering glycolysis, glycerol can be converted to pyruvate and can help in cellular energy production!

before fatty acids can be catabolized, what must happen?

they must be activated

activation involves the conversion of fatty acyl-CoA by acyl-CoA synthetase

(this is a part of BETA-OXIDATION-1)

where does fatty acyl-CoA enter and through what shuttle?

fatty acyl-CoA enters the mitochondria through the carnitine shuttle

(this is a part of BETA-OXIDATION-1)

what is BETA-OXIDATION-2

the pathway by which a fatty acyl-CoA is broken down into molecules of acetyl-CoA in the mitochondrial matrix

also involves the process of 2 carbon removal by acetyl-CoA having 2 carbons

what are the end products of the BETA-OXIDATION-2 pathway?

FADH2

NADH

ACETYL-COA

what are ketone bodies and where are they creates?

ketone bodies are created in the liver when excess acetyl-CoA is produced by fatty acid oxidation than can be processed by the citric acid cycle

what is ketogenesis?

condition of veryyyy low carbohydrate level in the body (usually due to starvation or diabetes)

during ketogenesis, what does the body use as the primary energy source?

fat is used as primary energy source during ketogenesis

what are the two things that happen when the body is in a state of ketogenesis?

1. fatty acids are oxidized (beta-oxidation ramps up) and therefore forms a lot of acetyl CoA

2. Acetyl CoA accumulates and usually, acetyl-CoA would enter the TCA cycle but in ketogenesis, oxaloacetate is being siphoned off for gluconeogenesis so the TCA cycle slows, acetyl-CoA has nowhere to go so it builds up in the liver mitochondria.

3. the liver uses ketogenesis as a “pressure-release valve so excess acetyl-CoA → converted into ketone bodies

describe fatty acid synthesis: where it occurs, what it involves (enzyme) and the product

fatty acid synthesis occurs in the cytoplasm of several different cell types but mostly in the liver (most important organ involved)

fatty acid synthesis process involves fatty acid synthase

the end product is palmitic acid (16:0) and can be elongated, shortened, and/or desaturated to form other fatty acids

what is fatty acid synthase?

a multienzyme complex that catalyzes the synthesis of fatty acids using acetyl-CoA and malonyl-CoA. IT REQUIRES NADPH!!!!

why does fatty acid synthesis occur? what is the process?

this occurs when there is an excess of carbohydrate energy that is then turned into long-term storage.

the main building blocks of fatty acid synthesis are:

• ATP

• Acetyl-CoA (2-carbon unit)

• NADPH

the steps are:

1. move acetyl-CoA out of the mitochondria and into the cytosol using a citrate “shuttle”

2. acetyl-CoA carboxylase converts acetyl-CoA into malonyl-CoA

3. fatty acid synthase uses 1 caetyl-CoA to “start” the chain, adds malonyl-CoA units, and uses NADPH for reductions, repeatedly until it makes palmitic acid (16:0)

4. then, in the endoplasmic reticulum, it can elongate, shorten, or desaturate

discuss the conversion between glucose and fatty acids (in general)

excessive dietary intake of carbohydrates in the form of glucose can lead to de novo synthesis of fatty acids and consequent accumulation of body fat because pyruvate is converted to acetyl-CoA

acetyl-CoA cannot be converted to pyruvate; therefore, fatty acids cannot be converted to glucose

map out the steps of converting glucose to fatty acids

1. glucose enters the cell using GLUT-2 (insulin-independent)

2. glucose → pyruvate in the cytosol

3. pyruvate enters the mitochondria, converting into acetyl-CoA via pyruvate dehydrogenase IRREVERSIBLE STEP!

4. TCA cycle bottleneck: when energy is abundant, ATP is high, NADH is high, TCA cycle slows, citrate ACCUMULATES

   1. citrate exists mitochondria → cytosol to become acetyl-CoA again and enters fatty acid synthesis

5. fatty acid synthesis occurs by: palmitate → triglycerides → stored in adipose tissue

why do excess carbs become fat?

1. glycolysis is fast

2. TCA cycle has limited capacity

3. excess citrate spills into cytosol

4. insulin activate ACC and FAS

5. NADPH is abundant

6. body prefers to store long-term energy as fat NOT GLYCOGEN

discuss digestion of proteins

digestion of proteins begins in the stomach

• gastrin stimulates HCl secretion

• HCl denatures proteins and activates pepsin

• Pepsin begins protein digestion

name the cells in the stomach

1. neck (mucous) cells: produce mucous for protection

2. parietal (oxyntic) cells: produce hydrochloric acid (HCl) and intrinsic factor (IF)

3. chief (peptic or zymogenic) cells: produce gastrointestinal hormones (e.g. gastrin)

discuss protein digestion in the small intestine

pancreatic proteases digest protein to small peptides

trypsin, chymotrypsin, and carboxypeptidase are secreted from the pancreas as inactive precursors (zymogens)

what are the active forms of the three protein zymogens in the small intestine?

trypsinogen → trypsin (active)

chymotrypsinogen → chymotrypsin (active)

procarboxypeptidase → carboxypeptidase (active)

what is peptidase secreted by and why?

peptidase is secreted by enterocytes to further digest small peptides to amino acids, dipeptides, and tripeptides. Then, these are absorbed into the blood to travel to the liver via portal vein

discuss amino acid metabolism (general)

about 75% of amino acids in normal, healthy adults are utilized to provide building blocks for the synthesis of proteins

amino acid pool is the total supply of amino acids in the body that is derived from digestion of food, body’s own degraded tissue, and synthesis of some amino acids in the liver

also involves protein turn over which is the continuing process in which body proteins are hydrolyzed and resynthesized

what is the amino acid pool?

the total supply of amino acids in the body that is derived from digestion of food, the body’s own degraded tissue, and synthesis of some amino acids in the liver

basically, it is the body’s “bank account” of free amino acids that are available at any moment for whatever the body needs

what is protein turnover?

the continuing process in which body proteins are hydrolyzed and resynthesized

in addition to protein synthesis, what is the amino acid pool continually used for, and what are the examples?

in addition to protein synthesis, the amino acid pool is continually used for the synthesis of other nitrogen-containing biomolecules:

• Purine and pyrimidine bases of nucleic acids

• Heme structures for hemoglobin and myoglobin

• Neurotransmitters like dopamine, and GABA

• Nitric oxide, a vasodilator

• Glutathione, an antioxidant

discuss in detail the steps of the catabolic metabolism of amino acids

1. removal of the amino group (nitrogen)

   1. ammonia generated is disposed of in the form of urea

2. once an amino group has been removed from an amino acid, the remaining molecule is referred to as a carbon skeleton, which is further catabolized for different uses (e.g. energy and glucose production)

discuss the stages in nitrogen catabolism

1. transamination

2. deamination

3. urea formation

what happens during transamination?

the main enzyme is transaminases (=aminotransferases)

transaminases remove an amino group from the amino acid and transfers to a-ketoglutarate to form glutamate

transaminases remove an amino acid and transfers to oxaloacetate to form aspartate

what happens during deamination?

during deamination, glutamate dehydrogenase catalyzes the removal of the amino group and regenerates a-ketoglutarate

this is the principle source of ammonium ion (NH4+) in humans

what happens during the urea cycle?

this is the metabolic pathway in which ammonium ions are converted to urea

energy is derived from 2 molecules of ATP

this occurs in the liver

nitrogen atoms from deamination (in carbonyl phosphate) and aspartate form urea

after urea is formed, it diffuses out of liver cells into the blood — kidneys filer it out — and it is excreted in the urine

discuss the fate of the carbon skeleton

to start, the carbon skelly is the part of the amino acid left over after the nitrogen is removed

it gets turned into one of seven molecules that enter normal metabolism

1. pyruvate → can make glucose (glucogenic)

2. acetyl-CoA → makes ketones or fat (ketogenic)

3. acetoacetate → makes ketones (ketogeneic)

4. a-ketoglutarate → enters TCA → can make glucose (glucogenic)

5. succinyl-CoA → enters TCA → can make glucose (glucogenic)

6. fumarate → enters TCA → can make glucose (glucogenic)

7. oxaloacetate → direct gluconeogenesis → glucose (glucogenic)

the biosynthesis of amino acids is derived from what? and what does this sentence even mean?

glycolysis, the TCA cycle, and phenylalanine

it means your body makes (synthesizes) many amino acids using molecules that come from glycolysis, TCA cycle, and phenylalanine

what amino acids are synthesized from glycolysis intermediates?

glycolysis intermediates → 3- phosphoglycerate → serine → cysteine or glycine

glycolysis intermediates → pyruvate → alanine

what amino acids are synthesized from TCA cycle intermediates?

oxaloacetate → aspartate → asparagine

a-ketoglutarate → glutamate → proline or glutamine or arginine

what amino acid is synthesized from phenylalanine (an essential amino acid)?

tyrosine

discuss amino acid metabolism in a fasted versus fed state

fasted:

• carbon skelly of amino acids are used for the production of energy or glucose

• glucogenic amino acids produce glucose

• all amino acids can generate energy

fed:

• excess intake of all amino acids can result in fatty acid synthesis and consequent fat storage

• glucogenic amino acids → glucose → fatty acid synthesis → triglycerides

• ketogenic amino acids → acetyl-CoA → fatty acid synthesis → triglycerides

what are nucleic acids

biomolecules involved in the transfer of genetic information from existing cells to new cells

classified into:

• ribonucleic acid (RNA)

• deoxyribonucleic acid (DNA)

what are nucleotides?

repeating structural unit or monomer of polymeric nucleic acids

where is RNA and DNA found?

RNA: cytoplasm of cells

DNA: nuclei of cells

what is the structure of nucleic acids?

1. nitrogen containing base

   1. pyrimidine

   2. purine

2. pentose (sugar)

   1. deoxyribose

   2. ribose

3. phosphate

bases found in nucleic acids are derived from what?

heterocyclic compounds pyrimidine and purine

name the differences in structure between pyrimidine and purine

pyrimidine: single 6-membered ring containing 2 nitrogen atoms

purine: fused ring system containing both a 6-membered ring with 2 nitrogen atoms and a 5-membered ring with 2 nitrogen atoms

what amino acids are found in DNA versus RNA

DNA:

• cytosine

• adenine

• guanine

• thymine

RNA:

• uracil

• cytosine

• adenine

• guanine

sugar component of RNA is ___, and DNA is ___

ribose, deoxyribose

what is the main structural difference between ribose and deoxyribose?

The structural difference between ribose/deoxyribose is the presence versus the absence of a hydroxy group on the 2’ position in the furanose ring

what is the structure of DNA

nucleotides are joined together in nucleic acids by phosphate groups that connect the 5’ carbon of one nucleotide to the 3’ carbon of the next

linkages are phosphodiester bonds

nucleic acid backbone is the sugar-phosphate chain that is common to all nucleic acids and the order of the bases provides the primary structure of DNA

who proposed the structure of DNA and in what year?

watson and crick in 1953

two intertwined polynucleotide chains of the DNA double helix run in which direction?

opposite directions and their bases point inward

sugar and phosphate point outward (sugar-phosphate backbone)

complementary DNA strands in the double helix are held together by what?

hydrogen bonds

what are the complementary DNA base paris?

adenine and thymine (2 hydrogen bonds)

guanine and cytosine (3 hydrogen bonds)

discuss the structure of RNA

long, unbranched polymer consisting of nucleotides joined by 3’-5’ phosphodiester bonds

ranges from as few as 73 to many thousands of nucleotides

where is RNA found?

nucleus, cytoplasm, mitochondria

what are the different types of RNA?

1. messenger RNA (mRNA)

2. ribosomal RNA (rRNA)

3. transfer RNA (tRNA)

how does RNA differ from DNA?

• contains ribose sugar unit instead of deoxyribose

• contains the base uracil (U) instead of thymine (T)

• usually single-stranded (does not have complementary 1:1 bases)

• has regions with double-helical structure and loops

  • adenine (A) pairs witih uracil (U)

  • guanine (G) pairs with cytosine (C)

what are chromosomes?

tightly packed bundle of DNA and protein that is involved in cell division

each chromosome contains one molecule of DNA coiled tightly by histones

how many chromosomes do humans contain?

46

DNA contains segments called what?

genes → these are the fundamental units of heredity

• each gene directs the synthesis of a specific protein

what is an exon and an intron?

exon: coding sequences

intron: non-coding sequences

what are the four phases of the cell cycle?

1. G1 phase

2. S phase

3. G2 phase

4. M phase = mitosis!

explain what happens during the G1 phase of the cell cycle

1. the cell grows in size

2. the cell makes tons of protein

   1. especially enzymes needed for DNA replication

3. the cell checks the environment and asks:

   1. do we have enough nutrients? enough energy? growth signals? no DNA damage?

   2. G1 is like an “is it safe to divide?” checkpoint

4. if the checkpoint is good → cell commits to DNA replication; if not good → cell stops dividing and goes into the resting phase (G0)

explain what happens during the S phase of the cell cycle

*the entire purpose of S phase is to copy all the DNA so the cell has TWO complete sets BEFORE division

1. DNA is replicated (copied)

2. each chromosome becomes two sister chromatids and stay attached at the centromere

3. the amount of DNA doubles; goes from 2N → 4N

   1. DNA doubles but chromosome number stays the same

4. histones are made

5. cell checks for replication errors

*this phase takes 10-15h

explain what happens during the G2 phase of the cell cycle

1. cell grows more

2. cell makes proteins needed for mitosis

3. cell checks the newly replicated DNA (checkpoint)

4. cell prepares for mitosis

explain what happens during the M phase of the cell cycle

CELL DIVISION!

1. prophase

   1. chromosomes condense

2. metaphase

   1. chromosomes line up in the middle of the cell

3. anaphase

   1. sister chromatids separate

4. telophase

   1. two nuclei form

5. cytokinesis

   1. cell splits into TWO!

what is the central dogma of molecular biology?

well-established process by which genetic information stored in DNA molecules is expressed in the structure of synthesized proteins

AKA the flow of genetic information in cells from DNA → RNA → protein

what are the steps of the flow of genetic information?

1. transcription: transfer of genetic material from a DNA molecule to a molecule of messenger RNA (mRNA)

2. translation: conversion of the code carried by messenger RNA into an amino acid sequence of a protein

what is DNA replication?

process by which an exact copy of a DNA molecule is produced

when two strands of DNA separate…

each serves as a template for the construction of its own complement

• A is paired with T and C is paired with G

legging strand: continuous daughter strands form as nucleotides

lagging strand: discontinuous daughter strand

• also called okazaki fragments

• consists of 100-200 nucleotides

what is DNA polymerase?

an enzyme that synthesizes DNA molecules

newly synthesized DNA strand is _______

complementary (A with T and C with G)

DNA polymerase requires what to synthesize new DNA?

• DNA template: a single strand of DNA

• Primer: a short, complementary segment of nucleotides (approx. 20 bases long) with a free 3’ end

what is exonuclease?

an enzyme that removes nucleotides one at a time from the ends of a DNA or RNA strand

used for DNA proofreading, repair, and removal when a DNA polymerase makes a mistake

DNA polymerase does not work alone but works incorporated with multiple enzymes and proteins. What are they?

helicase:

• unwinding of the double helix

  • replication forks are exposed (replication forks are the point where the double helix unwinds during replication)

DNA ligase:

• closing the nicks (gaps between segments in the daughter strand)

what is mutation?

ANY CHANGE resulting in an incorrect base sequence on DNA

mutations can occur when?

naturally during DNA replication or can be induced by environmental factors like repeated exposure to ionizing radiation (x-rays, gamma rays, UV light) or mutagens which are chemicals that induce mutations by reacting with DNA

are mutations beneficial or harmful and why?

some mutations may be beneficial to an organism by making it more capable of surviving in its environment

some may be lethal or may produce genetic diseases

give examples of diseases caused by DNA mutations

sickle-cell disease, phenylketonuria (PKU), hemophilia, muscular dystrophy

what happens during transcription and how is pre-mRNA processed?

transcription = RNA synthesis (mRNA)

• copies a gene (DNA sequence) into an RNA sequence

• RNA polymerase builds up RNA using complementary base pairing

  • C ←→ G

  • T → A

  • A → U (uracil in RNA)

post-transcriptional modification

• primary transcript = pre-mRNA (it must be processed to become mature mRNA)

• 5’ cap:

  • adds 7-methylguanosine to the 5’ end

  • protects mRNA + helps ribosome binding

• RNA splicing

  • removes introns (non-coding)

  • joins exons (coding)

  • produces a continuous coding sequence

• poly-A tail

  • adds 50-200 adenine nucleotides to the 3’ end

  • stabilizes mRNA + helps export from the nucleus

what happens during translation, and what are codons, the start codon, and stop codons?

translation = RNA → protein

• converts the genetic code in mRNA into a protein

• ribosomes read mRNA in codons (3-base “words”)

• each codon matches a specific amino acid carried by tRNA

codon

• a 3-nucleotide sequence on mRNA

• each codon corresponds to one amino acid

start codon

• AUG

• codes for methionine

• signals the ribosome to begin translation

stop codons

• UAA

• UAG

• UGA

• do NOT code for amino acids

• signal translation to stop

what is tRNA and how does it function during translation?

tRNA function

• delivers individual amino acids to the ribosome for protien synthesis

• each amino acid has at least one specific tRNA

• smallest nucleic acid (73-93 nucleotides)

key regions of tRNA

• anticodon

  • three-base sequence that pairs with the codon on mRNA

  • ensures the correct amino acid is addedd

• 3'‘ End (CCA tail)

  • binds an amino acid via an ester bond

  • carries it to the ribosome

tRNA during translation

• a charged tRNA (with amino acid) enters the A site of the ribosome

• a peptide bond forms b/w the new amino acid and the growing chain

• the ribosome translocates:

  • tRNA in A→P site

  • tRNA in P→E site (exit)

  • a site becomes empty again

• a new tRNA enters the A site, and the old tRNA is released from the E site

discuss termination of translation

termination factor: a specific protein, binds to the stop codon (UAA, UAG, or UGA) and catalyzes the hydrolysis of the completed polypeptide chain from the final tRNA

growing peptide chains extend from the ribosomes into the cellular cytoplasm and fold to assume 3d secondary and tertiary configurations

what is nutrigenetics?

the science of the effect of genetic variation on dietary response

ex: lactose intolerance is people who lack lactase interfering lactose digestion

how is the effect of food or nutrients on gene expression studied?

by investigating molecular-level interaction between nutrients and genomes

ex: vitamin D upregulates genes that control calcium absorption