Advanced 1 EXAM 3 sessions 10 and 11

What two factors determine the "quality" of a protein source? ex of digestibility % of animal vs plant protein

-Amino acid composition- Complete or Incomplete, see below -Digestibility - % of AA in a food that are absorbed after ingesting that food. Animal is 90-99% digestible, Plant protein is 70-90% digestible

Explain the basis for the different numbers in the proteins ApoB48 and ApoB100. What is this an example of? Which organ are these proteins expressed in and what are their functions, respectively?

-ApoB48 and ApoB100- 48 comes from the fact that ApoB48 has 48% of amino acids of ApoB100. ApoB100 is a big protein encoded by big RNA, it gets edited so an early stop codon is introduced to create → ApoB48. -This winds up being a different protein. Example of tissue specific gene expression -Liver (100, vldl and ldl) and Enterocytes (48, chylomicrons)

what is a proteasome

A cellular structure responsible for degradation of proteins

What signals activate mTORC1? What signals inhibit mTORC1?

Activated by: Insulin leucine, arginine and SAM mechanical stress Inhibited by: high AMP (ATP inhibits via AMPK) tumor suppressor p53 which is activated by DNA damage

What transporter facilitates transport of di- and tri-peptides across the apical membranes of enterocytes? What about single amino acids?

Di- and tri-peptides (and H+) are co-transported across the apical/luminal membranes of enterocytes via the transporter PEPT-1. Single amino acids use individual "AA transporters" Generic name as there are many individual AA transporters that operate via a variety of mechanisms Most common AA transporters are Na+ symporters

List two populations for which the RDA for protein is likely too low to support maintenance of lean mass

Elderly- need to maintain muscle mass so they need to increase intake >1.5g/kg/day strenuously training athletes- need to maximize muscle protein synthesis

At which ETC complex are the electrons from FADH2 accepted? What is the name of this complex?

Electrons from FADH2 are accepted at Complex II, also known as Succinate Dehydrogenase.

At which ETC complex are the electrons from NADH accepted? What is the name of this complex?

Electrons from NADH are accepted at Complex I of ETC, also known as NADH Dehydrogenase or NADH Ubiquinone Oxidoreductase.

Name a non-food source of protein that is digested and absorbed in the small intestine. And what do they do

Endogenous protein example → mucins Mucins are glycoproteins that form mucus layer of GI tract Desquamated (sloughed-off) enterocytes are digested and constituent nutrients are absorbed in the small intestine, and provide a significant amount of protein!

what work together to form the absorbable units of proteins and what are those units (3)

Endopeptidases and exopeptidases work in tandem to produce the absorbable units of proteins which include single AA, dipeptides, and tripeptides.

Compare and contrast the functions of endopeptidases and exopeptidases (they both cleave peptide bonds, but one cleaves "internal" and the other cleaves "external" peptide bonds)

Endopeptidases: cleaves larger polypeptide into smaller ones by cleaving "internal" peptide bonds Ex.: pepsin Exopeptidases: break external or end of peptide bonds to release single AA off a protein

List at least 5 functions of proteins - provide an example (from class) of a protein that carries out each of the listed functions.

Enzymes: glucokinase; ALT Hormones: preproinsulin; GLP-1 Receptors: insulin receptor (IR) Transporters: Glut4 Structural Proteins: ApoB48 Contractile Proteins: myosin DNA Packaging: histones Transcription Factors: Rev-erb

Where in the cell do each of the two major proteolysis pathways occur? 3

Every cell except RBCs Cytoplasm (ubiquitin proteasome pathway) Lysosomes (lysosomal degradation)

Provide a one-sentence summary of the following process: transamination

Exchange of amino group between AA and keto acid (KA)- so what was once an AA becomes a KA and vis versa

High levels of plasma homocysteine may indicate deficiency of which two vitamins?

Folate (b9) or cobalamin (b12)

How is the translation of intracellular vs. secreted and membrane-bound proteins different?

Intracellular proteins are synthesized on free ribosomes in the cytoplasm. Secreted and membrane-bound proteins are synthesized on ribosomes associated with rough ER.

What is the difference between an intron and exon? Which is "spliced out" during alternative splicing?

Intron = non coding sequence; exon = coding sequence; splicing (@nucleus)- introns removed, purely exons leftover.

- S-adenosyl methionine is synthesized from which two molecules?

Methionine Adenosine (ATP)

What are the two sulfur-containing amino acids? what is the NPNC mol?

Methionine Cysteine SAM (s-adenosylmethionine)

How do animal and plant derived proteins differ with respect to their digestibility and AA composition? veg low in? nuts/seeds low in?

Most plant foods except soy, chia, quinoa are incomplete. Veg are low in methionine, nuts and seeds low in lysine and threonine.

Which amino acid is most abundant in the whole body AA pool? Which is second most abundant?

Most- Glutamine - 5C Second most- Alanine - 3C

Which enzyme combines ornithine and carbamoyl phosphate to form citrulline?

Ornithine transcarbamoylase (OTC) is the enzyme combines ornithine and carbamoyl phosphate to form citrulline

What category of metabolic pathways generally requires NADPH as a co-factor?

Oxidative

At which ETC Complex is oxygen consumed? What is the name of this complex?

Oxygen is consumed at Complex IV of ETC, also known as Cytochrome C Oxidase.

During which stage are rates of muscle proteolysis the highest?

Starvation

How does the partial catabolism of amino acids for ATP production by enterocytes benefit other organs? (HINT: two words)

The partial catabolism of AAs for ATP production by enterocytes benefits the other organs because it is a glucose sparing process.

List 5 types of post-translational protein modifications. For each type of modification, provide an example from class. UBIQUINATION

Ubiquination: this one is here to preview one of the two major proteolysis pathways (metabolic pathways for the catabolism of proteins), which we will cover on the next slide

Which of the two major proteolysis pathway is responsible for the lion's share of protein degradation in most cells?

Ubiquitin proteasome pathway

how does proteasome recognize proteins for degradation and what does it do to proteins marked for degradation

Ubiquitin-proteasome degradation process- a tag added to proteins that they should be degraded. E1, e2 e3 go around looking for the proteins to degrade and mark them with ubiquitin then the proteasome recognizes the tags, grabs onto them and pulls them into the protein's opening to unfold it, cut its peptide bonds,and what comes out are constituent AA. Costs a lot of ATP, most common route of protein degradation.

During which stage are rates of protein synthesis the highest?

absorptive/fed state

Which AA/KA pairs does ALT interconvert?

alanine into pyruvate and AKG to glutamate

List 4 other non-protein nitrogen containing molecules that are synthesized via SAM-mediated methylation

creatine, carnitine, choline, epinephrine

under what conditions does proteolysis occur at accelerated rates?

fasting/starvation Wasting conditions

ex of intracellular proteins

hexokinase, glucokinase, PDHC, LDH, fatty acid synthase, ALT, AST, etc. literally any enzyme in any metabolic pathway is acceptable here.

examples membrane bound receptors

insulin receptor, glucagon receptor, GLP-1 receptor, etc.

examples of secreted proteins

insulin, glucagon, GLP-1, inflammatory cytokines.

Which intracellular compartment does mTORC1 associate with?

lysosome

The start codon recognition...

marks the beginning of the first stage. AUG → Methionine is always the first amino acid added to a protein, represented by the start codon.

The stop codon recognition...

marks the end of the last stage. There are three stop codons with no amino acid associated with them, but it signals to protein that it is done. UAG, UAA, and UGA

List 5 types of post-translational protein modifications. For each type of modification, provide an example from class. LIPIDATION

membrane transporters and other integral proteins are often lipidated (bonded with lipids) to facilitate their integration into the membrane

Briefly describe the sequence of events starting with CCK-mediated stimulation of pancreatic zymogen release and ending with absorption of absorbable units of proteins.

-CKK release stimulates pancreatic acinar cells to release inactive peptidases. -Trypsinogen is activated at brush border by the enzyme enterokinase to its active form trypsin. -Trypsin activates chymotrypsin from chymotrypsinogen, carboxypeptidase from procarboxypeptidase, and elastase from proelastase. -Endopeptidases cleave larger polypeptides into smaller ones and exopeptidases cleave end of peptide bonds to release single AA off a protein- these are absorbable units. -Endopeptidases and exopeptidases work in tandem to produce the absorbable units of proteins which include single AA, dipeptides, and tripeptides.

What are the three primary metabolic fates of amino acids in enterocytes?

-Can be transported to the liver via HPV. -Can be used for protein synthesis. -Up to 50% of dietary AA are partially catabolized in enterocytes for ATP production (This is a glucose-sparing process where we make ATP not from glycolysis and pyruvate but by taking nitrogen of AA and putting it through TCA and ETC)

What is meant by "complete" and "incomplete" in the context of protein quality?

-Complete- contain all essential amino acids (most animal foods aside from gelatin) -Incomplete- contain too little of one or more essential amino acids. Most plant foods except soy, chia, quinoa. Veg are low in methionine, nuts and seeds low in lysine and threonine.

I: Absorptive (fed) State 4

-Proteins digested single AAs, di- and tri-peptides absorbed liver via hepatic portal vein general circulation -Liver regulates AA composition of AA pool, which supplies all tissues with AAs -If excess AAs consumed, increase urea production -Insulin and AAs stimulate protein synthesis via mTOR

Briefly describe the role of AMPK in the regulation of cell metabolism. What does AMPK sense? When is AMPK active? What is the general effect of AMPK activation on metabolic pathway activity?

-Sense intracellular energy levels and maintains balance between ATP production and consumption -It is activated by increasing AMP levels -Generally it activates ATP producing pathways (catabolic) and inhibits ATP consuming (anabolic) pathways [inhibits mTOR]

What is the role of mRNA in translation?

-mRNA carries genetic information from dna in the nucleus to the ribosomes in the cytoplasm, acts as a template for protein synthesis by carrying genetic code from DNA to the ribosome where it is translated into a sequence of amino acids

What is the role of rRNA in translation?

-rRNA is a component of ribosomes which are the cellular structures responsible for protein synthesis, helps to catalyze the formation of peptide bonds between amino acids during protein synthesis

What is the role of tRNA in translation?

-tRNA is responsible for bringing amino acids to the ribosomes during protein synthesis, binds to a specific amino acid and carries it to the ribosome where it is added to the growing protein chain

what are the names of the 5 starvation stages

1- absorptive (fed) state 2 & 3- post absorptive and early starvation (fasted) 4 & 5- intermediate and prolonged starvation

Which urea cycle enzyme voraciously consumes arginine? What are the products this reaction?

Arginase Products are ornithine and urea

Arginine is broken down to ----- and ---- by ----- Ornithine is combined with ---- to form ----

Arginine is broken down to ornithine and urea by arginase. Ornithine is combined with carbamoyl phosphate to form citrulline.

Which AA/KA pairs does AST interconvert?

Aspartate into oxaloacetate, and AKG to Glutamate

Which AA/KA pairs does BCAT interconvert?

BCAA + aKG and BCKA + Glu

- How was protein adequacy traditionally assessed? Does this method tend to overestimate or underestimate protein needs? Why?

By nitrogen balance, nitrogen (protein) intake - nitrogen lost in urine, feces primarily and also in smaller amounts via sweat, skin cell sloughing, etc. Nitrogen Balance tends to UNDERESTIMATE protein needs (outdated...)

what is the generic chemical structure of an amino acid (4)

Central carbon atom Carboxyl group Amino group R group (variable)

What is the RDA for protein for children, healthy adults, pregnancy and lactation? What are the units?

Children .95g/kg/day Healthy adults .8g/kg/day Pregnancy 1.10g/kg/day During lactation 1.3g/kg/day

Which non-proteogenic amino acid is the product of the ornithine transcarbamolyase reaction?

Citrulline

what is splicing ____ removed with only ___ leftover.... plus explanation

During mRNA, pieces of pre-mRNA introns are revived during splicing, and the remaining parts (exons) are joined together. Alternative splicing, certain exons are either included or excluded resulting in different slice products. Alternative splicing: the same gene can be expressed in different forms in different tissues depending upon which exons get included in final mRNA that → cytoplasm.

What is the starting material for the pentose phosphate pathway? What are the two major outputs?

G6P (starting material) NADPH + Ribose-5-phosphate (major outputs)

Which enzyme catalyzes the first step of the pentose phosphate pathway?

G6p dehydrogenase

examples of membrane-bound transporters

GLUT transporters, CD36, PEPT1, AA transporters, MCT, SGLT1, etc.

What is the general effect of mTORC1 activation on protein synthesis, proteolysis and cell growth?

Generally, mTORC1 activation increases the rate of protein synthesis, and suppresses major proteolysis pathways It is a kinase that integrates nutrient related signals (AA, insulin, ATP) to modulate rates of protein synthesis and cell growth

You should know that glutamine can be used to synthesize all of the non-essential amino acids except for tyrosine ______ ____is the most abundant AA in blood

Glutamine is the most abundant AA in blood Glutamine can be used to make all essential AA except for tyrosine

describe the general difference between the chemical structures of glutamine, glutamate and alpha-ketoglutarate

Glutamine: amino acid with 2 N groups Glutamate: amino acid with 1 N group Alpha-ketoglutarate (aKG): keto acid with no N groups

List 5 types of post-translational protein modifications. For each type of modification, provide an example from class. GLYCOSYLATION

Glycosylation (the covalent bonding of glucose to a protein): oAn example of this from the course is HBA1c - the glycosylation of hemoglobin, which is irreversible and provides a way to estimate average blood glucose concentrations over a roughly 90-day period (recall that red blood cells survive in circulation for roughly 90 days)

Cori and Cahill Cycles: you should be able to explain the flow of lactate, alanine and glucose between myocytes and hepatocytes during extended duration exercise and/or fasting. Cahill Cycle (glucose/alanine cycle)

Highest activity during extended fasting/starvation Muscle: pyruvate generated via glycolysis is converted to alanine via ALT & exported to liver Liver: alanine from muscle converted to pyruvate via ALT Pyruvate used for GNG and resulting glucose is exported to blood

What is the breakdown product of SAM? How is this breakdown product cleared? Which vitamin cofactors are required to clear the breakdown product of SAM?

Homocysteine is breakdown product Converted back to methionine via a vitamin b9 and b12 dependent reaction

What is the primary role of creatine in metabolic physiology? How is this related to the preservation of muscle glucose and glycogen?

It's a high energy phosphate donor, allows fro rapid resynthesis of ATP, without it we'd need to burn glucose and/or mobilize glycogen stores Creatine kinase catalyzes phosphorylation of creatine (reversible) Phosphagen energy system allows for seconds of muscle contraction before glucose and glycogenolysis are needed Creatine phosphate group can be transferred to ADP in a one step reaction catalyzed by creatine kinase Happens very fast so it gets exhausted very quickly, and is useful for preserving muscle glucose and glycogen

Cori and Cahill Cycles: you should be able to explain the flow of lactate, alanine and glucose between myocytes and hepatocytes during extended duration exercise and/or fasting. Cori Cycle

Lactate generated in skeletal muscle via anaerobic glycolysis is exported to liver via monocarboxylate transporter (MCT) Lactate dehydrogenase (LDH) converts lactate to pyruvate Pyruvate then used for GNG. Resulting glucose is exported to blood

What are the three branched chain amino acids (BCAAs)?

Leucine Isoleucine Valine

Which of the essential amino acids is needed in the highest quantities per day?

Leucine (I LOVE LUCY!)

What is meant by "complementary" incomplete proteins?

Like eating rice and beans, two incomplete proteins in one dish combine to be a complete source of protein

Which organ produces most of the body's urea? Which organ clears urea from the blood? Liver produces most of the body's urea

Liver produces most of the body's urea Kidneys are responsible for clearing the urea from the blood

What causes marasmus? What about kwashiorkor?

Marasmus- CALORIE DEFICIENCY Very skinny, low muscle mass, little energy stored as fat tissue, susceptible to acute insults of injury and disease. Kwashiorkor- PROTEIN DEFICIENCY rounded belly, swollen legs Energy is there (enough calories) but not enough protein

intracellular proteins are made by _____ secreted and membrane proteins are made from ____

NTRACELLULAR proteins (like the enzymes in metabolic pathways) are made by free ribosomes SECRETED & MEMBRANE proteins (like hormones, receptors and transporters) are made from ER ribosomes.

What is the primary role of carnitine in metabolic physiology?

Needed for transport of long chain fatty acids across mitochnodrial membranes (carnitine shuttle)

What is the primary protein digesting enzyme in the stomach? Is it secreted in its active form? Why or why not?

Pepsin is the primary protein digesting enzyme in the stomach. It is secreted in its inactive (pepsinogen) zymogen form in the body. Once it hits the stomach, the low acidity removes the "kiddy cover" and activates it to pepsin. If it were secreted in its active form, the body's proteins would be vulnerable to self-digestion.

List 5 types of post-translational protein modifications. For each type of modification, provide an example from class. PHOSPHORYLATION

Phosphorylation: oWe've seen this many times in this course! The phosphorylation of metabolic pathway enzymes changes their activity

How does the RDA for protein change for growing children, pregnant mothers, and lactating mothers?

Populations that are growing (kids) or growing a person/supporting them (pregnancy and lactation) need more protein

II & III: Post-Absorptive & Early Starvation (Fasted) 2

Protein synthesis rate gradually declines as insulin concentrations and supply of incoming AAs drop Proteolysis rate gradually increases to provide substrate (carbon skeletons) for gluconeogenesis

List at least 3 functions of amino acids

Proteogenic AA = building blocks of proteins Building blocks of non protein, nitrogen containing molecules (NPNC) Clearance of ammonia as urea (urea cycle) Transport of ammonia (NH3) in non-toxic form Carbon skeletons can be used to "fill" TCA cycle for ATP production and biosynthesis Support acid/base and fluid balance

IV & V: Intermediate & Prolonged Starvation 1

Proteolysis rate continues to increase and eventually surpasses rate of protein synthesis

What is the primary function of SAM in metabolism (methyl donor in 1-carbon metabolism)

Provides methyl groups (1 carbon metabolism) for synthesis of other NPNC molecules (creatine, carnitine, choline, epinephrine)

Why don't red blood cells have mitochondria? How does this relate to the primary biological function of the iron-containing proteins in RBCs and mitochondria?

RBCs job is to carry oxygen to tissues that consume oxygen. The protein that transfers it is hemoglobin. There are no mitochondria in RBCs because hemoglobins are iron-containing proteins that transfer electrons and mitochondria have ETCs that CONSUME oxygen; we do not want RBCs to consume oxygen that they're supposed to be delivering to tissues that need to consume that oxygen.

High rates of pentose phosphate pathway activity occur in what kind of cells/tissues?

Rapidly proliferating tissues with high demand for NADPH & nucleotide synthesis

Where in the cell are secretory and membrane proteins synthesized? Where in the cell are intracellular proteins synthesized?

Rough Endoplasmic Reticulum cytoplasm

What are the definitions of stunting and wasting? What causes each? Can they occur simultaneously?

Stunting- low height for age caused by nutritional deficiency Wasting- low weight for height Typically, caused by acute nutritional deficiency However, it can also occur with adequate nutrition in disease states (i.e., cancer cachexia) Can occur simultaneously

What is meant by "conditionally essential" amino acids? List 3 circumstances in which non-essential amino acids become essential? (5)

Synthesized in adequate amounts except in certain circumstances, such as: illness stress organ damage rapid growth and/or in-born errors of metabolism (MSUD - BCAA metabolism error; PKU).

What are the 9 essential amino acids?

TV TILL PMH Tryptophan (W) Valine (V) Threonine (T) Isoleucine (I) Leucine (L) Lysine (K) Phenylalanine (F) Methionine (M) Histidine (H)

What are the three stages of translation? What marks the beginning of the first stage? What marks the end of the last stage?

Three stages of translation: Initiation: start codon recognition Elongation cycle: growing polypeptide Termination: stop codon

what is transcription what do rna polymerases make (3)

Transcription: transcription factors (TF) bind promoter, enhancer and silencer regions on DNA to recruit and allow binding of RNA-polymerase Makes three different kinds of RNA from DNA in the nucleus RNA polymerases I-III make: rRNA: ribosomes mRNA: protein-coding RNA tRNA: transfer RNAs

what is translation

Translation: all RNAs work together -RNA transcript binds ribosome (made of rRNA + protein) -rRNAs make ribosomes, the hub for protein synthesis -mRNA: not ready to go right after it's made, needs to be processed which involves splicing and RNA editing -Splicing: removing introns, non-coding sequences of mRNA from the mRNA transcript to leave only the exons, protein-coding pieces -tRNA: bring amino acids to the ribosomes to match up with specific codons on the mRNA to grow the protein chain -tRNA binds amino acid corresponding to its anti-codon → ribosome

List 5 types of post-translational protein modifications. For each type of modification, provide an example from class. TRIMMING

Trimming: proteins are often produced as prohormones or zymogens that require trimming or activation to produce the active form. Some examples of this from this course are preproinsulin, which is trimmed to form insulin and C-peptide, and the zymogens involved in the chemical digestion of proteins

Which of the zymogens that are active in the small intestine is responsible for activating all of the other zymogens? + 3 steps

Trypsin is the zymogen that is active in the small intestine and is responsible for activating all of the other pancreatic zymogens: Chymotrypsinogen → chymotrypsin Procarboxypeptidase → carboxypeptidaase Proelastase → elastase

Briefly summarize the sequence of events starting with the formation of an autophagosome vesicle and ending with the release of amino acids from a degraded protein

Vesicles form called phagosomes, to escort them to a lysosome which will fuse and rip apart anything enclosed within autophagosome. Transporters let out AA and other breakdown products from the lysosome to retrieve constituent AA

Which B-vitamin is a required co-factor in transamination reactions? What form must this vitamin be in?

Vitamin B6 Pyridoxal 5 phosphate (PLP)

Which two vitamins are required for nucleotide synthesis?

Vitamin B9 (folate) Vitamin B12 (cobalamin)

What is a zymogen? Why are protein digesting enzymes, but not carbohydrate or lipid digesting enzymes, produced as zymogens?

Zymogen is an inactive enzyme (protein) precursor. Zymogens protect the body from potent protein digesting enzymes. They prevent "self digestion" and protect digestive organs.

What are the two phases of the of the pentose phosphate pathway? Generally speaking, what are outputs of each phase?

oxidative phase: NADPH and ribose-5-phosphate; carbon shuffling phase: glycolysis intermediates

Which organ supplies most of the body's glutamine and alanine in the fasted state and beyond?

skeletal muscle