CHAPTER 6: Proteins: Workers in the Cellular Factory summary

Introduction

Most cellular jobs are performed by proteins

Proteins interact with other molecules in specific ways to perform cellular functions

Levels of protein structure

• Proteins are amino acid polymers
• The amino acid polymer is called a polypeptide
• Once polypeptides are functional after being folded, the polypeptides are called proteins
• Some proteins are generated by folding more than one chain of polypeptides

Categories of protein structure

• Primary structure-amino acid sequence in the protein
• Secondary structure-are small regions folded into pleated sheets and alpha helices
• Tertiary structure-is the 3D final structure of a single folded chain of amino acids
• Quaternary structure- is a protein structure that consists of two or more chains of amino acids

Primary structure

• Is the amino acid sequence in the protein
• There are twenty amino acids in human cells hence ordering of the amino acids makes up the primary structure
• On every amino acid, a central carbon atom is bonded to various chemical groups
  • Nitrogen-containing  amino group (–NH2 or –NH₃)
  • A hydrogen atom (-H)
  • Carboxyl group(-COOH)
  • Sidechain (R) which varies among the twenty amino acids

Amino acids bond to each other by condensation.

Water is formed as covalent bond forms between two amino acids

The bond being formed is called a peptide bond

Secondary structure

Chains of polypeptide fold into the final structure and some regions of the chain form regular folded patterns

There are two-fold patterns;

• Alpha helix twists around  a spiral-like staircase
• Pleated sheets wound back and forth
• Secondary structure types and number in a protein depends on the protein.

Tertiary structure

• Is the 3D final structure of a single folded chain of amino acids
• Categories of 3D proteins include:
  • Globular proteins-they contain an overall rounded shape or irregular shape. Most enzymes are globular
  • Fibrous proteins-cable like and long proteins.
• The tertiary structure is held together by several types of bonds between atoms of amino acid R groups.

• The  bonds forming between R groups include:
  • Covalent bonds-include the bond formed between to cysteine amino acids.
  • Hydrogen bonds- occur in R groups with polar covalent bonds which create differences in negative and positive charges in atoms.
  • Ionic bonds- formed when R groups that are ionized come close to each other in a folded polypeptide chain
  • Hydrophobic interaction-formed when hydrophobic R groups get pushed together in small pockets inside polypeptide chains that are folded resulting in hydrophobic interactions.

Quaternary structure

• They contain many chains of polypeptides.
• the bonds that attach polypeptide chains to build up a protein are the same ones in the tertiary structure.

Functions of proteins

• proteins are enzymes- enzymes make biochemical reactions faster
• proteins reinforce structures- proteins form the structure of plasma membranes and cytoskeletal proteins strengthen internal cell structures
• proteins transport materials inside and outside cells
• proteins play a big part in cellular identification
• proteins promote cell movements
• proteins help in cell communication
• proteins promote the organization of molecules in cells
• proteins promote immunity
• proteins regulate the use of DNA  in cells

Enzymes and substrates

• enzymes are specific
• the correct enzyme folding creates a region called an active site
• substrate- are molecules that fit correctly into enzymes active sites

Inhibiting enzymes

There are two main types of enzyme inhibition

• Competitive inhibition- occurs from another molecule of the same shape as the substrate competing for the active site on enzymes
• Non-competitive inhibition-occurs if a regulatory molecule binds to another site apart from the active site

Membrane proteins

Proteins on the plasma membrane coordinate  many activities of the plasma membrane

The activities include;

• transport proteins
• receptor proteins
• protein adhesion
• protein identification
• enzymes production

DNA Binding Proteins

• The genetic material contains many functional and structural instructions of the cell
• DNA binding proteins control part of the DNA to be expressed
• Many DNA proteins are known and most of the proteins have repeating units called motifs
• Commonly DNA binding protein motifs are;
  • Helix turn helix motifs- contain 2 alpha-helices which are connected  by short amino acid sequences between the helices
  • Leucine zipper motifs- contain 2 alpha-helices which cross over each other
  • Zinc finger motifs-contain 2 pleated sheats and 2 alpha-helices held by a zinc atom.

Revision

Terms in this set (52)

Original
what is the name of the basic unit that proteins are made of?
-amino acids

-which element are part of ALL amino acids?
-carbon, oxygen, hydrogen and nitrogen

describe the basic structure of the amino acid
contains:
-amino group: H-N-H
-carbon in middle with -H
-acid group: C-O-H and a double bond of O on C
-side group will vary

How many amino acids are there?
-20 (9 essential, 11 nonessential)

essential amino acids
-you must consume them in your diet because your body cannot make them or cannot make them in required amounts
-9 essential

indispensable (nonessential) amino acids
-your body can make them from other compounds
-11 nonessential

3 major steps of protein synthesis:
-Step 1: Cell signaling
-Step 2: Transcription
-Step 3: Translation

STEPS OF PROTEIN SYNTHESIS: Cell Signaling
-Cell receives a signal that tells it to make a protein
-Often involves the cell membrane
-Cell receives a signal that tells it to make a protein

Up-regulation: “turning on” protein synthesis
Down-regulation: “turning off” protein synthesis

STEPS OF PROTEIN SYNTHESIS: Transcription
-Synthesis of messenger RNA (mRNA) using a DNA template
-In the nucleus, mRNA subunits bind to the gene and form an mRNA strand (a transcription of the DNA sequence)
-mRNA transcription moves from nucleus to cytoplasm for translation

STEPS OF PROTEIN SYNTHESIS: Translation
-Process by which amino acids are linked together via peptide bonds on ribosomes using mRNA and tRNA
-Ribosome reads the mRNA sequence
-tRNA molecules carry specified amino acids to the ribosome
-Ribosome links amino acids into polypeptides via peptide bonds

genes
-chromosomes subdivided into thousands of units
-a gene is one subunit
-it specifies the sequence of amino acids needed TO SYNTHESIZE ONE SPECIFIC PROTEIN
-30,000 genes in body

chromosome
-strand of DNA, packaged with proteins in the nucleus
-23 pairs

ribosome
-Organelle where mRNA is translated
-Associated with endoplasmic reticulum in the cytoplasm

protein synthesis
-cells link amino acids together (ribosomes) by means of condensation reactions (elongation)
-amino acids are added and peptide bonds are formed

dipeptide
2 amino acids w/ peptide bond (condensation reaction)

amino acids are joined by forming……..
peptide bonds

primary structure of proteins
the primary structure of a protein is the sequence and number of the amino acids in the polypeptide chain

why is the primary structure important?
-critical to its function because it determines the protein’s most basic chemical and physical characteristics
-represents the basic identity of the protein

secondary structure
-Folding of a protein because of hydrogen bonds that form between amino and acid groups

tertiary structure
-More folding because of interactions between the R-groups

quaternary structure
-Several polypeptide chains coming together to form the final protein

denaturation
-alter or unfold 3D form,
-causing a loss of biological activity
-altered because of heat, agitation, acid, or basic solutions, heavy metals

where does protein digestion begin?
stomach

STEP 1 OF PROTEIN DIGESTION:
-gastric cells release the hormone gastrin, which enters the blood, causing release of gastric juices

STEP 2 OF PROTEIN DIGESTION:
-hydrochloric acid in gastric juice denatures proteins and converts pepsinogen to pepsin, which begins to digest proteins by hydrolizing peptide bonds

STEP 3 OF PROTEIN DIGESTION:
-partially digested proteins enter the small intestine and cause release of the hormones secretin and CCK

STEP 4 OF PROTEIN DIGESTION:
-Secretin stimulates the pancreas to release bicarbonate into the intestine. Bicarbonate neutralizes chyme. CCK stimulates the pancreas to release proenzymes (e.g., trypsinogen) into the small intestine

STEP 5 OF PROTEIN DIGESTION:
-pancreatic proenzymes are converted to active enzymes (e.g., trypsin) in the small intestine. These enzymes digest polypeptides into tripeptides, dipeptides, and free amino acids

STEP 6 OF PROTEIN DIGESTION:
-intestinal enzymes in the lumen of the small intestine and within mucosal cells complete protein digestion

absorption of amino acids and the route of transportation
-amino acids, di and tripeptides- taken up by enterocytes
-more digestion= amino acids
-route: amino acids travel in the blood (portal) route
-what is the route? : small intestine, to liver, to the heart

“ase” designates that….
its an enzyme

proteases
enzymes that break down proteins (dipeptides, tripeptides, amino acids)

after transportation, list and discuss the 5 ways the body cells metabolize amino acids! What is the other major source of amino acids in addition to diet?
1.protein synthesis- from dietary and endogenous sources

2. making nonessential a.a.
3. energy production
4. glucose production (critical)
5. conversion to body fat

other: Biosynthesis or (synthetic) : Naturally synthesized by the body (Non-esential amino acids

3 major sites of body protein
40% in skeletal muscle***
30% skin and blood
25% body organs
*** decreases mean a loss of functional tissue

deamination
-the removal of an amino group (NH2) from an amino acid in order to convert amino acids to fat, glucose, or energy

where does deamination occur? Describe the process
-in the liver the amino group is removed via deamination
-NH2 converted into urea (a less toxic substance) in the liver and is then released into the blood
-the kidneys filter urea out of the blood, and urea is excreted in the urine.

what is the purpose of deamination? Why do we deamination some amino acids?
-so then when we can metabolize the glucose that we made from deamination to form ATP

MAJOR FUNCTION OF PROTEIN: Structure
-proteins making up the basic structure of tissues such as bones, teeth, skin
-example: hydroxyapatite in bones, collagen in skin, teeth, ligaments, and tendons, keratin in hair and fingernails

MAJOR FUNCTION OF PROTEIN: Catalysis
-enzymes
-increases rate of chemical reaction without being consumed in the process
-anabolic and catabolic
-example: lingual lipase digests lipids in mouth, pancreatic amylase digests carbohydrates in intestine, pepsin digests proteins in intestine

MAJOR FUNCTION OF PROTEIN: Movement
-proteins found in muscles, ligaments, and tendons
-example: actin and myosin in muscle

MAJOR FUNCTION OF PROTEIN: Transport
-proteins involved in the movement of substances across cell membranes and within the circulatory system
-example: glucose and sodium transporters in cell membranes, lipoproteins and hormone transport proteins in blood

MAJOR FUNCTION OF PROTEIN: Communication
-protein hormones and cell-signaling proteins
-example: insulin and glucagon regulate blood glucose, CCK regulates digestion in the small intestine, cell-signaling proteins initiate protein synthesis

MAJOR FUNCTION OF PROTEIN: Protection
-skin proteins and immune proteins
-example: collagen in skin, fibrinogen helps blood clot, antibodies fight off infection

MAJOR FUNCTION OF PROTEIN: Regulation of fluid balance
-proteins that- via the process of osmosis- regulate the distribution of fluid in the body’s various compartments
-example: albumin is a major regulator of fluid balance in circulatory system

MAJOR FUNCTION OF PROTEIN: Regulation of pH
-proteins that readily take up and release hydrogen ions (H+) to maintain pH of the body
-example: hemoglobin is an important regulator of blood pH

edema and proteins role in it
-the buildup of fluid in the interstitial spaces
-severe protein deficiency can impair albumin synthesis, resulting in low levels of this important protein in the blood and, in turn, accumulation of fluid in the interstitial space (long description of edema)
-can be seen in swelling in the hands, feet, and abdominal cavity in severely malnourished individuals

protein functions (in-class notes)
-building: cells, muscle, connective tissue, bones, ect.
-as enzymes: catalyze reactions-anabolic and catabolic
-as hormones: messenger molecules (insulin)
-energy source: 4 kcal/g
-glucose formation: critical function
-fluid balance: proteins attract water, help keep it where it is suppose to be (ex. blood proteins, albumins & globulins)
-acid/base balance: protein acts as a buffer (-acid solution has many (free) H+ ions and pH range is 1-14)

complete protein foods
-contain all essential amino acids
-mean, poultry, fish, eggs, dairy

incomplete protein foods
-nuts, seeds, legumes, grains, vegetables
-complementary proteins

what is the major food source of protein in the american diet?
beef

protein needs for those over 30?
25g-30g…………… 3X a day?

RDA for protein equation
-Weight in lbs (divided by) 2.2= Weight in kilograms X 0.8 grams= grams of protein daily