6- Important Molecules of Living Systems. Proteins Nucleic Acids Taft College Human Physiology

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1 6- Important Molecules of Living Systems Proteins Nucleic Acids Taft College Human Physiology

2 Proteins Proteins- made from: C, H, O, N, and S. Proteins are very large molecules composed of long chains of nitrogen containing molecules known as amino acids. Since proteins are so large, they are known as macromolecules. Amino acids are the building blocks of proteins. Proteins have a large range of functions, both structural and physiological roles.

3 The major protein functions include: 1. Structural- They can be structural elements within cells. Examples: Collagen is a protein in bone and other C.T. Keratin is found in skin hair and nails. Silk, wool, horns, and antlers are made from structural proteins. 2. Regulatory (hormones)- chemical messengers in the body that regulates various physiological processes, and, control growth and development. Examples: Insulin regulates blood glucose level by controlling entry into cells and is a protein hormone. 3. Contractile- Allows shortening of muscle tissue which produces movement. Examples: Myosin and actin form contractile filaments that pull against each other and shorten the muscle. 4. Immunological- provides a specific response to protect the body against foreign substances and invading pathogens. Examples: Antibodies and interleukins (IL2, TNF). 5. Transport- serve to carry vital substances throughout the body. Example: Hemoglobin carries 02 from the lungs to the body. 6. Catalytic (enzymes)- enzymes are catalysts in cells. They speed up chemical reactions. These reactions can build up or breakdown biological compounds. All enzymes are proteins, but not all proteins are enzymes. Examples: Amylase breaks down starch. Lipase breaks down lipids. Lactase breaks down lactose.

4 Enzyme (Catalyst) Function Sucrose W/ sucrase Glucose Enzyme + Fructose

5 Amino Acids and Polypeptides Proteins are made of amino acids. There are 20 different amino acids used to make proteins. Amino acids are strung together in polymers to form individual types of proteins. Polymers are larger molecules composed of many repeating molecular subunits. Example: Insulin is composed of 51 amino acids strung together. You can see that with 20 different amino acids, there are many different types of combinations possible. The sequence in which the amino acids are arranged in the polypeptide chains(protein) determines the biological characteristics of the protein molecule. Even one small variation in this sequence can cause disaster. One change (substitution) of an amino acid in a protein can alter the shape of the protein and render it non-functional. Example: Hemoglobin has 574 amino acids. One wrong amino acid causes the hemoglobin to change shape under low oxygen levels to create sickle-cell shaped red blood cells. Cells get stuck in microcirculation causing hypoxia and tissue damage. The spleen can become quite enlarged.

6 Amino Acid Structure: Amino acids, since they make up proteins, are composed of the same elements as protein: C,H,O, as well as N. Some amino acids will contain S that will bond with other S containing amino acids to create covalent bonds to reinforce the shape of the protein, as we will review later. Every amino acid contains an amino group (-NH2) and a carboxyl group (-COOH) bonded to a carbon atom: R R Group = Radical H 2 N C- C -OH Amino group C Carboxyl group H O This is the basic structure of the molecule. It is the same in all amino acids. R (side chain) Radical- a group of atoms that acts as a single functional unit. The R group gives the amino acids its particular chemical behavior. Only the R group changes from one amino acid to another.

7 Amino Acid Structure Amino Group - C - Carboxyl Group

8 H When R = H Glycine (gly) H 2 N-C-C-OH H O H HCH When R = CH3 Alanine (ala) H 2 N-C-C-OH H O OH CH 2 When R = CH2-OH Serine (ser) H 2 N-C-C-OH H O

9 Examples: Amino Acids Radical Note The only thing that changes from one amino acid to another is R group = radical

10 Building Proteins out of Amino Acids Since proteins are made of chains of amino acids. Let's look at how amino acids are bound together to make proteins. The amino "head" of the molecule can be linked to the carboxyl "tail" of another by the removal of a water molecule. This is called dehydration synthesis.

11 Connecting Amino Acids Together with Peptide Bonds Amino Head Carboxyl Tail 1 Amino Acid = peptide 2 Amino Acids = dipeptide Many Amino Acids = polypeptide

12 Amino Acid = Peptide When several of these linkages form, combining several amino acids, the molecule is called a polypeptide. Polypeptides are assembled in the ribosome, linking the head of one amino acid to the tail of another, like a line of box cars. The sequence of the box cars (amino acids) is determined by information from the nucleus of the cell. As the amino acids produce a linear chain on the ribosome the primary structure of the protein is determined. The primary structure is the unique sequence of amino acids making up a protein. It will ultimately determine the shape and function of the protein. (Remember shape is determined by function.)

13 Protein Structure The primary structure is the unique sequence of amino acids making up a protein. It will ultimately determine the shape and function of the protein. (Remember shape is determined by function.) 3 other levels of protein organization are important to their function: Secondary structure- the protein, commonly assumes an alpha helix (clockwise spirals similar to a phone cord) or a pleated sheet repeating pattern. Tertiary structure- this level of protein structure describes the 3D shape of the protein molecule. It is determined by the side chain (R group) interactions that form hydrogen bonds, ionic bonds, covalent bonds, hydrophobic interactions. This level determines the proteins primary function. It is similar to the irritating secondary winding of the phone cord that occurs with use. Quaternary structure- some proteins contain more than 1 polypeptide chain. This level describes the bonding of individual polypeptide chains relative to each other. They are held in place by bonds as mentioned under tertiary structure. Example: Hemoglobin consists of 2 alpha chains and 2 beta chains to form one functional protein. Small changes in temperature, ph, or electrolyte concentrations in the body can cause protein structures to unravel and lose their characteristic shape. This process is called denaturation. This will effect the ability of the protein to perform its function.

14 Levels of Structural Organization in Proteins (a) Primary structure = amino acid sequence (b) Secondary Structure = Twisting and folding by H+ bonds (c) Tertiary Structure = 3 dimensional shape (d) Quaternary Shape = 2 or more polypeptide chains

15 Important Molecules of Living Systems Nucleic Acids Nucleic acids include 2 types: 1. Deoxyribonucleic acid (DNA)- forms the inherited genetic information (material) in the nucleus of each cell. DNA = blueprints for the control of cellular activity. 2. Ribonucleic acid (RNA)- one type (mrna) carries instructions from DNA to the ribosomes to make amino acids into proteins.

16 Control by Nucleic Acids DNA along with certain proteins (histones) make up chromosomes that contain the blueprint of life. The genetic information (blueprints) in chromosomes (DNA) has to get out of the nucleus and into the cytoplasm to control cell activities. A certain type of RNA is responsible for this: messenger RNA or mrna. mrna carries the genetic message from DNA out of the nucleus to the cytoplasm. The end result being that the genetic message is taken from the mrna and translated into a sequence of amino acids to make proteins. In order to understand how this works, it is necessary to take a closer look at nucleic acid chemistry.

17 DNA + Proteins = Chromosomes

18 Chemistry of Nucleic Acids The primary elements found in nucleic acids are C,H,O,N,P. The basic unit of a nucleic acid = nucleotide. DNA is made of thousands of nucleotide subunits strung together. DNA molecules are huge, the largest molecules in the cell. Molecular weight = 1 million to several billion = Macromolecules. Up to 100,000 times the size of most proteins which are also macromolecules.

19 Chemistry of Nucleic Acids Each nucleotide is made of 3 components: 1. Phosphate group. 2. Sugar- deoxyribose in DNA, ribose in RNA. 3. Base (nitrogenous base). The base is the only thing that differs from one nucleotide to another.

20 Nucleotide Bases of DNA and RNA There are only 4 different kinds of bases in DNA: Adenine (A) Guanine (G) Cytosine (C) Thymine (T) The 4 bases of RNA are: Adenine (A) Guanine (G) Cytosine (C) Uracil (U) only Uracil differs from DNA bases Uracil in RNA replaces Thymine in DNA

21 Components of a Nucleotide The organization of the components of a nucleotide is as follows: where phosphate = P sugar = S base = B P \ S-B = 1 nucleotide

22 Strand of (4) nucleotides Nucleotides join together to form a strand of DNA like this: P \ S-B = 1 nucleotide / P \ S-B = 1 nucleotide / P \ S-B = 1 nucleotide / P \ S-B = 1 nucleotide

23 Strand of (4) nucleotides Further simplification: 1 strand of nucleotide looks like 1/2 ladder, where: rungs = base, side of ladder = sugar + phosphate -B -B -B -B

24 DNA Structure In 1952, 2 men, Watson and Crick formulated current model of molecular of DNA. They postulated that DNA is made up of 2 strands of nucleotides wrapped around each other. This has been confirmed through decades of research. The overall shape is a double helix (double coil), with the bases of each strand sticking outwards from the backbone and bonding with each other. The 2 opposing strands have bases that pair with each other.

25 DNA looks like a twisted ladder. DNA consists of thousands of nucleotides strung together. How many are shown here? Double Helix

26 Nucleotide = phosphate + sugar + base DNA Double Helix= Double Coil

27 Base Pairing of DNA Nucleotides Bases =Adenine (A) Guanine (G) Cytosine (C) Thymine (T) A will only pair with T: A-T or T-A G will only pair with C: G-C or C-G Note- A and G are larger bases while T and C are smaller bases. A large base must bind to a small base for the DNA molecule to fit together correctly.

28 Base Pairs = A-T & T-A G-C & C-G

29 DNA Base Pairing Therefore, base pairs of DNA strand could look like this: -T -A -C -G -T -A DNA Strand 1 DNA Strand 2? On exam if you are given the bases in one strand of DNA you should be able to determine the nucleotide sequence of the complementary strand.

30 Base Pairing in RNA Nucleotides Bases =Adenine (A) Guanine (G) Cytosine (C) Uracil (U) (uracil replaces thymine) G will only pair with C: G-C or This is the same as DNA. U will only pair with A: U-A or U takes the place of T in RNA. This will make sense shortly. C-G A-U

31 Other Differences Between DNA and RNA RNA sugar = Ribose RNA consists of a single strand of nucleotides. mrna is smaller, containing nucleotides.

32 RNA If only single-stranded, what does RNA base pair with? RNA may twist upon itself to give a 2 stranded look in (trna)= Transfer RNA or will exist as single-stranded in mrna = Messenger RNA. What does mrna pair with? Remember we talked about mrna taking the genetic message from DNA in the nucleus to the site of protein synthesis. Therefore, mrna must base pair with DNA

33 mrna Where does mrna take it s information? To the ribosome. Where are ribosomes? In the cytoplasm or ER. mrna leaves the nucleus through a nuclear pore to enter the cytoplasm and then to free ribosomes or ER with ribosomes.

34 Transcription The process where genetic information of DNA is used to specify base sequences of mrna is called "transcription". Transcription is when RNA is made from DNA Be prepared to transcribe an mrna strand from a DNA strand that I will provide for you. -T A- - -A T- - -C G- - -G C- - -T A- - -A T- - DNA RNA =?

35 Transcription of RNA from DNA -T A- -U -A T- -A -C G- -C -G C- -G -T A- -U -A T- -A DNA RNA How does each newly formed cell in your body obtain genetic information? Before mitosis, the cell creates a second set of chromosomes in a process called DNA replication.

36 The Genetic Code We have been talking about how DNA is transcribed into mrna which travels to the ribosome and tells ribosome what amino acids to connect together to make protein= (translation). Translation = information in mrna dictates sequence of amino acids in protein molecules. a.a- a.a- a.a.- a.a.- a.a. And so on.

37 The Genetic Code How does DNA code for 1 of 20 specific amino acids in sequence to make protein? Through tedious research it has been found that a 3 base sequence in DNA or mrna is a code for a particular amino acid. The code for a particular amino acid has been termed a "codon".

38 Codons code for amino acid DNA Codon mrna Codon Amino acid A U phenylalanine (phe) =codon A U A U A U serine (ser) G C A U T A lysine (lys) T A T A G C arginine (arg) C G A U

39 The Genetic Code The bases are analogous to a 4 letter alphabet, and the codons are analogous to words. There are 64 different codons as follows: four bases, 3 = 3 bases/codon. 4 3 = 64, where 4 = the 64 different ways that A,T,G,C can combine to form 3 letter codons. We will see that most (18/20) amino acids have more than 1 codon. Example: Valine 4 codons for valine. GUU GUC GUA GUG Some amino acids have 6 codons (leucine, serine, arginine). Most amino acids have between 2-6 codons.

40 The Genetic Code As you can see some different codons code for the same amino acid, demonstrating a redundant or degenerate code. Some codons act as punctuation marks, 1 start, 3 stop codons, that tell the ribosome when to start and stop and amino acid chain. The stop codons are also known, less appropriately, as "nonsense" codons.

41 Control by Nucleic Acids in Protein Synthesis The synthesis of a protein requires that certain things are present within the cell: In Nucleus 1. DNA 2. Free nucleotides floating around that nucleus combine to form mrna. In Cytoplasm 1. Ribosomes 2. The 20 various amino acids that will eventually be joined together in proper sequence to form protein. 3. ATP = energy source (which is also a nucleotide). 4. trna = transfer RNA. trna is made in the nucleolus and moves out of the nucleus and into the cytoplasm through nuclear pores. trna carries the amino acids to corresponding mrna codon. trna binds by anticodon to codon

42 Sequence of Events for Protein Synthesis 1. Free nucleotides are attracted to DNA strand where complementary base pairing occurs. 2. Nucleotides link to form mrna strand. Steps 1&2, process = Transcription. 3. mrna separates from DNA and moves out of nucleus to associate with ribosomes. Structurally, a ribosome consists of 2 subunits, one about half the size of the other. The smaller ribosomal subunit complexes with trna, mrna, and proteins to initiate reading of the mrna message. 4. Free amino acids in cytoplasm combine to trna carriers. 5. trna anticodon with associated amino acids, base pairs with mrna codons at ribosome. The ribosome then moves along the mrna strand. 6. Ribosome continues moving along mrna strand to new codons, where amino acids are added to growing polypeptide chain. trna molecules are released as the amino acids are joined by a peptide bonds. The next trna carrying an amino acid attaches by anticodon to the next codon to continue the process. Steps 5 and 6 represent the translation process. 7. Polypeptide disconnects from ribosome and mrna strand when a "stop" codon is reached.

43 Protein Synthesis In Nucleus STEP 1 (Transcription = DNA to mrna) Peptide =amino acid mrna codon In Cytoplasm STEP 2 (Translation = mrna determines Amino Acid Sequence of Protein) trna anticodon Peptide bond Protein or polypeptide chain

44 1. Transcription occurs in Nucleus 2. Translation occurs in Cytoplasm In nucleus: Transcription = DNA used to make RNA In cytoplasm: Translation = RNA used to determine amino acid sequence of protein

45 Transcription = RNA from DNA

46 Ribosome subunits Large subunit binds with trna Small subunit binds with mrna Binds with trna Binds with mrna

47 Translation Occurs in Polypeptide = protein Cytoplasm

48 Protein Synthesis Another view of Transcription in Nucleus

49 Translation in Cytoplasm Another View

50 Nucleotide Fill-in Practice DNA Strand 1 A T T G G A C T A DNA Strand 2 _ mrna _ trna _

51 Nucleotide Fill-in Practice DNA Strand 1 A _ T _ C DNA Strand 2 _ C _ G _ C _ mrna U trna G U _

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