BIOL 118 Lecture Notes - Lecture 3: Beta Sheet, Tata Box, Protein Folding

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chocolatetortoise260

13 Oct 2016

School

Binghamton University

Department

Biology

Course

BIOL 118

Professor

Jeane Lawless

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Document Summary

Proteins are made up of building blocks called amino acids. There are 20 of these amino acid building blocks. Amino acids have a central carbon atom bonded to h, nh2, cooh, and a variable side chain. In water the amino and carboxyl groups ionize to nh3+ and coo- This makes amino acids stay in solution and more reactive. The 20 amino acids differ only in the side chain (r group) attached to central carbon. Amino acids can be grouped into 4 types: 1. ) To determine nature of the amino acid ask 3 questions. If so it is uncharged polar b/c of high electronegativity of oxygen. If it is not any of the previous then it is a nonpolar amino acid. R groups differ in size shape reactivity and interactions with water. They do not h bond b/c they lack charged or highly electronegative atoms capable of forming h bonds with water.

Related Questions

Question 401 pts

Kinetic energy is the stored energy that can be used for motion.

True

False

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Question 411 pts

When an electron is transferred from one atom to another, and the two atoms are then electrically attracted to one another, a(n) ________________ bond is formed.

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Question 421 pts

Changing the number of ____________ of an atom would change the chemical properties of the atom.

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Question 431 pts

Forming molecules and breaking down molecules in biological organisms usually requires the use of _________ to help the reaction proceed faster.

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Question 441 pts

Organic molecules have a core composed of .

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Question 451 pts

The building blocks of carbohydrates are

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Question 461 pts

Water molecules crossing a membrane from high to low concentration is .

active transport

cell fate

facilitated diffusion

osmosis

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Question 471 pts

Choose the membrane molecule responsible for the passage of polar molecules and ions into and out of the cell.

phospholipids

transmembrane channel proteins

cell surface proteins

carbohydrate chains

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Question 481 pts

The simplest cells are .

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Question 491 pts

Which of the following membrane bound organelles are found inside bacterial cells:

nucleus

organelles are not found in prokaryotic cells

mitochondria

chloroplasts

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Question 501 pts

Which of the following is a specialized components of the cell, is associated with the rough endoplasmic reticulum, and is responsible for making proteins.

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Question 511 pts

Proteins are sorted, modified, and packaged by the _____________ and later transported to the outside of the cell.

ribosomes

golgi bodies (golgi apparatus)

nucleus

mitochondria

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Question 521 pts

Dehydration synthesis is a process of linking two smaller subunits together to form a polymer. Which of the following statements below is true of dehydration synthesis?

Oxygen is consumed.

A water molecule is removed from the molecules.

A water molecule is added to the molecules

Carbon dioxide is given off.

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Question 531 pts

Proteins are made up of _________ held together by peptide bonds.

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Question 541 pts

Which of the following gives an amino acid its properties?

NH2

R Group or functional group

COOH

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Question 551 pts

The final three-dimensional shape of a protein that includes the bonding of two or more polypeptide chains is call its _____ structure.

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Question 561 pts

How do DNA and RNA differ?

all statements are differences between DNA and RNA.

DNA is double stranded while RNA is single stranded.

They have different sugars.

Thymine is present in DNA but not in RNA.

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Question 571 pts

Which of the following is a component of a DNA nucleotide?

phosphate

a nitrogen containing base

All are components of a nucleotide.

5-carbon sugar

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Question 581 pts

Cell membranes are made up of several different types of molecules. Select the membrane molecule below that is made up of a polar region and two non-polar fatty acid tails.

transmembrane proteins

carbohydrate chains

phospholipids

cell surface proteins

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Question 591 pts

Two organelles which are believed to have once been free-living bacterial cells are ____________ and ______________.

chloroplasts and mitochondria

golgi apparatus and endoplasmic reticulum

ribosomes and nucleolus

peroxisomes and lysosomes

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Question 601 pts

The is an extensive system of internal membranes responsible for producing carbohydrates and lipids.

smooth endoplasmic reticulum

rough endoplasmic reticulum

nucleolus

mitochondria

sangriarat617

1. What is an organic molecule?

2.Name three hydrocarbons and be able to draw their structural formulas.

3. What is an isomer? List and describe the three types (structural, geometric, and enantiomers).

4. Be able to recognize and describe the properties of these functional groups: aldehyde, ketone, hydroxyl, sulfhydryl, carboxyl, amino, and phosphate groups.

5. What is a monosaccharide? Give two examples of these molecules and their functions.

6. Describe these chemical reactions: dehydration synthesis (condensation reaction) and hydrolysis (rehydration).

7. What is a disaccharide? List two and give their functions.

8. What is a polysaccharide? List two storage forms and two structural forms. How are they formed and what is their specific function?

9. How do the pancreatic hormones insulin and glucagon regulate blood sugar levels?

10. What is molting and why is it necessary in certain animals?

11. What four molecules are bonded together to form a triglyceride or fat? Why are fats nonpolar? What are some functions of fats as well as other lipids such as oils and waxes?

12. How do saturated and unsaturated fats differ? Discuss bonding patterns and possible sources of these fats. Which type is healthier for you? Why?

13. Why do animals store most of their excess glucose as fats or oils rather than as glycogen or protein? Give two reasons.

14. What are phospholipids? Identify parts of the phospholipid bilayer that are hydrophobic or hydrophilic? What important cell structure do these molecules help create?

15. Describe the structure of a steroid. How is cholesterol used in beneficial ways in your body?

16. What are LDLs and HDLs? Which is considered good or bad cholesterol? What condition could result from high blood pressure?

17. What are four ways to either reduce high blood cholesterol or maintain a safe level?

18. What is the composition of an amino acid? Why would they be considered nonpolar, polar, acidic, or basic?

19. Define dipeptides and polypeptides.

20. Describe the primary structure of a protein. What type of bonding creates it?

21. What is the secondary structure of a protein? Name two types of secondary structure and indicate what type of bonding holds them together. List three fibrous proteins.

22. What is the tertiary structure of a protein? What types of bonds or chemical interactions allow a protein to maintain this structure? List three globular proteins.

23. What is the quaternary structure of a protein? Describe a hemoglobin molecule.

24. What are the subunits of nucleic acids and what is their composition? How are these subunits bonded together? What is DNS's basic shape?

25. List three differences between DNA and RNA.

1. You have the following prokaryotic DNA sequence: 5â²-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3â² 3â²-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5â² If the top strand is the template strand which sequence below is the correct mRNA transcript? A. 5â²-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAAâ3â² B. 5'-UUUCGGAAUCUCUAGGUCCCUAUUGUCUAGUCC-3' C. 5'-CCUGAUCUGUUAUCCCUGGAUCUCUAAGGCUUU-3' D. None of the above are correct

2.Starting in the cytoplasm with a fully mature mRNA explain the process of translation initiation and then elongation and termination to me.

3.Prior to export from the nucleus, pre-mRNA must be processed. What specifically does this entail?

4.The biosynthetic pathway for the two amino acids E and H is shown schematically in the figure. You are able to show experimentally that E inhibits enzyme V, and H inhibits enzyme X. The most logical hypothesis regarding the regulation of Enzyme T would be that it is most likely subject to feedback inhibition by E alone. True or False?

5. A. kinase B. ligase C. polymerase D. oxido-reductase E. Phosphatase F. protease G. nuclease H. ATPase 1. Removes a phosphate group from a molecule 2. Hydrolyzes ATP 3. Hydrolyzes bonds between nucleotides 4. Adds phosphate groups to molecules 5. Catalyzes reactions in which one molecule is oxidized and another is reduced 6. Hydrolyzes peptide bonds 7. Joins two ends of DNA together 8. Catalyzes the synthesis of polymers such as RNA and DNA

6. Looking at the figure showing the change in reaction rate for two different enzymes that both utilize the same substrate, answer the following questions. a. What is the approximate Vmax for enzyme B ? b. What is the approximate Vmax for enzyme A ? c. What is the approximate Km for the enzyme which has a higher affinity for the substrate uM.

7. Answer the following question either yes or no (spell out the word, do not abbreviate as y or n). Looking at the following coupled reaction: Luciferase luciferin + O 2 ==========> oxyluciferin + light âG = + + Mg2+ ATP <=> AMP + PPi âG = - - - a. Based on your knowledge of free energy change and reactions would this coupled reaction occur ? b. Would changing the second step from ATP<=> AMP + PPi âG = - - - to ATP <=> ADP + Pi âG = - change your answer

7.Spontaneous reactions by definition will happen instantaneously. Why false?

8. Each of the following questions apply to the image of the channel protein. The purple sphere is a charged ion. Type your response to each question in the blank provided. a. Based you on what you know about cells and ions, what does the tri-lobed red and white molecule represent (although there aren't anywhere near enough of them shown) ? b. Since the question stated the purple sphere was a charged particle, using what you know about the tri-lobed red and white molecule what is the charge of the purples sphere c. On the extracellular space, on the right side of the purple sphere, there are two tri-lobed red and white molecules in close proximity to one another. The red of one appears to be attracted to the white of the other. What type of bond is this ? d. Based on your knowledge of proteins that interact with the membrane and the properties of the membrane, to what family of amino acids would the amino acid marked by A. most likely belong? ?

BIOL 118 Lecture Notes - Lecture 3: Beta Sheet, Tata Box, Protein Folding

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