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12U Biology > 1.5 Proteins and Nucleic Acids > Flashcards

1.5 Proteins and Nucleic Acids Flashcards

To learn and understand proteins and nucleic acids

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1
Q

What are proteins?

A

The principal constituents of organs and soft structures of the animal body. A polymer made up of many amino acid subunits folded into 3D structures which determine its function.

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2
Q

How many proteins do humans have?

A

Tens of thousands of different proteins, each unique with its own structure and function

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3
Q

What is the key concept of 1.5 - Proteins?

A

Form/structure fits function (shape matters!)

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4
Q

What are the 7 protein functions?

A

Structural support
Enzymatic functions
Defense against foreign substances
Transport of molecules
Storage
Movement
Regulating cellular processes

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5
Q

What are proteins made from

A

Proteins are polymers made from amino acids

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6
Q

What does a proteins 3D structure determine?

A

The proteins function in an organism

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7
Q

How many amino acids do protein polymer chains have?

A

100-200 amino acids

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8
Q

What is the basic structure of all amino acids?

A

An asymmetric carbon (a-carbon) bonded to four covalent partners –> amino, hydrogen, carboxyl, and “R” which changes

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9
Q

Why are amino acids called acids?

A

They are composed of an amino (amine) and acid (carboxyl)

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10
Q

Why are there 20 different amino acids?

A

Because there are 20 different R groups found in organisms

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11
Q

What are the three classes of amino acids?

A

Nonpolar (hydrophobic), polar (hydrophilic) and electrically charged (acidic or basic)

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12
Q

What is a chain of amino acids called?

A

A polypeptide

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13
Q

What are the two nutritional categories of amino acids?

A

Essential and nonessential

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14
Q

What is the difference between essential and nonessential amino acids?

A

Essential amino acids are those that cannot be made from the body, and must come from food

Nonessential amino acids are those we make enough of so that we don’t need them from food

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15
Q

What are the 9 essential amino acids (must obtain through food)

A

Histidine, Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Leucine, and Lysine

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16
Q

What amino acids are likely abundant in a protein found in a basic solution (pH above 7)?

A

Basic amino acids (e.g., lysine, arginine, histidine) with amino groups (-NH₂) in their side chains, which become positively charged in basic conditions.

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17
Q

What is hemoglobin made up of?

A

Four specific 3D subunits, each having one polypeptide chain and one heme group

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18
Q

How many possible proteins can be made from amino acids?

A

There are nearly limitless possible proteins that can be made from different combinations of the 20 amino acids, as each sequence can vary in length and order, leading to countless unique proteins.

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19
Q

For a polypeptide chain that is 10 amino acids long, how many possible proteins can be made?

A

For a 10-amino-acid-long chain, 20^10 (10,240,000,000) possible proteins can be made due to the 20 different amino acids and 10 positions for variation.

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20
Q

How many amino acids are in one polypeptide chain?

A

50 or more

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21
Q

Which amino acid is most insoluble in water, isoleucine or alanine? Why?

A

Isoleucine is more hydrophobic and thus more insoluble in water. Its side chain contains a larger branched alkyl group (hydrocarbon chain), which is nonpolar and does not interact well with water.

Alanine has a smaller methyl group (-CH3), which is also nonpolar but less hydrophobic due to its smaller size, making it slightly more water-soluble than isoleucine.

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22
Q

Which amino acid is most soluble in water, lysine or serine? Why?

A

Serine is more soluble in water due to its side chain containing a hydroxyl group, which is polar and capable of forming hydrogen bonds with water, making serine more hydrophilic.

Lysine, while polar because of its amino group at the end of its side chain, as a longer hydrophobic chain, making lysine less hydrophilic.

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23
Q

How are amino acids linked together in a protein?

A

Amino acids are linked by peptide bonds, which are formed through dehydration synthesis between the amino group (-NH₂) of one amino acid and the carboxyl group (-COOH) of another.

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24
Q

What are the four levels of protein structure?

A

Primary Structure: The sequence of amino acids in a polypeptide chain.

Secondary Structure: The folding or coiling of the chain into alpha-helices or beta-pleated sheets due to hydrogen bonding.

Tertiary Structure: The overall 3D shape of a protein, formed by interactions between R groups of amino acids.

Quaternary Structure: The arrangement of multiple polypeptide chains into a single functional protein complex.

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25
Q

What are the two common types of secondary structures in proteins?

A

The two common secondary structures are the alpha-helix (a coiled shape) and the beta-pleated sheet (side-by-side chains).

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25
Q

What gives amino acids their unique properties?

A

Amino acids have unique properties due to their R groups (side chains), which can be polar, non-polar, acidic, basic, or even form rings.

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26
Q

What is the difference between a polypeptide and a protein?

A

A polypeptide is a chain of amino acids, while a protein is one or more polypeptides folded into a functional 3D shape.

27
Q

What is a disulfide bridge, and why is it important?

A

A disulfide bridge is a strong covalent bond between two cysteine amino acids that helps stabilize a protein’s tertiary structure.

28
Q

How do nucleic acids relate to proteins?

A

Nucleic acids like DNA and RNA carry genetic information needed for the synthesis of proteins in cells.

28
Q

What happens when a protein is denatured?

A

When a protein is denatured, it loses its 3D structure and function, often due to extreme conditions like heat or changes in pH.

29
Q

What are essential amino acids?

A

Essential amino acids are the eight amino acids humans must get from their diet because the body cannot synthesize/create them.

30
Q

What are nucleic acids, and what is their role in cells?

A

Nucleic acids, like DNA and RNA, carry genetic information needed for protein production in cells, ensuring proper cellular function.

31
Q

What are the components of an amino acid?

A

An amino acid consists of a central carbon atom attached to an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a variable R group (side chain).

32
Q

How do hydrogen bonds influence the secondary structure of proteins?

A

Hydrogen bonds form between different parts of the amino acid chain in a protein. These bonds help keep the protein’s shape by supporting structures like alpha-helices (spirals) and beta-pleated sheets (folds). This arrangement is what makes up the protein’s secondary structure.

33
Q

How is a protein’s tertiary structure formed?

A

The tertiary structure is formed by interactions between R groups, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

34
Q

Why are proteins called the “workers” of the cell?

A

Proteins carry out vital functions such as structural support, enzyme activity, transportation of substances, and chemical signaling in cells.

35
Q

What are peptide bonds, and how are they formed?

A

Peptide bonds are covalent bonds between amino acids, formed by a dehydration synthesis reaction between the amino and carboxyl groups of two amino acids.

35
Q

How do changes in the primary structure affect a protein?

A

A change in the amino acid sequence can alter or destroy a protein’s function by affecting its shape and folding. Even a single amino acid change can disrupt the protein’s ability to perform its specific role.

36
Q

What is the primary structure of a protein?

A

The primary structure is the linear sequence of amino acids in a polypeptide chain, which determines the protein’s overall structure and function

37
Q

What is the importance of proteins in nature?

A

Proteins are crucial in living systems because they perform diverse functions such as structural support, enzymatic reactions, chemical signaling, and transport within cells.

38
Q

What are the roles of storage proteins?

A

Storage proteins, like those found in egg whites, provide essential chemical building blocks for developing embryos.

39
Q

What is the relationship between DNA, RNA, and proteins?

A

DNA carries the genetic information of an organism, which is then transcribed into RNA, which then directs the synthesis (creation) of proteins in cells.

39
Q

What is the quaternary structure of a protein?

A

Quaternary structure refers to the arrangement of two or more polypeptide chains (subunits) into a single functional protein. Bonds such as hydrogen bonds, ionic interactions, and disulfide linkages hold these subunits together.

40
Q

What are motile proteins, and what do they do?

A

Motile proteins enable movement within cells and cellular structures, such as muscle contractions or the movement of cilia and flagella.

40
Q

How do proteins function in cell membranes?

A

Proteins in cell membranes act as transporters, moving substances across the membrane, and as receptors for cell signaling.

41
Q

What is the significance of hydrophobic interactions in protein structure?

A

Hydrophobic interactions occur when non-polar R groups cluster together, helping to stabilize the protein’s tertiary structure.

41
Q

How do proteins assist in oxygen transport?

A

Hemoglobin, a transport protein in red blood cells, binds to oxygen and delivers it to tissues and organs in the body.

42
Q

What role do enzymes play in biochemical reactions?

A

Enzymes are proteins that act as catalysts, speeding up the rate of biochemical reactions in the body.

43
Q

What are prosthetic groups in proteins?

A

Prosthetic groups are non-protein components that are essential for a protein’s function. For example, in hemoglobin, heme groups with iron ions bind oxygen, aiding in its transport.

44
Q

How does protein shape relate to its function?

A

The shape of a protein is crucial for its function. For example, elongated proteins like silk provide strength, while compact globular proteins like hemoglobin are efficient for transport.

45
Q

What does each nucleotide consist of?

A

Each nucleotide consists of three parts: a nitrogenous base (A,G,C,U/T), a 5-carbon sugar (either deoxyribose in DNA or ribose in RNA), and one to three phosphate groups.

45
Q

What is the structure of DNA and RNA?

A

DNA is a double-stranded molecule with strands running antiparallel, held together by hydrogen bonds between bases (A with T, G with C). RNA is usually single-stranded and can fold into various shapes.

46
Q

How do ATP and GTP function in cells?

A

ATP and GTP are nucleotides that transport and regulate chemical energy in cells. They are crucial for energy transfer between reactions and for adjusting cellular activities.

46
Q

What are the two types of nitrogenous bases in nucleotides?

A

Pyrimidines; single ringed bases (cytosine, thymine, and uracil)

Purines; double ringed bases (adenine and guanine)

47
Q

How does one differentiate between the ribose and deoxyribose sugar structures?

A

Ribose has C-2 as OH, however deoxyribose has C-2 as just H.

48
Q

Why must adenine bond to thymine, and similarly, guanine bond to cytosine?

A

Because adenine and thymine can both form 2 hydrogen bonds and guanine and cytosine can both bond 3 hydrogen bonds.

49
Q

What bonds are nucleotides connected together by?

A

Phosphodiester bonds

50
Q

Why is it advantageous that DNA has hydrogen bonds instead of covalent bonds between its strands?

A

Hydrogen bonds are advantageous because they are weaker and allow the DNA strands to separate easily during processes like replication and transcription, whereas covalent bonds would make separation more difficult.

51
Q

Describe the difference between the primary and secondary protein structures.

A

The primary structure is the unique linear sequence of amino acids in a protein chain. The secondary structure involves the folding or coiling of this chain into patterns like alpha-helices or beta-pleated sheets due to hydrogen bonding between the backbone atoms.

52
Q

What is an alpha-helix?

A

A spiral or coil shape formed by hydrogen bonds between every fourth amino acid. This structure looks like a spring and provides strength and flexibility.

53
Q

What is a beta-pleated sheet?

A

A flat, zigzag pattern where segments of the protein chain line up side by side. Hydrogen bonds form between these aligned segments, giving the sheet strength and stability.

54
Q

What amino acids would you predict to NOT be abundant in a protein if the solution has a pH above 7?

A

Acidic amino acids (e.g., aspartic acid, glutamic acid) with carboxyl groups (-COOH) in their side chains, which are negatively charged in basic conditions.

55
Q

What is the role of the sugar and phosphate groups in the structure of nucleic acids?

A

They form the backbone of nucleic acids (DNA and RNA) by linking nucleotides through phosphodiester bonds. The sugar (deoxyribose in DNA, ribose in RNA) and phosphate groups are arranged in a repeating sequence, creating a strong and stable chain that supports the nitrogenous bases.

56
Q

What are alpha helices?

A

Alpha helices are a type of secondary protein structure where the polypeptide chain coils into a spiral shape, stabilized by hydrogen bonds between every fourth amino acid.

57
Q

What are beta pleated sheets?

A

Beta pleated sheets are a type of secondary protein structure formed by two or more strands of polypeptide chains lying side by side, with hydrogen bonds between them, creating a folded or pleated shape.

12U Biology (10 decks)

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