CHEM EXAM 3

Denaturation

a process that disrupts the stabilizing attractive forces in the secondary, tertiary, or quaternary structure of a protein caused by heat, acids, bases, heavy metals, small organic compounds, or mechanically digest.

** WHEN A PROTEIN IS DENATURED, ITS PRIMARY STRUCTURE IS NOT CHANGED.

Hair relaxing and perming involve protein denaturation. Both of these processes involve denaturing the proteins in your hair by disrupting what type of bonds?

disulfide bonds

found in the hair protein, keratin reshaping the hair and forcing the disulfide bonds to re-form at different points.

Denaturing proteins can be used as a treatment for what type of poisoning?

Lead or mercury poisoning

A person who accidentally ingested heavy metals like lead or mercury are given egg whites to drink. The proteins in the egg white are denatured by mercury/lead, and the combination forms a precipitate.

Proteins can act as?

Messengers, Receptors, and Transporter!

Receptors

a protein facing the outer surface of a cell that binds to a hormone or other messenger, triggering a signal inside the cell.

integral membrane protein

a protein found within or spanning the phospholipid bilayer of a membrane; many serve as passages for polar compounds to move across the membrane.

conformational change

a change in the tertiary or quaternary structure of a protein the occurs through bonds ROTATING, not bonds breaking.

antigen

the foreign substance recognized by an antibody

steady state

a reaction rate describing maximum enzyme activity when substrate is being converted to product as efficiently as possible.

Conditions that affect enzyme activity

-pH

-Temperature

-Inhibitors

pH optimum

the pH at which an enzyme functions most efficiently

** (same as temperature optimum)

inhibitors

a molecule that causes an enzyme’s catalytic activity to DECREASE

reversible inhibition

the lowering of enzyme catalytic activity caused by a competitive or noncompetitive inhibitor (however if the inhibitor is removed, the enzyme becomes functional again)

-can be reversed!

Competitive Inhibitors

a molecule structurally similar to the substrate that COMPETES for the active site.

-can be reversed!

if more substrate is added

Noncompetitive inhibitors

a molecule that inhibits an enzyme’s catalytic activity by interacting with a site other than the active site resulting in distortion of the shape of active site.

-can be reversed!

typically requires a special chemical reagent to remove the inhibitor and restore the catalytic activity of the enzyme.

Irreversible inhibition

PERMANENTLY inactivate enzymes

the inhibitor forms a covalent bond with an amino acid side chain on the enzyme. With the inhibitor covalently bonded in the active site, the substrate is excluded or the catalytic reaction is blocked.

Penicillin acts as an antibiotic

-an irreversible inhibitor.

-penicillin binds to the active site of an enzyme that bacteria use in the synthesis of their cell walls. (the cell wall is a structure present in bacterial cells, not human cells)

-when the bacterial enzyme bonds with penicillin, the enzyme loses its catalytic activity, and the growth of the bacteria cell wall slows.

-without a proper cell wall for protection, bacteria cannot survive, and the infection stops.

DNA

Deoxyribonucleic acid; the genetic material of all cells containing nucleotides with deoxyribose sugar, phosphate, and the four nitrogenous bases adenine, thymine, guanine, and cytosine

RNA

Ribonucleic acid; a type of nucleic acid that is a single strand of nucleotides containing adenine, cytosine, guanine, and uracil.

Nucleotides

A pentose sugar condensed with one of the five nitrogenous bases (adenine, thymine, guanine, cytosine, or uracil) at C1 and up to 3 phosphates.

3 basic components-

a nitrogenous base (purine or pyrimidine)

a five carbon sugar (pentose)

a phosphate functional group.

proteins are strings of?

amino acids

nucleic acids are strings of molecules known as…

nucleotides

DNA contains 2 purine and 2 pyrimidines:

2 purines- adenine (A) and guanine (G)

3 pyrimidines- thymine (T), cytosine(C),

RNA contains 2 purine and 2 pyrimidines:

2 purines- adenine (A) and guanine (G)

3 pyrimidines- uracil (U), cytosine(C)

DNA contains the pentose?

-deoxyribose (the “D” in DNA)

-LACKS oxygen on carbon 2’ of the pentose

RNA contains the pentose?

-ribose (the “R” in RNA)

Nucleoside

a pentose sugar condensed with one of the five nitrogenous bases (adenine, thymine, guanine, cytosine, or uracil) at C1.

**the formation of a nucleoside is the FIRST step in the synthesis of a nucleotide.

RNA nucleoside and nucleotide names

nucleoside-

Adenosine (A),Guanosine(G),Cytidine(C),Uridine(U)

nucleotide-

Adenosine monophosphate (AMP)

Guanosine monophosphate (GMP)
Cytidine monophosphate (CMP)
Uridine monophosphate (UMP)

DNA nucleoside and nucleotide names

nucleoside-

deoxyadenosine(A), deoxyguanosine(G), deoxycytidine(C), deoxythymidine(T)

nucleotide-

deoxyAdenosine monophosphate (dAMP)

deoxyGuanosine monophosphate (dGMP)
deoxyCytidine monophosphate (dCMP)
deoxythymidine monophosphate (dTMP)

many nucleotides linked together form?

nucleic acids

Nucleic acids

Large molecules composed of nucleotides, found in cells as double–stranded helical DNA and single–stranded RNA.

amino acids in proteins are linked together by?

PEPTIDE BONDS!

Nucleotides are linked together through…

Phosphodiester bonds!!

This bond connects the 3ʹ –OH of one nucleotide to the phosphate linked to C5ʹ of a second nucleotide

Primary structure:

Nucleic acid sequence

The backbone of a nucleic acid runs directionally, with the phosphates connected between the 3′ carbon of one sugar and the 5′ carbon of the neighboring sugar.

Secondary Structure:

Complementary base pairing

DNA’s secondary structure is described by the interaction of two nucleic acids to form a double helix.

The two strands both have the bases in the center. Their backbones run in opposite directions, aka the backbones run antiparallel to each other.

One strand goes in the 5′ to 3′ direction, and the other strand goes in the 3′ to 5′ direction.

complementary base pairs

In DNA,adenine and thymine are always paired (A–T or T–A) and guanine and cytosine are always paired (G–C or C–G).

In RNA, adenine pairs with uracil (A–U or U–A) and same for G-C as in DNA

Tertiary Structure:

chromosomes

As in proteins, tertiary structure refers to a large biomolecule’s overall shape when it folds onto itself. Because DNA has a helical twist (the double helix), any further twisting (doubling it up on itself) that makes the DNA more compact constitutes its tertiary structure.

This further twisting is called supercoiling. The DNA in a human cell is separated into 46 pieces (23 from mother, 23 from father) that are super coiled around proteins called histones.

These pieces of DNA wound around histones pack into chromosomes. Chromosomes are an efficient package for lots of DNA information.

messenger RNA (mRNA)

produced in the nucleus by DNA to carry the genetic information to the ribosomes for the construction of a protein

ribosomal RNA (rRNA)

A major component of the cell structure called the ribosome

transfer RNA (tRNA)

An RNA that places a specific amino acid into a peptide chain at the ribosome. There is one or more tRNA for each of the 20 different amino acids

Transcription

The transfer of a gene copy from DNA via the formation of an mRNA.

RNA polymerase

The enzyme complex that catalyzes the construction of mRNA from a DNA template

ribosome

the organelle in cells where protein synthesis takes place.

anticodon

The triplet of bases in the center loop of tRNA that is complementary to a codon on mRNA.

codon

A sequence of three bases in mRNA that specifies a certain amino acid to be placed in a protein.

A few codons signal the start or stop of transcription.

translation

The interpretation of the codons in the mRNA as amino acids in a peptide.

mutation

a change in the DNA sequence

No change in protein sequence…

Sometimes, a change in a DNA base will have no effect.

For example, if the codon UUU were changed to UUC, the amino acid phenylalanine would still be placed in the growing polypeptide chain.

These types of mutations are called silent mutations.

silent mutations

a change in DNA sequence that has NO effect on protein sequence

A change in protein sequence occurs, but it has NO effect on protein function…

If, for example, the codon AUU were mutated to GUU, the amino acid isoleucine would be changed to valine.

These two amino acids are similar in polarity and size, and it is likely that such a substitution would not have much of an effect on the protein function. This is another type of silent mutation.

A change in protein sequence occurs and AFFECTS protein function…

If, for example, the codon AUU were mutated to AAU, isoleucine would be changed to asparagine. In this case, a nonpolar amino acid is replaced with a polar amino acid, which could affect the structure and the function of the protein.

Other mutations that can have a negative effect on protein synthesis include mutating a codon into a stop codon or inserting or deleting a base.

The latter has the effect of shifting the triplets that are read in the mRNA and would change the identity of all subsequent amino acids after the insertion or deletion.

mutagens

An environmental agent that causes a mutation

carcinogen

a mutagen that causes cancers

spontaneous mutation

Mutations arising from random errors during DNA replication.

metabolites

chemical intermediates formed by enzyme-catalyzed reactions in the body.

common metabolites:

Pyruvate (3 carbon molecule)

Acetyl group (2 carbons)

biochemical reactions

chemical reactions that occur in living systems

catabolism

refers to chemical reactions in which LARGER molecules are broken down into a few common metabolites.

we see many hydrolysis and oxidation reactions in catabolic pathways.

these reactions tend to be EXERGONIC (- delta G)

Anabolism

refers to chemical reactions in which metabolites combine to form larger molecules.

many of the reactions are condensation or reduction reactions

these reactions tend to be ENDERGONIC (+ delta G)

The energy released during catabolic reactions is captured in molecules such as ATP, and is used to drive the ______ reactions.

Anabolic

cytoplasm

consists of all the cellular contents between the cell membrane and nucleus

Cytosol

The fluid part of the cytoplasm that contains enzymes for many of the cells chemical reaction

mitochondria

contain the structure for the synthesis of ATP from energy-producing reactions.

nucleus

contain genetic information for the replication of DNA and synthesis of protein

High-Energy Form Nucleotides

ATP

NADH (reduced form)

FADH₂ (reduced form)

Acetyl Coenzyme A

Low-Energy form

ADP

NAD⁺ (oxidized form)

FAD (oxidized form)

Coenzyme A

Identify the metabolic nucleotide described by:

contains a form of the vitamin riboflavin

FAD

Identify the metabolic nucleotide described by:

contains a thioester functional group

Coenzyme A

Identify the metabolic nucleotide described by:

contains a form of the vitamin niacin

NAD+

Identify the metabolic nucleotide described by:

the main energy currency in the body

ATP

Identify the metabolic nucleotide described by:

Exchanges energy when a phosphate bond is hydrolyzed

ATP

Identify the metabolic nucleotide described by:

Exchanges energy when a C–S bond is hydrolyzed

Coenzyme A

digestion

The breakdown of large molecules into smaller components for absorption, usually through hydrolysis.

Why do saltine crackers start to taste sweet when you chew them?

Salivary α-amylase breaks down starch (amylose & amylopectin) into glucose, maltose, and oligosaccharides.

The sweetness comes from the glucose produced.

(carbohydrates)

Why is fat digestion difficult in the body?

Fats are nonpolar, and digestive fluids are water-based (polar), so they don’t mix well.

What is the role of bile in fat digestion?

Bile helps break fats into smaller droplets so they can be digested.

What are bile salts?

Amphipathic molecules (have a polar and nonpolar part) that act like soap

What is emulsification?

The process of breaking large fat globules into small droplets (micelles).

What do micelles do in digestion?

They carry fats to the intestinal wall for absorption.

What enzyme digests triglycerides?

Pancreatic lipase

What are the products of triglyceride digestion?

Free fatty acids + monoglycerides

Where does fat digestion mainly occur?

In the duodenum (small intestine)

What happens to fatty acids and monoglycerides after absorption?

They are reassembled into triglycerides inside intestinal cells.

What happens to cholesterol after absorption?

It combines with a fatty acid to form a cholesterol ester.

What are chylomicrons?

Lipoproteins that package triglycerides and cholesterol for transport in the blood.

What is the function of chylomicrons?

They transport fats through the bloodstream to tissues for energy or storage.

Where does protein digestion begin and what happens first?

n the stomach; proteins are denatured (unfolded) by acid.

Which enzymes digest proteins?

Pepsin, trypsin, and chymotrypsin (they break peptide bonds).

What are the final products of protein digestion and where do they go?

Amino acids, absorbed into the bloodstream and sent to tissues.

what enzyme digest lactose?

Lactase (breaks lactose → glucose + galactose)

What enzyme digests triglycerides?

Pancreatic lipase (breaks triglycerides → fatty acids + monoglyceride)

what enzyme digest proteins?

Pepsin, trypsin, chymotrypsin (break into amino acids)

End products of protein digestion:

amino acids

End products of starch digestion

Glucose

α-Amylase is produced in the __________ and it catalyzes the breakdown of _______ (α-glycosidic bonds)

salivary glands ; starch

Where does carbohydrate digestion occur in the body?

• Mouth: Starch

• Stomach: NO carbohydrates

• Small intestine: oligosaccharides + disaccharides (maltose, lactose,sucrose)

gluconeogenesis

The anabolic process of synthesizing glucose.

How many reactions are there in GLYCOLYSIS?

10 reactions!

what reactions in glycolysis are catalyzed by kinases?

reactions: 1,3,7,10

what reactions in glycolysis are catalyzed by Isomerases?

reaction: 5 and 8

What enzymes catalyze steps 6 and 9 of glycolysis?

Rxn 6: glyceraldehyde-3-phosphate dehydrogenase (oxidation-reduction)
Rxn 9: enolase (dehydration/lyase reaction)